Unit 5 - The evolutionary history of biological diversity

The major groups of living eutherians are thought to have diverged from one another in a burst of evolutionary change. The timing of this burst is uncertain: Molecular data suggest it occurred about 100 million years ago, while morphological data suggest it was about 60 million years ago. Figure 34.42 explores several major eutherian orders and their phylogenetic relationships with each other as well as with the monotremes and marsupials.

Primates: The mammalian order Primates includes the lemurs, tarsiers, monkeys, and apes. Humans are members of the ape group.

Figure 34.24 A mobile nursery. A female marsupial frog (Flectonotus fitzgeraldi) incubates her eggs in pouches of skin on her back.

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Table 27.2 A Comparison of the Three Domains of Life

memorize

Figure 26.10 Monophyletic, paraphyletic, and polyphyletic groups. (a) Monophyletic group (clade): Group I, consisting of three species (A, B, C) and their common ancestor , is a monophyletic group (clade), meaning that it consists of an ancestral species and all of its descendants. (b) Paraphyletic group: Group II is paraphyletic, meaning that it consists of an ancestral species and some of its descendants (species D, E, F) but not all of them (does not include species G).

(c) Polyphyletic group Group III, consisting of four species (A, B, C, D), is polyphyletic, meaning that the most recent common ancestor of its members is not part of the group.

Figure 30.9 Flower symmetry: In radial symmetry, the sepals, petals, stamens, and carpels radiate out from a center. Any line through the central axis divides the flower into two equal parts. In bilateral symmetry, the flower can only be divided into two equal parts by a single line.

Figure 30.8 The structure of an idealized flower.

Figure 34.21 Steps in the origin of limbs with digits. The white bars on the branches of this diagram place known fossils in time; arrowheads indicate lineages that extend to today. The drawings of extinct organisms are based on fossilized skeletons, but the colors are fanciful.

Amphibians: The amphibians are represented today by about 6,150 species in three clades: salamanders (clade Urodela, "tailed ones"), frogs (clade Anura, "tail-less ones"), and caecilians (clade Apoda, "legless ones").

Moss and hornwort sporophytes are often larger and more complex than those of liverworts. For example, hornwort sporophytes, which superficially resemble grass blades, have a cuticle. Moss and hornwort sporophytes also have stomata, as do all vascular plants (but not liverworts). Figure 29.8 shows some examples of gametophytes and sporophytes in the bryophyte phyla.

The Ecological and Economic Importance of Mosses: Wind dispersal of lightweight spores has distributed mosses throughout the world. These plants are particularly common and diverse in moist forests and wetlands. Some mosses colonize bare, sandy soil, where, researchers have found, they help retain nitrogen in the soil (Figure 29.9).

Figure 32.9 Body cavities of triploblastic animals. The organ systems develop from the three embryonic germ layers. (a) Coelomate: Coelomates, such as earthworms, have a true coelom, a body cavity completely lined by tissue derived from mesoderm. Tissue layer lining coelom and suspending internal organs (from mesoderm). Body covering (from ectoderm). Digestive tract (from endoderm).

(b) Pseudocoelomate: Pseudocoelomates, such as roundworms, have a body cavity lined by tissue derived from mesoderm and by tissue derived from endoderm. Muscle layer (from mesoderm). Pseudocoelom. Digestive tract (from endoderm). Body covering (from ectoderm). (c) Acoelomate: Acoelomates, such as planarians, lack a body cavity between the digestive cavity and outer body wall. Body covering (from ectoderm). Tissuefilled region (from mesoderm).Wall of digestive cavity (from endoderm)

Fruits: As seeds develop from ovules after fertilization, the ovary wall thickens and the ovary matures into a fruit. A pea pod is an example of a fruit, with seeds (mature ovules, the peas) encased in the ripened ovary (the pod). Fruits protect seeds and aid in their dispersal. Mature fruits can be either fleshy or dry (Figure 30.10). Tomatoes, plums, and grapes are examples of fleshy fruits, in which the wall (pericarp) of the ovary becomes soft during ripening. Dry fruits include beans, nuts, and grains. Some dry fruits split open at maturity to release seeds, whereas others remain closed. The dry, wind-dispersed fruits of grasses, harvested while on the plant, are major staple foods for humans. The cereal grains of maize, rice, wheat, and other grasses, though easily mistaken for seeds, are each actually a fruit with a dry outer covering (the former wall of the ovary) that adheres to the seed coat of the seed within.

As shown in Figure 30.11, various adaptations of fruits and seeds help to disperse seeds (see also Figure 38.12). The seeds of some flowering plants, such as dandelions and maples, are contained within fruits that function like parachutes or propellers, adaptations that enhance dispersal by wind. Some fruits, such as coconuts, are adapted to dispersal by water. And the seeds of many angiosperms are carried by animals. Some angiosperms have fruits modified as burrs that cling to animal fur (or the clothes of humans). Others produce edible fruits, which are usually nutritious, sweet tasting, and vividly colored, advertising their ripeness. When an animal eats the fruit, it digests the fruit's fleshy part, but the tough seeds usually pass unharmed through the animal's digestive tract. When the animal defecates, it may deposit the seeds, along with a supply of natural fertilizer, many kilometers from where the fruit was eaten.

Frogs: Numbering about 5,420 species, anurans, or frogs, are better suited than salamanders to locomotion on land (Figure 34.22b). Adult frogs use their powerful hind legs to hop along the terrain. Although often distinctive in appearance, the animals known as "toads" are simply frogs that have leathery skin or other adaptations for life on land. A frog nabs insects and other prey by flicking out its long, sticky tongue, which is attached to the front of the mouth. Frogs display a great variety of adaptations that help them avoid being eaten by larger predators. Their skin glands secrete distasteful or even poisonous mucus. Many poisonous species have color patterns that camouflage them or have bright coloration, which predators appear to associate with danger (see Figure 54.5).

Caecilians: The approximately 170 species of apodans, or caecilians, are legless and nearly blind, and superficially they resemble earthworms (Figure 34.22c). Their absence of legs is a secondary adaptation, as they evolved from a legged ancestor. Caecilians inhabit tropical areas, where most species burrow in moist forest soil.

The reproductive adaptations of angiosperms include flowers and fruits: Commonly known as flowering plants, angiosperms are seed plants with the reproductive structures called flowers and fruits. The name angiosperm (from the Greek angion, container) refers to seeds contained in fruits. Angiosperms are the most diverse and widespread of all plants, with more than 250,000 species (about 90% of all plant species)..

Characteristics of Angiosperms: All angiosperms are classified in a single phylum, Anthophyta. Before considering the evolution of angiosperms, we will examine two of their key adaptations—flowers and fruits— and the roles of these structures in the angiosperm life cycle.

Figure 33.12 Anatomy of a tapeworm. The inset shows a close-up of the scolex (colorized SEM). Molluscs: Snails and slugs, oysters and clams, and octopuses and squids are all molluscs (phylum Mollusca). There are over 100,000 known species, making them the second most diverse phylum of animals (after the arthropods, discussed later). Although the majority of molluscs are marine, roughly 8,000 species inhabit fresh water, and 28,000 species of snails and slugs live on land. All molluscs are soft-bodied, and most secrete a hard protective shell made of calcium carbonate. Slugs, squids, and octopuses have a reduced internal shell or have lost their shell completely during their evolution.

Despite their apparent differences, all molluscs have a similar body plan (Figure 33.16). Molluscs are coelomates, and their bodies have three main parts: a muscular foot, usually used for movement; a visceral mass containing most of the internal organs; and a mantle, a fold of tissue that drapes over the visceral mass and secretes a shell (if one is present). In many molluscs, the mantle extends beyond the visceral mass, producing a water-filled chamber, the mantle cavity, which houses the gills, anus, and excretory pores. Many molluscs feed by using a straplike organ called a radula to scrape up food.

Mollusca (100,000 species): Molluscs (including snails, clams, squids, and octopuses) have a soft body that in many species is protected by a hard shell (see Concept 33.3).

Ecdysozoa: Loricifera (10 species): Loriciferans (from the Latin lorica, corset, and ferre, to bear) are tiny animals that inhabit sediments on the sea floor. A loriciferan can telescope its head, neck, and thorax in and out of the lorica, a pocket formed by six plates surrounding the abdomen. Though the natural history of loriciferans is mostly a mystery, at least some species likely eat bacteria. A loriciferan (LM) Priapula (16 species): Priapulans are worms with a large, rounded proboscis at the anterior end. (They are named after Priapos, the Greek god of fertility, who was symbolized by a giant penis.) Ranging from 0.5 mm to 20 cm in length, most species burrow through seafloor sediments. Fossil evidence suggests that priapulans were among the major predators during the Cambrian period. A priapulan

Figure 34.7 The neural crest, embryonic source of many unique vertebrate traits. The neural crest consists of bilateral bands of cells near the margins of the embryonic folds that form the neural tube. Neural crest cells migrate to distant sites in the embryo. ) The migrating neural crest cells give rise to some of the anatomical structures unique to vertebrates, including some of the bones and cartilage of the skull. (A fetal human skull is depicted here.)

Figure 34.9 A sea lamprey. Parasitic lampreys use their mouth (inset) and tongue to bore a hole in the side of a fish. The lamprey then ingests the blood and other tissues of its host.

Figure 34.54 Art, a human hallmark. The engravings on this 77,000-year-old piece of ochre, discovered in South Africa's Blombos Cave, are among the earliest signs of symbolic thought in humans . Figure 34.53 Fossils of hand bones and foot bones (top and side views) of Homo naledi. A 160,000-year-old fossil of Homo sapiens.

Figure 34.51 Inquiry Did gene flow occur between Neanderthals and humans? Experiment Fossils discovered in Europe have been interpreted by some researchers as showing a mixture of Neanderthal and human features, suggesting that humans may have bred with Neanderthals. To assess this idea, researchers extracted DNA from several Neanderthal fossils and used this DNA to construct a draft sequence of the Neanderthal genome. Under the hypothesis that little or no gene flow occurred between Neanderthals and H. sapiens after their evolutionary lineages diverged, the Neanderthal genome should be equally similar to all human genomes, regardless of the geographic region from which the human genomes were obtained. To test this hypothesis, the researchers compared the Neanderthal genome to the genomes of five living humans: one from southern Africa, one from western Africa, and three from regions outside of Africa (France, China, and Papua New Guinea). They used a genetic similarity index, D, equal to the percentage of Neanderthal DNA that matched one human population minus the percentage of Neanderthal DNA that matched a second human population. If little or no gene flow occurred between Neanderthals and humans, D should be close to zero for each such comparison. Values of D that are substantially greater than zero indicate that Neanderthals are more similar genetically to the first of the two comparison populations—providing evidence of gene flow between Neanderthals and members of that population. Results Neanderthals consistently shared more genetic variants with non-Africans than with Africans. In contrast, the Neanderthal genome was equally close to the genomes of humans from each of the three different regions outside of Africa. Conclusion Genomic analyses indicate that gene flow occurred between Neanderthals and human populations outside of Africa (where the ranges of the two species overlapped).

A lancelet frequently leaves its burrow to swim to a new location. Though feeble swimmers, these invertebrate chordates display, in a simple form, the swimming mechanism of fishes. Coordinated contraction of muscles arranged like rows of chevrons 17 7 7 72 along the sides of the notochord flexes the notochord, producing side-to-side undulations that thrust the body forward. This serial arrangement of muscles is evidence of the lancelet's segmentation. The muscle segments develop from blocks of mesoderm called somites, which are found along each side of the notochord in all chordate embryos.

Globally, lancelets are rare, but in a few areas (such as Tampa Bay, on the Florida coast), they may reach densities of more than 5,000 individuals per square meter.

On May 18, 1980, Mount St. Helens erupted with a force 500 times that of the Hiroshima atomic bomb. Traveling at over 300 miles per hour, the blast destroyed hundreds of hectares of forest, leaving the region covered in ash and devoid of visible life. Within a few years, however, plants such as fireweed (Chamerion angustifolium) had colonized the barren landscape (Figure 30.1).

Fireweed and other early arrivals reached the blast zone as seeds. A seed consists of an embryo and its food supply, surrounded by a protective coat. When mature, seeds are dispersed from their parent by wind or other means, enabling them to colonize distant locations.

Flattening: By having a body that is only a few cells thick, an organism such as this flatworm can use its entire body surface for exchange. 1 μm Thylakoid (See Figure 40.3.)

Folding: This TEM shows portions of two chloroplasts in a plant leaf. Photosynthesis occurs in chloroplasts, which have a flattened and interconnected set of internal membranes called thylakoid membranes. The foldings of the thylakoid membranes increase their surface area, enhancing the exposure to light and thus increasing the rate of photosynthesis. (See Figure 10.4.)

Early in the Cambrian period, some 530 million years ago, an immense variety of invertebrate animals inhabited Earth's oceans. Predators used sharp claws and mandibles to capture and break apart their prey. Many animals had protective spikes or armor as well as modified mouthparts that enabled their bearers to filter food from the water. Amidst this bustle, it would have been easy to overlook certain slender, 3-cm-long creatures gliding through the water: members of the species Myllokunmingia fengjiaoa (Figure 34.1). Although lacking armor and appendages, this ancient species was closely related to one of the most successful groups of animals ever to swim, walk, slither, or fly: the vertebrates, which derive their name from vertebrae, the series of bones that make up the vertebral column, or backbone.

For more than 150 million years, vertebrates were restricted to the oceans, but about 365 million years ago, the evolution of limbs in one lineage of vertebrates set the stage for these vertebrates to colonize land. Over time, as the descendants of these early colonists adapted to life on land, they gave rise to the three groups of terrestrial vertebrates alive today: the amphibians, the reptiles (including birds), and the mammals.

Fungi as Mutualists: Fungi may form mutualistic relationships with plants, algae, cyanobacteria, and animals. Mutualistic fungi absorb nutrients from a host organism, but they reciprocate with actions that benefit the host—as we already saw for the key mycorrhizal associations that fungi form with most vascular plants.

Fungus-Plant Mutualisms: Along with mycorrhizal fungi, all plant species studied to date appear to harbor symbiotic endophytes, fungi (or bacteria) that live inside leaves or other plant parts without causing harm. Most fungal endophytes identified to date are ascomycetes. Fungal endophytes benefit certain grasses and other nonwoody plants by making toxins that deter herbivores or by increasing host plant tolerance of heat, drought, or heavy metals. As described in Figure 31.20, researchers studying how fungal endophytes affect a woody plant tested whether leaf endophytes benefit seedlings of the cacao tree, Theobroma cacao. Their findings show that the fungal endophytes of woody flowering plants can play an important role in defending against pathogens.

Green Algae: The grass-green chloroplasts of green algae have a structure and pigment composition much like the chloroplasts of plants. Molecular systematics and cellular morphology leave little doubt that green algae and plants are closely related. In fact, some systematists now advocate including green algae in an expanded "plant" kingdom, Viridiplantae (from the Latin viridis, green). Phylogenetically, this change makes sense, since otherwise the green algae are a paraphyletic group.

Green algae can be divided into two main groups, the charophytes and the chlorophytes. The charophytes include the algae most closely related to plants, and we will discuss them along with plants in Chapter 29.

Monilophytes (Phylum Monilophyta): Ferns: Unlike the lycophytes, ferns have megaphylls (see Figure 29.13). The sporophytes typically have horizontal stems that give rise to large leaves called fronds, often divided into leaflets. A frond grows as its coiled tip, the fiddlehead, unfurls. Almost all species are homosporous. The gametophyte in some species shrivels and dies after the young sporophyte detaches itself. In most species, sporophytes have stalked sporangia with springlike devices that catapult spores several meters. Airborne spores can be carried far from their origin. Some species produce more than a trillion spores in a plant's lifetime.

Horsetails: The group's name refers to the brushy appearance of the stems, which have a gritty texture that made them historically useful as "scouring rushes" for pots and pans. Some species have separate fertile (conebearing) and vegetative stems. Horsetails are homosporous, with cones releasing spores that typically give rise to bisexual gametophytes. Horsetails are also called arthrophytes ("jointed plants") because their stems have joints. Rings of small leaves or branches emerge from each joint, but the stem is the main photosynthetic organ. Large air canals carry oxygen to the roots, which often grow in waterlogged soil.

Figure 26.9 A molecular homoplasy.

Inquiry What is the species identity of food being sold as whale meat? Experiment C. S. Baker and S. R. Palumbi purchased 13 samples of "whale meat" from Japanese fish markets. They sequenced part of the mitochondrial DNA (mtDNA) from each sample and compared their results with the comparable mtDNA sequence from known whale species. To infer the species identity of each sample, the team constructed a gene tree, a phylogenetic tree that shows patterns of relatedness among DNA sequences rather than among taxa. Results Of the species in the resulting gene tree, only Minke whales caught in the Southern Hemisphere can be sold legally in Japan. Conclusion This analysis indicated that mtDNA sequences of six of the unknown samples (in red) were most closely related to mtDNA sequences of whales that are not legal to harvest.

Although the demands of flight have rendered the general body forms of many flying birds similar to one another, experienced bird-watchers can distinguish species by their profile, colors, flying style, behavior, and beak shape. The skeleton of a hummingbird's wing is unique, making it the only bird that can hover and fly backward (Figure 34.34). Adult birds lack teeth, but during the course of avian evolution their beaks have taken on a variety of shapes suited to different diets. Some birds, such as parrots, have crushing beaks with which they can crack open hard nuts and seeds. Other birds, such as flamingoes, are filter feeders. Their beaks have "strainers" that enable them to capture food particles from the water (Figure 34.35). Foot structure, too, shows considerable variation. Various birds use their feet for perching on branches (Figure 34.36), grasping food, defense, swimming or walking, and even courtship (see Figure 24.3e)..

Mammals are amniotes that have hair and produce milk: The reptiles we have been discussing represent one of the two living lineages of amniotes. The other amniote lineage is our own, the mammals. Today, there are more than 5,300 known species of mammals on Earth.

Brown Algae: The largest and most complex algae are brown algae. All are multicellular, and most are marine. Brown algae are especially common along temperate coasts that have cold-water currents. They owe their characteristic brown or olive color to the carotenoids in their plastids.

Many of the species commonly called "seaweeds" are brown algae. Some brown algal seaweeds have specialized structures that resemble organs in plants, such as a rootlike holdfast, which anchors the alga, and a stemlike stipe, which supports the leaflike blades (Figure 28.12). Unlike plants, however, brown algae lack true tissues and organs. Moreover, morphological and DNA data show that these similarities evolved independently in the algal and plant lineages and are thus analogous, not homologous. In addition, while plants have adaptations (such as rigid stems) that provide support against gravity, brown algae have adaptations that enable their main photosynthetic surfaces (the leaflike blades) to be near the water surface. Some brown algae accomplish this task with gas-filled, bubble-shaped floats.

Derived Characters of Chordates: All chordates share a set of derived characters, though many species possess some of these traits only during embryonic development. Figure 34.3 illustrates four key characters of chordates: a notochord; a dorsal, hollow nerve cord; pharyngeal slits or clefts; and a muscular, post-anal tail.

Notochord: Chordates are named for a skeletal structure, the notochord, present in all chordate embryos as well as in some adult chordates. The notochord is a longitudinal, flexible rod located between the digestive tube and the nerve cord. It is composed of large, fluid-filled cells encased in fairly stiff, fibrous tissue. The notochord provides skeletal support throughout most of the length of a chordate, and in larvae or adults that retain it, it also provides a firm but flexible structure against which muscles can work during swimming. In most vertebrates, a more complex, jointed skeleton develops around the ancestral notochord, and the adult retains only remnants of the embryonic notochord. In humans, for example, the notochord is reduced and forms part of the gelatinous disks sandwiched between the vertebrae.

Rhizarians: Our next subgroup of SAR is the rhizarians. Many species in this group are amoebas, protists that move and feed by means of pseudopodia, extensions that may bulge from almost anywhere on the cell surface. As it moves, an amoeba extends a pseudopodium and anchors the tip; more cytoplasm then streams into the pseudopodium. Amoebas do not constitute a monophyletic group; instead, they are dispersed across many distantly related eukaryotic taxa. Most amoebas that are rhizarians differ morphologically from other amoebas by having threadlike pseudopodia. Rhizarians also include flagellated (non-amoeboid) protists that feed using threadlike pseudopodia. We'll examine three groups of rhizarians here: radiolarians, forams, and cercozoans.

Radiolarians: The protists called radiolarians have delicate, intricately symmetrical internal skeletons that are generally made of silica. The pseudopodia of these mostly marine protists radiate from the central body (Figure 28.18) and are reinforced by bundles of microtubules. The microtubules are covered by a thin layer of cytoplasm, which engulfs smaller microorganisms that become attached to the pseudopodia. Cytoplasmic streaming then carries the captured prey into the main part of the cell. After radiolarians die, their skeletons settle to the seafloor, where they have accumulated as an ooze that is hundreds of meters thick in some locations.

This diversity of food sources corresponds to the varied roles of fungi in ecological communities: Different species live as decomposers, parasites, or mutualists. Fungi that are decomposers break down and absorb nutrients from nonliving organic material, such as fallen logs, animal corpses, and the wastes of living organisms. Parasitic fungi absorb nutrients from the cells of living hosts. Some parasitic fungi are pathogenic, including many species that cause diseases in plants and others that cause diseases in animals. Mutualistic fungi also absorb nutrients from a host organism, but they reciprocate with actions that benefit the host. For example, mutualistic fungi that live within the digestive tracts of certain termite species use their enzymes to break down wood, as do mutualistic protists in other termite species (see Figure 28.27).

The versatile enzymes that enable fungi to digest a wide range of food sources are not the only reason for their ecological success. Another important factor is how their body structure increases the efficiency of nutrient absorption.

Horizontal gene transfer can also spread genes associated with virulence, turning normally harmless bacteria into potent pathogens. E. coli, for instance, is ordinarily a harmless symbiont in the human intestines, but pathogenic strains that cause bloody diarrhea have emerged. One of the most dangerous strains, O157:H7, is a global threat; in the United States alone, there are 75,000 cases of O157:H7 infection per year, often from contaminated beef or produce. Scientists have sequenced the genome of O157:H7 and compared it with the genome of a harmless strain of E. coli called K-12.

They discovered that 1,387 out of the 5,416 genes in O157:H7 have no counterpart in K-12. Many of these 1,387 genes are found in chromosomal regions that include phage DNA. This suggests that at least some of the 1,387 genes were incorporated into the genome of O157:H7 through phage-mediated horizontal gene transfer (transduction). Some of the genes found only in O157:H7 are associated with virulence, including genes that code for adhesive fimbriae that enable O157:H7 to attach itself to the intestinal wall and extract nutrients.

Medusozoans: All cnidarians that produce a medusa are members of clade Medusozoa, a group that includes the scyphozoans (jellies) and cubozoans (box jellies) shown in Figure 33.7a, along with the hydrozoans. Most hydrozoans alternate between the polyp and medusa forms, as seen in the life cycle of Obelia (Figure 33.8). The polyp stage, a colony of interconnected polyps in the case of Obelia, is more conspicuous than the medusa. Hydras, among the few cnidarians found in fresh water, are also unusual hydrozoans in that they exist only in polyp form.

Unlike hydrozoans, most scyphozoans and cubozoans spend the majority of their life cycles in the medusa stage. Coastal scyphozoans, for example, often have a brief polyp stage during their life cycle, whereas those that live in the open ocean generally lack the polyp stage altogether. As their name (which means "cube animals") suggests, cubozoans have a box-shaped medusa stage. Most cubozoans live in tropical oceans and are equipped with highly toxic cnidocytes. For example, the sea wasp (Chironex fleckeri), a cubozoan that lives off the coast of northern Australia, is one of the deadliest organisms known: Its sting causes intense pain and can lead to respiratory failure, cardiac arrest, and death within minutes.

Zygentoma (silverfish; 450 species): These small, wingless insects have a flattened body and reduced eyes. They live in leaf litter or under bark. They can also infest buildings, where they can become pests.

Winged insects (many orders; six are shown below):

Future Directions in Animal Systematics: While many scientists think that current evidence supports the evolutionary relationships shown in Figure 32.11, aspects of this phylogeny continue to be debated. Although it can be frustrating that the phylogenies in textbooks cannot be memorized as set-in-stone truths, the uncertainty inherent in these diagrams is a healthy reminder that science is an ongoing, dynamic process of inquiry. We'll conclude with three questions that are the focus of ongoing research. 1. Are sponges monophyletic? Traditionally, sponges were placed in a single phylum, Porifera. This view was challenged in the 1990s, when molecular studies indicated that sponges were paraphyletic; as a result, sponges were placed into several different phyla that branched near the base of the animal tree. Since 2009, however, several morphological and molecular studies have concluded that sponges are monophyletic after all, as traditionally thought and as shown in Figure 32.11. Researchers are currently sequencing the entire genomes of various sponges to investigate whether sponges are indeed monophyletic.

2. Are ctenophores basal metazoans? Many researchers have concluded that sponges are basal metazoans (see Figure 32.11). This conclusion was supported in a 2016 phylogenomic analysis, but several other recent studies have placed the comb jellies (phylum Ctenophora) at the base of the animal tree. In addition to the most recent phylogenomic results, data consistent with placing sponges at the base of the animal tree include fossil steroid evidence, molecular clock analyses, the morphological similarity of sponge collar cells to the cells of choanoflagellates (see Figure 32.3), and the fact that sponges are one of the few animal groups that lack tissues (as might be expected for basal animals). Ctenophores, on the other hand, have tissues, and their cells do not resemble the cells of choanoflagellates. At present, the idea that ctenophores are basal metazoans remains an intriguing but controversial hypothesis.

Figure 28.23 The life cycle of Chlamydomonas, a unicellular chlorophyte 1 )In Chlamydomonas, mature cells are haploid and contain a single cup-shaped chloroplast. 2) In response to a nutrient shortage, drying of the enviroment, or other stress, cells develop into gametes. 3) Gametes of different mating types (designated + and -) fuse (fertilization), forming a diploid zygote.

4)The zygote secretes a durable coat that protects the cell from harsh conditions. 5)After a dormant period, meiosis produces four haploid individuals (two of each mating type) that emerge and mature. 6)When a mature cell reproduces asexually, it resorbs its flagella and then undergoes two rounds of mitosis, forming four cells (more in some species). 7) These daughter cells develop flagella and cell walls and then emerge as swimming zoospores from the parent cell. The zoospores develop into mature haploid cells.

Figure 34.40 Australian marsupials. (a) A young brushtail possum. The offspring of marsupials are born very early in their development. They finish their growth while nursing from a nipple (in their mother's pouch in most species).

(b) A greater bilby. The greater bilby is a digger and burrower that eats termites and other insects, along with the seeds, roots, and bulbs of various plants. The female's rear-opening pouch helps protect the young from dirt as the mother digs. Other marsupials, such as kangaroos, have a pouch that opens to the front.

Figure 27.3 Gram staining.: (a) Gram-positive bacteria: Gram-positive bacteria have a thick wall made of peptidoglycan. The crystal violet enters the cell, where it forms a complex with the iodine in the stain. This complex is too large to pass through the thick cell wall, so it is not removed by the alcohol rinse. Result: The darker crystal violet dye masks the red safranin dye.

(b) Gram- negative bacteria- Gram-negative bacteria have a thin layer of peptidoglycan, which is located between the plasma membrane and an outer membrane. The crystal violet-iodine complex can pass through this thin cell wall and hence is removed by the alcohol rinse. Result: The safranin dye stains the cell pink or red.

Figure 30.3 From ovule to seed in a gymnosperm. (a)Unfertilized ovule. In this longitudinal section through the ovule of a pine (a gymnosperm), a fleshy megasporangium is surrounded by a protective layer of tissue called an integument. The micropyle, the only opening through the integument, allows entry of a pollen grain. (b)Fertilized ovule. A megaspore develops into a female gametophyte, which produces an egg. The pollen grain, which had entered through the micropyle, contains a male gametophyte. The male gametophyte develops a pollen tube that discharges sperm, thereby fertilizing the egg.

(c)Gymnosperm seed. Fertilization initiates the transformation of the ovule into a seed, which consists of a sporophyte embryo, a food supply, and a protective seed coat derived from the integument. The megasporangium dries out and collapses.

1. All animals share a common ancestor. Current evidence indicates that animals are monophyletic, forming a clade called Metazoa. All extant and extinct animal lineages have descended from a common ancestor. 2. Sponges are the sister group to all other animals. Sponges (phylum Porifera) are basal animals, having diverged from all other animals early in the history of the group. Recent morphological and molecular analyses indicate that sponges are monophyletic, as shown here. 3. Eumetazoa is a clade of animals with tissues. All animals except for sponges and a few others belong to a clade of eumetazoans ("true animals"). Members of this group have tissues, such as muscle tissue and nervous tissue. Basal eumetazoans, which include the phyla Ctenophora (comb jellies) and Cnidaria, are diploblastic and generally have radial symmetry.

4. Most animal phyla belong to the clade Bilateria. Bilateral symmetry and the presence of three prominent germ layers are shared derived characters that help define the clade Bilateria. This clade contains the majority of animal phyla, and its members are known as bilaterians. The Cambrian explosion was primarily a rapid diversification of bilaterians. 5. There are three major clades of bilaterian animals. Bilaterians have diversified into three main lineages, Deuterostomia, Lophotrochozoa, and Ecdysozoa. With one exception, the phyla in these clades consist entirely of invertebrates, animals that lack a backbone; Chordata is the only phylum that includes vertebrates, animals with a backbone.

Applying Phylogenies: Understanding phylogeny can have practical applications. Consider maize (corn), which originated in the Americas and is now an important food crop worldwide. From a phylogeny of maize based on DNA data, researchers have been able to identify two species of wild grasses that may be maize's closest living relatives. These two close relatives may be useful as "reservoirs" of beneficial alleles that can be transferred to cultivated maize by cross-breeding or genetic engineering.

A different use of phylogenetic trees is to infer species identities by analyzing the relatedness of DNA sequences from different organisms. Researchers have used this approach to investigate whether "whale meat" had been harvested illegally from whale species protected under international law rather than from species that can be harvested legally (Figure 26.6). How do researchers construct phylogenetic trees like those we've considered here? In the next section, we'll begin to answer that question by examining the data used to determine phylogenies.

Flowers: The flower is a unique angiosperm structure that is specialized for sexual reproduction. In many angiosperm species, insects or other animals transfer pollen from one flower to the sex organs on another flower, which makes pollination more directed than the wind-dependent pollination of most species of gymnosperms. However, some angiosperms are wind-pollinated, particularly those species that occur in dense populations, such as grasses and tree species in temperate forests.

A flower is a specialized shoot that can have up to four types of modified leaves called floral organs: sepals, petals, stamens, and carpels (Figure 30.8). Starting at the base of the flower are the sepals, which are usually green and enclose the flower before it opens (think of a rosebud). Interior to the sepals are the petals, which are brightly colored in most flowers and can aid in attracting pollinators. Flowers that are windpollinated, such as grasses, generally lack brightly colored parts. In all angiosperms, the sepals and petals are sterile floral organs, meaning that they do not produce sperm or eggs. Within the petals are two types of fertile floral organs that produce spores, the stamens and carpels. Stamens and carpels are sporophylls, modified leaves that are specialized for reproduction.

Stamens are microsporophylls: They produce microspores that develop into pollen grains containing male gametophytes. A stamen consists of a stalk called the filament and a terminal sac, the anther, where pollen is produced. Carpels are megasporophylls: They produce megaspores that give rise to female gametophytes. The carpel is the "container" mentioned earlier in which seeds are enclosed; as such, it is a key structure that distinguishes angiosperms from gymnosperms. At the tip of the carpel is a sticky stigma that receives pollen. A style leads from the stigma to a structure at the base of the carpel, the ovary; the ovary contains one or more ovules. As in gymnosperms, each angiosperm ovule contains a female gametophyte. If fertilized, an ovule develops into a seed.

A flower may have one or more carpels. In many species, multiple carpels are fused into one structure. The term pistil is sometimes used to refer to a single carpel (a simple pistil) or two or more fused carpels (a compound pistil). Flowers also vary in symmetry (Figure 30.9) and other aspects of shape, as well as size, color, and odor. Much of this diversity results from adaptation to specific pollinators (see Figures 38.4 and 38.5).

Vascular plants, which form a clade that comprises about 93% of all extant plant species, can be categorized further into smaller clades. Two of these clades are the lycophytes (the club mosses and their relatives) and the monilophytes (ferns and their relatives). The plants in each of these clades lack seeds, which is why collectively the two clades are often informally called seedless vascular plants. However,notice in Figure 29.6 that, like bryophytes, seedless vascular plants do not form a clade.

A group such as the bryophytes or the seedless vascular plants is sometimes referred to as a grade, a collection of organisms that share key biological features. Grades can be informative by grouping organisms according to their features, such as having a vascular system but lacking seeds. But members of a grade, unlike members of a clade, do not necessarily share the same ancestry. For example, even though monilophytes and lycophytes are all seedless vascular plants, monilophytes share a more recent common ancestor with seed plants. As a result, we would expect monilophytes and seed plants to share key traits not found in lycophytes—and they do, as you'll read in Concept 29.3.

The basic body plan of a cnidarian is a sac with a central digestive compartment, the gastrovascular cavity. A single opening to this cavity functions as both mouth and anus. There are two variations on this body plan: the largely sessile polyp and the more motile medusa (Figure 33.5). Polyps are cylindrical forms that adhere to the substrate by the aboral end of their body (the end opposite the mouth) and extend their tentacles, waiting for prey. Examples of the polyp form include hydras and sea anemones. Although they are primarily sedentary, many polyps can move slowly across their substrate using muscles at the aboral end of their body. When threatened by a predator, some sea anemones can detach from the substrate and "swim" by bending their body column back and forth, or thrashing their tentacles.

A medusa (plural, medusae) resembles a flattened, mouth-down version of the polyp. It moves freely in the water by a combination of passive drifting and contractions of its bell-shaped body. Medusae include free-swimming jellies. The tentacles of a jelly dangle from the oral surface, which points downward. Some cnidarians exist only as polyps or only as medusae; others have both a polyp stage and a medusa stage in their life cycle. Cnidarians are predators that often use tentacles arranged in a ring around their mouth to capture prey and push the food into their gastrovascular cavity, where digestion begins.

Free-Living Species: Free-living rhabditophorans are important as predators and scavengers in a wide range of freshwater and marine habitats. The best-known members of this group are freshwater species in the genus Dugesia, commonly called planarians. Abundant in unpolluted ponds and streams, planarians prey on smaller animals or feed on dead animals. They move by using cilia on their ventral surface, gliding along a film of mucus they secrete. Some other rhabditophorans also use their muscles to swim through water with an undulating motion.

A planarian's head features a pair of light-sensitive eyespots as well as lateral flaps that function mainly to detect specific chemicals. The planarian nervous system is more complex and centralized than the nerve nets of cnidarians (Figure 33.10). Experiments have shown that planarians can learn to modify their responses to stimuli. Some planarians can reproduce asexually through fission. The parent constricts roughly in the middle of its body, separating into a head end and a tail end; each end then regenerates the missing parts. Sexual reproduction also occurs. Planarians are hermaphrodites, and copulating mates typically cross-fertilize each other.

Figure 33.44 Anatomy of a sea star, an echinoderm (top view). The photograph shows a sea star surrounded by sea urchins, which are members of the echinoderm clade Echinoidea. Radial canal. The water vascular system consists of a ring canal in the central disk and five radial canals, each running in a groove down the entire length of an arm. Branching from each radial canal are hundreds of hollow, muscular tube feet filled with fluid. Digestive glands secrete digestive juices and aid in the absorption and storage of nutrients. Central disk. The central disk has a nerve ring and nerve cords radiating from the ring into the arms

A short digestive tract runs from the mouth on the bottom of the central disk to the anus on top of the disk. The surface of a sea star is covered by spines that help defend against predators, as well as by small gills that provide gas exchange. Madreporite. Water can flow in or out of the water vascular system into the surrounding water through the madreporite. Each tube foot consists of a bulb-like ampulla and a podium (foot portion). When the ampulla squeezes, water is forced into the podium, which expands and contacts the substrate. Adhesive chemicals are then secreted from the base of the podium, attaching it to the substrate. To detach the tube foot, de-adhesive chemicals are secreted and muscles in the podium contract, forcing water back into the ampulla and shortening the podium. As it moves, a sea star leaves an observable "footprint" of adhesive material on the substrate.

Early Evolution of Mammals: Mammals belong to a group of amniotes known as synapsids. Early nonmammalian synapsids lacked hair, had a sprawling gait, and laid eggs. A distinctive characteristic of synapsids is the single temporal fenestra, a hole behind the eye socket on each side of the skull. Humans retain this feature; your jaw muscles pass through the temporal fenestra and anchor on your temple. Fossil evidence shows that the jaw was remodeled as mammalian features arose gradually in successive lineages of earlier synapsids (see Figure 25.7); in all, these changes took more than 100 million years. In addition, two of the bones that formerly made up the jaw joint (the quadrate and the articular) were incorporated into the mammalian middle ear (Figure 34.38).

. This evolutionary change is reflected in changes that occur during development. For example, as a mammalian embryo grows, the posterior region of its jaw—which in a reptile forms the articular bone—can be observed to detach from the jaw and migrate to the ear, where it forms the malleus. Synapsids evolved into large herbivores and carnivores during the Permian period (299-252 million years ago), and for a time they were the dominant tetrapods. However, the Permian-Triassic extinctions took a heavy toll on them, and their diversity fell during the Triassic (252-201 million years ago). Increasingly mammal-like synapsids emerged by the end of the Triassic. While not true mammals, these synapsids had acquired a number of the derived characters that distinguish mammals from other amniotes. They were small and probably hairy, and they likely fed on insects at night. Their bones show that they grew faster than other synapsids, suggesting that they probably had a relatively high metabolic rate; however, they still laid eggs.

Like many molluscs, arthropods have an open circulatory system, in which fluid called hemolymph is propelled by a heart through short arteries and then into spaces called sinuses surrounding the tissues and organs. (The term blood is generally reserved for fluid in a closed circulatory system.) Hemolymph reenters the arthropod heart through pores that are usually equipped with valves. The hemolymph-filled body sinuses are collectively called the hemocoel, which is not part of the coelom. Although arthropods are coelomates, in most species the coelom that forms in the embryo becomes much reduced as development progresses, and the hemocoel becomes the main body cavity in adults.

A variety of specialized gas exchange organs have evolved in arthropods. These organs allow the diffusion of respiratory gases in spite of the exoskeleton. Most aquatic species have gills with thin, feathery extensions that expose a large surface area to the surrounding water. Terrestrial arthropods generally have internal surfaces specialized for gas exchange. For example, most insects have tracheal systems, branched air ducts leading into the interior of the body from pores in the cuticle. Morphological and molecular data suggest that living arthropods consist of three major lineages that diverged early in the phylum's evolution: chelicerates (sea spiders, horseshoe crabs, scorpions, ticks, mites, and spiders); myriapods (centipedes and millipedes); and pancrustaceans (a recently defined, diverse group that includes insects as well as lobsters, shrimp, barnacles, and other crustaceans).

The largest sharks and rays are suspension feeders that consume plankton. Most sharks, however, are carnivores that swallow their prey whole or use their powerful jaws and sharp teeth to tear flesh from animals too large to swallow in one piece. Sharks have several rows of teeth that gradually move to the front of the mouth as old teeth are lost. The digestive tract of many sharks is proportionately shorter than that of many other vertebrates. Within the shark intestine is a spiral valve, a corkscrew-shaped ridge that increases surface area and prolongs the passage of food through the digestive tract.

Acute senses are adaptations that go along with the active, carnivorous lifestyle of sharks. Sharks have sharp vision but cannot distinguish colors. The nostrils of sharks, like those of most aquatic vertebrates, open into dead-end cups. They function only for olfaction (smelling), not for breathing. Like some other vertebrates, sharks have a pair of regions in the skin of their head that can detect electric fields generated by the muscle contractions of nearby animals. Like all nonmammalian aquatic vertebrates, sharks have no eardrums, structures that terrestrial vertebrates use to transmit sound waves in air to the auditory organs. Sound reaches a shark through water, and the animal's entire body transmits the sound to the hearing organs of the inner ear.

Apical Meristems: In terrestrial habitats, a photosynthetic organism finds essential resources in two very different places. Light and CO2 are mainly available above ground; water and mineral nutrients are found mainly in the soil. Though plants cannot move from place to place, most plants have roots and shoots that can elongate, increasing exposure to environmental resources. Growth in length is sustained throughout the plant's life by the activity of apical meristems, regions at growing tips of the plant body where one or more cells divide repeatedly. Cells produced by apical meristems differentiate into the outer epidermis, which protects the body, and various types of internal tissues. Apical meristems of shoots also generate leaves in most plants. Thus, the complex bodies of most plants have specialized below- and aboveground organs.

Additional derived traits that relate to terrestrial life have evolved in many plant species. For example, the epidermis in many species has a covering, the cuticle, that consists of wax and other polymers. Permanently exposed to the air, plants run a far greater risk of desiccation (drying out) than do their algal relatives. The cuticle acts as waterproofing, helping prevent excessive water loss from the aboveground plant organs, while also providing some protection from microbial attack. Most plants also have specialized pores called stomata (singular, stoma), which support photosynthesis by allowing the exchange of CO2 and O2 between the outside air and the plant (see Figure 10.4). Stomata are also the main avenues by which water evaporates from the plant; in hot, dry conditions, the stomata close, minimizing water loss

Lancelets: The most basal (earliestdiverging) group of living chordates are animals called lancelets (Cephalochordata), which get their name from their bladelike shape (Figure 34.4). As larvae, lancelets develop a notochord; a dorsal, hollow nerve cord; numerous pharyngeal slits; and a post-anal tail. The larvae feed on plankton in the water column, alternating between upward swimming and passive sinking. As the larvae sink, they trap plankton and other suspended particles in their pharynx.

Adult lancelets can reach 6 cm in length. They retain key chordate traits, closely resembling the idealized chordate shown in Figure 34.3. Following metamorphosis, an adult lancelet swims down to the seafloor and wriggles backward into the sand, leaving only its anterior end exposed. Cilia draw seawater into the lancelet's mouth. A net of mucus secreted across the pharyngeal slits removes tiny food particles as the water passes through the slits, and the trapped food enters the intestine. The pharynx and pharyngeal slits play a minor role in gas exchange, which occurs mainly across the external body surface.

Seeds and pollen grains are key adaptations for life on land: We begin with an overview of terrestrial adaptations that seed plants added to those already present in nonvascular plants (bryophytes) and seedless vascular plants (see Concept 29.1). In addition to seeds, all seed plants have reduced gametophytes, heterospory, ovules, and pollen. As we'll see, these adaptations helped seed plants cope with conditions such as drought and exposure to ultraviolet (UV) radiation in sunlight. They also freed seed plants from requiring water for fertilization, enabling reproduction under a broader range of conditions than in seedless plants.

Advantages of Reduced Gametophytes: Mosses and other bryophytes have life cycles dominated by gametophytes, whereas ferns and other seedless vascular plants have sporophyte-dominated life cycles. The evolutionary trend of gametophyte reduction continued further in the vascular plant lineage that led to seed plants. While the gametophytes of seedless vascular plants are visible to the naked eye, the gametophytes of most seed plants are microscopic.

By concentrating growth in the hyphae of mushrooms, a basidiomycete mycelium can erect its fruiting structures in just a few hours; a mushroom pops up as it absorbs water and as cytoplasm streams in from the dikaryotic mycelium. By this process, in some species a ring of mushrooms, popularly called a "fairy ring," may appear literally overnight (Figure 31.19). The mycelium below the fairy ring expands outward at a rate of about 30 cm per year, decomposing organic matter in the soil as it grows. Some giant fairy rings are produced by mycelia that are centuries old.

After a mushroom forms, its cap supports and protects a large surface area of dikaryotic basidia on gills. During karyogamy, the two nuclei in each basidium fuse, producing a diploid nucleus (see Figure 31.18). This nucleus then undergoes meiosis, yielding four haploid nuclei, each of which ultimately develops into a basidiospore. Large numbers of basidiospores are produced: The gills of a common white mushroom have a surface area of about 200 cm2 and may drop a billion basidiospores, which blow away.

The pollen grain absorbs water and germinates after it adheres to the stigma of a carpel. The tube cell produces a pollen tube that grows down within the style of the carpel. After reaching the ovary, the pollen tube penetrates through the micropyle, a pore in the integuments of the ovule, and discharges two sperm cells into the female gametophyte (embryo sac). One sperm fertilizes the egg, forming a diploid zygote. The other sperm fuses with the two nuclei in the large central cell of the female gametophyte, producing a triploid cell. This type of double fertilization, in which one fertilization event produces a zygote and the other produces a triploid cell, is unique to angiosperms.

After double fertilization, the ovule matures into a seed. The zygote develops into a sporophyte embryo with a rudimentary root and one or two seed leaves called cotyledons. The triploid central cell of the female gametophyte develops into endosperm, tissue rich in starch and other food reserves that nourish the developing embryo.

The Angiosperm Life Cycle: You can follow a typical angiosperm life cycle in Figure 30.12. The flower of the sporophyte produces microspores that form male gametophytes and megaspores that form female gametophytes. The male gametophytes are in the pollen grains, which develop within microsporangia in the anthers. Each male gametophyte has two haploid cells: a generative cell that divides, forming two sperm, and a tube cell that produces a pollen tube. Each ovule, which develops in the ovary, contains a female gametophyte, also known as an embryo sac. The embryo sac consists of only a few cells, one of which is the egg.

After its release from the anther, the pollen is carried to the sticky stigma at the tip of a carpel. Although some flowers self-pollinate, most have mechanisms that ensure crosspollination, which in angiosperms is the transfer of pollen from an anther of a flower on one plant to the stigma of a flower on another plant of the same species. Cross-pollination enhances genetic variability. In some species, stamens and carpels of a single flower may mature at different times, or they may be so arranged that self-pollination is unlikely.

Acanthocephalans: Acanthocephalans (1,100 species) are sexually reproducing parasites of vertebrates that lack a complete digestive tract and usually are less than 20 cm long. They are commonly called spiny-headed worms because of the curved hooks on the proboscis at the anterior end of their body (Figure 33.14). Although they once were placed in their own phylum, recent studies have shown that acanthocephalans originated from within the group traditionally known as Rotifera. In particular, rotifers in the genus Seison share a more recent common ancestor with acanthocephalans than they do with other rotifers, making the acanthocephalans a group of highly modified "rotifers."

All acanthocephalans are parasites that have complex life cycles with two or more hosts. Some species manipulate the behavior of their intermediate hosts (generally arthropods) in ways that increase their chances of reaching their final hosts (generally vertebrates). For example, acanthocephalans that infect New Zealand mud crabs cause their hosts to move to more visible areas on the beach, where the crabs are more likely to be eaten by birds, the worms' final hosts.

Dinosaurs once were considered slow, sluggish creatures. Since the 1970s, however, fossil discoveries and research have led to the conclusion that many dinosaurs were agile and fast moving. Dinosaurs had a limb structure that enabled them to walk and run more efficiently than could earlier tetrapods, which had a sprawling gait. Fossilized footprints and other evidence suggest that some species were social—they lived and traveled in groups, much as many mammals do today. Paleontologists have also discovered evidence that some dinosaurs built nests and brooded their eggs, as birds do today (see Figure 26.17). Finally, some anatomical evidence supports the hypothesis that at least some dinosaurs were endotherms.

All dinosaurs except birds became extinct by the end of the Cretaceous period (66 million years ago). Their extinction may have been caused at least in part by the asteroid or comet impact described in Concept 25.4. Some analyses of the fossil record are consistent with this idea in that they show a sudden decline in dinosaur diversity at the end of the Cretaceous. However, other analyses indicate that the number of dinosaur species had begun to decline several million years before the Cretaceous ended. Further fossil discoveries and new analyses will be needed to resolve this debate. Next, we'll discuss the two extant lineages of reptiles, the lepidosaurs (tuataras, lizards, and snakes) and the archosaurs (turtles, crocodilians, and birds).

Hagfishes: The hagfishes are jawless vertebrates that have highly reduced vertebrae and a skull that is made of cartilage. They swim in a snakelike fashion by using their segmental muscles to exert force against their notochord, which they retain in adulthood as a strong, flexible rod of cartilage. Hagfishes have a small brain, eyes, ears, and a nasal opening that connects with the pharynx. Their mouths contain tooth-like formations made of the protein keratin.

All of the 30 living species of hagfishes are marine. Measuring up to 60 cm in length, most are bottom-dwelling scavengers (Figure 34.8) that feed on worms and sick or dead fish. Rows of slime glands on a hagfish's flanks secrete a substance that absorbs water, forming a slime that may repel other scavengers when a hagfish is feeding. When attacked by a predator, a hagfish can produce several liters of slime in less than a minute. The slime coats the gills of the attacking fish, sending it into retreat or even suffocating it. Biologists and engineers are investigating the properties of hagfish slime as a model for developing a space-filling gel that could be used, for instance, to stop bleeding during surgery.

Giant brown algae known as kelps that live in deep waters have such floats in their blades, which are attached to stipes that can rise as much as 60 m from the seafloor—more than half the length of a football field. Brown algae are important commodities for humans. Some species are eaten, such as Laminaria (Japanese "kombu"), which is used in soups. In addition, the cell walls of brown algae contain a gel-forming substance, called algin, which is used to thicken many processed foods, including pudding and salad dressing.

Alternation of Generations: A variety of life cycles have evolved among the multicellular algae. The most complex life cycles include an alternation of generations, the alternation of multicellular haploid and diploid forms. Although haploid and diploid conditions alternate in all sexual life cycles—human gametes, for example, are haploid—the term alternation of generations applies only to life cycles in which both haploid and diploid stages are multicellular. As you will read in Concept 29.1, alternation of generations also evolved in plants.

Figure 29.3 Exploring Derived Traits of Plants: Charophyte algae lack the key traits of plants described in this figure: alternation of generations; multicellular, dependent embryos; walled spores produced in sporangia; multicellular gametangia; and apical meristems. This suggests that these traits were absent in the ancestor common to plants and charophytes but instead evolved as derived traits of plants. Not every plant exhibits all of these traits; certain lineages of plants have lost some traits over time.

Alternation of Generations: The life cycles of all plants alternate between two generations of distinct multicellular organisms: gametophytes and sporophytes. As shown in the diagram below (using a fern as an example), each generation gives rise to the other, a process that is called alternation of generations. This type of reproductive cycle evolved in various groups of algae but does not occur in the charophytes, the algae most closely related to plants. Take care not to confuse the alternation of generations in plants with the haploid and diploid stages in the life cycles of other sexually reproducing organisms (see Figure 13.6). Alternation of generations is distinguished by the fact that the life cycle includes both multicellular haploid organisms and multicellular diploid organisms. The multicellular haploid gametophyte ("gamete-producing plant") is named for its production by mitosis of haploid gametes—eggs and sperm—that fuse during fertilization, forming diploid zygotes. Mitotic division of the zygote produces a multicellular diploid sporophyte ("spore-producing plant"). Meiosis in a mature sporophytes produces haploid spores, reproductive cells that can develop into a new haploid organism without fusing with another cell. Mitotic division of the spore cell produces a new multicellular gametophyte, and the cycle begins again.

Bipedalism: Our anthropoid ancestors of 30-35 million years ago were still tree-dwellers. By about 10 million years ago, the Himalayan mountain range had formed, thrust up in the aftermath of the Indian plate's collision with the Eurasian plate (see Figure 25.16). The climate became drier, and the forests of what are now Africa and Asia contracted. The result was an increased area of savanna (grassland) habitat, with fewer trees. Researchers have hypothesized that as the habitat changed, natural selection may have favored adaptations that made moving over open ground more efficient. Underlying this idea is the fact that while nonhuman apes are superbly adapted for climbing trees, they are less well suited for ground travel. For example, as a chimpanzee walks, it uses four times the amount of energy used by a human.

Although elements of this hypothesis survive, the picture now appears somewhat more complex. Even though all fossils of early hominins show indications of bipedalism, none of these hominins lived in savannas. Instead, they lived in mixed habitats ranging from forests to open woodlands. Furthermore, whatever the selective pressure that led to bipedalism, hominins did not become more bipedal in a simple, linear fashion. Ardipithecus had skeletal elements indicating that it could switch to upright walking but also was well suited for climbing trees. Australopiths seem to have had various locomotor styles, and some species spent more time on the ground than others. Only about 1.9 million years ago did hominins begin to walk long distances on two legs. These hominins lived in more arid environments, where bipedal walking requires less energy than walking on all fours.

The Evolutionary Advantage of Seeds: If a sperm fertilizes an egg of a seed plant, the zygote grows into a sporophyte embryo. As shown in Figure 30.3c, the ovule develops into a seed: the embryo, with a food supply, packaged in a protective coat derived from the integument(s). Until the advent of seeds, the spore was the only protective stage in any plant life cycle. Moss spores, for example, may survive even if the local environment becomes too cold, too hot, or too dry for the mosses themselves to live. Their tiny size enables the spores to be dispersed in a dormant state to a new area, where they can germinate and give rise to new moss gametophytes if and when conditions are favorable enough for them to break dormancy. Spores were the main way that mosses, ferns, and other seedless plants spread over Earth for the first 100 million years of plant life on land.

Although mosses and other seedless plants continue to be very successful today, seeds represent a major evolutionary innovation that contributed to the opening of new ways of life for seed plants. What advantages do seeds provide over spores? Spores are usually single-celled, whereas seeds are multicellular, consisting of an embryo protected by a layer of tissue, the seed coat. A seed can remain dormant for days, months, or even years after being released from the parent plant, whereas most spores have shorter lifetimes. Also, unlike spores, seeds have a supply of stored food. Most seeds land close to their parent sporophyte plant, but some are carried long distances (up to hundreds of kilometers) by wind or animals. If conditions are favorable where it lands, the seed can emerge from dormancy and germinate, with its stored food providing critical support for growth as the sporophyte embryo emerges as a seedling. As we explore in the Scientific Skills Exercise, some seeds have germinated after more than 1,000 years.

Shark eggs are fertilized internally. The male has a pair of claspers on its pelvic fins that transfer sperm into the female's reproductive tract. Some species of sharks are oviparous; they lay eggs that hatch outside the mother's body. These sharks release their fertilized eggs after encasing them in protective coats. Other species are ovoviviparous; they retain the fertilized eggs in the oviduct. Nourished by the egg yolk, the embryos develop into young that are born after hatching within the uterus. A few species are viviparous; the young develop within the uterus and obtain nourishment prior to birth by receiving nutrients from the mother's blood through a yolk sac placenta, by absorbing a nutritious fluid produced by the uterus, or by eating other eggs. The reproductive tract of the shark empties along with the excretory system and digestive tract into the cloaca, a common chamber that has a single opening to the outside.

Although rays are closely related to sharks, they have adopted a very different lifestyle. Most rays are bottomdwellers that feed by using their jaws to crush molluscs and crustaceans. They have a flattened shape and use their greatly enlarged pectoral fins like water wings to propel themselves through the water. The tail of many rays is whiplike and, in some species, bears venomous barbs that function in defense. Chondrichthyans have thrived for over 400 million years. Today, however, they are severely threatened by overfishing. A 2012 report, for example, indicated that shark populations in the Pacific have plummeted by up to 95%, and shark populations that live closest to people have declined the most.

Figure 31.24 Examples of fungal diseases of plants.: (a) Corn smut on corn b) Tar spot fungus on maple leaves Figure 31.23 Anatomy of an ascomycete lichen (colorized SEM).

Although slow-moving on its feet, the chameleon in Figure 32.1 can wield its long, sticky tongue with blinding speed to capture its unsuspecting prey. Many species of chameleons can also change their color and thereby blend into their surroundings— making them hard to detect, both by their prey and by the animals that would eat them.

Reproduction and Development: Most animals reproduce sexually, and the diploid stage usually dominates the life cycle. In the haploid stage, sperm and egg cells are produced directly by meiotic division, unlike what occurs in plants and fungi (see Figure 13.6). In most animal species, a small, flagellated sperm fertilizes a larger, nonmotile egg, forming a diploid zygote. The zygote then undergoes cleavage, a succession of mitotic cell divisions without cell growth between the divisions. During the development of most animals, cleavage leads to the formation of a multicellular embryonic stage called a blastula, which in many animals takes the form of a hollow ball (Figure 32.2). Following this stage is the process of gastrulation, during which the layers of embryonic tissues that will develop into adult body parts are produced (see also Figure 47.8). The resulting developmental stage is called a gastrula.

Although some animals, including humans, develop directly into adults, the life cycles of most animals include at least one larval stage. A larva is a sexually immature form of an animal that is morphologically distinct from the adult, usually eats different food, and may even have a different habitat than the adult, as in the case of the aquatic larva of a mosquito or dragonfly. Animal larvae eventually undergo metamorphosis, a developmental transformation that turns the animal into a juvenile that resembles an adult but is not yet sexually mature. Though adult animals vary widely in morphology, the genes that control animal development are similar across a broad range of taxa.

Ascomycetes vary in size and complexity from unicellular yeasts to elaborate cup fungi and morels (see Figure 31.15). They include some of the most devastating plant pathogens, which we will discuss later. However, many ascomycetes are important decomposers, particularly of plant material. More than 25% of all ascomycete species live with green algae or cyanobacteria in beneficial symbiotic associations called lichens. Some ascomycetes form mycorrhizae with plants. Many others live between mesophyll cells in leaves; some of these species release toxic compounds that help protect the plant from insects.

Although the life cycles of various ascomycete groups differ in the details of their reproductive structures and processes, we'll illustrate some common elements using the bread mold Neurospora crassa (Figure 31.16). Ascomycetes reproduce asexually by producing enormous numbers of asexual spores called conidia (singular, conidium). Unlike the asexual spores of most zygomycetes, in most ascomycetes, conidia are not formed inside sporangia. Rather, they are produced externally at the tips of specialized hyphae called conidiophores, often in clusters or long chains, from which they may be dispersed by the wind.

Over the past 30 years, zoologists have documented a rapid and alarming decline in amphibian populations in locations throughout the world. There appear to be several causes, including the spread of a disease-causing chytrid fungus (see Figure 31.25), habitat loss, climate change, and pollution. In some cases, declines have become extinctions. Recent studies indicate that at least 9 amphibian species have become extinct within the last four decades; more than 100 other species have not been observed in that time and are considered possibly extinct. In the Problem-Solving Exercise, you can explore one possible strategy to prevent amphibian deaths from fungal infections.

Amniotes are tetrapods that have a terrestrially adapted egg: The amniotes are a group of tetrapods whose extant members are the reptiles (including birds, as we'll discuss in this section) and mammals (Figure 34.25). During their evolution, amniotes acquired a number of new adaptations to life on land.

Another example is the wood-digesting protists that inhabit the gut of many termite species (Figure 28.27). Unaided, termites cannot digest wood, and they rely on protistan or prokaryotic symbionts to do so. Termites cause over $3.5 billion in damage annually to wooden homes in the United States. Symbiotic protists also include parasites that have compromised the economies of entire countries. Consider the malaria-causing protist Plasmodium: Income levels in countries hard hit by malaria are 33% lower than in similar countries free of the disease. Protists can have devastating effects on other species too. Massive fish kills have been attributed to Pfiesteria shumwayae (see Figure 28.15), a dinoflagellate parasite that attaches to its victims and eats their skin.

Among species that parasitize plants, the stramenopile Phytophthora ramorum has emerged as a major new forest pathogen. This species causes sudden oak death (SOD), a disease that has killed millions of oaks and other trees in the United States and Great Britain (Figure 28.28; also see Concept 54.5). A closely related species, P. infestans, causes potato late blight, which turns the stalks and stems of potato plants into black slime. Late blight contributed to the devastating Irish famine of the 19th century, in which a million people died and at least that many were forced to leave Ireland. The disease continues to be a major problem today, causing crop losses as high as 70% in some regions.

As you read earlier, the seed consists of the embryo, the endosperm, and a seed coat derived from the integuments. An ovary develops into a fruit as its ovules become seeds. After being dispersed, a seed may germinate if environmental conditions are favorable. The coat ruptures and the embryo emerges as a seedling, using food stored in the endosperm and cotyledons until it can produce its own food by photosynthesis.

Angiosperm Evolution: Charles Darwin once referred to the origin of angiosperms as an "abominable mystery." He was particularly troubled by the relatively sudden and geographically widespread appearance of angiosperms in the fossil record (about 100 million years ago, based on fossils known to Darwin). Recent fossil evidence and phylogenetic analyses have led to progress in solving Darwin's mystery, but we still do not fully understand how angiosperms arose from earlier seed plants.

Can we infer traits of the angiosperm common ancestor from traits found in early fossil angiosperms? Archaefructus, for example, was herbaceous and had bulbous structures that may have served as floats, suggesting it was aquatic. But investigating whether the angiosperm common ancestor was herbaceous and aquatic also requires examining fossils of other seed plants thought to have been closely related to angiosperms. All of those plants were woody, indicating that the common ancestor was probably woody and probably not aquatic. As we'll see, this conclusion has been supported by recent phylogenetic analyses.

Angiosperm Phylogeny: To shed light on the body plan of early angiosperms, scientists have sought to identify which seed plants, including fossil species, are most closely related to angiosperms. Molecular and morphological evidence suggests that extant gymnosperm lineages had diverged from the lineage leading to angiosperms by 305 million years ago. Note that this does not imply that angiosperms originated 305 million years ago, but that the most recent common ancestor of extant gymnosperms and angiosperms lived at that time. Indeed, angiosperms may be more closely related to several extinct lineages of woody seed plants than they are to gymnosperms.

Incomplete metamorphosis: Hemiptera (85,000 species): Hemipterans include so-called "true bugs," such as stink bugs, bed bugs, and assassin bugs. (Insects in other orders are sometimes erroneously called bugs.) Hemipterans have two pairs of wings, one pair partly leathery, the other pair membranous. They have piercing or sucking mouthparts and undergo incomplete metamorphosis, as shown in this image of an adult stink bug guarding its offspring (nymphs). Orthoptera (13,000 species): Grasshoppers, crickets, and their relatives are mostly herbivorous. They have large hind legs adapted for jumping, two pairs of wings (one leathery, one membranous), and biting or chewing mouthparts. This aptly named spiny devil katydid (Panacanthus cuspidatus) has a face and legs specialized for making a threatening display. Male orthopterans commonly make courtship sounds by rubbing together body parts, such as ridges on their hind legs.

Animals as numerous, diverse, and widespread as insects are bound to affect the lives of most other terrestrial organisms, including humans. Insects consume enormous quantities of plant matter; play key roles as predators, parasites, and decomposers; and are an essential source of food for larger animals such as lizards, rodents, and birds. Humans depend on bees, flies, and many other insects to pollinate crops and orchards. In addition, people in many parts of the world eat insects as an important source of protein. On the other hand, insects are carriers for many diseases, including African sleeping sickness (spread by tsetse flies that carry the protist Trypanosoma; see Figure 28.7) and malaria (spread by mosquitoes that carry the protist Plasmodium; see Figure 23.18 and Figure 28.16). Insects also compete with humans for food. In parts of Africa, for instance, insects claim about 75% of the crops. In the United States, billions of dollars are spent each year on pesticides, spraying crops with massive doses of some of the deadliest poisons ever invented. Try as they may, not even humans have challenged the preeminence of insects and their arthropod kin. As one prominent entomologist put it: "Bugs are not going to inherit the Earth. They own it now. So we might as well make peace with the landlord."

Cenozoic Era (66 Million Years Ago to the Present): Mass extinctions of both terrestrial and marine animals ushered in a new era, the Cenozoic. Among the groups of species that disappeared were the large, nonflying dinosaurs and the marine reptiles. The fossil record of the early Cenozoic documents the rise of large mammalian herbivores and predators as mammals began to exploit the vacated ecological niches. The global climate gradually cooled throughout the Cenozoic, triggering significant shifts in many animal lineages. Among primates, for example, some species in Africa adapted to the open woodlands and savannas that replaced many of the former dense forests. The ancestors of our own species were among those grassland apes.

Animals can be characterized by "body plans": Animal species vary tremendously in morphology, but their great diversity in form can be described by a relatively small number of major "body plans." A body plan is a particular set of morphological and developmental traits, integrated into a functional whole—the living animal. The term plan here does not imply that animal forms are the result of conscious planning or invention. But body plans do provide a succinct way to compare and contrast key animal features. They also are of interest in the study of evo-devo, the interface between evolution and development.

Unikonts include protists that are closely related to fungi and animals: Unikonta is an extremely diverse supergroup of eukaryotes that includes animals, fungi, and some protists. There are two major clades of unikonts, the amoebozoans and the opisthokonts (animals, fungi, and closely related protist groups). Each of these two major clades is strongly supported by molecular systematics. The close relationship between amoebozoans and opisthokonts is more controversial. Support for this close relationship is provided by comparisons of myosin proteins and by some (but not all) studies based on multiple genes or whole genomes.

Another controversy involving the unikonts concerns the root of the eukaryotic tree. Recall that the root of a phylogenetic tree anchors the tree in time: Branch points close to the root are the oldest. At present, the root of the eukaryotic tree is uncertain; hence, we do not know which supergroup of eukaryotes was the first to diverge from all other eukaryotes. Some hypotheses, such as the amitochondriate hypothesis described earlier, have been abandoned, but researchers have yet to agree on an alternative. If the root of the eukaryotic tree were known, it would help scientists infer characteristics of the common ancestor of all eukaryotes.

Derived Characters of Vertebrates: Living vertebrates share a set of derived characters that distinguish them from other chordates. For example, as a result of gene duplication, vertebrates possess two or more sets of Hox genes (lancelets and tunicates have only one). Other important families of genes that produce transcription factors and signaling molecules are also duplicated in vertebrates. The resulting additional genetic complexity may be associated with innovations in the vertebrate nervous system and skeleton, including the development of a skull and a backbone composed of vertebrae. In some vertebrates, the vertebrae are little more than small prongs of cartilage arrayed dorsally along the notochord. In the majority of vertebrates, however, the vertebrae enclose the spinal cord and have taken over the mechanical roles of the notochord.

Another feature unique to vertebrates is the neural crest, a collection of cells that appears along the edges of the closing neural tube of an embryo (Figure 34.7). Neural crest cells disperse throughout the embryo, where they give rise to a variety of structures, including teeth, some of the bones and cartilage of the skull, several types of neurons, and the sensory capsules in which eyes and other sense organs develop.

As the diversity of animal phyla increased during the Cambrian, the diversity of Ediacaran life-forms declined. What caused these trends? Fossil evidence suggests that during the Cambrian period, predators acquired novel adaptations, such as forms of locomotion that helped them catch prey, while prey species acquired new defenses, such as protective shells. As new predator-prey relationships emerged, natural selection may have led to the decline of the softbodied Ediacaran species and the rise of various bilaterian phyla.

Another hypothesis focuses on an increase in atmospheric oxygen that preceded the Cambrian explosion. More plentiful oxygen would have enabled animals with higher metabolic rates and larger body sizes to thrive, while potentially harming other species. A third hypothesis proposes that genetic changes affecting development, such as the origin of Hox genes and the addition of new microRNAs (small RNAs involved in gene regulation), facilitated the evolution of new body forms. In the Scientific Skills Exercise, you can investigate whether there is a correlation between microRNAs (miRNAs; see Figure 18.14) and body complexity in various animal phyla.

At the risk of oversimplifying, we could say that A. afarensis had fewer of the derived characters of humans above the neck than below. Lucy's brain was the size of a softball, a size similar to that expected for a chimpanzee of Lucy's body size. A. afarensis skulls also have a long lower jaw. Skeletons of A. afarensis suggest that these hominins were capable of arboreal locomotion, with arms that were relatively long in proportion to body size (compared to the proportions in humans). However, fragments of pelvic and skull bones indicate that A. afarensis walked on two legs. Fossilized footprints in Laetoli, Tanzania, corroborate the skeletal evidence that hominins living at the time of A. afarensis were bipedal (Figure 34.49).

Another lineage of australopiths consisted of the "robust" australopiths. These hominins, which included species such as Paranthropus boisei, had sturdy skulls with powerful jaws and large teeth, adapted for grinding and chewing hard, tough foods. They contrast with the "gracile" (slender) australopiths, including A. afarensis and A. africanus, which had lighter feeding equipment adapted for softer foods. Combining evidence from the earliest hominins with the much richer fossil record of later australopiths makes it possible to formulate hypotheses about significant trends in hominin evolution. In the Scientific Skills Exercise, you'll examine one such trend: how hominin brain volume has changed over time. Here we'll consider two other trends: the emergence of bipedalism and tool use.

Note that the characters that distinguish humans from other living apes did not all evolve in tight unison. While early hominins were showing signs of bipedalism, their brains remained small—about 300-450 cm3 in volume, compared with an average of 1,300 cm3 for Homo sapiens. The earliest hominins were also small overall. A. ramidus, for example, is estimated to have been about 1.2 m tall, with relatively large teeth and a jaw that projected beyond the upper part of the face. Humans, in contrast, average about 1.7 m in height and have a relatively flat face; compare your own face with that of the chimpanzees in Figure 34.46d. It's important to avoid two common misconceptions about early hominins. One is to think of them either as chimpanzees or as having evolved from chimpanzees. Chimpanzees represent the tip of a separate branch of evolution, and they acquired derived characters of their own after they diverged from their common ancestor with humans.

Another misconception is to think of human evolution as a ladder leading directly from an ancestral ape to Homo sapiens. This error is often illustrated as a parade of fossil species that become progressively more like ourselves as they march across the page. If human evolution is a parade, it is a very disorderly one, with many groups breaking away to wander other evolutionary paths. At times, several hominin species coexisted. These species often differed in skull shape, body size, and diet (as inferred from their teeth). Ultimately, all but one lineage— the one that gave rise to Homo sapiens—ended in extinction. Overall, considering the characteristics of all hominins that lived over the past 6.5 million years, H. sapiens appears not as the end result of a straight evolutionary path, but rather as the only surviving member of a highly branched evolutionary tree.

What is the function of double fertilization in angiosperms? One hypothesis is that double fertilization synchronizes the development of food storage in the seed with the development of the embryo. If a particular flower is not pollinated or sperm cells are not discharged into the embryo sac, fertilization does not occur, and neither endosperm nor embryo forms. So perhaps double fertilization is an adaptation that prevents flowering plants from squandering nutrients on infertile ovules.

Another type of double fertilization occurs in some gymnosperm species belonging to the phylum Gnetophyta. However, double fertilization in these species gives rise to two embryos rather than to an embryo and endosperm.

Recently, the prokaryotic CRISPR-Cas system, which helps bacteria and archaea defend against attack by viruses (see Figure 19.7), has been developed into a powerful new tool for altering genes in virtually any organism. The genomes of many prokaryotes contain short DNA repeats, called CRISPRs, that interact with proteins known as the Cas (CRISPR-associated) proteins. Cas proteins, acting together with "guide RNA" made from the CRISPR region, can cut any DNA sequence to which they are directed. Scientists have been able to exploit this system by introducing a Cas protein (Cas9) to guide RNA into cells whose DNA they want to alter (see Figure 20.14). Among other applications, this CRISPR-Cas9 system has already opened new lines of research on HIV, the virus that causes AIDS (Figure 27.21). While the CRISPR-Cas9 system can potentially be used in many different ways, care must be taken to guard against the unintended consequences that could arise when applying such a new and powerful technology.

Another valuable application of bacteria is to reduce our use of petroleum. Consider the plastics industry. Globally, each year about 350 billion pounds of plastic are produced from petroleum and used to make toys, storage containers, soft drink bottles, and many other items. These products degrade slowly, creating environmental problems. Bacteria produce natural plastics (Figure 27.22). For example, some bacteria synthesize a type of polymer known as PHA (polyhydroxyalkanoate), which they use to store chemical energy. The PHA can be extracted, formed into pellets, and used to make durable, yet biodegradable, plastics.

Dinoflagellates (a) Dinoflagellate flagella. Beating of the spiral flagellum, which lies in a groove that encircles the cell, makes this specimen of Pfiesteria shumwayae spin (colorized SEM). (b) Red tide in the Gulf of Carpentaria in northern Australia. The red color is due to high concentrations of a carotenoid-containing dinoflagellate.

Apicomplexans: Nearly all apicomplexans are parasites of animals—and virtually all animal species examined so far are attacked by these parasites. The parasites spread through their host as tiny infectious cells called sporozoites. Apicomplexans are so named because one end (the apex) of the sporozoite cell contains a complex of organelles specialized for penetrating host cells and tissues. Although apicomplexans are not photosynthetic, recent data show that they retain a modified plastid (apicoplast), most likely of red algal origin.

SAR: This supergroup contains (and is named after) three large and very diverse clades: Stramenopila, Alveolata, and Rhizaria. Stramenopiles include some of the most important photosynthetic organisms on Earth, such as the diatoms shown here. Alveolates also include photosynthetic species, as well as important pathogens, such as Plasmodium, which causes malaria. According to one current hypothesis, stramenopiles and alveolates originated by secondary endosymbiosis when a heterotrophic protist engulfed a red alga. Diatom diversity. These beautiful single-celled protists are important photosynthetic organisms in aquatic communities (LM). The rhizarian subgroup of SAR includes many species of amoebas, most of which have pseudopodia that are threadlike in shape. Pseudopodia are extensions that can bulge from any portion of the cell; they are used in movement and in the capture of prey Globigerina, a rhizarian in SAR. This species is a foram, a group whose members have threadlike pseudopodia that extend through pores in the shell, or test (LM). The inset shows a foram test, which is hardened by calcium carbonate.

Archaeplastida: This supergroup of eukaryotes includes red algae and green algae, along with plants. Red algae and green algae include unicellular species, colonial species, and multicellular species (including the green alga Volvox). Many of the large algae known informally as "seaweeds" are multicellular red or green algae. Protists in Archaeplastida include key photosynthetic species that form the base of the food web in many aquatic communities. Volvox, a multicellular freshwater green alga. This alga has two types of differentiated cells, and so it is considered multicellular rather than colonial. It resembles a hollow ball whose wall is composed of hundreds of biflagellated cells (see inset LM) embedded in a gelatinous extracellular matrix; if isolated, these cells cannot reproduce. However, the alga also contains cells that are specialized for either sexual or asexual reproduction. The large algae shown here will eventually release the small "daughter" algae that can be seen within them (LM)

Nematoda (25,000 species): Also called roundworms, nematodes are enormously abundant and diverse in the soil and in aquatic habitats; many species parasitize plants and animals. Their most distinctive feature is a tough cuticle that coats their body (see Concept 33.4). A roundworm.

Arthropoda (1,000,000 species): The vast majority of known animal species, including insects, crustaceans, and arachnids, are arthropods. All arthropods have a segmented exoskeleton and jointed appendages (see Concept 33.4). A spider (an arachnid).

When the arthropod exoskeleton first evolved in the sea, its main functions were probably protection and anchorage for muscles, but it later enabled certain arthropods to live on land. The exoskeleton's relative impermeability to water helped prevent desiccation, and its strength provided support when arthropods left the buoyancy of water. Fossil evidence suggests that arthropods were among the first animals to colonize land, roughly 450 million years ago. These fossils include fragments of arthropod remains, as well as possible millipede burrows. Arthropod fossils from several continents indicate that by 410 million years ago, millipedes, centipedes, spiders, and a variety of wingless insects all had colonized land.

Arthropods have well-developed sensory organs, including eyes, olfactory (smell) receptors, and antennae that function in both touch and smell. Most sensory organs are concentrated at the anterior end of the animal, although there are interesting exceptions. Female butterflies, for example, "taste" plants using sensory organs on their feet.

Figure 33.28 Juveniles of the parasitic nematode Trichinella spiralis encysted in human muscle tissue.

Arthropods: Zoologists estimate that there are about a billion billion (1018) arthropods living on Earth. More than 1 million arthropod species have been described, most of which are insects. In fact, two out of every three known species are arthropods, and members of the phylum Arthropoda can be found in nearly all habitats of the biosphere. By the criteria of species diversity, distribution, and sheer numbers, arthropods must be regarded as the most successful of all animal phyla.

New findings continually update our understanding of the human evolutionary lineage. For example, in 2015, the human family gained a new member, Homo naledi. The structure of its foot indicates that H. naledi was fully bipedal, and the shape of its hand suggests that H. naledi had fine motor skills (Figure 34.53), as in H. sapiens, Neanderthals, and other species that used tools extensively. But H. naledi also had a small brain, a flared upper pelvis, and other features that have led researchers to conclude that it was an early member of our genus.

As an early member of our genus, it is likely that H. naledi originated more than 2 million years ago—yet estimates of the age of the H. naledi fossils range from 3 million years old to just 100,000 years old. Scientists don't know how old the fossils are because they were found on the floor of a deep cave, not encased in rocks that could be dated using radioactive isotopes. If new evidence shows that the fossils are only 100,000 years old, that would suggest that H. naledi arose several million years ago (like other early members of our genus) and then persisted almost until the present.

Some morphological and DNA sequence data suggest that two of these groups, the stramenopiles and alveolates, originated more than a billion years ago, when a common ancestor of these two clades engulfed a single-celled, photosynthetic red alga. Because red algae are thought to have originated by primary endosymbiosis (see Figure 28.3), such an origin for the stramenopiles and alveolates is referred to as secondary endosymbiosis. Others question this idea, noting that some species in these groups lack plastids or their remnants (including any trace of plastid genes in their nuclear DNA).

As its lack of a formal name suggests, SAR is one of the most controversial of the four supergroups we describe in this chapter. Even so, for many scientists, this supergroup represents the best current hypothesis for the phylogeny of the three large protist clades to which we now turn.

Lampreys: The second group of living jawless vertebrates, the lampreys, consists of about 38 species inhabiting various marine and freshwater environments (Figure 34.9). Some are parasites that feed by clamping their round, jawless mouth onto the flank of a live fish, their "host." Parasitic lampreys use their rasping mouth and tongue to penetrate the skin of the fish and ingest the fish's blood and other tissues.

As larvae, lampreys live in freshwater streams. The larva is a suspension feeder that resembles a lancelet and spends much of its time partially buried in sediment. About 20 species of lampreys are not parasitic. These species feed only as larvae; following several years in streams, they mature sexually, reproduce, and die within a few days. In contrast, parasitic species of lampreys migrate to the sea or lakes as they mature into adults. One such parasite, the sea lamprey (Petromyzon marinus), has invaded the Great Lakes over the past 170 years and devastated a number of fisheries there.

Phylum Monilophyta: Ferns, Horsetails, and Whisk Ferns and Relatives Ferns radiated extensively from their Devonian origins and grew alongside lycophyte trees and horsetails in the great Carboniferous swamp forests. Today, ferns are by far the most widespread seedless vascular plants, numbering more than 12,000 species. Though most diverse in the tropics, many ferns thrive in temperate forests, and some species are even adapted to arid habitats.

As mentioned earlier, ferns and other monilophytes are more closely related to seed plants than to lycophytes. As a result, monilophytes and seed plants share traits that are not found in lycophytes, including megaphyll leaves and roots that can branch at various points along the length of an existing root. In lycophytes, by contrast, roots branch only at the growing tip of the root, forming a Y-shaped structure. The monilophytes called horsetails were very diverse during the Carboniferous period, some growing as tall as 15 m. Today, only 15 species survive as a single, widely distributed genus, Equisetum, often found in marshy places and along streams.

Figure 31.15 Ascomycetes (sac fungi).: Tuber melanosporum is a truffle species that forms ectomycorrhizae with trees. The ascocarp grows underground and emits a strong odor. These ascocarps have been dug up and the middle one sliced open. The edible ascocarp of Morchella esculenta, the tasty morel, is often found under trees in orchards.

Ascomycetes: Mycologists have described 65,000 species of ascomycetes, fungi in the phylum Ascomycota, from a wide variety of marine, freshwater, and terrestrial habitats. The defining feature of ascomycetes is the production of spores (called ascospores) in saclike asci (singular, ascus); thus, they are commonly called sac fungi. During their sexual stage, most ascomycetes develop fruiting bodies, called ascocarps, which range in size from microscopic to macroscopic (Figure 31.15). The ascocarps contain the spore-forming asci.

The union of the cytoplasms of two parent mycelia is known as plasmogamy (see Figure 31.5). In most fungi, the haploid nuclei contributed by each parent do not fuse right away. Instead, parts of the fused mycelium contain coexisting, genetically different nuclei. Such a mycelium is said to be a heterokaryon (meaning "different nuclei"). In some species, the haploid nuclei pair off two to a cell, one from each parent. Such a mycelium is dikaryotic (meaning "two nuclei"). As a dikaryotic mycelium grows, the two nuclei in each cell divide in tandem without fusing. Because these cells retain two separate haploid nuclei, they differ from diploid cells, which have pairs of homologous chromosomes within a single nucleus. Hours, days, or (in some fungi) even centuries may pass between plasmogamy and the next stage in the sexual cycle, karyogamy. During karyogamy, the haploid nuclei contributed by the two parents fuse, producing diploid cells. Zygotes and other transient structures form during karyogamy, the only diploid stage in most fungi. Meiosis then restores the haploid condition, ultimately leading to the formation of genetically diverse spores. Meiosis is a key step in sexual reproduction, so spores produced in this way are sometimes referred to as "sexual spores." The sexual processes of karyogamy and meiosis generate extensive genetic variation, a prerequisite for natural selection. (See Concepts 13.2 and 23.1 to review how sex can increase genetic diversity.) The heterokaryotic condition also offers some of the advantages of diploidy in that one haploid genome may compensate for harmful mutations in the other.

Asexual Reproduction: Although many fungi can reproduce both sexually and asexually, some 20,000 species are only known to reproduce asexually. As with sexual reproduction, the processes of asexual reproduction vary widely among fungi. Many fungi reproduce asexually by growing as filamentous fungi that produce (haploid) spores by mitosis; such species are informally referred to as molds if they form visible mycelia. Depending on your housekeeping habits, you may have observed molds in your kitchen, forming furry carpets on bread or fruit (Figure 31.6). Molds typically grow rapidly and produce many spores asexually, enabling the fungi to colonize new sources of food. Many species that produce such spores can also reproduce sexually if they happen to contact a member of their species of a different mating type.

Australopiths: The fossil record indicates that hominin diversity increased dramatically between 4 and 2 million years ago. Many of the hominins from this period are collectively called australopiths. Their phylogeny remains unresolved on many points, but as a group, they are almost certainly paraphyletic. The earliest member of the group, Australopithecus anamensis, lived 4.2-3.9 million years ago, close in time to older hominins such as Ardipithecus ramidus

Australopiths got their name from the 1924 discovery in South Africa of Australopithecus africanus ("southern ape of Africa"), which lived between 3 and 2.4 million years ago. With the discovery of more fossils, it became clear that A. africanus walked fully erect (was bipedal) and had human-like hands and teeth. However, its brain was only about one-third the size of the brain of a present-day human. In 1974, in the Afar region of Ethiopia, scientists discovered a 3.2-million-year-old Australopithecus skeleton that was 40% complete. "Lucy," as the fossil was named, was short—only about 1 m tall. Lucy and similar fossils have been given the species name Australopithecus afarensis (for the Afar region). Fossil evidence shows that A. afarensis existed as a species for at least 1 million years.

Basidiomycetes: About 30,000 species, including mushrooms, puffballs, and shelf fungi, are called basidiomycetes and are classified in the phylum Basidiomycota (Figure 31.17). This phylum also includes mutualists that form mycorrhizae and two groups of destructive plant parasites: rusts and smuts. The name of the phylum derives from the basidium (plural, basidia; Latin for "little pedestals"), a cell in which karyogamy occurs, followed immediately by meiosis. The club-like shape of the basidium also gives rise to the common name club fungus.

Basidiomycetes are important decomposers of wood and other plant material. Of all the fungi, certain basidiomycetes are the best at decomposing the complex polymer lignin, an abundant component of wood. Many shelf fungi break down the wood of weak or damaged trees and continue to decompose the wood after the tree dies. The life cycle of a basidiomycete usually includes a longlived dikaryotic mycelium. As in ascomycetes, this extended dikaryotic stage provides many opportunities for genetic recombination events, in effect multiplying the result of a single mating. Periodically, in response to environmental stimuli, the mycelium reproduces sexually by producing elaborate fruiting bodies called basidiocarps (Figure 31.18). The common white mushrooms in the supermarket are familiar examples of a basidiocarp.

Derived Characters of Humans: Many characters distinguish humans from other apes. Most obviously, humans stand upright and are bipedal (walk on two legs). Humans have a much larger brain and are capable of language, symbolic thought, artistic expression, and the manufacture and use of complex tools. Humans also have reduced jawbones and jaw muscles, along with a shorter digestive tract. At the molecular level, the list of derived characters of humans is growing as scientists compare the human and chimpanzee genomes. Although the two genomes are 99% identical, a difference of 1% can represent many changes in a genome with 3 billion base pairs. Furthermore, changes in a small number of genes can have large effects. This point was highlighted by recent results showing that humans and chimpanzees differ in the expression of 19 regulatory genes. These genes turn other genes on and off and hence may account for many differences between humans and chimpanzees.

Bear in mind that such genomic differences—and whatever derived phenotypic traits they encode—separate humans from other living apes. But many of these new characters first emerged in our ancestors, long before our own species appeared. We will consider some of these ancestors to see how these characters originated.

Photosynthetic Protists: Many protists are important producers, organisms that use energy from light (or in some prokaryotes, inorganic chemicals) to convert CO2 to organic compounds. Producers form the base of ecological food webs. In aquatic communities, the main producers are photosynthetic protists and prokaryotes (Figure 28.29). All other organisms in the community depend on them for food, either directly (by eating them) or indirectly (by eating an organism that ate a producer). Scientists estimate that roughly 30% of the world's photosynthesis is performed by diatoms, dinoflagellates, multicellular algae, and other aquatic protists. Photosynthetic prokaryotes contribute another 20%, and plants are responsible for the remaining 50%.

Because producers form the foundation of food webs, factors that affect producers can dramatically affect their entire community. In aquatic environments, photosynthetic protists are often held in check by low concentrations of nitrogen, phosphorus, or iron. Various human actions can increase the concentrations of these elements in aquatic communities. For example, when fertilizer is applied to a field, some of the fertilizer may be washed by rainfall into a river that drains into a lake or ocean. When people add nutrients to aquatic communities in this or other ways, the abundance of photosynthetic protists can increase spectacularly. Such increases can have major ecological consequences, including the formation of large "dead zones" in marine ecosystems (see Figure 56.23).

As seen in Figure 32.11, hemichordates (acorn worms), echinoderms (sea stars and relatives), and chordates are members of the bilaterian clade Deuterostomia; thus, the term deuterostome refers not only to a mode of animal development, but also to the members of this clade. (The dual meaning of this term can be confusing since some organisms with a deuterostome developmental pattern are not members of clade Deuterostomia.) Hemichordates share some characteristics with chordates, such as gill slits and a dorsal nerve cord; echinoderms lack these characteristics. These shared traits may have been present in the common ancestor of the deuterostome clade (and lost in the echinoderm lineage). As mentioned above, phylum Chordata, the only phylum with vertebrate members, also includes invertebrates.

Bilaterians also diversified in two major clades that are composed entirely of invertebrates: the ecdysozoans and the lophotrochozoans. The clade name Ecdysozoa refers to a characteristic shared by nematodes, arthropods, and some of the other ecdysozoan phyla that are not included in our survey. These animals secrete external skeletons (exoskeletons); the stiff covering of a cricket and the flexible cuticle of a nematode are examples. As the animal grows, it molts, squirming out of its old exoskeleton and secreting a larger one. The process of shedding the old exoskeleton is called ecdysis. Though named for this characteristic, the clade was proposed mainly on the basis of molecular data that support the common ancestry of its members. Furthermore, some taxa excluded from this clade by their molecular data, such as certain species of leeches, do in fact molt.

Crocodilians: Alligators and crocodiles (collectively called crocodilians) belong to a lineage that reaches back to the late Triassic. The earliest members of this lineage were small terrestrial quadrupeds with long, slender legs. Later species became larger and adapted to aquatic habitats, breathing air through their upturned nostrils. Some Mesozoic crocodilians grew as long as 12 m and may have attacked dinosaurs and other prey at the water's edge. The 23 known species of living crocodilians are confined to warm regions of the globe. In the southeastern United States, the American alligator (Figure 34.29e) has made a comeback after spending years on the endangered species list.

Birds: There are about 10,000 species of birds in the world. Like crocodilians, birds are archosaurs, but almost every feature of their anatomy has been modified in their adaptation to flight. Derived Characters of Birds :Many of the characters of birds are adaptations that facilitate flight, including weightsaving modifications that make flying more efficient. For example, birds lack a urinary bladder, and the females of most species have only one ovary. The gonads of both females and males are usually small, except during the breeding season, when they increase in size. Living birds are also toothless, an adaptation that trims the weight of the head.

Many bryophyte species can increase the number of individuals in a local area through various methods of asexual reproduction. For example, some mosses reproduce asexually by forming brood bodies, small plantlets (as shown here) that detach from the parent plant and grow into new, genetically identical copies of their parent.

Bryophyte Sporophytes: The cells of bryophyte sporophytes contain plastids that are usually green and photosynthetic when the sporophytes are young. Even so, bryophyte sporophytes cannot live independently. A bryophyte sporophyte remains attached to its parental gametophyte throughout the sporophyte's lifetime, dependent on the gametophyte for supplies of sugars, amino acids, minerals, and water.

Bryophyte Gametophytes: Unlike vascular plants, in all three bryophyte phyla the haploid gametophytes are the dominant stage of the life cycle: They are usually larger and longer-living than the sporophytes, as shown in the moss life cycle in Figure 29.7. The sporophytes are typically present only part of the time. When bryophyte spores are dispersed to a favorable habitat, such as moist soil or tree bark, they may germinate and grow into gametophytes. Germinating moss spores, for example, characteristically produce a mass of green, branched, one-cell-thick filaments known as a protonema (plural, protonemata). A protonema has a large surface area that enhances absorption of water and minerals. In favorable conditions, a protonema produces one or more "buds." (Note that when referring to nonvascular plants, we often use quotation marks for structures similar to the buds, stems, and leaves of vascular plants because the definitions of these terms are based on vascular plant organs.) Each of these budlike growths has an apical meristem that generates a gameteproducing structure known as a gametophore. Together, a protonema and one or more gametophores make up the body of a moss gametophyte.

Bryophyte gametophytes generally form ground-hugging carpets, partly because their body parts are too thin to support a tall plant. A second constraint on the height of many bryophytes is the absence of vascular tissue, which would enable long-distance transport of water and nutrients. (The thin structure of bryophyte organs makes it possible to distribute materials for short distances without specialized vascular tissue.) However, some mosses have conducting tissues in the center of their "stems." A few of these mosses can grow as tall as 60 cm (2 feet) as a result. Phylogenetic analyses suggest that conducting tissues similar to those of vascular plants arose independently in these mosses by convergent evolution.

The gametophytes are anchored by delicate rhizoids, which are long, tubular single cells (in liverworts and hornworts) or filaments of cells (in mosses). Unlike roots, which are found in vascular plant sporophytes, rhizoids are not composed of tissues. Bryophyte rhizoids also lack specialized conducting cells and do not play a primary role in water and mineral absorption. Gametophytes can form multiple gametangia, each of which produces gametes and is covered by protective tissue. Each archegonium produces one egg, whereas each antheridium produces many sperm. Some bryophyte gametophytes are bisexual, but in mosses the archegonia and antheridia are typically carried on separate female and male gametophytes. Flagellated sperm swim through a film of water toward eggs, entering the archegonia in response to chemical attractants. Eggs are not released but instead remain within the bases of archegonia. After fertilization, embryos are retained within the archegonia. Layers of placental transfer cells help transport nutrients to the embryos as they develop into sporophytes.

Bryophyte sperm typically require a film of water to reach the eggs. Given this requirement, it is not surprising that many bryophyte species are found in moist habitats. The fact that sperm swim through water to reach the egg also means that in species with separate male and female gametophytes (most species of mosses), sexual reproduction is likely to be more successful when individuals are located close to one another.

Bryophytes have the smallest sporophytes of all extant plant groups, consistent with the hypothesis that larger sporophytes evolved only later, in the vascular plants. A typical bryophyte sporophyte consists of a foot, a seta, and a sporangium. Embedded in the archegonium, the foot absorbs nutrients from the gametophyte. The seta (plural, setae), or stalk, conducts these materials to the sporangium, also called a capsule, which produces spores by meiosis.

Bryophyte sporophytes can produce enormous numbers of spores. A single moss capsule, for example, can generate over 5 million spores. In most mosses, the seta becomes elongated, enhancing spore dispersal by elevating the capsule. Typically, the upper part of the capsule features a ring of interlocking, tooth-like structures known as the peristome (see Figure 29.7). These "teeth" open under dry conditions and close again when it is moist. This allows moss spores to be discharged gradually, via periodic gusts of wind that can carry them long distances.

During the Jurassic (201-145 million years ago), the first true mammals arose and diversified into many short-lived lineages. A diverse set of mammal species coexisted with dinosaurs in the Jurassic and Cretaceous periods, but these species were not abundant or dominant members of their communities, and most measured less than 1 m in length. One factor that may have contributed to their small size is that dinosaurs already occupied ecological niches of large-bodied animals.

By the early Cretaceous (140 million years ago), the three major lineages of mammals had emerged: those leading to monotremes (egg-laying mammals), marsupials (mammals with a pouch), and eutherians (placental mammals). After the extinction of large dinosaurs, pterosaurs, and marine reptiles during the late Cretaceous period, mammals underwent an adaptive radiation, giving rise to large predators and herbivores as well as flying and aquatic species.

Lobe-Fins: Like the ray-finned fishes, the other major lineage of osteichthyans, the lobe-fins (Sarcopterygii), also originated during the Silurian period (Figure 34.18). The key derived character of lobe-fins is the presence of rod-shaped bones surrounded by a thick layer of muscle in their pectoral and pelvic fins. During the Devonian (419-359 million years ago), many lobe-fins lived in brackish waters, such as in coastal wetlands. There they may have used their lobed fins to help them move across logs or the muddy bottom (as do some living lobe-fins). Some Devonian lobe-fins were gigantic predators. It is not uncommon to find spike-shaped fossils of Devonian lobe-fin teeth as big as your thumb.

By the end of the Devonian period, lobe-fin diversity was dwindling, and today only three lineages survive. One lineage, the coelacanths (Actinistia), was thought to have become extinct 75 million years ago. However, in 1938, fishermen caught a living coelacanth off the east coast of South Africa (Figure 34.19). Until the 1990s, all subsequent discoveries were near the Comoros Islands in the western Indian Ocean. Since 1999, coelacanths have also been found at various places along the eastern coast of Africa and in the eastern Indian Ocean, near Indonesia. The Indonesian population may represent a second species

Plasmodial Slime Molds: Many plasmodial slime molds are brightly colored, often yellow or orange (Figure 28.25). As they grow, they form a mass called a plasmodium, which can be many centimeters in diameter. (Don't confuse a slime mold's plasmodium with the genus Plasmodium, which includes the parasitic apicomplexan that causes malaria.) Despite its size, the plasmodium is not multicellular; it is a single mass of cytoplasm that is undivided by plasma membranes and that contains many nuclei. This "supercell" is the product of mitotic nuclear divisions that are not followed by cytokinesis. The plasmodium extends pseudopodia through moist soil, leaf mulch, or rotting logs, engulfing food particles by phagocytosis as it grows. If the habitat begins to dry up or there is no food left, the plasmodium stops growing and differentiates into fruiting bodies that function in sexual reproduction.

Cellular Slime Molds: The life cycle of the protists called cellular slime molds can prompt us to question what it means to be an individual organism. The feeding stage of these organisms consists of solitary cells that function individually, but when food is depleted, the cells form a slug-like aggregate that functions as a unit (Figure 28.26). Unlike the feeding stage (plasmodium) of a plasmodial slime mold, these aggregated cells remain separated by their individual plasma membranes. Ultimately, the aggregated cells form an asexual fruiting body.

Forams: The protists called foraminiferans (from the Latin foramen, little hole, and ferre, to bear), or forams, are named for their porous shells, called tests (see Figure 28.2). Foram tests consist of a single piece of organic material that typically is hardened with calcium carbonate. The pseudopodia that extend through the pores function in swimming, test formation, and feeding. Many forams also derive nourishment from the photosynthesis of symbiotic algae that live within the tests. Forams are found in both the ocean and fresh water. Most species live in sand or attach themselves to rocks or algae, but some live as plankton. The largest forams, though singlecelled, have tests several centimeters in diameter. Ninety percent of all identified species of forams are known from fossils. Along with the calcium-containing remains of other protists, the fossilized tests of forams are part of marine sediments, including sedimentary rocks that are now land formations. Foram fossils are excellent markers for correlating the ages of sedimentary rocks in different parts of the world. Researchers are also studying these fossils to obtain information about climate change and its effects on the oceans and their life (Figure 28.19).

Cercozoans: First identified in molecular phylogenies, the cercozoans are a large group of amoeboid and flagellated protists that feed using threadlike pseudopodia. Cercozoan protists are common inhabitants of marine, freshwater, and soil ecosystems. Most cercozoans are heterotrophs. Many are parasites of plants, animals, or other protists; many others are predators. The predators include the most important consumers of bacteria in aquatic and soil ecosystems, along with species that eat other protists, fungi, and even small animals. One small group of cercozoans, the chlorarachniophytes (mentioned earlier in the discussion of secondary endosymbiosis), are mixotrophic: These organisms ingest smaller protists and bacteria as well as perform photosynthesis. At least one other cercozoan, Paulinella chromatophora, is an autotroph, deriving its energy from light and its carbon from CO2. As described in Figure 28.20, Paulinella appears to represent an intriguing additional evolutionary example of a eukaryotic lineage that obtained its photosynthetic apparatus directly from a cyanobacterium.

Most molluscs have separate sexes, and their gonads (ovaries or testes) are located in the visceral mass. Many snails, however, are hermaphrodites. The life cycle of many marine molluscs includes a ciliated larval stage, the trochophore (see Figure 32.12b), which is also characteristic of marine annelids (segmented worms) and some other lophotrochozoans. The basic body plan of molluscs has evolved in various ways in the phylum's eight major clades. We'll examine four of those clades here: Polyplacophora (chitons), Gastropoda (snails and slugs), Bivalvia (clams, oysters, and other bivalves), and Cephalopoda (squids, octopuses, cuttlefishes, and chambered nautiluses). We will then focus on threats facing some groups of molluscs.

Chitons: Chitons have an oval-shaped body and a shell composed of eight dorsal plates (Figure 33.17). The chiton's body itself, however, is unsegmented. You can find these marine animals clinging to rocks along the shore during low tide. If you try to dislodge a chiton by hand, you will be surprised at how well its foot, acting as a suction cup, grips the rock. A chiton can also use its foot to creep slowly over the rock surface. Chitons use their radula to scrape algae off the rock surface.

Figure 34.14 Fossil of an early gnathostome. A formidable predator, the placoderm Dunkleosteus grew up to 10 m in length. Its jaw structure indicates that Dunkleosteus could exert a force of 560 kg/cm2 (8,000 pounds per square inch) at the tip of its jaws.

Chondrichthyans (Sharks, Rays, and Their Relatives): Sharks, rays, and their relatives include some of the biggest and most successful vertebrate predators in the oceans. They belong to the clade Chondrichthyes, which means "cartilage fish." As their name indicates, the chondrichthyans have a skeleton composed predominantly of cartilage, though often impregnated with calcium.

Deuterostomia: Hemichordata (85 species): Like echinoderms and chordates, hemichordates are members of the deuterostome clade (see Chapter 32). Hemichordates share some traits with chordates, such as gill slits and a dorsal nerve cord. The largest group of hemichordates is the enteropneusts, or acorn worms. Acorn worms are marine and generally live buried in mud or under rocks; they may grow to more than 2 m in length. An acorn worm.

Chordata (57,000 species): More than 90% of all known chordate species have backbones (and thus are vertebrates). However, the phylum Chordata also includes two groups of invertebrates: lancelets and tunicates. See Chapter 34 for a full discussion of this phylum. A tunicate.

Holothuroidea: Sea Cucumbers: On casual inspection, sea cucumbers do not look much like other echinoderms. They lack spines, and their endoskeleton is much reduced. They are also elongated in their oral-aboral axis, giving them the shape for which they are named and further disguising their relationship to sea stars and sea urchins (Figure 33.49). Closer examination, however, reveals that sea cucumbers have five radially arranged sections of tube feet, as in other echinoderms. Some of the tube feet around the mouth are developed as feeding tentacles.

Chordates: Phylum Chordata consists of two basal groups of invertebrates, the lancelets and the tunicates, as well as the vertebrates. Chordates are bilaterally symmetrical coelomates with segmented bodies. The close relationship between echinoderms and chordates does not mean that one phylum evolved from the other. In fact, echinoderms and chordates have evolved independently of one another for over 500 million years. We will trace the phylogeny of chordates in Chapter 34, focusing on the history of vertebrates.

Fungi have radiated into a diverse set of lineages: In the past decade, molecular analyses have helped clarify the evolutionary relationships between fungal groups, although there are still areas of uncertainty. Figure 31.10 presents a simplified version of one current hypothesis. In this section, we will survey each of the major fungal groups identified in this phylogenetic tree. The fungal groups shown in Figure 31.10 may represent only a small fraction of the diversity of extant fungal groups. (Extant lineages are those that have surviving members.) While there are roughly 100,000 known species of fungi, scientists have estimated that the actual diversity may be closer to 1.5 million species. Two recent metagenomic studies support such higher estimates: the cryptomycota (see Concept 31.3) and other entirely new groups of unicellular fungi were discovered, and the genetic variation found in some of these groups is as large as that found across all of the groups shown in Figure 31.10.

Chytrids: The fungi classified in the phylum Chytridiomycota, called chytrids, are ubiquitous in lakes and soil, and as described in several recent metagenomic studies, more than 20 new clades of chytrids have been found in hydrothermal vent and other marine communities. Some of the approximately 1,000 chytrid species are decomposers, while others are parasites of protists, other fungi, plants, or animals; as we'll see later in the chapter, one such chytrid parasite has likely contributed to the global decline of amphibian populations. Still other chytrids are important mutualists. For example, anaerobic chytrids that live in the digestive tracts of sheep and cattle help to break down plant matter, thereby contributing significantly to the animal's growth.

(b) Conjugation and reproduction.: Two cells of compatible mating strains align side by side and partially fuse. Meiosis of micronuclei produces four haploid micronuclei in each cell Three micronuclei in each cell disintegrate. The remaining micronucleus in each cell divides by mitosis The cells swap one micronucleus. The cells separate. The two micronuclei fuse.Three rounds of mitosis produce eight micronuclei. Four micronuclei become macronuclei.Two rounds of binary fission yield four daughter cells.

Ciliates: The ciliates are a large and varied group of protists named for their use of cilia to move and feed (Figure 28.17a). Most ciliates are predators, typically of bacteria or of other protists. Their cilia may completely cover the cell surface or may be clustered in a few rows or tufts. In certain species, rows of tightly packed cilia function collectively in locomotion. Other ciliates scurry about on leg-like structures constructed from many cilia bonded together. A distinctive feature of ciliates is the presence of two types of nuclei: tiny micronuclei and large macronuclei. A cell has one or more nuclei of each type. Genetic variation results from conjugation, a sexual process in which two individuals exchange haploid micronuclei but do not reproduce (Figure 28.17b). Ciliates generally reproduce asexually by binary fission, during which the existing macronucleus disintegrates and a new one is formed from the cell's micronuclei. Each macronucleus typically contains multiple copies of the ciliate's genome. Genes in the macronucleus control the everyday functions of the cell, such as feeding, waste removal, and maintaining water balance.

Most seedless vascular plant species are homosporous: They have one type of sporophyll bearing one type of sporangium that produces one type of spore, which typically develops into a bisexual gametophyte, as in most ferns. In contrast, a heterosporous species has two types of sporophylls: megasporophylls and microsporophylls. Megasporophylls have megasporangia, which produce megaspores, spores that develop into female gametophytes. Microsporophylls have microsporangia, which produce microspores, smaller spores that develop into male gametophytes. All seed plants and a few seedless vascular plants are heterosporous. The following diagram compares the two conditions:

Classification of Seedless Vascular Plants: As we noted earlier, biologists recognize two clades of living seedless vascular plants: the lycophytes (phylum Lycophyta) and the monilophytes (phylum Monilophyta). The lycophytes include the club mosses, the spikemosses, and the quillworts. The monilophytes include the ferns, the horsetails, and the whisk ferns and their relatives. Although ferns, horsetails, and whisk ferns differ greatly in appearance, recent anatomical and molecular comparisons provide convincing evidence that these three groups make up a clade. Accordingly, many systematists now classify them together as the phylum Monilophyta, as we do in this chapter. Others refer to these groups as three separate phyla within a clade. Figure 29.14 describes the two main groups of seedless vascular plants.

Protostome and Deuterostome Development: Based on certain aspects of early development, many animals can be described as having one of two developmental modes: protostome development or deuterostome development. These modes can generally be distinguished by differences in cleavage, coelom formation, and fate of the blastopore.

Cleavage: Many animals with protostome development undergo spiral cleavage, in which the planes of cell division are diagonal to the vertical axis of the embryo; as seen in the eight-cell stage of the embryo, smaller cells are centered over the grooves between larger, underlying cells (Figure 32.10a, left). Furthermore, the so-called determinate cleavage of some animals with protostome development rigidly casts ("determines") the developmental fate of each embryonic cell very early. A cell isolated from a snail at the four-cell stage, for example, cannot develop into a whole animal. Instead, after repeated divisions, such a cell will form an inviable embryo that lacks many parts.

Tissues: Animal body plans also vary with regard to tissue organization. Recall that tissues are collections of specialized cells that act as a functional unit. Sponges and a few other groups lack tissues. In all other animals, the embryo becomes layered during gastrulation (see Figure 47.8, "Visualizing Gastrulation," which will help you understand this three-dimensional folding process). As development progresses, these layers, called germ layers, form the various tissues and organs of the body. Ectoderm, the germ layer covering the surface of the embryo, gives rise to the outer covering of the animal and, in some phyla, to the central nervous system. Endoderm, the innermost germ layer, lines the pouch that forms during gastrulation (the archenteron) and gives rise to the lining of the digestive tract (or cavity) and to the lining of organs such as the liver and lungs of vertebrates.

Cnidarians and a few other animal groups that have only these two germ layers are said to be diploblastic. All bilaterally symmetrical animals have a third germ layer, called the mesoderm, which fills much of the space between the ectoderm and endoderm. Thus, animals with bilateral symmetry are also said to be triploblastic (having three germ layers). In triploblasts, the mesoderm forms the muscles and most other organs between the digestive tract and the outer covering of the animal. Triploblasts include a broad range of animals, from flatworms to arthropods to vertebrates. (Although some diploblasts actually do have a third germ layer, it is not nearly as well developed as the mesoderm of animals considered to be triploblastic.)

Unikonta: This supergroup of eukaryotes includes amoebas that have lobe- or tube-shaped pseudopodia, as well as animals, fungi, and non-amoeba protists that are closely related to animals or fungi. According to one current hypothesis, the unikonts were the first eukaryotic supergroup to diverge from all other eukaryotes; however, this hypothesis has yet to be widely accepted. A unikont amoeba. This amoeba, the tubulinid Amoeba proteus, is using its pseudopodia to move

Collectively, such studies indicate that mitochondria arose from an alpha proteobacterium (see Figure 27.16). Results from mtDNA sequence analyses also indicate that the mitochondria of protists, animals, fungi and plants descended from a single common ancestor, thus suggesting that mitochondria arose only once over the course of evolution. Similar analyses provide evidence that plastids descended from a single common ancestor—a cyanobacterium that was engulfed by a eukaryotic host cell.

Conidia may also be involved in sexual reproduction, fusing with hyphae from a mycelium of a different mating type, as occurs in Neurospora. Fusion of two different mating types is followed by plasmogamy, resulting in the formation of dikaryotic cells, each with two haploid nuclei representing the two parents. The cells at the tips of these dikaryotic hyphae develop into many asci. Within each ascus, karyogamy combines the two parental genomes, and then meiosis forms four genetically different nuclei. This is usually followed by a mitotic division, forming eight ascospores. The ascospores develop in and are eventually discharged from the ascocarp.

Compared to the life cycle of zygomycetes, the extended dikaryotic stage of ascomycetes (and also basidiomycetes) provides additional opportunities for genetic recombination. In Neurospora, for example, many dikaryotic cells can develop into asci. The haploid nuclei in these asci fuse, and their genomes then recombine during meiosis, resulting in a multitude of genetically different offspring from one mating event (see steps 3-5 in Figure 31.16).

Enzymes are secreted into the cavity, thus breaking down the prey into a nutrient-rich broth. Cells lining the cavity then absorb these nutrients and complete the digestive process; any undigested remains are expelled through the cnidarian's mouth/anus. The tentacles are armed with batteries of cnidocytes, cells unique to cnidarians that function in defense and prey capture. Cnidocytes contain cnidae (from the Greek cnide, nettle), capsule-like organelles that are capable of exploding outward and that give phylum Cnidaria its name (Figure 33.6). Specialized cnidae called nematocysts contain a stinging thread that can penetrate the body wall of the cnidarian's prey. Other kinds of cnidae have long threads that stick to or entangle small prey that bump into the cnidarian's tentacles.

Contractile tissues and nerves occur in their simplest forms in cnidarians. Cells of the epidermis (outer layer) and gastrodermis (inner layer) have bundles of microfilaments arranged into contractile fibers. The gastrovascular cavity acts as a hydrostatic skeleton (see Concept 50.6) against which the contractile cells can work. When a cnidarian closes its mouth, the volume of the cavity is fixed, and contraction of selected cells causes the animal to change shape. Cnidarians have no brain. Instead, movements are coordinated by a noncentralized nerve net that is associated with sensory structures distributed around the body. Thus, the animal can detect and respond to stimuli from all directions. Fossil and molecular evidence suggests that early in its evolutionary history, the phylum Cnidaria diverged into two major clades, Medusozoa and Anthozoa (Figure 33.7).

Echinoidea: Sea Urchins and Sand Dollars: Sea urchins and sand dollars have no arms, but they do have five radially arranged groups of tube feet that function in slow movement. Sea urchins also have muscles that pivot their long spines, which aid in locomotion as well as protection (Figure 33.47). A sea urchin's mouth, located on its underside, is ringed by highly complex, jaw-like structures that are well adapted to eating seaweed. Sea urchins are roughly spherical, whereas sand dollars are flat disks.

Crinoidea: Sea Lilies and Feather Stars: Sea lilies live attached to the substrate by a stalk; feather stars crawl about by using their long, flexible arms. Both use their arms in suspension feeding. The arms encircle the mouth, which is directed upward, away from the substrate (Figure 33.48). Crinoidea is an ancient group whose morphology has changed little over the course of evolution; fossilized sea lilies some 500 million years old are extremely similar to present-day members of the clade.

Pancrustaceans: A series of recent papers, including a 2010 phylogenomic study, present evidence that terrestrial insects are more closely related to lobsters and other crustaceans than they are to the terrestrial group we just discussed, the myriapods (millipedes and centipedes). These studies also suggest that the diverse group of organisms referred to as crustaceans are paraphyletic: Some lineages of crustaceans are more closely related to insects than they are to other crustaceans (Figure 33.36). However, together the insects and crustaceans form a clade, which systematists have named Pancrustacea (from the Greek pan, all). We turn next to a description of the members of Pancrustacea, focusing first on crustaceans and then on the insects.

Crustaceans: Crustaceans (crabs, lobsters, shrimps, barnacles, and many others) thrive in a broad range of marine, freshwater, and terrestrial environments. Many crustaceans have highly specialized appendages. Lobsters and crayfishes, for instance, have a toolkit of 19 pairs of appendages (see Figure 33.31). The anterior-most appendages form two pairs of antennae; crustaceans are the only arthropods with two pairs. Three or more pairs of appendages are modified as mouthparts, including the hard mandibles. Walking legs are present on the thorax, and, unlike their terrestrial relatives, the insects, crustaceans also have appendages on their postgenital region, or "tail."

The Origin of Fungi: Phylogenetic analyses suggest that fungi evolved from a flagellated ancestor. While the majority of fungi lack flagella, some of the earliest-diverging lineages of fungi (the chytrids, as we'll discuss shortly) do have flagella. Moreover, most of the protists that share a close common ancestor with animals and fungi also have flagella. DNA sequence data indicate that these three groups of eukaryotes—the fungi, the animals, and their protistan relatives—form a monophyletic group, or clade (Figure 31.8). As discussed in Concept 28.5, members of this clade are called opisthokonts, a name that refers to the posterior (opistho-) location of the flagellum in these organisms.

DNA sequence data also indicate that fungi are more closely related to several groups of single-celled protists than they are to animals, suggesting that the ancestor of fungi was unicellular. One such group of unicellular protists, the nucleariids, consists of amoebas that feed on algae and bacteria. DNA evidence further indicates that animals are more closely related to a different group of protists (the choanoflagellates) than they are to either fungi or nucleariids. Together, these results suggest that multicellularity evolved in animals and fungi independently, from different single-celled ancestors.

Gnathostomes are vertebrates that have jaws: Hagfishes and lampreys are survivors from the early Paleozoic era, when jawless vertebrates were common. Since then, jawless vertebrates have been far outnumbered by the jawed vertebrates, the gnathostomes. Living gnathostomes are a diverse group that includes sharks and their relatives, ray-finned fishes, lobe-finned fishes, amphibians, reptiles (including birds), and mammals.

Derived Characters of Gnathostomes: Gnathostomes ("jaw mouth") are named for their jaws, hinged structures that, especially with the help of teeth, enable gnathostomes to grip food items firmly and slice them. According to one hypothesis, gnathostome jaws evolved by modification of the skeletal rods that had previously supported the anterior pharyngeal (gill) slits. Figure 34.13 shows a stage in this evolutionary process in which several of these skeletal rods have been modified into precursors of jaws (green) and their structural supports (red). The remaining gill slits, no longer required for suspension feeding, remained as the major sites of respiratory gas exchange with the external environment.

Today, what adaptations are unique to plants? The answer depends on where you draw the boundary dividing plants from algae (Figure 29.2). Since the placement of this boundary is the subject of ongoing debate, this text uses a traditional definition that equates the kingdom Plantae with embryophytes (plants with embryos). In this context, let's now examine the derived traits that separate plants from their closest algal relatives.

Derived Traits of Plants: Several adaptations that facilitate survival and reproduction on dry land emerged after plants diverged from their algal relatives. Figure 29.3 depicts five such traits that are found in plants but not in charophyte algae.

Excavates include protists with modified mitochondria and protists with unique flagella: Now that we have examined some of the broad patterns in eukaryotic evolution, we will look more closely at the four main groups of protists shown in Figure 28.2. We begin with Excavata (the excavates), a clade that was originally proposed based on morphological studies of the cytoskeleton. Some members of this diverse group also have an "excavated" feeding groove on one side of the cell body. The excavates include the diplomonads, parabasalids, and euglenozoans. Molecular data indicate that each of these three groups is monophyletic, and recent genomic studies support the monophyly of the excavate supergroup.

Diplomonads and Parabasalids: The protists in these two groups lack plastids and have highly reduced mitochondria (until recently, they were thought to lack mitochondria altogether). Most diplomonads and parabasalids are found in anaerobic environments. Diplomonads have reduced mitochondria called mitosomes. These organelles lack functional electron transport chains and hence cannot use oxygen to help extract energy from carbohydrates and other organic molecules. Instead, diplomonads get the energy they need from anaerobic biochemical pathways. Many diplomonads are parasites, including the infamous Giardia intestinalis (see Figure 28.2), which inhabits the intestines of mammals. Structurally, diplomonads have two equal-sized nuclei and multiple flagella. Recall that eukaryotic flagella are extensions of the cytoplasm, consisting of bundles of microtubules covered by the cell's plasma membrane (see Figure 6.24). They are quite different from prokaryotic flagella, which are filaments composed of globular proteins attached to the cell surface (see Figure 27.7).

Figure 34.3 Chordate characteristics. All chordates possess the four highlighted structural trademarks at some point during their development.

Dorsal, Hollow Nerve Cord: The nerve cord of a chordate embryo develops from a plate of ectoderm that rolls into a neural tube located dorsal to the notochord. The resulting dorsal, hollow nerve cord is unique to chordates. Other animal phyla have solid nerve cords, and in most cases they are ventrally located. The nerve cord of a chordate embryo develops into the central nervous system: the brain and spinal cord.

Errantians: Clade Errantia (from the Old French errant, traveling) is a large and diverse group, most of whose members are marine (Figure 33.23). As their name suggests, many errantians are mobile; some swim among the plankton (small, drifting organisms), while many others crawl on or burrow in the seafloor. Many are predators, while others are grazers that feed on large, multicellular algae. The group also includes some relatively immobile species, such as the tube-dwelling Platynereis, a marine species that recently has become a model organism for studying neurobiology and development. In many errantians, each body segment has a pair of prominent paddle-like or ridge-like structures called parapodia ("beside feet") that function in locomotion (see Figure 33.23).

Each parapodium has numerous chaetae. (Possession of parapodia with numerous chaetae is not unique to Errantia, however, as some members of the other major clade of annelids, Sedentaria, also have these features.) In many species, the parapodia are richly supplied with blood vessels and also function as gills. Errantians also tend to have well-developed jaws and sensory organs, as might be expected of predators or grazers that move about in search of food.

In most pine species, each tree has both types of cones. From the time pollen and ovulate cones appear on the tree, it takes nearly three years for the male and female gametophytes to be produced and brought together and for mature seeds to form from fertilized ovules. The scales of each ovulate cone then separate, and seeds are dispersed by the wind. A seed that lands in a suitable environment germinates, its embryo emerging as a pine seedling.

Early Seed Plants and the Rise of Gymnosperms: The origins of characteristics found in pines and other living seed plants date back to the late Devonian period (380 million years ago). Fossils from that time reveal that some plants had acquired features that are also present in seed plants, such as megaspores and microspores. For example, Archaeopteris was a heterosporous tree with a woody stem. But it did not bear seeds and therefore is not classified as a seed plant. Growing up to 20 m tall, it had fernlike leaves. The earliest evidence of seed plants comes from 360-million-year-old fossils of plants in the genus Elkinsia (Figure 30.5). These and other early seed plants lived 55 million years before the first fossils classified as gymnosperms and more than 200 million years before the first fossils of angiosperms. These early seed plants became extinct, and we don't know which extinct lineage gave rise to the gymnosperms.

The skeleton of lampreys is made of cartilage. Unlike the cartilage found in most vertebrates, lamprey cartilage contains no collagen. Instead, it is a stiff matrix of other proteins. The notochord of lampreys persists as the main axial skeleton in the adult, as it does in hagfishes. However, lampreys also have a flexible sheath around their rodlike notochord. Along the length of this sheath, pairs of cartilaginous projections related to vertebrae extend dorsally, partially enclosing the nerve cord.

Early Vertebrate Evolution: In the late 1990s, paleontologists working in China discovered a vast collection of fossils of early chordates that appear to straddle the transition to vertebrates. The fossils were formed during the Cambrian explosion 530 million years ago, when many animal groups were undergoing rapid diversification (see Concept 32.2). The most primitive of the fossils are the 3-cm-long Haikouella (Figure 34.10). In many ways, Haikouella resembled a lancelet. Its mouth structure indicates that, like lancelets, it probably was a suspension feeder. However, Haikouella also had some of the characters of vertebrates. For example, it had a well-formed brain, small eyes, and muscle segments along the body, as do the vertebrate fishes. Unlike the vertebrates, however, Haikouella did not have a skull or ear organs, suggesting that these characters emerged with further innovations to the chordate nervous system. (The earliest "ears" were organs for maintaining balance, a function still performed by the ears of humans and other living vertebrates.)

As you might expect since all their cells are close to water, flatworms have no organs specialized for gas exchange, and their relatively simple excretory apparatus functions mainly to maintain osmotic balance with their surroundings. This apparatus consists of protonephridia, networks of tubules with ciliated structures called flame bulbs that pull fluid through branched ducts opening to the outside (see Figure 44.9). Most flatworms have a gastrovascular cavity with only one opening. Though flatworms lack a circulatory system, the fine branches of the gastrovascular cavity distribute food directly to the animal's cells.

Early in their evolutionary history, flatworms separated into two lineages, Catenulida and Rhabditophora. Catenulida is a small clade of about 100 flatworm species, most of which live in freshwater habitats. Catenulids typically reproduce asexually by budding at their posterior end. The offspring often produce their own buds before detaching from the parent, thereby forming a chain of two to four genetically identical individuals—hence their informal name, "chain worms."The other ancient flatworm lineage, Rhabditophora, is a diverse clade of about 20,000 freshwater and marine species, one example of which is shown in Figure 33.9. We'll explore the rhabditophorans in more detail, focusing on free-living and parasitic members of this clade.

Until the 20th century, leeches were frequently used for bloodletting. Today they are used to drain blood that accumulates in tissues following certain injuries or surgeries. In addition, forms of hirudin produced with recombinant DNA techniques can be used to dissolve unwanted blood clots that form during surgery or as a result of heart disease.

Earthworms: Earthworms eat their way through the soil, extracting nutrients as the soil passes through the alimentary canal. Undigested material, mixed with mucus secreted into the canal, is eliminated as fecal castings through the anus. Farmers value earthworms because the animals till and aerate the earth, and their castings improve the texture of the soil. (Charles Darwin estimated that one acre of farmland contains about 50,000 earthworms, producing 18 tons of castings per year.) A guided tour of the anatomy of an earthworm, which is representative of annelids, is shown in Figure 33.26.

Echinoderms and chordates are deuterostomes: Sea stars, sea urchins, and other echinoderms (phylum Echinodermata) may seem to have little in common with vertebrates (animals that have a backbone) and other members of phylum Chordata. Nevertheless, DNA evidence indicates that echinoderms and chordates are closely related, with both phyla belonging to the Deuterostomia clade of bilaterian animals. Echinoderms and chordates also share features characteristic of a deuterostome mode of development, such as radial cleavage and formation of the anus from the blastopore (see Figure 32.10). As discussed in Concept 32.4, however, some animal phyla with members that have deuterostome developmental features, including ectoprocts and brachiopods, are not in the deuterostome clade. Hence, despite its name, the clade Deuterostomia is defined primarily by DNA similarities, not developmental similarities.

Echinoderms: Sea stars (commonly called starfish) and most other groups of echinoderms (from the Greek echin, spiny, and derma, skin) are slow-moving or sessile marine animals. Echinoderms are coelomates. A thin epidermis covers an endoskeleton of hard calcareous plates, and most species are prickly from skeletal bumps and spines. Unique to echinoderms is the water vascular system, a network of hydraulic canals branching into extensions called tube feet that function in locomotion and feeding (Figure 33.44). Sexual reproduction of echinoderms usually involves separate male and female individuals that release their gametes into the water. Echinoderms descended from bilaterally symmetrical ancestors, yet on first inspection most species seem to have a radially symmetrical form. The internal and external parts of most adult echinoderms radiate from the center, often as five spokes. However, echinoderm larvae have bilateral symmetry. Furthermore, the symmetry of adult echinoderms is not truly radial. For example, the opening (madreporite) of a sea star's water vascular system is not central but shifted to one side. Living echinoderms are divided into five clades.

Lophophorates: Ectoprocts and Brachiopods: Bilaterians in the phyla Ectoprocta and Brachiopoda are among those known as lophophorates. These animals have a lophophore, a crown of ciliated tentacles around their mouth (see Figure 32.12a). As the cilia draw water toward the mouth, the tentacles trap suspended food particles. Other similarities, such as a U-shaped alimentary canal and the absence of a distinct head, reflect these organisms' sessile existence. In contrast to flatworms, which lack a body cavity, and rotifers, which have a pseudocoelom, lophophorates are coelomates, organisms with a body cavity that is completely lined by mesoderm (see Figure 32.9a).

Ectoprocts (from the Greek ecto, outside, and procta, anus) are colonial animals that superficially resemble clumps of moss. (In fact, their common name, bryozoans, means "moss animals.") In most species, the colony is encased in a hard exoskeleton studded with pores through which the lophophores extend (Figure 33.15a). Most ectoproct species live in the sea, where they are among the most widespread and numerous sessile animals. Several species are important reef builders. Ectoprocts also live in lakes and rivers. Colonies of the freshwater ectoproct Pectinatella magnifica grow on submerged sticks or rocks and can grow into a gelatinous, ball-shaped mass more than 10 cm across.

Tubulinids: Tubulinids constitute a large and varied group of amoebozoans that have lobe- or tube-shaped pseudopodia. These unicellular protists are ubiquitous in soil as well as freshwater and marine environments. Most are heterotrophs that actively seek and consume bacteria and other protists; one such tubulinid species, Amoeba proteus, is shown in Figure 28.2. Some tubulinids also feed on detritus (nonliving organic matter).

Entamoebas: Whereas most amoebozoans are free-living, those that belong to the genus Entamoeba are parasites. They infect all classes of vertebrate animals as well as some invertebrates. Humans are host to at least six species of Entamoeba, but only one, E. histolytica, is known to be pathogenic. E. histolytica causes amebic dysentery and is spread via contaminated drinking water, food, or eating utensils. Responsible for up to 100,000 deaths worldwide every year, the disease is the third-leading cause of death due to eukaryotic parasites, after malaria (see Figure 28.16) and schistosomiasis (see Figure 33.11).

Most eukaryotes are single-celled organisms: Protists, along with plants, animals, and fungi, are classified as eukaryotes; they are in domain Eukarya, one of the three domains of life. Unlike the cells of prokaryotes, eukaryotic cells have a nucleus and other membrane-enclosed organelles, such as mitochondria and the Golgi apparatus. Such organelles provide specific locations where particular cellular functions are accomplished, making the structure and organization of eukaryotic cells more complex than those of prokaryotic cells

Eukaryotic cells also have a well-developed cytoskeleton that extends throughout the cell (see Figure 6.20). The cytoskeleton provides the structural support that enables eukaryotic cells to have asymmetric (irregular) forms, as well as to change in shape as they feed, move, or grow. In contrast, prokaryotic cells lack a well-developed cytoskeleton, thus limiting the extent to which they can maintain asymmetric forms or change shape over time.

Marsupials existed worldwide during the Mesozoic era, but today they are found only in the Australian region and in North and South America. The biogeography of marsupials illustrates the interplay between biological and geologic evolution (see Concept 25.4). After the breakup of the supercontinent Pangaea, South America and Australia became island continents, and their marsupials diversified in isolation from the eutherians that began an adaptive radiation on the northern continents. Australia has not been in contact with another continent since early in the Cenozoic era, 66 million years ago. In Australia, convergent evolution has resulted in a diversity of marsupials that resemble eutherians in similar ecological roles in other parts of the world (Figure 34.41). In contrast, although South America had a diverse marsupial fauna throughout the Paleogene, it has experienced several immigrations of eutherians. One of the most important occurred about 3 million years ago, when North and South America joined at the Panamanian isthmus and extensive two-way traffic of animals took place over the land bridge. Today, only three families of marsupials live outside the Australian region, and the only marsupials found in the wild in North America are a few species of opossum.

Eutherians (Placental Mammals): Eutherians are commonly called placental mammals because their placentas are more complex than those of marsupials. Eutherians have a longer pregnancy than marsupials. Young eutherians complete their embryonic development within the uterus, joined to their mother by the placenta. The eutherian placenta provides an intimate and long-lasting association between the mother and her developing young.

Figure 28.2 Exploring Protistan Diversity: The tree below represents a phylogenetic hypothesis for the relationships among eukaryotes on Earth today. The eukaryotic groups at the branch tips are related in larger "supergroups," labeled vertically at the far right of the tree. Groups that were formerly classified in the kingdom Protista are highlighted in yellow. Dotted lines indicate evolutionary relationships that are uncertain and proposed clades that are under active debate. For clarity, this tree only includes representative clades from each supergroup. In addition, the recent discoveries of many new groups of eukaryotes indicate that eukaryotic diversity is actually much greater than shown here.

Excavata: Some members of this supergroup have an "excavated" groove on one side of the cell body. Two major clades (the parabasalids and diplomonads) have highly reduced mitochondria; members of a third clade (the euglenozoans) have flagella that differ in structure from those of other organisms. Excavates include parasites such as Giardia, as well as many predatory and photosynthetic species. Giardia intestinalis, a diplomonad parasite. This diplomonad (colorized SEM), which lacks the characteristic surface groove of the Excavata, inhabits the intestines of mammals. It can infect people when they drink water contaminated with feces containing Giardia cysts. Drinking such water—even from a seemingly pristine stream—can cause severe diarrhea. Boiling the water kills the parasite.

Euglena, a euglenid commonly found in pond water.

Eyespot: pigmented organelle that functions as a light shield, allowing light from only a certain direction to strike the light detector Light detector: swelling near the base of the long flagellum; detects light that is not blocked by the eyespot. As a result, Euglena moves toward light of appropriate intensity, an important adaptation that enhances photosynthesis. Pellicle: protein bands beneath the plasma membrane that provide strength and flexibility

Coelom Formation: During gastrulation, an embryo's developing digestive tube initially forms as a blind pouch, the archenteron, which becomes the gut (Figure 32.10b). As the archenteron forms in protostome development, initially solid masses of mesoderm split and form the coelom. In contrast, in deuterostome development, the mesoderm buds from the wall of the archenteron, and its cavity becomes the coelom.

Fate of the Blastopore: Protostome and deuterostome development often differ in the fate of the blastopore, the indentation that during gastrulation leads to the formation of the archenteron (Figure 32.10c). After the archenteron develops, in most animals a second opening forms at the opposite end of the gastrula. In many species, the blastopore and this second opening become the two openings of the digestive tube: the mouth and the anus. In protostome development, the mouth generally develops from the first opening, the blastopore, and it is for this characteristic that the term protostome derives (from the Greek protos, first, and stoma, mouth). In deuterostome development (from the Greek deuteros, second), the mouth is derived from the secondary opening, and the blastopore usually forms the anus.

Figure 27.22 Bacteria synthesizing and storing PHA, a component of biodegradable plastics.

Figure 27.23 Bioremediation of an oil spill. Spraying fertilizer stimulates the growth of native bacteria that metabolize oil, increasing the speed of the breakdown process up to fivefold.

Figure 28.12 Seaweeds: adapted to life at the ocean's margins. The sea palm (Postelsia) lives on rocks along the coast of the northwestern United States and western Canada. The body of this brown alga is well adapted to maintaining a firm foothold despite the crashing surf

Figure 28.11 Dinobryon, a colonial golden alga found in fresh water (LM).

The complex life cycle of the brown alga Laminaria provides an example of alternation of generations (Figure 28.13). The diploid individual is called the sporophyte because it produces spores. The spores are haploid and move by means of flagella; they are called zoospores. The zoospores develop into haploid, multicellular male and female gametophytes, which produce gametes. The union of two gametes (fertilization) results in a diploid zygote, which matures and gives rise to a new multicellular sporophyte. In Laminaria, the two generations are heteromorphic, meaning that the sporophytes and gametophytes are structurally different. Other algal life cycles have an alternation of isomorphic generations, in which the sporophytes and gametophytes look similar to each other, although they differ in chromosome number.

Figure 28.13 The life cycle of the brown alga Laminaria: an example of alternation of generations.: The sporophytes are usually found in water just below the line of the lowest tides, attached to rocks by branching holdfasts. Cells on the surface of the blade develop into sporangia. Sporangia produce zoospores by meiosis. The zoospores are all structurally alike, but about half of them develop into male gametophytes and half into female gametophytes. The gametophytes are short, branched laments that grow on subtidal rocks. Male gametophytes release sperm, and female gametophytes produce eggs, which remain attached to the female gametophyte. Eggs secrete a chemical signal that attracts sperm of the same species, thereby increasing the probability of fertilization in the ocean. Sperm fertilize the eggs. The zygotes grow into new sporophytes while attached to the remains of the female gametophyte.

Alveolates: Members of the next subgroup of SAR, the alveolates, have membrane-enclosed sacs (alveoli) just under the plasma membrane (Figure 28.14). Alveolates are abundant in many habitats and include a wide range of photosynthetic and heterotrophic protists. We'll discuss three alveolate clades here: a group of flagellates (the dinoflagellates), a group of parasites (the apicomplexans), and a group of protists that move using cilia (the ciliates).

Figure 28.14 Alveoli. These sacs under the plasma membrane are a characteristic that distinguishes alveolates from other eukaryotes (TEM).

Figure 28.16 The two-host life cycle of Plasmodium, the apicomplexan that causes malaria.: An infected Anopheles mosquito bites a person, injecting Plasmodium sporozoites in its saliva. The sporozoites enter the person's liver cells. After several days, the sporozoites undergo multiple divisions and become merozoites, which use their apical complex to penetrate red blood cells (see TEM below). The merozoites divide asexually inside the red blood cells. At intervals of 48 or 72 hours (depending on the species), large numbers of merozoites break out of the blood cells, causing periodic chills and fever. Some of the merozoites infect other red blood cells. Some merozoites form gametocytes. Another Anopheles mosquito bites the infected person and picks up Plasmodium gametocytes along with blood. Gametes form from gametocytes; each male 5 gametocyte produces several slender male gametes. Fertilization occurs in the mosquito's digestive tract, and a zygote forms.An oocyst develops from the zygote in the wall of the mosquito's gut. The oocyst releases thousands of sporozoites, which migrate to the mosquito's salivary gland.

Figure 28.17 Structure and function in the ciliate Paramecium caudatum. Paramecium constantly takes in water by osmosis from its hypotonic environment. Bladderlike contractile vacuoles accumulate excess water from radial canals and periodically expel it through the plasma membrane. Cilia along a funnel-shaped oral groove move food (mainly bacteria) into the cell mouth, where the food is engulfed into food vacuoles by phagocytosis. Food vacuoles fuse with lysosomes (not shown). As the food is digested, the vacuoles follow a looping path through the cell. Wastes are released when the vacuoles fuse with a specialized region of the plasma membrane that functions as an anal pore. (a) Feeding, waste removal, and water balance.

Figure 28.20 A second case of primary endosymbiosis? The cercozoan Paulinella conducts photosynthesis in a unique sausageshaped structure called a chromatophore (LM). Chromatophores are surrounded by a membrane with a peptidoglycan layer, suggesting that they are derived from a bacterium. DNA evidence indicates that chromatophores are derived from a different cyanobacterium than that from which plastids are derived.

Figure 28.18 A radiolarian. Numerous threadlike pseudopodia radiate from the central body of this radiolarian (LM). Figure 28.19 Fossil forams. By measuring the magnesium content in fossilized forams like these, researchers seek to learn how ocean temperatures have changed over time. Forams take up more magnesium in warmer water than in colder water.

Most red algae are multicellular. Although none are as big as the giant brown kelps, the largest multicellular red algae are included in the informal designation "seaweeds." You may have eaten one of these multicellular red algae, Porphyra (Japanese "nori"), as crispy sheets or as a wrap for sushi (see Figure 28.21). Red algae reproduce sexually and have diverse life cycles in which alternation of generations is common. However, unlike other algae, red algae do not have flagellated gametes, so they depend on water currents to bring gametes together for fertilization.

Figure 28.21 Red algae. Bonnemaisonia hamifera. This red alga has a filamentous form. Dulse (Palmaria palmata). This edible species has a "leafy" form. ▼ Nori. The red alga Porphyra is the source of a traditional Japanese food. The seaweed is grown on nets in shallow coastal waters. Paper-thin, glossy sheets of dried nori make a mineral-rich wrap for rice, seafood, and vegetables in sushi.

In trying to determine the root of the eukaryotic tree, researchers have based their phylogenies on different sets of genes, some of which have produced conflicting results. Researchers have also tried a different approach, based on tracing the occurrence of a rare evolutionary event (Figure 28.24). Results from this "rare event" approach indicate that Excavata, SAR, and Archaeplastida share a more recent common ancestor than any of them does with Unikonta. This suggests that the root of the tree is located between the unikonts and all other eukaryotes, which implies that the unikonts were the first eukaryotic supergroup to diverge from all other eukaryotes. This idea remains controversial and will require more supporting evidence to be widely accepted.

Figure 28.24 Inquiry What is the root of the eukaryotic tree? Experiment Responding to the difficulty in determining the root of the eukaryotic phylogenetic tree, Alexandra Stechmann and Thomas Cavalier-Smith proposed a new approach. They studied two genes, one coding for the enzyme dihydrofolate reductase (DHFR) and the other coding for the enzyme thymidylate synthase (TS). The scientists' approach took advantage of a rare evolutionary event: In some organisms, the genes for DHFR and TS have fused, leading to the production of a single protein with both enzyme activities. Stechmann and Cavalier-Smith amplified (using PCR; see Figure 20.8) and sequenced the genes for DHFR and TS in nine species (one choanoflagellate, two amoebozoans, one euglenozoan, one stramenopile, one alveolate, and three rhizarians). They combined their data with previously published data for species of bacteria, animals, plants, and fungi. Results The bacteria studied all have separate genes coding for DHFR and TS, suggesting that this is the ancestral condition (red dot on the tree below). Other taxa with separate genes are denoted by red type. Fused genes are a derived character, found in certain members (blue type) of the supergroups Excavata, SAR, and Archaeplastida: Conclusion The results show that Excavata, SAR, and Archaeplastida form a clade, which supports the hypothesis that the root of the tree is located between the unikonts and all other eukaryotes. Because support for this hypothesis is based on only one trait—the fusion of the genes for DHFR and TS—more data are needed to evaluate its validity.

Dictyostelium discoideum, a cellular slime mold commonly found on forest floors, has become a model organism for studying the evolution of multicellularity. One line of research has focused on the slime mold's fruiting body stage. During this stage, the cells that form the stalk die as they dry out, while the spore cells at the top survive and have the potential to reproduce (see Figure 28.26). Scientists have found that mutations in a single gene can turn individual Dictyostelium cells into "cheaters" that never become part of the stalk. Because these mutants gain a strong reproductive advantage over noncheaters, why don't all Dictyostelium cells cheat? Recent discoveries suggest an answer to this question. Cheating cells lack a specific surface protein, and noncheating cells can recognize this difference. Noncheaters preferentially aggregate with other noncheaters, thus depriving cheaters of the chance to exploit them. Such a recognition system may have been important in the evolution of other multicellular eukaryotes, such as animals and plants.

Figure 28.25 A plasmodial slime mold. The photograph shows a mature plasmodium, the feeding stage in the life cycle of a plasmodial slime mold. When food becomes scarce, the plasmodium forms stalked fruiting bodies that produce haploid spores that function in sexual reproduction. 1)The feeding stage is a multinucleate plasmodium. 2) The plasmodium erects stalked fruiting bodies (sporangia) when conditions become harsh. 3) In the sporangia, meiosis produces haploid spores, which disperse through the air 4) The resistant spores germinate in favorable conditions, releasing motile cells. 5)The motile haploid cells are either amoeboid or flagellated; the two forms readily convert from one to the other. 6)The cells fuse, forming diploid zygotes. 7)Repeated mitotic divisions of the zygote's nucleus, without cytoplasmic division, form the plasmodium.

Opisthokonts: Opisthokonts are an extremely diverse group of eukaryotes that includes animals, fungi, and several groups of protists. We will discuss the evolutionary history of fungi and animals in Chapters 31-34. Of the opisthokont protists, we will discuss the nucleariids in Chapter 31 because they are more closely related to fungi than they are to other protists. Similarly, we will discuss choanoflagellates in Chapter 32, since they are more closely related to animals than they are to other protists. The nucleariids and choanoflagellates illustrate why scientists have abandoned the former kingdom Protista: A monophyletic group that includes these single-celled eukaryotes would also have to include the multicellular animals and fungi that are closely related to them.

Figure 28.26 The life cycle of Dictyostelium, a cellular slime mold.: In the feeding stage, solitary haploid amoebas engulf bacteria; these solitary cells periodically divide by mitosis (asexual reproduction). During sexual reproduction, two haploid amoebas fuse and form a zygote. The zygote becomes a giant cell by consuming haploid amoebas (not shown). After developing a resistant wall, the giant cell undergoes meiosis followed by several mitotic divisions. The wall ruptures, releasing new haploid amoebas. When food is depleted, hundreds of amoebas congregate in response to a chemical attractant and form a slug-like aggregate (see photo). The aggregate migrates for a while and then stops. Some of the cells dry up after forming a stalk that supports an asexual fruiting body Other cells crawl up the stalk and develop into spores. Spores are released. In favorable conditions, amoebas emerge from the spore coats and feed.

Figure 28.28 Sudden oak death. Many dead oak trees are visible in this Monterey County, California landscape. Infected trees lose their ability to adjust to cycles of wet and dry weather.

Figure 28.27 A symbiotic protist. This organism is a hypermastigote, a member of a group of parabasalids that live in the gut of termites and certain cockroaches and enable the hosts to digest wood (SEM).

A pressing question is how global warming will affect photosynthetic protists and other producers. As shown in Figure 28.30, the growth and biomass of photosynthetic protists and prokaryotes have declined in many ocean regions as sea surface temperatures have increased. By what mechanism do rising sea surface temperatures reduce the growth of marine producers? One hypothesis relates to the rise or upwelling of cold, nutrient-rich waters from below. Many marine producers rely on nutrients brought to the surface in this way. However, rising sea surface temperatures can cause the formation of a layer of light, warm water that acts as a barrier to nutrient upwelling—thus reducing the growth of marine producers. If sustained, the changes shown in Figure 28.30 would likely have far-reaching effects on marine ecosystems, fishery yields, and the global carbon cycle (see Figure 55.14). Global warming can also affect producers on land, but there the base of food webs is occupied not by protists but by plants, which we will discuss in Chapters 29 and 30.

Figure 28.29 Protists: key producers in aquatic communities. Arrows in this simplified food web lead from food sources to the organisms that eat them. Figure 28.30 Effects of climate change on marine producers. (a) Researchers studied 10 ocean regions, identified with letters on the map (see (b) for the corresponding names). SSTs have increased since 1950 in most areas of these regions. (b) The concentration of chlorophyll, an index for the biomass and growth of marine producers, has decreased over the same time period in most ocean regions.

Progress has also been made toward identifying the host cell that engulfed an alpha proteobacterium, thereby setting the stage for the origin of eukaryotes. In 2015, for example, researchers reported the discovery of a new group of archaea, the lokiarchaeotes. In phylogenomic analyses, this group was identified as the sister group of the eukaryotes and its genome was found to encode many eukaryote-specific features. Was the host cell that engulfed an alpha proteobacterium a lokiarchaeote? While this may have been the case, it is also possible that the host was closely related to the archaeans (but was not itself an archaean). Either way, current evidence indicates that the host was a relatively complex cell in which certain features of eukaryotic cells had evolved, such as a cytoskeleton that enabled it to change shape (and thereby engulf the alpha proteobacterium).

Figure 28.3 Diversity of plastids produced by endosymbiosis. Studies of plastid-bearing eukaryotes suggest that plastids evolved from a cyanobacterium that was engulfed by an ancestral heterotrophic eukaryote (primary endosymbiosis). That ancestor then diversified into red algae and green algae, some of which were subsequently engulfed by other eukaryotes (secondary endosymbiosis).

Parabasalids also have reduced mitochondria; called hydrogenosomes, these organelles generate some energy anaerobically, releasing hydrogen gas as a by-product. The best-known parabasalid is Trichomonas vaginalis, a sexually transmitted parasite that infects some 5 million people each year. T. vaginalis travels along the mucus-coated lining of the human reproductive and urinary tracts by moving its flagella and by undulating part of its plasma membrane (Figure 28.5). In females, if the vagina's normal acidity is disturbed, T. vaginalis can outcompete beneficial microorganisms there and infect the vagina. (Trichomonas infections also can occur in the urethra of males, though often without symptoms.) T. vaginalis has a gene that allows it to feed on the vaginal lining, promoting infection. Studies suggest that the protist acquired this gene by horizontal gene transfer from bacterial parasites in the vagina.

Figure 28.5 The parabasalid parasite Trichomonas vaginalis (colorized SEM).

Figure 28.6 Euglenozoan flagellum. Most euglenozoans have a crystalline rod inside one of their flagella (the TEM is a flagellum shown in cross section). The rod lies alongside the 9 + 2 ring of microtubules found in all eukaryotic flagella (compare with Figure 6.24).

Figure 28.7 Trypanosoma, the kinetoplastid that causes sleeping sickness (colorized SEM).

Figure 28.10 The diatom Triceratium morlandii (colorized SEM).

Figure 28.9 Stramenopile flagella. Most stramenopiles, such as Synura petersenii, have two flagella: one covered with fine, stiff hairs and a shorter one that is smooth.

Stramenopiles: One major subgroup of SAR, the stramenopiles, includes some of the most important photosynthetic organisms on the planet. Their name (from the Latin stramen, straw, and pilos, hair) refers to their characteristic flagellum, which has numerous fine, hairlike projections. In most stramenopiles, this "hairy" flagellum is paired with a shorter "smooth" (nonhairy) flagellum (Figure 28.9). Here we'll focus on three groups of stramenopiles: diatoms, golden algae, and brown algae.

Figure 28.9 Stramenopile flagella. Most stramenopiles, such as Synura petersenii, have two flagella: one covered with fine, stiff hairs and a shorter one that is smooth.

Peat has long been a fuel source in Europe and Asia, and it is still harvested for fuel today, notably in Ireland and Canada. Peat moss is also useful as a soil conditioner and for packing plant roots during shipment because it has large dead cells that can absorb roughly 20 times the moss's weight in water. Peatlands cover 3% of Earth's land surface and contain roughly 30% of the world's soil carbon: Globally, an estimated 450 billion tons of organic carbon is stored as peat. Current overharvesting of Sphagnum—primarily for use in peat-fired power stations—may contribute to global warming by releasing stored CO2. In addition, if global temperatures continue to rise, the water levels of some peatlands are expected to drop. Such a change would expose peat to air and cause it to decompose, thereby releasing additional stored CO2 and contributing further to global warming. The historical and expected future effects of Sphagnum on the global climate underscore the importance of preserving and managing peatlands. Mosses may have a long history of affecting climate change. In the Scientific Skills Exercise, you will explore the question of whether they did so during the Ordovician period by contributing to the weathering of rocks.

Figure 29.10 Sphagnum, or peat moss: a bryophyte with economic, ecological, and archaeological significance. (a) Peat being harvested from a peatland (b) "Tollund Man," a bog mummy dating from 405-100 B.C.E. The acidic, oxygen-poor conditions produced by Sphagnum can preserve human or other animal bodies for thousands of years.

Early vascular plants had some derived traits of today's vascular plants, but they lacked roots and some other adaptations that evolved later. The main traits that characterize living vascular plants are life cycles with dominant sporophytes, transport in vascular tissues called xylem and phloem, and well-developed roots and leaves, including spore-bearing leaves called sporophylls.

Figure 29.11 Sporophytes of Aglaophyton major, an ancient relative of living vascular plants. This reconstruction from 405-million-year-old fossils exhibits dichotomous (Y-shaped) branching with sporangia at the ends of branches. Sporophyte branching characterizes living vascular plants but is lacking in living nonvascular plants (bryophytes). Aglaophyton had structures called rhizoids that anchored it to the ground. The inset shows a fossilized stoma of A. major (colorized LM).

Lignified vascular tissue helped enable vascular plants to grow tall. Their stems became strong enough to provide support against gravity, and they could transport water and mineral nutrients high above the ground. Tall plants could also outcompete short plants for access to the sunlight needed for photosynthesis. In addition, the spores of tall plants could disperse farther than those of short plants, enabling tall species to colonize new environments rapidly. Overall, the ability to grow tall gave vascular plants a competitive edge over nonvascular plants, which typically are less than 5 cm in height. Competition among vascular plants also would have increased, leading to selection for taller growth forms—a process that eventually gave rise to the trees that formed the first forests about 385 million years ago.

Figure 29.12 The life cycle of a fern. Sporangia release spores. Most fern species produce a single type of spore that develops into a bisexual photosynthetic gametophyte. Each gametophyte develops sperm-producing organs called antheridia and egg-producing organs called archegonia. Although this simplified diagram shows a sperm fertilizing an egg from the same gametophyte, in most fern species a gametophyte produces sperm and eggs at different times. Therefore, typically an egg from one gametophyte is fertilized by a sperm from another gametophyte. Sperm use flagella to swim to eggs in the archegonia. An attractant secreted by archegonia helps direct the sperm. A zygote develops into a new sporophyte, and the young plant grows out from an archegonium of its parent, the gametophyte.. On the underside of the sporophyte's reproductive leaves are spots called sori. Each sorus is a cluster of sporangia.

Psilotum (whisk ferns) and a closely related genus, Tmesipteris, form a clade consisting mainly of tropical epiphytes. Plants in these two genera, the only vascular plants lacking true roots, once were called "living fossils" because of their resemblance to fossils of ancient relatives of living vascular plants (see Figures 29.11 and 29.14). However, much evidence, including analyses of DNA sequences and sperm structure, indicates that the genera Psilotum and Tmesipteris are closely related to ferns. This hypothesis suggests that their ancestor's true roots were lost during evolution. Today, plants in these two genera absorb water and nutrients through numerous absorptive rhizoids.

Figure 29.15 Artist's conception of a Carboniferous forest based on fossil evidence. Lycophyte trees, with trunks covered with small leaves, thrived in the "coal forests" of the Carboniferous, along with giant ferns and horsetails

The earliest plants lacked true roots and leaves. Without roots, how did these plants absorb nutrients from the soil? Fossils dating from 420 million years ago reveal an adaptation that may have aided early plants in nutrient uptake: They formed symbiotic associations with fungi. We'll describe these associations, called mycorrhizae, and their benefits to both plants and fungi in more detail in Concept 31.1. For now, the main point is that mycorrhizal fungi form extensive networks of filaments through the soil and transfer nutrients to their symbiotic plant partner. This benefit may have helped plants without roots to colonize land.

Figure 29.4 Ancient plant spores and tissue (colorized SEMs). a) Fossilized spores. The chemical composition and wall structure of these 450-millionyear-old spores match those found in plants. b) Fossilized sporophyte tissue. The spores were embedded in tissue that appears to be from plants.

A third clade of vascular plants consists of seed plants, which represent the vast majority of living plant species. A seed is an embryo packaged with a supply of nutrients inside a protective coat. Seed plants can be divided into two groups, gymnosperms and angiosperms, based on the absence or presence of enclosed chambers in which seeds mature. Gymnosperms (from the Greek gymnos, naked, and sperm, seed) are known as "naked seed" plants because their seeds are not enclosed in chambers. Living gymnosperm species, the most familiar of which are the conifers, form a clade. Angiosperms (from the Greek angion, container) are a huge clade consisting of all flowering plants; their seeds develop nside chambers that originate within flowers. Nearly 90% of living plant species are angiosperms.

Figure 29.6 Highlights of plant evolution. The phylogeny shown here illustrates a leading hypothesis about the relationships between plant groups. Table 29.1 Ten Phyla of Extant Plants

Figure 29.7 The life cycle of a moss.: Spores develop into threadlike protonemata. The haploid protonemata produce "buds" that divide by mitosis and grow into gametophores. Sperm must swim through a film of moisture to reach the egg. The zygote develops into a sporophyte embryo The sporophyte grows a long stalk (seta) that emerges from the archegonium. Attached by its foot, the sporophyte remains nutritionally dependent on the gametophyte. Meiosis occurs and haploid spores develop in the capsule. When the capsule is mature, its lid pops off, and the spores are released.

Figure 29.8 Exploring Bryophyte Diversity: Liverworts (Phylum Hepatophyta): This phylum's common and scientific names (from the Latin hepaticus, liver) refer to the liver-shaped gametophytes of its mem- bers, such as Marchantia, shown below. In medieval times, their shape was thought to be a sign that the plants could help treat liver diseases. Some liverworts, including Marchantia, are described as "thalloid" because of the flattened shape of their gametophytes. Marchantia gametangia are elevated on gametophores that look like miniature trees. You would need a magnifying glass to see the sporophytes, which have a short seta (stalk) with an oval or round capsule. Other liverworts, such as Plagiochila, below, are called "leafy" because their stemlike gametophytes have many leaflike appendages. There are many more species of leafy liverworts than thalloid liverworts.

Figure 30.10 Some variations in fruit structure.: ▼ Tomato, a fleshy fruit with soft outer and inner layers of pericarp (fruit wall) ▼ Ruby grapefruit, a fleshy fruit with a firm outer layer and soft inner layer of pericarp ▼ Nectarine, a fleshy fruit with a soft outer layer and hard inner layer (pit) of pericarp ▼ Hazelnut, a dry fruit that remains closed at maturity ◀ Milkweed, a dry fruit that splits open at maturity

Figure 30.11 Fruit adaptations that enhance seed dispersal. Some plants have mechanisms that disperse seeds by explosive action. Wings enable maple fruits to be carried by the wind. Seeeds within berries and other edible fruits are often dispersed in animal feces. The barbs of cockleburs facilitate seed dispersal by allowing the fruits to "hitchhike" on animals.

Figure 30.16 Characteristics of monocots and eudicots.

Figure 30.15 A bee pollinating a bilaterally symmetrical flower. To harvest nectar (a sugary solution secreted by flower glands) from this Scottish broom flower, a honeybee must land as shown. This releases a tripping mechanism that arches the flower's stamens over the bee and dusts it with pollen. Later, some of this pollen may rub off onto the stigma of the next flower of this species that the bee visits.

Angiosperm Diversity: From their humble beginnings in the Cretaceous period, angiosperms have diversified into more than 250,000 living species. Until the late 1990s, most systematists divided flowering plants into two groups, based partly on the number of cotyledons, or seed leaves, in the embryo. Species with one cotyledon were called monocots, and those with two were called dicots. Other features, such as flower and leaf structure, were also used to define the two groups. Recent DNA studies, however, indicate that the species traditionally called dicots are paraphyletic. The vast majority of species once categorized as dicots form a large clade, now known as eudicots ("true" dicots)

Figure 30.16 compares the main characteristics of monocots and eudicots. The rest of the former dicots are now grouped into four small lineages. Three of these lineages— Amborella, water lilies, and star anise and relatives—are informally called basal angiosperms because they diverged from other angiosperms early in the history of the group (see Figure 30.14b). A fourth lineage, the magnoliids, evolved later. Figure 30.17 provides an overview of angiosperm diversity

Figure 30.14 Angiosperm evolutionary history. (a)A close relative of the angiosperms? This reconstruction shows a longitudinal section through the flowerlike structures found in the Bennettitales, an extinct group of seed plants hypothesized to be more closely related to extant angiosperms than to extant gymnosperms. (b) Angiosperm phylogeny. This tree represents a current hypothesis of angiosperm evolutionary relationships, based on morphological and molecular evidence. Angiosperms originated about 140 million years ago. The dotted line indicates the uncertain position of the Bennettitales, a possible sister group to extant angiosperms.

Figure 30.17 Exploring Angiosperm Diversity: Basal Angiosperms: Surviving basal angiosperms consist of three lineages comprising only about 100 species. The first lineage to have diverged from other angiosperms is represented today by a single species, Amborella trichopoda (right). The other surviving lineages diverged later: a clade that includes water lilies and a clade consisting of the star anise and its relatives. ◀ Water lily (Nymphaea "Rene Gerard"). Species of water lilies are found in aquatic habitats throughout the world. Water lilies belong to a clade that diverged from other angiosperms early in the group's history. Amborella trichopoda. This small shrub,found only on the South Pacific island of New Caledonia, may be the sole survivor of a branch at the base of the angiosperm tree. ◀ Star anise (Illicium). This genus belongs to a third surviving lineage of basal angiosperms.

Many people have ethical concerns about contributing to the extinction of species. In addition, there are practical reasons to be concerned about the loss of plant diversity. So far, we have explored the potential uses of only a tiny fraction of the more than 290,000 known plant species. For example, almost all our food is based on the cultivation of only about two dozen species of seed plants. And fewer than 5,000 plant species have been studied as potential sources of medicines. The tropical rain forest may be a medicine chest of healing plants that could be extinct before we even know they exist. If we begin to view rain forests and other ecosystems as living treasures that can regenerate only slowly, we may learn to harvest their products at sustainable rates.

Figure 30.18 Clear-cutting of tropical forests. Over the past several hundred years, nearly half of Earth's tropical forests have been cut down and converted to farmland and other uses. A satellite image from 1975 (left) shows a dense forest in Brazil. By 2012, much of this forest had been cut down. Deforested and urban areas are shown as light purple.

This miniaturization allowed for an important evolutionary innovation in seed plants: Their tiny gametophytes can develop from spores retained within the sporangia of the parental sporophyte. This arrangement can protect the gametophytes from environmental stresses. For example, the moist reproductive tissues of the sporophyte shield the gametophytes from UV radiation and protect them from drying out. This relationship also enables the developing gametophytes to obtain nutrients from the parental sporophyte. In contrast, the free-living gametophytes of seedless vascular plants must fend for themselves. Figure 30.2 provides an overview of the gametophyte-sporophyte relationships in nonvascular plants, seedless vascular plants, and seed plants.

Figure 30.2 Gametophyte-sporophyte relationships in different plant groups

Gymnosperm Diversity: Although angiosperms now dominate most terrestrial ecosystems, gymnosperms remain an important part of Earth's flora. For example, vast regions in northern latitudes are covered by forests of conifers (see Figure 52.12). Of the ten plant phyla (see Table 29.1), four are gymnosperms: Cycadophyta, Ginkgophyta, Gnetophyta, and Coniferophyta. It is uncertain how the four phyla of gymnosperms are related to each other. Figure 30.7 surveys the diversity of extant gymnosperms.

Figure 30.5 A fossil of the early seed plant Elkinsia.

Figure 30.6 An ancient pollinator. This 110-million-year-old fossil shows pollen on an insect, the thrip Gymnopollisthrips minor. Structural features of the pollen suggest that it was produced by gymnosperms (most likely by species related to extant ginkgos or cycads). Although most gymnosperms today are wind-pollinated, many cycads are insect-pollinated.

Figure 30.7 Exploring Gymnosperm Diversity Phylum Cycadophyta: The 300 species of living cycads have large cones and palmlike leaves (true palm species are angiosperms). Unlike most seed plants, cycads have flagellated sperm, indicating their descent from seedless vascular plants that had motile sperm. Cycads thrived during the Mesozoic era, known as the age of cycads as well as the age of dinosaurs. Today, however, cycads are the most endangered of all plant groups: 75% of their species are threatened by habitat destruction and other human actions.

Figure 31.14 Arbuscular mycorrhizae. Most glomeromycetes form arbuscular mycorrhizae with plant roots, supplying minerals and other nutrients to the roots. This SEM depicts the branched hyphae— an arbuscule—of Glomus mosseae bulging into a root cell by pushing in the membrane (the root has been treated to remove the cytoplasm). Figure 31.11 Flagellated chytrid zoospore (TEM).

Figure 31.12 The life cycle of the zygomycete Rhizopus stolonifer (black bread mold). Mycelia have various mating types (here designated (-), with red nuclei, and (+), with blue nuclei). Neighboring mycelia of different mating types form hyphal extensions (gametangia), each of which encloses several haploid nuclei. A zygosporangium forms, containing multiple haploid nuclei from the two parents. The zygosporangium develops a rough, thick-walled coating that can resist harsh conditions for months.When conditions are favorable, karyogamy occurs, then meiosis. The zygosporangium germinates into a sporangium on a short stalk. The sporangium disperses genetically diverse haploid spores. The spores germinate and grow into new mycelia. Mycelia can also reproduce asexually by forming sporangia that produce genetically identical haploid spores.

Glomeromycetes: The glomeromycetes, fungi assigned to the phylum Glomeromycota, were formerly thought to be zygomycetes. But recent molecular studies, including a phylogenetic analysis of DNA sequence data from hundreds of fungal species, indicate that glomeromycetes form a separate clade. Although only 200 species have been described to date, molecular studies indicate that the actual number of species may be much higher. The glomeromycetes are an ecologically significant group in that nearly all of them form arbuscular mycorrhizae (Figure 31.14). The tips of the hyphae that push into plant root cells branch into tiny treelike arbuscules. More than 80% of all plant species have such mutualistic partnerships with glomeromycetes.

Figure 31.13 Pilobolus aiming its sporangia. This zygomycete decomposes animal dung. Its spore-bearing hyphae bend toward light, where there are likely to be openings in the vegetation through which spores may reach fresh grass. The fungus then launches its sporangia in a jet of water that can travel up to 2.5 m. Grazing animals ingest the fungi with the grass and then scatter the spores in feces, thereby enabling the next generation of fungi to grow.

Figure 31.19 A fairy ring. According to legend, mushroom rings spring up where fairies have danced on a moonlit night. The text provides a biological explanation of how these rings form.

Figure 31.18 The life cycle of a mushroom-forming basidiomycete. Two haploid mycelia 1 of different mating types undergo plasmogamy. A dikaryotic mycelium forms, growing faster than, and ultimately crowding out, the haploid parental mycelia. Environmental cues such as rain or change in temperature induce the dikaryotic mycelium to form compact masses that develop into basidiocarps (mushrooms, in this case). The basidiocarp gills are lined with terminal dikaryotic cells called basidia. Karyogamy in each basidium produces a diploid nucleus, which then undergoes meiosis. Each diploid nucleus yields four haploid nuclei, each of which develops into a basidiospore (SEM). When mature, the basidiospores are ejected and then dispersed by the wind. In a suitable environment, the basidiospores germinate and grow into short-lived haploid mycelia.

Figure 31.21 Fungus-gardening insects. These leaf-cutting ants depend on fungi to convert plant material to a form the insects can digest. The fungi, in turn, depend on the nutrients from the leaves the ants feed them. Figure 31.22 Variation in lichen growth forms: ◀ A fruticose (shrublike) lichen ▶ A foliose (leaflike) lichen ◀ Crustose (encrusting) lichens

Figure 31.20 Inquiry Do fungal endophytes benefit a woody plant? Experiment Fungal endophytes are symbiotic fungi found within the bodies of all plants examined to date. A. Elizabeth Arnold, at the University of Arizona, Tucson, and colleagues tested whether fungal endophytes benefit the cacao tree (Theobroma cacao). This tree, whose name means "food of the gods" in Greek, is the source of the beans used to make chocolate, and it is cultivated throughout the tropics. A particular mixture of fungal endophytes was added to the leaves of some cacao seedlings, but not others. (In cacao, fungal endophytes colonize leaves after the seedling germinates.) The seedlings were then inoculated with a virulent pathogen, the protist Phytophthora. Results Fewer leaves were killed by the pathogen in seedlings with fungal endophytes than in seedlings without endophytes. Among leaves that survived, pathogens damaged less of the leaf surface area in seedlings with endophytes than in seedlings without endophytes. Conclusion The presence of endophytes appears to benefit cacao trees by reducing the leaf mortality and damage caused by Phytophthora.

Figure 31.26 Can this fungus be used to produce biofuels? The ascomycete Gliocladium roseum can produce hydrocarbons similar to those in diesel fuel (colorized SEM).

Figure 31.25 Amphibians under attack. Could a fungal parasite have caused some of the many declines and extinctions of amphibian populations in recent decades? One study found that the number of yellow-legged frogs (Rana muscosa) plummeted after the chytrid Batrachochytrium dendrobatidis reached the Sixty Lake Basin area of California. In the years leading up to the chytrid's 2004 arrival, there had been more than 2,300 frogs in these lakes. By 2009, only 38 frogs remained; all the survivors were in two lakes (yellow) where frogs had been treated with a fungicide to reduce the chytrid's impact.

Figure 31.4 Specialized hyphae: (a) Hyphae adapted for trapping and killing prey. In Arthrobotrys, a soil fungus, portions of the hyphae are modified as hoops that can constrict around a nematode (roundworm) in less than a second. The growing hyphae then penetrate the worm's body, and the fungus digests its prey's inner tissues (SEM). (b) Arbuscules. Some mutualistic fungi have specialized hyphae called arbuscules that can exchange nutrients with living plant cells. Arbuscules remain separated from a plant cell's cytoplasm by the plasma membrane of the plant cell (orange).

Figure 31.3 Two forms of hyphae. (a) Septate hypha (b) Coenocytic hypha

Using molecular clock analyses, scientists have estimated that the ancestors of animals and fungi diverged into separate lineages more than a billion years ago. Fossils of certain unicellular, marine eukaryotes that lived as early as 1.5 billion years ago have been interpreted as fungi, but those claims remain controversial. Furthermore, although most scientists think that fungi originated in aquatic environments, the oldest fossils that are widely accepted as fungi are of terrestrial species that lived about 460 million years ago (Figure 31.9). Overall, more fossils are needed to help clarify when fungi originated and what features were present in their earliest lineages.

Figure 31.9 Fossil fungal hyphae and spores from the Ordovician period (about 460 million years ago) (LM).

In contrast to the spiral cleavage pattern, deuterostome development is predominantly characterized by radial cleavage. The cleavage planes are either parallel or perpendicular to the vertical axis of the embryo; as seen at the eight-cell stage, the tiers of cells are aligned, one directly above the other (see Figure 32.10a, right). Most animals with deuterostome development also have indeterminate cleavage, meaning that each cell produced by early cleavage divisions retains the capacity to develop into a complete embryo. For example, if the cells of a sea urchin embryo are separated at the four-cell stage, each can form a complete larva. Similarly, it is the indeterminate cleavage of the human zygote that makes identical twins possible.

Figure 32.10 A comparison of protostome and deuterostome development. These are useful general distinctions, though there are many variations and exceptions to these patterns. (a) Cleavage. In general, protostome development begins with spiral, determinate cleavage. Deuterostome development is characterized by radial, indeterminate cleavage. (b) Coelom formation. Coelom formation begins in the gastrula stage. In protostome development, the coelom forms from splits in the mesoderm. In deuterostome development, the coelom forms from mesodermal outpocketings of the archenteron. (c) Fate of the blastopore. In protostome development, the mouth forms from the blastopore. In deuterostome development, the mouth forms from a secondary opening.

The name Lophotrochozoa refers to two different features observed in some animals belonging to this clade. Some lophotrochozoans, such as ectoprocts, develop a unique structure called a lophophore (from the Greek lophos, crest, and pherein, to carry), a crown of ciliated tentacles that function in feeding (Figure 32.12a). Individuals in other phyla, including molluscs and annelids, go through a distinctive developmental stage called the trochophore larva (Figure 32.12b)—hence the name lophotrochozoan.

Figure 32.11 A phylogeny of living animals. This phylogeny shows a leading hypothesis about the relationships among selected animal phyla. The bilaterians are divided into three main lineages: deuterostomes, lophotrochozoans, and ecdysozoans. The dates of origin identified here are based on the results of a recent molecular clock study. Figure 32.12 Morphological characteristics of lophotrochozoans. (a)Lophophore feeding structures of an ectoproct (b) Structure of a trochophore larva

DNA analyses generally agree with this fossil biochemical evidence; for example, one recent molecular clock study estimated that sponges originated about 700 million years ago. These findings are also consistent with molecular analyses suggesting that the common ancestor of all extant animal species lived about 770 million years ago. What was this common ancestor like, and how did animals arise from their single-celled ancestors?

Figure 32.3 Three lines of evidence that choanoflagellates are closely related to animals. Morphologically, choanoflagellate cells and the collar cells (or choanocytes) of sponges are almost indistinguishable. Similar collar cells have been identified in other animals, including cnidarians, flatworms, and echinoderms—but they have never been observed in non-choanoflagellate protists or in plants or fungi. DNA sequence data indicate that choanoflagellates and animals are sister groups. In addition, genes for signaling and adhesion proteins previously known only from animals have been discovered in choanoflagellates.

Figure 33.13 A rotifer. These pseudocoelomates, smaller than many protists, are generally more anatomically complex than flatworms (LM). Figure 33.12 Anatomy of a tapeworm. The inset shows a close-up of the scolex (colorized SEM).

Figure 33.10 Anatomy of a planarian. Digestion is completed within the cells lining the gastrovascular cavity, which has many fine subbranches that provide an extensive surface area. Pharynx. A muscular pharynx can be extended through the mouth. Digestive juices are spilled onto prey, and the pharynx sucks small pieces of food into the gastrovascular cavity, where digestion continues. Undigested wastes are egested through an opening at the tip of the pharynx. Ventral nerve cords. From the ganglia, a pair of ventral nerve cords runs the length of the body. Ganglia. At the anterior end of the worm, near the main sources of sensory input, is a pair of ganglia, dense clusters of nerve cells

Brachiopods, or lamp shells, superficially resemble clams and other hinge-shelled molluscs, but the two halves of the brachiopod shell are dorsal and ventral rather than lateral, as in clams (Figure 33.15b). All brachiopods are marine. Most live attached to the seafloor by a stalk, opening their shell slightly to allow water to flow through the lophophore. The living brachiopods are remnants of a much richer past that included 30,000 species in the Paleozoic and Mesozoic eras. Some living brachiopods, such as those in the genus Lingula, appear nearly identical to fossils of species that lived 400 million years ago.

Figure 33.15 Lophophorates. (a) Ectoprocts, such as this creeping bryozoan (Plumatella repens), are colonial lophophorates. (b) Brachiopods, such as this lampshell (Terebratulina retusa), have a hinged shell. The two parts of the shell are dorsal and ventral. Figure 33.14 Paratenuisentis ambiguus, an acanthocephalan. The inset photograph shows the curved hooks that give the spiny-headed worms their name.

Figure 33.17 A chiton. Note the eight-plate shell characteristic of molluscs in the clade Polyplacophora.

Figure 33.18 Gastropods. The many species of gastropods have colonized terrestrial as well as aquatic environments. (a) A land snail (b) A sea slug. Nudibranchs, or sea slugs, lost their shell during their evolution.

Cephalopods: Cephalopods are active marine predators (Figure 33.21). They use their tentacles to grasp prey, which they then bite with beak-like jaws and immobilize with a poison present in their saliva. The foot of a cephalopod has become modified into a muscular excurrent siphon and part of the tentacles. Squids dart about by drawing water into their mantle cavity and then firing a jet of water through the excurrent siphon; they steer by pointing the siphon in different directions. Octopuses use a similar mechanism to escape predators. The mantle covers the visceral mass of cephalopods, but the shell is generally reduced and internal (in most species) or missing altogether (in some cuttlefishes and some octopuses).

Figure 33.21 Cephalopods. Squids are speedy carnivores with beak-like jaws and well-developed eyes. Octopuses are considered among the most intelligent invertebrates. ▶ Chambered nautiluses are the only living cephalopods with an external shell. Figure 33.19 A bivalve. This scallop has many eyes (dark blue spots) lining each half of its hinged shell. Figure 33.20 Anatomy of a clam. Food particles suspended in water that enters through the incurrent siphon are collected by the gills and passed via cilia and the palps to the mouth.

Threats faced by freshwater and terrestrial molluscs include habitat loss, pollution, competition or predation by non-native species, and overharvesting by humans. Is it too late to protect these molluscs? In some locations, reducing water pollution and changing how water is released from dams have led to dramatic rebounds in pearl mussel populations. Such results provide hope that with corrective measures, other endangered mollusc species can be revived.

Figure 33.22 The silent extinction. Molluscs account for a largely unheralded but sobering 40% of all documented extinctions of animal species. These extinctions have resulted from habitat loss, pollution, introduced species, overharvesting, and other human actions. Many pearl mussel populations, for example, were driven to extinction by overharvesting for their shells, which were used to make buttons and other goods. Land snails are highly vulnerable to the same threats; like pearl mussels, they are among the world's most imperiled animal groups.

Earthworms are hermaphrodites, but they do cross-fertilize. Two earthworms mate by aligning themselves in opposite directions in such a way that they exchange sperm, and then they separate. Some earthworms can also reproduce asexually by fragmentation followed by regeneration. As a group, Lophotrochozoa encompasses a remarkable range of body plans, as illustrated by members of such phyla as Syndermata, Ectoprocta, Mollusca, and Annelida. Next we'll explore the diversity of Ecdysozoa, a dominant presence on Earth in terms of sheer number of species.

Figure 33.24 The Christmas tree worm, Spirobranchus giganteus. This sedentarian's two tree-shaped whorls are tentacles, which it uses in gas exchange and to collect food particles from the water. The tentacles emerge from a calcium carbonate tube secreted by the worm that protects and supports its soft body. Figure 33.23 An errantian, the predator Nereimyra punctata. This marine annelid ambushes prey from burrows it has constructed on the seafloor. N. punctata hunts by touch, detecting its prey with long sensory organs called cirri that extend from the burrow.

Figure 33.25 A leech. A nurse applied this medicinal leech (Hirudo medicinalis) to a patient's sore thumb to drain blood from a hematoma (an abnormal accumulation of blood around an internal injury).

Figure 33.26 Anatomy of an earthworm, a sedentarian. Cerebral ganglia. The earthworm nervous system features a brainlike pair of cerebral ganglia above and in front of the pharynx. A ring of nerves around the pharynx connects to a subpharyngeal ganglion, from which a fused pair of nerve cords runs posteriorly. Chaetae. Each segment has four pairs of chaetae, bristles that provide traction for burrowing. Many of the internal structures are repeated within each segment of the earthworm. Each segment is surrounded by longitudinal muscle, which in turn is surrounded by circular muscle. Earthworms coordinate the contraction of these two sets of muscles to move. Coelom. The coelom of the earthworm is partitioned by septa. Metanephridium. Each segment of the worm contains a pair of excretory tubules, called metanephridia, that discharge wastes from the blood and coelomic fluid through exterior pores. Tiny blood vessels are abundant in the earthworm's skin, which functions as its respiratory organ. Ventral nerve cords. The nerve cords penetrate the septa and run the length of the animal, as do the digestive tract and longitudinal blood vessels. The circulatory system, a network of vessels, is closed. The dorsal and ventral vessels are linked by segmental pairs of vessels, some of which are muscular and pump blood through the circulatory system.

What genetic changes led to the increasing complexity of the arthropod body plan? Arthropods today have two unusual Hox genes, both of which influence segmentation. To test whether these genes could have driven the evolution of increased body segment diversity in arthropods, researchers studied Hox genes in onychophorans (see Figure 33.3), close relatives of arthropods (Figure 33.30). Their results indicate that the diversity of arthropod body plans did not arise from the acquisition of new Hox genes. Instead, the evolution of body segment diversity in arthropods was probably driven by changes in the sequence or regulation of existing Hox genes (see Concept 25.5).

Figure 33.29 A trilobite fossil. Trilobites were common denizens of the shallow seas throughout the Paleozoic era but disappeared with the great Permian extinctions about 250 million years ago. Paleontologists have described about 4,000 trilobite species.

Figure 33.2 Review of animal phylogeny. Except for sponges (phylum Porifera) and a few other groups, all animals have tissues and are eumetazoans. Most animals are bilaterians (see Figure 32.11).

Figure 33.3 (continued) Exploring Invertebrate Diversity Gastrotricha (800 species): Gastrotrichans are tiny worms whose ventral surface is covered with cilia, leading them to be called hairy bellies. Most species live on the bottoms of lakes or oceans, where they feed on small organisms and partially decayed organic matter. This individual has consumed algae, visible as the greenish material inside its gut. A gastrotrichan (differentialinterference-contrast LM)

Figure 33.31 External anatomy of an arthropod. Many of the distinctive features of arthropods are apparent in this dorsal view of a lobster. The body is segmented, but this character is obvious only in the post-genital region or "tail," located behind the genitals. The appendages (including antennae, pincers, mouthparts, walking legs, and swimming appendages) are jointed. The head bears a pair of compound (multilens) eyes. The whole body, including appendages, is covered by an exoskeleton.

Figure 33.30 Inquiry Did the arthropod body plan result from new Hox genes? Experiment One hypothesis suggests that the arthropod body plan resulted from the origin (by gene duplication and subsequent mutations) of two unusual Hox genes found in arthropods: Ultrabithorax (Ubx) and abdominal-A (abd-A). Researchers tested this hypothesis using onychophorans, a group of invertebrates closely related to arthropods. Unlike many living arthropods, onychophorans have a body plan in which most body segments are identical to one another. If the origin of the Ubx and abd-A Hox genes drove the evolution of body segment diversity in arthropods, these genes probably arose on the arthropod branch of the evolutionary tree: According to this hypothesis, Ubx and abd-A would not have been present in the common ancestor of arthropods and onychophorans; hence, onychophorans should not have these genes. The researchers examined the Hox genes of the onychophoran Acanthokara kaputensis. Results The onychophoran A. kaputensis has all arthropod Hox genes, including Ubx and abd-A. Red indicates the body regions of this onychophoran embryo in which Ubx or abd-A genes were expressed. (The inset shows this area enlarged.) Conclusion The evolution of increased body segment diversity in arthropods was not related to the origin of new Hox genes.

Lobsters, crayfishes, crabs, and shrimps are all relatively large crustaceans called decapods (Figure 33.37). The cuticle of decapods is hardened by calcium carbonate. Most decapod species are marine. Crayfishes, however, live in fresh water, and some tropical crabs live on land. Many small crustaceans are important members of marine and freshwater plankton communities. Planktonic crustaceans include many species of copepods, which are among the most numerous of all animals. Some copepods are grazers that feed upon algae, while others are predators that eat small animals (including smaller copepods!). Copepods are rivaled in abundance by the shrimplike krill, which grow to about 5 cm long (Figure 33.38). A major food source for baleen whales (including blue whales, humpbacks, and right whales), krill are now being harvested in great numbers by humans for food and agricultural fertilizer. The larvae of many larger-bodied crustaceans are also planktonic.

Figure 33.38 Krill. These planktonic crustaceans are consumed in vast quantities by some whales. Figure 33.39 Barnacles. The jointed appendages projecting from the barnacles' shells capture organisms and organic particles suspended in the water. Figure 33.37 A ghost crab, an example of a decapod. Ghost crabs live on sandy ocean beaches worldwide. Primarily nocturnal, they take shelter in burrows during the day

Reproduction in insects is usually sexual, with separate male and female individuals. Adults come together and recognize each other as members of the same species by advertising with bright colors (as in butterflies), sounds (as in crickets), or odors (as in moths). Fertilization is generally internal. In most species, sperm are deposited directly into the female's vagina at the time of copulation, though in some species the male deposits a sperm packet outside the female, and the female picks it up. An internal structure in the female called the spermatheca stores the sperm, usually enough to fertilize more than one batch of eggs. Many insects mate only once in a lifetime. After mating, a female often lays her eggs on an appropriate food source where the next generation can begin eating as soon as it hatches. Insects are classified in more than 30 orders, 8 of which are introduced in Figure 33.43.

Figure 33.40 Anatomy of a grasshopper, an insect. The insect body has three regions: head, thorax, and post-genital region. The segmentation of the thorax and post-genital region is obvious, but the segments that form the head are fused. Malpighian tubules. Metabolic wastes are removed from the hemolymph by excretory organs called Malpighian tubules, which are outpocketings of the digestive tract. Heart. The insect heart drives hemolymph through an open circulatory system. Cerebral ganglia. The two nerve cords meet in the head, where the ganglia of several anterior segments are fused into a brain (colored white below). The antennae, eyes, and other sense organs are concentrated on the head. Insect mouthparts are formed from several pairs of modified appendages. The mouthparts include mandibles, which grasshoppers use for chewing. In other insects, mouthparts are specialized for lapping, piercing, or sucking. Nerve cords. The insect nervous system consists of a pair of ventral nerve cords with several segmental ganglia. Tracheal tubes. Gas exchange in insects is accomplished by a tracheal system of branched, chitin-lined tubes that infiltrate the body and carry oxygen directly to cells. The tracheal system opens to the outside of the body through spiracles, pores that can control air flow and water loss by opening or closing.

Figure 33.42 Complete metamorphosis of a butterfly. (a) The larva (caterpillar) spends its time eating and growing, molting as it grows. (b) After several molts, the larva develops into a pupa. (c) Within the pupa, the larval tissues are broken down, and the adult is built by the division and differentiation of cells that were quiescent in the larva. (d) Eventually, the adult begins to emerge from the pupal cuticle. (e) Hemolymph is pumped into veins of the wings and then withdrawn, leaving the hardened veins as struts supporting the wings. The insect will fly off and reproduce, deriving much of its nourishment from the food reserves stored by the feeding larva. (a) Larva (caterpillar) (b) Pupa (c) Later-stage pupa d) Emerging adult (e) Adult

Figure 33.43 Exploring Insect Diversity: Although there are more than 30 orders of insects, we'll focus on just 8 here. Two orders of wingless insects, the bristletails (Archaeognatha) and silverfish (Zygentoma), diverged from other insects early in insect evolution. Evolutionary relationships among the other groups discussed here are under debate and so are not depicted on the tree. Archaeognatha (bristletails; 350 species): These wingless insects are found under bark and in other moist, dark habitats such as leaf litter, compost piles, and rock crevices. They feed on algae, plant debris, and lichens.

Figure 33.48 A feather star (clade Crinoidea). Figure 33.47 A sea urchin (clade Echinoidea). Figure 33.49 A sea cucumber (clade Holothuroidea).

Figure 33.45 A sea daisy (clade Asteroidea). Figure 33.46 A brittle star (clade Ophiuroidea).

Cnidarians are an ancient phylum of eumetazoans: All animals except sponges and a few other groups are eumetazoans ("true animals"), members of a clade of animals with tissues. One of the first lineages to have diverged from others in this clade is the phylum Cnidaria, which originated about 680 million years ago according to DNA analyses. Cnidarians have diversified into a wide range of sessile and motile forms, including hydras, corals, and jellies (commonly called "jellyfish"). Yet most cnidarians still exhibit the relatively simple, diploblastic, radial body plan that existed in early members of the group some 560 million years ago.

Figure 33.5 Polyp and medusa forms of cnidarians. The body wall of a cnidarian has two layers of cells: an outer layer of epidermis (darker blue; derived from ectoderm) and an inner layer of gastrodermis (yellow; derived from endoderm). Digestion begins in the gastrovascular cavity and is completed inside food vacuoles in the gastrodermal cells. Sandwiched between the epidermis and gastrodermis is a gelatinous layer, the mesoglea.

Anthozoans: Sea anemones and corals belong to the clade Anthozoa (see Figure 33.7b). These cnidarians occur only as polyps. Corals live as solitary or colonial forms, often forming symbioses with algae. Many species secrete a hard exoskeleton (external skeleton) of calcium carbonate. Each polyp generation builds on the skeletal remains of earlier generations, constructing rocklike reefs with shapes characteristic of their species. These skeletons are what we usually think of as coral. Coral reefs are to tropical seas what rain forests are to tropical land areas: They provide habitat for many other species. Unfortunately, these reefs are being destroyed at an alarming rate. Pollution, overharvesting, and ocean acidification (see Figure 3.12) are major threats; global warming is likely also contributing to their demise by raising seawater temperatures above the range in which corals thrive.

Figure 33.8 The life cycle of the hydrozoan Obelia. The polyp is asexual, and the medusa is sexual, releasing eggs and sperm. These two stages alternate, one producing the other. A colony of interconnected polyps (inset, LM) results from asexual reproduction by budding. Some of the colony's polyps, equipped with tentacles, are specialized for feeding. Other polyps, specialized for reproduction, lack tentacles and produce tiny medusae by asexual budding. Medusae swim off, grow, and reproduce sexually. The zygote develops into a solid ciliated larva called a planula. The planula eventually settles and develops into a new polyp.

Figure 33.11 The life cycle of a blood fluke (Schistosoma mansoni), a trematode. Mature flukes live in the blood vessels of the human intestine. A female fluke fits into a groove running the length of the larger male's body, as shown in the LM at right. Blood flukes reproduce sexually in the human host. The fertilized eggs exit the host in feces. If the human feces reach a pond or other source of water, the eggs develop into ciliated larvae. These larvae infect snails, the intermediate host. Asexual reproduction within a snail results in another type of motile larva, which escapes from the snail host. These larvae penetrate the skin and blood vessels of humans working in fields irrigated with water contaminated with fluke larvae.

Figure 33.9 Make Connections: Maximizing Surface Area: In general, the amount of metabolic or chemical activity an organism can carry out is proportional to its mass or volume. Maximizing metabolic rate, however, requires the efficient uptake of energy and raw materials, such as nutrients and oxygen, as well as the effective disposal of waste products. For large cells, plants, and animals, these exchange processes have the potential to be limiting due to simple geometry. When a cell or organism grows without changing shape, its volume increases more rapidly than its surface area (see Figure 6.7). As a result, there is proportionately less surface area over which exchange processes can occur. The challenge posed by the relationship of surface area and volume occurs in diverse contexts and organisms, but the evolutionary adaptations that meet this challenge are similar. Structures that maximize surface area through flattening, folding, branching, and projections have an essential role in biological systems.

Finally, note that the human skeleton is heavily mineralized bone, whereas cartilage plays a fairly minor role. But a bony internal skeleton was a relatively late development in the history of vertebrates. Instead, the vertebrate skeleton evolved initially as a structure made of unmineralized cartilage. Steps toward a bony skeleton began 470 million years ago, with the appearance of mineralized bone on the outer surface of the skull in some jawless vertebrates. Shortly after that time, the internal skeleton began to mineralize, first as calcified cartilage. By 430 million years ago, some vertebrates had a thin layer of bone lining the cartilage of their internal skeleton. The bones of vertebrates underwent even more mineralization in the group we turn to next, the jawed vertebrates.

Figure 34.12 Jawless armored vertebrates. Pteraspis and Pharyngolepis were two of many genera of jawless vertebrates that emerged during the Ordovician, Silurian, and Devonian periods Figure 34.11 A conodont. Conodonts were early jawless vertebrates that lived from 500 million to 200 million years ago. Unlike hagfishes and lampreys, conodonts had mineralized mouthparts, which they used for either predation or scavenging. Figure 34.10 Fossil of an early chordate. Discovered in 1999 in southern China, Haikouella had eyes and a brain but lacked a skull, a trait found in vertebrates. The organism's color in the drawing is fanciful. Figure 34.9 A sea lamprey. Parasitic lampreys use their mouth (inset) and tongue to bore a hole in the side of a fish. The lamprey then ingests the blood and other tissues of its host. Figure 34.8 A hagfish.

Figure 34.10 Fossil of an early chordate. Discovered in 1999 in southern China, Haikouella had eyes and a brain but lacked a skull, a trait found in vertebrates. The organism's color in the drawing is fanciful. Figure 34.11 A conodont. Conodonts were early jawless vertebrates that lived from 500 million to 200 million years ago. Unlike hagfishes and lampreys, conodonts had mineralized mouthparts, which they used for either predation or scavenging.

Figure 34.12 Jawless armored vertebrates. Pteraspis and Pharyngolepis were two of many genera of jawless vertebrates that emerged during the Ordovician, Silurian, and Devonian periods Figure 34.13 Possible step in the evolution of jawbones.

Figure 34.5 A tunicate, a urochordate.: (a)A tunicate larva is a free-swimming but nonfeeding "tadpole" in which all four main characters of chordates are evident. (b) In the adult, prominent pharyngeal slits function in suspension feeding, but other chordate characters are not obvious. (c) An adult tunicate, or sea squirt, is a sessile animal (photo is approximately life-sized).

Figure 34.15 Chondrichthyans. (a) Blacktip reef shark (Carcharhinus melanopterus). Sharks are fast swimmers with acute senses. Like all gnathostomes, they have paired pectoral and pelvic fins. b) Southern stingray (Dasyatis americana). Most rays are bottomdwellers that feed on molluscs and crustaceans. Some rays cruise in open water and scoop food into their gaping mouths. (c) Spotted ratfish (Hydrolagus colliei). Ratfishes, or chimaeras, typically live at depths greater than 80 m and feed on shrimp, molluscs, and sea urchins. Some species have a venomous spine at the front of their first dorsal fin.

Chordates have a notochord and a dorsal, hollow nerve cord: Vertebrates are members of the phylum Chordata, the chordates. Chordates are bilaterian (bilaterally symmetrical) animals, and within Bilateria, they belong to the clade of animals known as Deuterostomia (see Figure 32.11). As shown in Figure 34.2, there are two groups of invertebrate deuterostomes that are more closely related to vertebrates than they are to other invertebrates: the cephalochordates and the urochordates. Thus, along with the vertebrates, these two invertebrate groups are classified within the chordates.

Figure 34.2 Phylogeny of living chordates. This phylogenetic hypothesis shows the major clades of chordates in relation to the other main deuterostome clade, Echinodermata (see Concept 33.5). Derived characters are listed for selected clades; for example, only gnathostomes have a jaw. In some lineages, derived traits have been lost over time or occur in reduced form; hagfishes and lampreys, for example, are vertebrates with reduced vertebrae.

We'll discuss later how some of these characters were dramatically altered or lost in various lineages of tetrapods. In birds, for example, the pectoral limbs became wings, and in whales, the entire body converged toward a fishlike shape.

Figure 34.20 Discovery of a "fishapod": Tiktaalik. Paleontologists were on the hunt for fossils that could shed light on the evolutionary origin of tetrapods. Based on the ages of previously discovered fossils, researchers were looking for a dig site with rocks about 365-385 million years old. Ellesmere Island, in the Canadian Arctic, was one of the few such sites that was also likely to contain fossils, because it was once a river. The search at this site was rewarded by the discovery of fossils of a 375-million-year-old lobe-fin, named Tiktaalik. As shown in the chart and photographs, Tiktaalik exhibits both fish and tetrapod characters.

Salamanders: There are about 550 known species of urodeles, or salamanders. Some are entirely aquatic, but others live on land as adults or throughout life. Most salamanders that live on land walk with a side-to-side bending of the body, a trait also found in early terrestrial tetrapods (Figure 34.22a). Paedomorphosis is common among aquatic salamanders; the axolotl, for instance, retains larval features even when sexually mature (see Figure 25.24).

Figure 34.22 Amphibians. Order Urodela. Urodeles (salamanders) retain their tail as adults. Order Anura. Anurans (toads and frogs) lack a tail as adults. Order Apoda. Apodans, or caecilians, are legless, mainly burrowing amphibians

Figure 34.23 The "dual life" of a frog (Rana temporaria). The tadpole is an aquatic herbivore with a fishlike tail and internal gills. During metamorphosis, the gills and tail are resorbed, and walking legs develop. The adult frog will live on land. The adults return to water to mate. The male grasps the female, stimulating her to release eggs. The eggs are laid and fertilized in water. They have a jelly coat but lack a shell and would desiccate in air

Figure 34.24 A mobile nursery. A female marsupial frog (Flectonotus fitzgeraldi) incubates her eggs in pouches of skin on her back.

Figure 34.27 Artist's reconstruction of Hylonomus, an early amniote. About 25 cm long, this species lived 310 million years ago and probably ate insects and other small invertebrates.

Figure 34.25 A phylogeny of amniotes. Extant groups are named at the tips of the branches in boldface type. The dagger symbols (†) indicate extinct groups.

Figure 34.28 Hatching reptiles. These baby panther chameleons (Furcifer pardalis) are breaking out of their parchment-like shells, a common type of shell among living reptiles other than birds

Figure 34.26 The amniotic egg. The embryos of reptiles and mammals form four extraembryonic membranes: the allantois, chorion, amnion, and yolk sac. This diagram shows these membranes in the shelled egg of a reptile Extraembryonic membranes: Allantois. The allantois is a disposal sac for certain metabolic wastes produced by the embryo., Chorion. The chorion and the membrane of the allantois exchange gases between the embryo and the air. Amnion. The amnion protects the embryo in a fluid-filled cavity that cushions against mechanical shock. Yolk sac. The yolk sac contains the yolk, a stockpile of nutrients. Other nutrients are stored in the albumen ("egg white").

Figure 34.30 Form fits function: the avian wing and feather. (a) A wing is a remodeled version of the tetrapod forelimb. (b) The bones of many birds have a honeycombed internal structure and are filled with air. (c) A feather consists of a central air-filled shaft, from which radiate the vanes. The vanes are made up of barbs, which bear small branches called barbules. Birds have contour feathers and downy feathers. Contour feathers are stiff and contribute to the aerodynamic shapes of the wings and body. Their barbules have hooks that cling to barbules on neighboring barbs. When a bird preens, it runs the length of each contour feather through its beak, engaging the hooks and uniting the barbs into a precise shape. Downy feathers lack hooks, and the free-form arrangement of their barbs produces a fluffiness that provides insulation by trapping air.

Figure 34.29 Extant reptiles (other than birds).

Figure 34.32 An emu (Dromaius novaehollandiae), a flightless bird native to Australia.

Figure 34.31 Was Archaeopteryx the first bird? Fossil evidence indicates that Archaeopteryx was capable of powered flight but retained many characters of nonbird dinosaurs. Although it has long been considered the first bird, recent fossil discoveries have sparked debate. Some analyses indicate that Archaeopteryx was a nonbird dinosaur closely related to the birds. Others indicate that Archaeopteryx was a bird—as traditionally thought—but that it was not the first bird.

Figure 34.37 Adaptations of the kangaroo rat to its extremely dry habitat. The kangaroo rat's thick, oily skin limits evaporative water loss. The animal stays in its cool, relatively 2 humid burrow during the heat of the day, emerging at night to forage. Due to the unusual shape of its nasal passages, very little water is lost when the animal exhales. A kangaroo rat does not need to drink: It obtains all of the water it needs from catabolic pathways and from moisture in food. The large intestine and kidney absorb water so effectively that little water is lost in feces and urine.

Figure 34.34 Hummingbird feeding while hovering. A hummingbird can rotate its wings in all directions, enabling it to hover and fly backward. Figure 34.36 Feet adapted to perching. This great tit (Parus major) is a member of the Passeriformes, the perching birds. The toes of these birds can lock around a branch or wire, enabling the bird to rest for long periods. Figure 34.35 A specialized beak. This greater flamingo (Phoenicopterus ruber) dips its beak into the water and strains out the food. Figure 34.33 A king penguin (Aptenodytes patagonicus) "flying" underwater. With their streamlined shape and powerful pectoral muscles, penguins are fast and agile swimmers.

Figure 34.39 Short-beaked echidna (Tachyglossus aculeatus), an Australian monotreme. Monotremes have hair and produce milk, but they lack nipples. Monotremes are the only mammals that lay eggs (inset)

Figure 34.38 The evolution of the mammalian ear bones. Biarmosuchus was a synapsid, a lineage that eventually gave rise to the mammals. Bones that transmit sound in the ear of mammals arose from the modification of bones in the jaw of nonmammalian synapsids. a)In Biarmosuchus, the meeting of the articular and quadrate bones formed the jaw joint. (b) During the evolutionary remodeling of the mammalian skull, a new jaw joint formed between the dentary and squamosal bones (see Figure 25.7). No longer used in the jaw, the quadrate and articular bones became incorporated into the middle ear as two of the three bones that transmit sound from the eardrum to the inner ear.

Figure 34.15 Chondrichthyans.: (a) Blacktip reef shark (Carcharhinus melanopterus). Sharks are fast swimmers with acute senses. Like all gnathostomes, they have paired pectoral and pelvic fins. (b) Southern stingray (Dasyatis americana). Most rays are bottomdwellers that feed on molluscs and crustaceans. Some rays cruise in open water and scoop food into their gaping mouths. (c) Spotted ratfish (Hydrolagus colliei). Ratfishes, or chimaeras, typically live at depths greater than 80 m and feed on shrimp, molluscs, and sea urchins. Some species have a venomous spine at the front of their first dorsal fin.

Figure 34.4 The lancelet Branchiostoma, a cephalochordate. This small invertebrate displays all four main chordate characters. Water enters the mouth and passes through the pharyngeal slits into the atrium, a chamber that vents to the outside via the atriopore; large particles are blocked from entering the mouth by tentacle-like cirri. The serially arranged segmental muscles produce the lancelet's wavelike swimming movements.

Memorize figure 34.42 Exploring mammalian diversity

Figure 34.41 Convergent evolution of marsupials and eutherians (placental mammals). (Drawings not to scale.)

Figure 34.43 Verreaux's sifakas (Propithecus verreauxi), a type of lemur.

Figure 34.42 Exploring Mammalian Diversity: Phylogenetic Relationships of Mammals: Evidence from numerous fossils and molecular analyses indicates that monotremes diverged from other mammals about 180 million years ago and that marsupials diverged from eutherians (placental mammals) about 140 million years ago. Molecular systematics has helped to clarify the evolutionary relationships between the eutherian orders, though there is still no broad consensus on a phylogenetic tree. One current hypothesis, represented by the tree shown below, clusters the eutherian orders into four main clades.

Figure 34.45 New World monkeys and Old World monkeys.: (a) New World monkeys, such as spider monkeys (shown here), squirrel monkeys, and capuchins, have a prehensile tail (one adapted for grasping) and nostrils that open to the sides. (b) Old World monkeys lack a prehensile tail, and their nostrils open downward. This group includes macaques (shown here), mandrils, baboons, and rhesus monkeys.

Figure 34.44 A phylogenetic tree of primates. The fossil record indicates that the lineage leading to anthropoids diverged from other primates about 55 million years ago. New World monkeys, Old World monkeys, and apes (the clade that includes gibbons, orangutans, gorillas, chimpanzees, and humans) have been evolving as separate lineages for more than 25 million years. The lineage leading to humans and Australopithecus branched off from other apes between 6 and 7 million years ago.

Figure 34.48 The skeleton of "Ardi," a 4.4-million-yearold hominin, Ardipithecus ramidus. Figure 34.47 A timeline for selected hominin species. Most of the fossils illustrated here come from sites in eastern and southern Africa. Note that at most times in hominin history, two or more hominin species were contemporaries. Some of the species are controversial, reflecting phylogenetic debates about the interpretation of skeletal details and biogeography.

Figure 34.46 Nonhuman apes. (a) Gibbons, such as this Muller's gibbon, are found only in southeastern Asia. Their very long arms and fingers are adaptations for brachiating (swinging by the arms from branch to branch). b) Orangutans are shy apes that live in the rain forests of Sumatra and Borneo. They spend most of their time in trees; note the foot adapted for grasping and the opposable thumb. (c) Gorillas are the largest apes; some males are almost 2 m tall and weigh about 200 kg. Found only in Africa, these herbivores usually live in groups of up to about 20 individuals. (d) Chimpanzees live in tropical Africa. They feed and sleep in trees but also spend a great deal of time on the ground. Chimpanzees are intelligent, communicative, and social. (e) Bonobos are in the same genus (Pan) as chimpanzees but are smaller. They survive today only in the African nation of Congo.

Figure 34.50 Fossil of Homo ergaster. This 1.7-million-year-old fossil from Kenya belongs to a young Homo ergaster male. This individual was tall, slender, and fully bipedal, and he had a relatively large brain. 34.52 Fossil evidence of humanNeanderthal interbreeding. This jawbone belonged to a human who lived 40,000 years ago and had a relatively recent Neanderthal ancestor.

Figure 34.49 Evidence that hominins walked upright 3.5 million years ago. (a) The Laetoli footprints, more than 3.5 million years old, confirm that upright posture evolved quite early in hominin history. (b)An artist's reconstruction of A. afarensis, a hominin alive at the time of the Laetoli footprints.

Figure 34.4 The lancelet Branchiostoma, a cephalochordate. This small invertebrate displays all four main chordate characters. Water enters the mouth and passes through the pharyngeal slits into the atrium, a chamber that vents to the outside via the atriopore; large particles are blocked from entering the mouth by tentacle-like cirri. The serially arranged segmental muscles produce the lancelet's wavelike swimming movements.

Figure 34.5 A tunicate, a urochordate. (a)A tunicate larva is a free-swimming but nonfeeding "tadpole" in which all four main characters of chordates are evident. (b) In the adult, prominent pharyngeal slits function in suspension feeding, but other chordate characters are not obvious. (c) An adult tunicate, or sea squirt, is a sessile animal (photo is approximately life-sized).

A bird's most obvious adaptations for flight are its wings and feathers (Figure 34.30). Feathers are made of the protein β@keratin, which is also found in the scales of other reptiles. The shape and arrangement of the feathers form the wings into airfoils, and they illustrate some of the same principles of aerodynamics as the wings of an airplane. Power for flapping the wings comes from contractions of large pectoral (breast) muscles anchored to a keel on the sternum (breastbone). Some birds, such as eagles and hawks, have wings adapted for soaring on air currents and flap their wings only occasionally; other birds, including hummingbirds, must flap continuously to stay aloft (see Figure 34.34). Among the fastest birds are the appropriately named swifts, which can fly up to 170 km/hr.

Flight provides numerous benefits. It enhances scavenging and hunting, including enabling many birds to feed on flying insects, an abundant, nutritious food resource. Flight also provides ready escape from earthbound predators and enables some birds to migrate great distances to exploit different food resources and seasonal breeding areas. Flying requires a great expenditure of energy from an active metabolism. Birds are endothermic; they use their own metabolic heat to maintain a high, constant body temperature. Feathers and in some species a layer of fat provide insulation that enables birds to retain body heat. The lungs have tiny tubes leading to and from elastic air sacs that improve airflow and oxygen uptake. This efficient respiratory system and a circulatory system with a four-chambered heart keep tissues well supplied with oxygen and nutrients, supporting a high rate of metabolism

Today's crops are the products of artificial selection—the result of plant domestication that began about 12,000 years ago. To appreciate the scale of this transformation, note how the number and size of seeds in domesticated plants are greater than those of their wild relatives, as in the case of maize and the grass teosinte (see Figure 38.16). Scientists can glean information about domestication by comparing the genes of crops with those of wild relatives. With maize, dramatic changes such as increased cob size and loss of the hard coating around teosinte kernels may have been initiated by as few as five mutations.

Flowering plants also provide other edible products. Two popular beverages come from tea leaves and coffee beans, and you can thank the cacao tree for cocoa and chocolate. Spices are derived from various plant parts, such as flowers (cloves, saffron), fruits and seeds (vanilla, black pepper, mustard), leaves (basil, mint, sage), and even bark (cinnamon). Many seed plants are sources of wood, which is absent in all living seedless plants. Wood consists of tough-walled xylem cells (see Figure 35.22). It is the primary source of fuel for much of the world, and wood pulp, typically derived from conifers such as fir and pine, is used to make paper. Wood remains the most widely used construction material.

On several occasions during eukaryotic evolution, red algae and green algae underwent secondary endosymbiosis, meaning they were ingested in the food vacuoles of heterotrophic eukaryotes and became endosymbionts themselves.

For example, protists known as chlorarachniophytes likely evolved when a heterotrophic eukaryote engulfed a green alga. Evidence for this process can be found within the engulfed cell, which contains a tiny vestigial nucleus, called a nucleomorph (Figure 28.4). Genes from the nucleomorph are still transcribed, and their DNA sequences indicate that the engulfed cell was a green alga.

Gnathostomes share other derived characters besides jaws. The common ancestors of all gnathostomes underwent an additional duplication of Hox genes, such that the single set present in early chordates became four. In fact, the entire genome appears to have duplicated, and together these genetic changes likely enabled the origin of jaws and other novel features in gnathostomes. The gnathostome forebrain is enlarged compared to that of other vertebrates, and it is associated with enhanced senses of smell and vision. Another characteristic of aquatic gnathostomes is the lateral line system, organs that form a row along each side of the body and are sensitive to vibrations in the surrounding water. Precursors of these organs were present in the head shields of some jawless vertebrates.

Fossil Gnathostomes: Gnathostomes appeared in the fossil record about 440 million years ago and steadily became more diverse. Their success probably resulted from a combination of anatomical features: Their paired fins and tail (which were also found in jawless vertebrates) allowed them to swim efficiently after prey, and their jaws enabled them to grab prey or simply bite off chunks of flesh. Over time, dorsal, ventral, and anal fins stiffened by bony structures called fin rays also evolved in some early gnathostomes. Fin rays provide thrust and steering control when aquatic vertebrates swim after prey or away from predators. Faster swimming was supported by other adaptations, including a more efficient gas exchange system in the gills.

Early Homo: The earliest fossils that paleoanthropologists place in our genus, Homo, include those of the species Homo habilis. These fossils, ranging in age from about 2.4 to 1.6 million years, show clear signs of certain derived hominin characters above the neck. Compared to the australopiths, H. habilis had a shorter jaw and a larger brain volume, about 550-750 cm3 . Sharp stone tools have also been found with some fossils of H. habilis (the name means "handy man").

Fossils from 1.9 to 1.5 million years ago mark a new stage in hominin evolution. A number of paleoanthropologists recognize these fossils as those of a distinct species, Homo ergaster..Homo ergaster had a substantially larger brain than H. habilis (over 900 cm3 ), as well as long, slender legs with hip joints well adapted for long-distance walking (Figure 34.50). The fingers were relatively short and straight, suggesting that H. ergaster did not climb trees like earlier hominins. Homo ergaster fossils have been discovered in far more arid environments than earlier hominins and have been associated with more sophisticated stone tools. Its smaller teeth also suggest that H. ergaster either ate different foods than australopiths (more meat and less plant material) or prepared some of its food before chewing, perhaps by cooking or mashing the food.

Another important structural feature of most fungi is that their hyphae are divided into cells by cross-walls, or septa (singular, septum) (Figure 31.3a). Septa generally have pores large enough to allow ribosomes, mitochondria, and even nuclei to flow from cell to cell. Some fungi lack septa (Figure 31.3b). Known as coenocytic fungi, these organisms consist of a continuous cytoplasmic mass having hundreds or thousands of nuclei. As we'll describe later, the coenocytic condition results from the repeated division of nuclei without cytokinesis.

Fungal hyphae form an interwoven mass called a mycelium (plural, mycelia) that infiltrates the material on which the fungus feeds (see Figure 31.2). The structure of a mycelium maximizes its surface-to-volume ratio, making feeding very efficient. Just 1 cm3 of rich soil may contain as much as 1 km of hyphae with a total surface area of 300 cm2 in contact with the soil. A fungal mycelium grows rapidly, as proteins and other materials synthesized by the fungus move through cytoplasmic streaming to the tips of the extending hyphae. The fungus concentrates its energy and resources on adding hyphal length and thus overall absorptive surface area, rather than on increasing hyphal girth. Multicellular fungi are not motile in the typical sense—they cannot run, swim, or fly in search of food or mates. However, as they grow, such fungi can move into new territory, swiftly extending the tips of their hyphae.

The hidden network of Russula filaments is a fitting symbol of the neglected grandeur of the kingdom Fungi. Most of us are barely aware of these eukaryotes beyond the mushrooms we eat or the occasional brush with athlete's foot. Yet fungi are a huge and important component of the biosphere. While about 100,000 species have been described, there may be as many as 1.5 million species of fungi. Some fungi are exclusively single-celled, though most have complex multicellular bodies. These diverse organisms are found in just about every imaginable terrestrial and aquatic habitat.

Fungi are not only diverse and widespread but also essential for the well-being of most ecosystems. They break down organic material and recycle nutrients, allowing other organisms to assimilate essential chemical elements. Humans make use of fungi as a food source, for applications in agriculture and forestry, and in manufacturing products ranging from bread to antibiotics. But it is also true that some fungi cause disease in plants and animals. In this chapter, we will investigate the structure and evolutionary history of fungi, survey the major groups of fungi, and discuss their ecological and commercial significance.

Fungi play key roles in nutrient cycling, ecological interactions, and human welfare: In our survey of fungal classification, we've touched on some of the ways fungi influence other organisms. We will now look more closely at these impacts, focusing on how fungi act as decomposers, mutualists, and pathogens.

Fungi as Decomposers: Fungi are well adapted as decomposers of organic material, including the cellulose and lignin of plant cell walls. In fact, almost any carbon-containing substrate—even jet fuel and house paint—can be consumed by at least some fungi. The same is true of bacteria. As a result, fungi and bacteria are primarily responsible for keeping ecosystems stocked with the inorganic nutrients essential for plant growth. Without these decomposers, carbon, nitrogen, and other elements would remain tied up in organic matter. If that were to happen, plants and the animals that eat them could not exist because elements taken from the soil would not be returned. Without decomposers, life as we know it would cease.

Figure 31.2 Structure of a multicellular fungus. The top photograph shows the sexual structures, in this case called mushrooms, of the penny bun fungus (Boletus edulis). The bottom photograph shows a mycelium growing on fallen conifer needles. The inset SEM shows hyphae. Reproductive structure. Tiny haploid cells called spores are produced inside the mushroom. Hyphae. The mushroom and its subterranean mycelium are a continuous network of hyphae.

Fungi produce spores through sexual or asexual life cycles: Most fungi propagate themselves by producing vast numbers of spores, either sexually or asexually. For example, puffballs, the reproductive structures of certain fungal species, may release trillions of spores (see Figure 31.17). Spores can be carried long distances by wind or water. If they land in a moist place where there is food, they germinate, producing a new mycelium. To appreciate how effective spores are at dispersing, leave a slice of melon exposed to the air. Even without a visible source of spores nearby, within a week, you will likely observe fuzzy mycelia growing from microscopic spores that have fallen onto the melon.

Gastropods: About three-quarters of all living species of molluscs are gastropods (Figure 33.18). Most gastropods are marine, but there are also freshwater species. Still other gastropods have adapted to life on land, where snails and slugs thrive in habitats ranging from deserts to rain forests.

Gastropods move literally at a snail's pace by a rippling motion of their foot or by means of cilia—a slow process that can leave them vulnerable to attack. Most gastropods have a single, spiraled shell into which the animal can retreat when threatened. The shell, which is secreted by glands at the edge of the mantle, has several functions, including protecting the animal's soft body from injury and dehydration. One of its most important roles is as a defense against predators, as is demonstrated by comparing populations with different histories of predation (see the Scientific Skills Exercise). As they move slowly about, most gastropods use their radula to graze on algae or plants. Several groups, however, are predators, and their radula has become modified for boring holes in the shells of other molluscs or for tearing apart prey. In the cone snails, the teeth of the radula act as poison darts that are used to subdue prey. Many gastropods have a head with eyes at the tips of tentacles. Terrestrial snails lack the gills typical of most aquatic gastropods. Instead, the lining of their mantle cavity functions as a lung, exchanging respiratory gases with the air.

In addition, the seedless vascular plants that formed the first forests eventually became coal, again removing CO2 from the atmosphere for long periods of time. In the stagnant waters of Carboniferous swamps, the dead bodies of early trees did not completely decay. This organic material turned to thick layers of peat, later covered by the sea. Marine sediments piled on top, and over millions of years, heat and pressure converted the peat to coal. In fact, Carboniferous coal deposits are the most extensive ever formed. Coal was crucial to the Industrial Revolution, and people worldwide still burn 6 billion tons a year. It is ironic that coal, formed from plants that contributed to a global cooling, now contributes to global warming by returning carbon to the atmosphere (see Figure 56.29).

Growing along with the seedless plants in Carboniferous swamps were primitive seed plants. Though seed plants were not dominant at that time, they rose to prominence after the swamps began to dry up at the end of the Carboniferous period. The next chapter traces the origin and diversification of seed plants, continuing our story of adaptation to life on land.

The oldest fossils of species from an extant lineage of gymnosperms are 305 million years old. These early gymnosperms lived in moist Carboniferous ecosystems that were dominated by lycophytes, horsetails, ferns, and other seedless vascular plants. As the Carboniferous period gave way to the Permian (299 to 252 million years ago), the climate became much drier. As a result, the lycophytes, horsetails, and ferns that dominated Carboniferous swamps were largely replaced by gymnosperms, which were better suited to the drier climate. Gymnosperms thrived as the climate dried, in part because they have the key terrestrial adaptations found in all seed plants, such as seeds and pollen. In addition, some gymnosperms were particularly well suited to arid conditions because of the thick cuticles and relatively small surface areas of their needle-shaped leaves.

Gymnosperms dominated terrestrial ecosystems throughout much of the Mesozoic era, which lasted from 252 to 66 million years ago. In addition to serving as the food supply for giant herbivorous dinosaurs, these gymnosperms were involved in many other interactions with animals. Recent fossil discoveries, for example, show that some gymnosperms were pollinated by insects more than 100 million years ago— the earliest evidence of insect pollination in any plant group (Figure 30.6). Late in the Mesozoic, angiosperms began to replace gymnosperms in some ecosystems.

Genetically modified fungi also hold much promise. For example, scientists have succeeded in engineering a strain of S. cerevisiae that produces human glycoproteins, including insulin-like growth factor. Such fungus-produced glycoproteins have the potential to treat people with medical conditions that prevent them from producing these compounds. Meanwhile, other researchers are sequencing the genome of Gliocladium roseum, an ascomycete that can grow on wood or agricultural waste and that naturally produces hydrocarbons similar to those in diesel fuel (Figure 31.26). They hope to decipher the metabolic pathways by which G. roseum synthesizes hydrocarbons, with the goal of harnessing those pathways to produce biofuels without reducing land area for growing food crops (as occurs when ethanol is produced from corn).

Having now completed our survey of the kingdom Fungi, we will turn in the rest of this unit to the closely related kingdom Animalia, to which we humans belong

▲ Recorded extinctions of animal species Annelids: Annelida means "little rings," referring to the annelid body's resemblance to a series of fused rings. Annelids are segmented worms that live in the sea, in most freshwater habitats, and in damp soil. Annelids are coelomates, and they range in length from less than 1 mm to more than 3 m. Traditionally, the phylum Annelida was divided into three main groups, Polychaeta (the polychaetes), Oligochaeta (the oligochaetes), and Hirudinea (the leeches). The names of the first two of these groups reflected the relative number of chaetae, bristles made of chitin, on their bodies: polychaetes (from the Greek poly, many, and chaitē, long hair) have many more chaetae per segment than do oligochaetes.

However, a 2011 phylogenomic study and other recent molecular analyses have indicated that the oligochaetes are a subgroup of the polychaetes, making the polychaetes (as defined morphologically) a paraphyletic group. Likewise, the leeches have been shown to be a subgroup of the oligochaetes. As a result, these traditional names are no longer used to describe the evolutionary history of the annelids. Instead, current evidence indicates that the annelids can be divided into two major clades, Errantia and Sedentaria—a grouping that reflects broad differences in lifestyle.

The other group of anthropoids consists of primates informally called apes (Figure 34.46). The ape group includes the genera Hylobates (gibbons), Pongo (orangutans), Gorilla (gorillas), Pan (chimpanzees and bonobos), and Homo (humans). The apes diverged from Old World monkeys about 25-30 million years ago. Today, nonhuman apes are found exclusively in tropical regions of the Old World. With the exception of gibbons, living apes are larger than either New or Old World monkeys. All living apes have relatively long arms, short legs, and no tail. Although all nonhuman apes spend time in trees, only gibbons and orangutans are primarily arboreal. Social organization varies among the apes; gorillas and chimpanzees are highly social. Finally, compared to other primates, apes have a larger brain in proportion to their body size, and their behavior is more flexible. These two characteristics are especially prominent in our next group, the hominins.

Humans are mammals that have a large brain and bipedal locomotion: In our tour of Earth's biodiversity, we turn now to our own species, Homo sapiens, which is about 200,000 years old. When you consider that life has existed on Earth for at least 3.5 billion years, we are clearly evolutionary newcomers.

Practical Uses of Fungi: The dangers posed by fungi should not overshadow their immense benefits. We depend on their ecological services as decomposers and recyclers of organic matter. In addition, mushrooms are not the only fungi of interest for human consumption. Fungi are used to ripen Roquefort and other blue cheeses. Morels and truffles, the edible fruiting bodies of various ascomycetes, are highly prized for their complex flavors (see Figure 31.15). These fungi can sell for hundreds to thousands of dollars a pound. Truffles release strong odors that attract mammals and insects, which in nature feed on them and disperse their spores. In some cases, the odors mimic the pheromones (sex attractants) of certain mammals. For example, the odors of several European truffles mimic the pheromones released by male pigs, which explains why truffle hunters sometimes use female pigs to help find these delicacies.

Humans have used yeasts to produce alcoholic beverages and bread for thousands of years. Under anaerobic conditions, yeasts ferment sugars to alcohol and CO2, which causes dough to rise. Only relatively recently have the yeasts involved been separated into pure cultures for more controlled use. The yeast Saccharomyces cerevisiae is the most important of all cultured fungi (see Figure 31.7). It is available as many strains of baker's yeast and brewer's yeast. Many fungi have great medical value as well. For example, a compound extracted from ergots is used to reduce high blood pressure and to stop maternal bleeding after childbirth. Some fungi produce antibiotics that are effective in treating bacterial infections. In fact, the first antibiotic discovered was penicillin, made by the ascomycete mold Penicillium. Other examples of pharmaceuticals derived from fungi include cholesterol-lowering drugs and cyclosporine, a drug used to suppress the immune system after organ transplants. Fungi also figure prominently in basic research. For example, the yeast Saccharomyces cerevisiae is used to study the molecular genetics of eukaryotes because its cells are easy to culture and manipulate. Scientists are gaining insight into the genes involved in Parkinson's disease by examining the functions of homologous genes in S. cerevisiae.

Complete metamorphosis: Coleoptera (beetles; 350,000 species): Beetles, such as this male snout weevil (Rhiastus lasternus), constitute the most species-rich order of insects. They have two pairs of wings, one of which is thick and stiff, the other membranous. They have an armored exoskeleton and mouthparts adapted for biting and chewing. Diptera (151,000 species): Dipterans have one pair of wings; the second pair has become modified into balancing organs called halteres. Their mouthparts are adapted for sucking, piercing, or lapping. Flies and mosquitoes are among the best-known dipterans, which live as scavengers, predators, and parasites. Like many other insects, flies such as this red tachinid (Adejeania vexatrix) have well-developed compound eyes that provide a wideangle view and excel at detecting fast movements.

Hymenoptera (125,000 species): Most hymenopterans, which include ants, bees, and wasps, are highly social insects. They have two pairs of membranous wings, a mobile head, and chewing or sucking mouthparts. The females of many species have a posterior stinging organ. Many species, such as this European paper wasp (Polistes dominulus), build elaborate nests. Lepidoptera (120,000 species): Butterflies and moths have two pairs of wings covered with tiny scales. To feed, they uncoil a long proboscis, visible in this photograph of a hummingbird hawkmoth (Macroglossum stellatarum). This moth's name refers to its ability to hover in the air while feeding from a flower. Most lepidopterans feed on nectar, but some species feed on other substances, including animal blood or tears.

What is the evolutionary relationship of Neanderthals to Homo sapiens? Genetic data indicate that the lineages leading to H. sapiens and to Neanderthals diverged about 400,000 years ago. This indicates that while Neanderthals and humans share a recent common ancestor, humans did not descend directly from Neanderthals (as was once thought). Another long-standing question is whether mating occurred between the two species, leading to interspecific gene flow. Some researchers have argued that evidence of gene flow can be found in fossils that show a mixture of human and Neanderthal characteristics. A recent analysis of the DNA sequence of the Neanderthal genome indicated that limited gene flow did occur between the two species (Figure 34.51).

In 2015, the most extensive evidence yet of such gene flow was reported: DNA extracted from the fossil of a human jawbone was found to contain long stretches of Neanderthal DNA (Figure 34.52). In fact, the amount of Neanderthal DNA in this fossil indicated that this individual's great-great-great-grandparent was a Neanderthal. Other recent genomic studies have shown that gene flow also occurred between Neanderthals and the "Denisovans," an as-yet unidentified hominin whose DNA was isolated from 40,000-year-old bone fragments discovered in a Siberian cave.

Figure 26.13 Branch lengths can represent genetic change. This tree was constructed by comparing sequences of homologs of a gene that plays a role in development; Drosophila was used as an outgroup. The branch lengths are proportional to the amount of genetic change in each lineage; varying branch lengths indicate that the gene has evolved at different rates in different lineages.

In Figure 26.13, for example, the branch length of the phylogenetic tree reflects the number of changes that have taken place in a particular DNA sequence in that lineage. Note that the total length of the horizontal lines from the base of the tree to the mouse is less than that of the line leading to the outgroup species, the fruit fly Drosophila. This implies that in the time since the mouse and fly lineages diverged from their common ancestor, more genetic changes have occurred in the Drosophila lineage than in the mouse lineage.

Derived Characters of Amniotes: Amniotes are named for the major derived character of the clade, the amniotic egg, which contains four specialized membranes: the amnion, the chorion, the yolk sac, and the allantois (Figure 34.26). Called extraembryonic membranes because they are not part of the body of the embryo itself, these membranes develop from tissue layers that grow out from the embryo. The amniotic egg is named for the amnion, which encloses a compartment of fluid that bathes the embryo and acts as a hydraulic shock absorber. The other membranes in the egg function in gas exchange, the transfer of stored nutrients to the embryo, and waste storage. The amniotic egg was a key evolutionary innovation for terrestrial life: It allowed the embryo to develop on land in its own private "pond," hence reducing the dependence of tetrapods on an aqueous environment for reproduction.

In contrast to the shell-less eggs of amphibians, the amniotic eggs of most reptiles and some mammals have a shell. A shell slows dehydration of the egg in air, an adaptation that helped amniotes to occupy a wider range of terrestrial habitats than amphibians, their closest living relatives. (Seeds played a similar role in the evolution of plants, as discussed in Concept 30.1.) Most mammals have lost the eggshell over the course of their evolution, and the embryo avoids desiccation by developing within the amnion inside the mother's body. Amniotes have acquired other key adaptations to life on land. For example, amniotes use their rib cage to ventilate their lungs. This method is more efficient than throat-based ventilation, which amphibians use as a supplement to breathing through their skin. The increased efficiency of rib cage ventilation may have allowed amniotes to abandon breathing through their skin and develop less permeable skin, thereby conserving water.

Most fishes can maintain a buoyancy equal to the surrounding water by filling an air sac known as a swim bladder. (If a fish swims to greater depths or toward the surface, where water pressure differs, the fish shuttles gas between its blood and swim bladder, keeping the volume of gas in the bladder constant.) Charles Darwin proposed that the lungs of tetrapods evolved from swim bladders, but strange as it may sound, the opposite seems to be true: Swim bladders arose from lungs. Osteichthyans in many early-branching lineages have lungs, which they use to breathe air as a supplement to gas exchange in their gills. This suggests that lungs arose in early osteichthyans; later, swim bladders evolved from lungs in some lineages.

In nearly all fishes, the skin is covered by flattened, bony scales that differ in structure from the tooth-like scales of sharks. Glands in the skin secrete a slimy mucus over the skin, an adaptation that reduces drag during swimming. Like the ancient aquatic gnathostomes mentioned earlier, fishes have a lateral line system, which is evident as a row of tiny pits in the skin on either side of the body. The details of fish reproduction vary extensively. Most species are oviparous, reproducing by external fertilization after the female sheds large numbers of small eggs. However, internal fertilization and birthing characterize other species.

Pollen and Production of Sperm: A microspore develops into a pollen grain that consists of a male gametophyte enclosed within the pollen wall. (The wall's outer layer is made of molecules secreted by sporophyte cells, so we refer to the male gametophyte as being in the pollen grain, not equivalent to the pollen grain.) Sporopollenin in the pollen wall protects the pollen grain as it is transported by wind or by hitchhiking on an animal. The transfer of pollen to the part of a seed plant that contains the ovules is called pollination. If a pollen grain germinates (begins growing), it gives rise to a pollen tube that discharges sperm into the female gametophyte within the ovule, as shown in Figure 30.3b.

In nonvascular plants and seedless vascular plants such as ferns, free-living gametophytes release flagellated sperm that swim through a film of water to reach eggs. Given this requirement, it is not surprising that many of these species live in moist habitats. But a pollen grain can be carried by wind or animals, eliminating the dependence on water for sperm transport. The ability of seed plants to transfer sperm without water likely contributed to their colonization of dry habitats. The sperm of seed plants also do not require motility because they are carried to the eggs by pollen tubes. The sperm of some gymnosperm species (such as cycads and ginkgos, shown in Figure 30.7) retain the ancient flagellated condition, but flagella have been lost in the sperm of most gymnosperms and all angiosperms.

Hagfishes and Lampreys: The hagfishes (Myxini) and the lampreys (Petromyzontida) are the only lineages of living vertebrates whose members lack jaws. Unlike most vertebrates, lampreys and hagfishes also do not have a backbone. Even so, lampreys are classified as vertebrates because they have rudimentary vertebrae (composed of cartilage, not bone). The hagfishes, in contrast, traditionally were thought to lack vertebrae altogether; hence, they were classified as invertebrate chordates closely related to vertebrates.

In the past few years, however, this interpretation has changed. Recent research has shown that hagfishes, like lampreys, have rudimentary vertebrae. In addition, a series of molecular phylogenetic studies have supported the hypothesis that hagfishes are vertebrates. Molecular analyses also indicate that hagfishes and lampreys are sister groups, as shown in Figure 34.2. Together, the hagfishes and lampreys form a clade of living jawless vertebrates, the cyclostomes. (All other vertebrates have jaws and make up a much larger clade, the gnathostomes, which we will discuss in Concept 34.3.)

The chameleon is just one example of an animal that is an efficient consumer of other organisms. Other predatory animals overwhelm their prey using their strength, speed, or toxins, while still others capture the unwary by building concealed traps such as webs. Likewise, herbivorous animals can strip the plants they eat bare of leaves or seeds, while parasitic animals weaken their hosts by consuming their tissues or body fluids. These and other animals are effective eating machines in part because they have specialized muscle and nerve cells that enable them to detect, capture, and eat other organisms—including those that can flee from attack. Animals are also very good at processing the food they have eaten; most animals do this using an efficient digestive system that has a mouth at one end and an anus at the other.

In this chapter, we embark on a tour of the animal kingdom that will continue in the next two chapters. Here we will consider the characteristics that all animals share, as well as the evolutionary history of this kingdom of consumers.

Plants not only have affected the recovery of regions such as Mount St. Helens but also have transformed Earth. Continuing the saga of how this occurred, this chapter follows the emergence and diversification of the group to which fireweed belongs, the seed plants. Fossils and comparative studies of living plants offer clues about the origin of seed plants some 360 million years ago. As this new group became established, it dramatically altered the course of plant evolution. Indeed, seed plants have become the dominant producers on land, and they make up the vast majority of plant biodiversity today.

In this chapter, we will first examine the general features of seed plants. Then we will look at their evolutionary history and enormous impact on human society.

Blue dragons are invertebrates: animals that lack a backbone. Invertebrates account for over 95% of known animal species. They occupy almost every habitat on Earth, from the scalding water released by deep-sea "black smoker" hydrothermal vents to the frozen ground of Antarctica. Evolution in these varied environments has produced an immense diversity of forms, including a species consisting of a flat bilayer of cells and species with features such as silk-spinning glands, pivoting spines, and tentacles covered with suction cups. Invertebrates range from microscopic organisms to organisms that can grow to 18 m long (1.5 times the length of a school bus).

In this chapter, we'll take a tour of the invertebrate world, using the phylogenetic tree in Figure 33.2 as a guide. Figure 33.3 surveys 23 invertebrate phyla as representatives of invertebrate diversity. Many of those phyla are explored in more detail in the rest of this chapter.

There are more than 57,000 species of vertebrates, a relatively small number compared to, say, the 1 million insect species on Earth. But what vertebrates may lack in number of species, they make up for in disparity, varying enormously in characteristics such as body mass. Vertebrates include the heaviest animals ever to walk on land, plant-eating dinosaurs that were as massive as 40,000 kg (more than 13 pickup trucks). The biggest animal ever to exist on Earth is also a vertebrate— the blue whale, which can exceed 100,000 kg. On the other end of the spectrum, the fish Schindleria brevipinguis is just 8.4 mm long and has a mass roughly 100 billion times smaller than that of a blue whale.

In this chapter, you will learn about current hypotheses regarding the origins of vertebrates from invertebrate ancestors. We will track the evolution of the vertebrate body plan, from a notochord to a head to a mineralized skeleton. We'll also explore the major groups of vertebrates (both living and extinct), as well as the evolutionary history of our own species—Homo sapiens.

With the exception of a few parasitic species, barnacles are a group of sessile crustaceans whose cuticle is hardened into a shell containing calcium carbonate (Figure 33.39). Most barnacles anchor themselves to rocks, boat hulls, pilings, and other submerged surfaces. Their natural adhesive is as strong as synthetic glues. These barnacles feed by extending appendages from their shell to strain food from the water. Barnacles were not recognized as crustaceans until the 1800s, when naturalists discovered that barnacle larvae resemble the larvae of other crustaceans. The remarkable mix of unique traits and crustacean homologies found in barnacles was a major inspiration to Charles Darwin as he developed his theory of evolution. We turn now to a group nested within the paraphyletic crustaceans, the insects.

Insects Insects and their six-legged terrestrial relatives form an enormous clade, Hexapoda; we'll focus here on the insects, since as a group they have more described species than all other eukaryotic groups combined. Insects live in almost every terrestrial habitat and in fresh water, and flying insects fill the air. Insects are rare, though not absent, in marine habitats. The internal anatomy of an insect includes several complex organ systems, which are highlighted in Figure 33.40. The oldest insect fossils date to about 415 million years ago. Later, an explosion in insect diversity took place when insect flight evolved during the Carboniferous and Permian periods (359-252 million years ago). An animal that can fly can escape predators, find food and mates, and disperse to new habitats more effectively than an animal that must crawl about on the ground. Many insects have one or two pairs of wings that emerge from the dorsal side of the thorax. Because the wings are extensions of the cuticle, insects can fly without sacrificing any walking legs (Figure 33.41). By contrast, the flying vertebrates— birds and bats—have one of their two pairs of walking legs modified into wings, making some of these species clumsy on the ground.

Euglenozoans: Protists called euglenozoans belong to a diverse clade that includes predatory heterotrophs, photosynthetic autotrophs, mixotrophs, and parasites. The main morphological feature that distinguishes protists in this clade is the presence of a rod with either a spiral or a crystalline structure inside each of their flagella (Figure 28.6). The two best-studied groups of euglenozoans are the kinetoplastids and the euglenids.

Kinetoplastids: Protists called kinetoplastids have a single, large mitochondrion that contains an organized mass of DNA called a kinetoplast. These protists include species that feed on prokaryotes in freshwater, marine, and moist terrestrial ecosystems, as well as species that parasitize animals, plants, and other protists. For example, kinetoplastids in the genus Trypanosoma infect humans and cause sleeping sickness, a neurological disease that is invariably fatal if not treated. The infection occurs via the bite of a vector (carrier) organism, the African tsetse fly (Figure 28.7). Trypanosomes also cause Chagas' disease, which is transmitted by bloodsucking insects and can lead to congestive heart failure. Trypanosomes evade immune responses with an effective "bait-and-switch" defense. The surface of a trypanosome is coated with millions of copies of a single protein. However, before the host's immune system can recognize the protein and mount an attack, new generations of the parasite switch to another surface protein with a different molecular structure. Frequent changes in the surface protein prevent the host from developing immunity. (The Scientific Skills Exercise in Chapter 43 explores this topic further.) About a third of Trypanosoma's genome is dedicated to producing these surface proteins.

The second group, the chlorophytes (from the Greek chloros, green), includes more than 7,000 species. Most live in fresh water, but there are also many marine and some terrestrial species. The simplest chlorophytes are unicellular organisms such as Chlamydomonas, which resemble gametes of more complex chlorophytes. Various species of unicellular chlorophytes live independently in aquatic habitats as phytoplankton or inhabit damp soil. Some live symbiotically within other eukaryotes, contributing part of their photosynthetic output to the food supply of their hosts. Still other chlorophytes live in environments exposed to intense visible and ultraviolet radiation; these species are protected by radiation-blocking compounds in their cytoplasm, cell wall, or zygote coat.

Larger size and greater complexity evolved in green algae by three different mechanisms: 1. The formation of colonies of individual cells, as seen in Zygnema (Figure 28.22a) and other species whose filamentous forms contribute to the stringy masses known as pond scum. 2. The formation of true multicellular bodies by cell division and differentiation, as in Volvox (see Figure 28.2) and Ulva (Figure 28.22b). 3. The repeated division of nuclei with no cytoplasmic division, as in Caulerpa (Figure 28.22c)

Sedentarians: Species in the other major clade of annelids, Sedentaria (from the Latin sedere, sit), tend to be less mobile than those in Errantia. Some species burrow slowly through marine sediments or soil, while others live within tubes that protect and support their soft bodies. Tube-dwelling sedentarians often have elaborate gills or tentacles used for filter feeding (Figure 33.24). Although the Christmas tree worm shown in Figure 33.24 once was classified as a "polychaete," current evidence indicates it is a sedentarian. The clade Sedentaria also contains former "oligochaetes," including the two groups we turn to next, the leeches and the earthworms.

Leeches: Some leeches are parasites that suck blood by attaching temporarily to other animals, including humans (Figure 33.25), but most are predators that feed on other invertebrates. Leeches range in length from 1 to 30 cm. Most leeches inhabit fresh water, but there are also marine species and terrestrial leeches, which live in moist vegetation. Some parasitic species use bladelike jaws to slit the skin of their host. The host is usually oblivious to this attack because the leech secretes an anesthetic. After making the incision, the leech secretes a chemical, hirudin, which keeps the blood of the host from coagulating near the incision. The parasite then sucks as much blood as it can hold, often more than ten times its own weight. After this gorging, a leech can last for months without another meal.

Plastid Evolution: A Closer Look: As you've seen, current evidence indicates that mitochondria are descended from a bacterium that was engulfed by a host cell that was an archaean (or a close relative of the archaeans). This event gave rise to the eukaryotes. There is also much evidence that later in eukaryotic history, a lineage of heterotrophic eukaryotes acquired an additional endosymbiont—a photosynthetic cyanobacterium—that then evolved into plastids. According to the hypothesis illustrated in Figure 28.3, this plastid-bearing lineage gave rise to two lineages of photosynthetic protists, or algae: red algae and green algae.

Let's examine some of the steps in Figure 28.3 more closely. First, recall that cyanobacteria are gram-negative and that gram-negative bacteria have two cell membranes, an inner plasma membrane and an outer membrane that is part of the cell wall (see Figure 27.3). Plastids in red algae and green algae are also surrounded by two membranes. Transport proteins in these membranes are homologous to proteins in the inner and outer membranes of cyanobacteria, providing further support for the hypothesis that plastids originated from a cyanobacterial endosymbiont.

In most lichens, each partner provides something the other could not obtain on its own. The alga or cyanobacterium provides carbon compounds; a cyanobacterium also fixes nitrogen (see Concept 27.3) and provides organic nitrogen compounds. The fungus provides its photosynthetic partner with a suitable environment for growth. The physical arrangement of hyphae allows for gas exchange, protects the photosynthetic partner, and retains water and minerals, most of which are absorbed from airborne dust or from rain. The fungus also secretes acids, which aid in the uptake of minerals.

Lichens are important pioneers on cleared rock and soil surfaces, such as volcanic flows and burned forests. They break down the surface by physically penetrating and chemically attacking it, and they trap windblown soil. Nitrogen-fixing lichens also add organic nitrogen to some ecosystems. These processes make it possible for a succession of plants to grow. Fossils show that lichens were on land 420 million years ago. These early lichens may have modified rocks and soil much as they do today, helping pave the way for plants.

Derived Characters of Tetrapods: The most significant character of tetrapods gives the group its name, which means "four feet" in Greek. In place of pectoral and pelvic fins, tetrapods have limbs with digits. Limbs support a tetrapod's weight on land, while feet with digits efficiently transmit muscle-generated forces to the ground when it walks.

Life on land selected for numerous other changes to the tetrapod body plan. In tetrapods, the head is separated from the body by a neck that originally had one vertebra on which the skull could move up and down. Later, with the origin of a second vertebra in the neck, the head could also swing from side to side. The bones of the pelvic girdle, to which the hind legs are attached, are fused to the backbone, permitting forces generated by the hind legs against the ground to be transferred to the rest of the body. Except for some fully aquatic species (such as the axolotl discussed below), the adults of living tetrapods do not have gills; during embryonic development, the pharyngeal clefts instead give rise to parts of the ears, certain glands, and other structures.

Derived Characters of Mammals: Mammals are named for their distinctive mammary glands, which produce milk for offspring. All mammalian mothers nourish their young with milk, a balanced diet rich in fats, sugars, proteins, minerals, and vitamins. Hair, another mammalian character, and a fat layer under the skin provide insulation that can conserve water and protect the body against extremes of heat or cold. Another mammalian adaptation for life on land is the kidney (see Figure 44.12), which is efficient at conserving water when removing wastes from the body. Some mammals, such as kangaroo rats, are so adept at conserving water that they can survive in arid environments while drinking little or no water at all (Figure 34.37).

Like birds, mammals are endothermic, and most have a high metabolic rate. Efficient respiratory and circulatory systems (including a four-chambered heart) support a mammal's metabolism. Also as in birds, mammals generally have a larger brain than other vertebrates of equivalent size, and many species are capable learners. The relatively long duration of parental care extends the time for offspring to learn important survival skills by observing their parents. In addition, whereas the teeth of reptiles are generally uniform in size and shape, the jaws of mammals bear a variety of teeth with sizes and shapes adapted for chewing many kinds of foods. Humans, like most mammals, have teeth modified for shearing (incisors and canine teeth) and for crushing and grinding (premolars and molars).

By about 160 million years ago, feathered theropods had evolved into birds. Many researchers consider Archaeopteryx, which was discovered in a German limestone quarry in 1861, to be the earliest known bird (Figure 34.31). It had feathered wings but retained ancestral characters such as teeth, clawed digits in its wings, and a long tail. Archaeopteryx flew well at high speeds, but unlike a present-day bird, it could not take off from a standing position. Fossils of later birds from the Cretaceous show a gradual loss of certain ancestral dinosaur features, such as teeth and clawed forelimbs, as well as the acquisition of innovations found in extant birds, including a short tail covered by a fan of feathers.

Living Birds Clear evidence of Neornithes, the clade that includes the 28 orders of living birds, can be found before the Cretaceous-Paleogene boundary 66 million years ago. Several groups of living and extinct birds include one or more flightless species. The ratites, an order of birds that includes the ostrich, rhea, kiwi, cassowary, and emu, are all flightless (Figure 34.32). In ratites, the sternal keel is absent, and the pectoral muscles are small relative to those of birds that can fly. Penguins make up another flightless order of birds, but, like flying birds, they have powerful pectoral muscles. They use these muscles to "fly" in the water: As they swim, they flap their flipper-like wings in a manner that resembles the flight stroke of a more typical bird (Figure 34.33). Certain species of rails, ducks, and pigeons are also flightless.

One such lineage is the Bennettitales, a group with flowerlike structures that may have been pollinated by insects (Figure 30.14a). However, the Bennettitales and other similar lineages of extinct woody seed plants did not have carpels or flowers and hence are not classified as angiosperms.

Making sense of the origin of angiosperms also depends on working out the order in which angiosperm clades diverged from one another. Here, dramatic progress has been made in recent years. Molecular and morphological evidence suggests that the shrub Amborella trichopoda, water lilies, and star anise are living representatives of lineages that diverged from other angiosperms early in the history of the group (Figure 30.14b). Amborella is woody, supporting the conclusion mentioned earlier that the angiosperm common ancestor was probably woody. Like the Bennettitales, Amborella, water lilies, and star anise lack vessel elements, efficient water-conducting cells that are found in most present-day angiosperms. Overall, based on the features of ancestral species and angiosperms like Amborella, researchers have hypothesized that early angiosperms were woody shrubs that had small flowers and relatively simple water-conducting cells.

Fertilization is external in most amphibians; the male grasps the female and spills his sperm over the eggs as the female sheds them (see Figure 34.23c). Some amphibian species lay vast numbers of eggs in temporary pools, and egg mortality is high. In contrast, other species lay relatively few eggs and display various types of parental care. Depending on the species, either males or females may house eggs on their back (Figure 34.24), in their mouth, or even in their stomach. Certain tropical tree frogs stir their egg masses into moist, foamy nests that resist drying.

Many amphibians exhibit complex and diverse social behaviors, especially during breeding seasons. Frogs are usually quiet, but the males of many species vocalize to defend heir breeding territory or to attract females. In some species, migrations to specific breeding sites may involve vocal communication, celestial navigation, or chemical signaling.

Golden Algae: The characteristic color of golden algae results from their yellow and brown carotenoids. The cells of golden algae are typically biflagellated, with both flagella attached near one end of the cell. Most species are unicellular, but some are colonial (Figure 28.11).

Many golden algae are components of freshwater and marine plankton, communities of mostly microscopic organisms that drift in currents near the water's surface. While all golden algae are photosynthetic, some species are mixotrophic. These mixotrophs can absorb dissolved organic compounds or ingest food particles, including living cells, by phagocytosis. If environmental conditions deteriorate, many species form protective cysts that can survive for decades.

Insects also radiated in response to the origin of new plant species, which provided new sources of food. By the speciation mechanisms described in Concept 24.2, an insect population feeding on a new plant species can diverge from other populations, eventually forming a new species of insect. A fossil record of diverse insect mouthparts, for example, suggests that specialized modes of feeding on gymnosperms and other Carboniferous plants contributed to early adaptive radiations of insects. Later, a major increase in insect diversity appears to have been stimulated by the evolutionary expansion of flowering plants during the mid-Cretaceous period (about 100 million years ago). Although insect and plant diversity decreased during the Cretaceous mass extinction, both groups have rebounded over the past 66 million years. Increases in the diversity of particular insect groups have often been associated with radiations of the flowering plants on which they fed.

Many insects undergo metamorphosis during their development. In the incomplete metamorphosis of grasshoppers and some other insect groups, the young (called nymphs) resemble adults but are smaller, have different body proportions, and lack wings. The nymph undergoes a series of molts, each time looking more like an adult. With the final molt, the insect reaches full size, acquires wings, and becomes sexually mature. Insects with complete metamorphosis have larval stages specialized for eating and growing that are known by such names as caterpillar, maggot, or grub. The larval stage looks entirely different from the adult stage, which is specialized for dispersal and reproduction. Metamorphosis from the larval stage to the adult occurs during a pupal stage (Figure 33.42).

Monotremes: Monotremes are found only in Australia and New Guinea and are represented by one species of platypus and four species of echidnas (spiny anteaters; Figure 34.39). Monotremes lay eggs, a character that is ancestral for amniotes and retained in most reptiles. Like all mammals, monotremes have hair and produce milk, but they lack nipples. Milk is secreted by glands on the belly of the mother. After hatching, the baby sucks the milk from the mother's fur.

Marsupials: Opossums, kangaroos, and koalas are examples of the group called marsupials. Both marsupials and eutherians share derived characters not found among monotremes. They have higher metabolic rates and nipples that provide milk, and they give birth to live young. The embryo develops inside the uterus of the female's reproductive tract. The lining of the uterus and the extraembryonic membranes that arise from the embryo form a placenta, a structure in which nutrients diffuse into the embryo from the mother's blood. A marsupial is born very early in its development and completes its embryonic development while nursing (Figure 34.40a). In most species, the nursing young are held within a maternal pouch called a marsupium. A red kangaroo, for instance, is about the size of a honeybee at its birth, just 33 days after fertilization. Its back legs are merely buds, but its front legs are strong enough for it to crawl from the exit of its mother's reproductive tract to a pouch that opens to the front of her body, a journey that lasts a few minutes. In other species, the marsupium opens to the rear of the mother's body; in greater bilbies, this protects the young as their mother burrows in the dirt (Figure 34.40b).

These various hypotheses are not mutually exclusive; predator-prey relationships, atmospheric changes, and changes in development may each have played a role. The Cambrian period was followed by the Ordovician, Silurian, and Devonian periods, when animal diversity continued to increase, although punctuated by episodes of mass extinction (see Figure 25.17). Vertebrates (fishes) emerged as the top predators of the marine food web. By 450 million years ago, groups that diversified during the Cambrian period began to make an impact on land. Arthropods were the first animals to adapt to terrestrial habitats, as indicated by fragments of arthropod remains and by well-preserved fossils from several continents of millipedes, centipedes, and spiders. Another clue is seen in fossilized fern galls—enlarged cavities that fern plants form in response to stimulation by resident insects, which then use the galls for protection. Fossils indicate that fern galls date back at least 302 million years, suggesting that insects and plants were influencing each other's evolution by that time. Vertebrates colonized land around 365 million years ago and diversified into numerous terrestrial groups. Two of these survive today: the amphibians (such as frogs and salamanders) and the amniotes (reptiles, including birds, and mammals). We will explore these groups, known collectively as the tetrapods, in more detail in Chapter 34.

Mesozoic Era (252-66 Million Years Ago): The animal phyla that had evolved during the Paleozoic now began to spread into new habitats. In the oceans, the first coral reefs formed, providing other marine animals with new places to live. Some reptiles returned to the water, leaving plesiosaurs (see Figure 25.5) and other large aquatic predators as their descendants. On land, descent with modification in some tetrapods led to the origin of wings and other flight equipment in pterosaurs and birds. Large and small dinosaurs emerged, both as predators and herbivores. At the same time, the first mammals—tiny nocturnal insect-eaters—appeared on the scene. In addition, as you read in Concept 30.3, flowering plants (angiosperms) and insects both underwent dramatic diversifications during the late Mesozoic.

Knowing that most prokaryotes are extremely small organisms, you might assume that Figure 28.1 depicts six prokaryotes and one much larger eukaryote. But in fact, the only prokaryote is the organism immediately above the scale bar. The other six organisms are members of diverse, mostly unicellular groups of eukaryotes informally known as protists. These very small eukaryotes have intrigued biologists for more than 300 years, ever since the Dutch scientist Antoni van Leeuwenhoek first laid eyes on them under a light microscope. Some protists change their forms as they creep along using blob-like appendages, while others resemble tiny trumpets or miniature jewelry. Recalling his observations, van Leeuwenhoek wrote, "No more pleasant sight has met my eye than this, of so many thousands of living creatures in one small drop of water." The protists that fascinated van Leeuwenhoek continue to surprise us today.

Metagenomic studies have revealed a treasure trove of previously unknown protists within the world of microscopic life. Many of these newly discovered organisms are just 0.5-2 µm in diameter—as small as many prokaryotes. Genetic and morphological studies have also shown that some protists are more closely related to plants, fungi, or animals than they are to other protists. As a result, the kingdom in which all protists once were classified, Protista, has been abandoned, and various protist lineages are now recognized as major groups in their own right. Most biologists still use the term protist, but only as a convenient way to refer to eukaryotes that are not plants, animals, or fungi. In this chapter, you will become acquainted with some of the most significant groups of protists. You will learn about their structural and biochemical adaptations as well as their enormous impact on ecosystems, agriculture, industry, and human health.

Lophotrochozoans, a clade identified by molecular data, have the widest range of animal body forms: The vast majority of animal species belong to the clade Bilateria, whose members exhibit bilateral symmetry and triploblastic development (see Concept 32.3). Most bilaterians also have a digestive tract with two openings (a mouth and an anus) and a coelom. Recent DNA analyses suggest that the common ancestor of living bilaterians lived about 670 million years ago. To date, however, the oldest fossil that is widely accepted as a bilaterian is of Kimberella, a mollusc (or close relative) that lived 560 million years ago (see Figure 32.5). Many other bilaterian groups first appeared in the fossil record during the Cambrian explosion (535 to 525 million years ago).

Molecular evidence suggests that today there are three major clades of bilaterally symmetrical animals: Lophotrochozoa, Ecdysozoa, and Deuterostomia. This section will focus on the first of these clades, the lophotrochozoans. Concepts 33.4 and 33.5 will explore the other two clades. Although the clade Lophotrochozoa was identified by molecular data, its name comes from features found in some of its members. Some lophotrochozoans develop a structure called a lophophore, a crown of ciliated tentacles that functions in feeding, while others go through a distinctive stage called the trochophore larva (see Figure 32.12). Other members of the group have neither of these features. Few other unique morphological features are widely shared within the group—in fact, the lophotrochozoans are the most diverse bilaterian clade in terms of body plan. This diversity in form is reflected in the number of phyla classified in the group: Lophotrochozoa includes 18 phyla, more than twice the number in any other clade of bilaterians. We'll now introduce six of the diverse lophotrochozoan phyla: the flatworms, rotifers and acanthocephalans, ectoprocts, brachiopods, molluscs, and annelids.

Magnoliids: Magnoliids consist of about 8,000 species, most notably magnolias, laurels, and black pepper plants. They include both woody and herbaceous species. Although they share some traits with basal angiosperms, such as a typically spiral rather than whorled arrangement of floral organs, magnoliids are more closely related to eudicots and monocots. ◀ Southern magnolia (Magnolia grandiflora). This member of the magnolia family is a large tree. The variety of southern magnolia shown here, called "Goliath," has flowers that measure up to about a foot across.

Monocots: About one-quarter of angiosperm species are monocots — about 70,000 species. Some of the largest groups are the orchids, grasses, and palms. Grasses include some of the most agriculturally important crops, such as maize, rice, and wheat. ◀ Orchid (Lemboglossum rossii) Barley (Hordeum vulgare), a grass ▲ Pygmy date palm (Phoenix roebelenii)

This clade of eutherians evolved in Africa when the continent was isolated from other landmasses. It includes Earth's largest living land animal (the African elephant), as well as species that weigh less than 10 g. All members of this clade, which underwent an adaptive radiation in South America, belong to the order Xenarthra. One species, the nine-banded armadillo, is found in the southern United States. This is the largest eutherian clade. It includes the rodents, which make up the largest mammalian order by far, with about 1,770 species. Humans belong to the order Primates. This diverse clade includes terrestrial and marine mammals as well as bats, the only flying mammals. A growing body of evidence, including Eocene fossils of whales with feet, supports putting whales in the same order (Cetartiodactyla) as pigs, cows, and hippos. Possible phylogenetic tree of mammals. All 20 extant orders of mammals are listed at the right of the tree. The orders in bold type are surveyed on the facing page.

Monotremata Platypuses, echidnas - Lay eggs; no nipples; young suck milk from fur of mother

Plants evolved from green algae: As you read in Chapter 28, green algae called charophytes are the closest relatives of plants. We'll begin with a closer look at the evidence for this relationship.

Morphological and Molecular Evidence: Many key traits of plants also appear in some algae. For example, plants are multicellular, eukaryotic, photosynthetic autotrophs, as are brown, red, and certain green algae. Plants have cell walls made of cellulose, and so do green algae, dinoflagellates, and brown algae. And chloroplasts with chlorophylls a and b are present in green algae, euglenids, and a few dinoflagellates, as well as in plants.

Hornworts (Phylum Anthocerophyta): This phylum's common and scientific names (from the Greek keras, horn) refer to the long, tapered shape of the sporophyte. A typical sporophyte can grow to about 5 cm high. Unlike a liverwort or moss sporophyte, a hornwort sporophyte lacks a seta and consists only of a sporangium. The sporangium releases mature spores by splitting open, starting at the tip of the horn. The gametophytes, which are usually 1-2 cm in diameter, grow mostly horizontally and often have multiple sporophytes attached. Hornworts are frequently among the first species to colonize open areas with moist soils; a symbiotic relationship with nitrogen-fixing cyanobacteria contributes to their ability to do this (nitrogen is often in short supply in such areas).

Mosses (Phylum Bryophyta): Moss gametophytes, which range in height from less than 1 mm up to 60 cm, are less than 15 cm tall in most species. The familiar carpet of moss you observe consists mainly of gametophytes. The blades of their "leaves" are usually only one cell thick, but more complex "leaves" that have ridges coated with cuticle can be found on the common hairy-cap moss (Polytrichum, below) and its close relatives. Moss sporophytes are typically elongated and visible to the naked eye, with heights ranging up to about 20 cm. Though green and photosynthetic when young, they turn tan or brownish red when ready to release spores.

Note that the phylogeny depicted in Figure 29.6 focuses only on the relationships between extant plant lineages. Paleobotanists have also discovered fossils belonging to extinct plant lineages. As you'll read later in the chapter, these fossils can reveal intermediate steps in the emergence of plant groups found on Earth today

Mosses and other nonvascular plants have life cycles dominated by gametophytes: The nonvascular plants (bryophytes) are represented today by three phyla of small, herbaceous (nonwoody) plants: liverworts (phylum Hepatophyta), mosses (phylum Bryophyta), and hornworts (phylum Anthocerophyta). Liverworts and hornworts are named for their shapes, plus the suffix wort (from the Anglo-Saxon for "herb"). Mosses are familiar to many people, although some plants commonly called "mosses" are not really mosses at all. These include Irish moss (a red seaweed), reindeer moss (a lichen), club mosses (seedless vascular plants), and Spanish mosses (lichens in some regions and flowering plants in others).

Lifestyle and Ecology of Amphibians: The term amphibian (derived from amphibious, meaning "both ways of life") refers to the life stages of many frog species that live first in water and then on land (Figure 34.23). The larval stage of a frog, called a tadpole, is usually an aquatic herbivore with gills, a lateral line system resembling that of aquatic vertebrates, and a long, finned tail. The tadpole initially lacks legs; it swims by undulating its tail. During the metamorphosis that leads to the "second life," the tadpole develops legs, lungs, a pair of external eardrums, and a digestive system adapted to a carnivorous diet. At the same time, the gills disappear; the lateral line system also disappears in most species. The young frog crawls onto shore and becomes a terrestrial hunter. In spite of their name, however, many amphibians do not live a dual— aquatic and terrestrial—life. There are some strictly aquatic or strictly terrestrial frogs, salamanders, and caecilians. Moreover, salamander and caecilian larvae look much like the adults, and typically both the larvae and the adults are carnivorous.

Most amphibians are found in damp habitats such as swamps and rain forests. Even those adapted to drier habitats spend much of their time in burrows or under moist leaves, where humidity is high. One reason amphibians require relatively wet habitats is that they rely heavily on their moist skin for gas exchange—if their skin dries out, they cannot get enough oxygen. In addition, amphibians typically lay their eggs in water or in moist environments on land; their eggs lack a shell and dehydrate quickly in dry air.

Bivalves: The molluscs of the clade Bivalvia are all aquatic and include many species of clams, oysters, mussels, and scallops. Bivalves have a shell divided into two halves (Figure 33.19). The halves are hinged, and powerful adductor muscles draw them tightly together to protect the animal's soft body. Bivalves have no distinct head, and the radula has been lost. Some bivalves have eyes and sensory tentacles along the outer edge of their mantle. The mantle cavity of a bivalve contains gills that are used for feeding as well as gas exchange in most species (Figure 33.20).

Most bivalves are suspension feeders. They trap small food particles in mucus that coats their gills, and cilia then convey those particles to the mouth. Water enters the mantle cavity through an incurrent siphon, passes over the gills, and then exits the mantle cavity through an excurrent siphon. Most bivalves lead sedentary lives, a characteristic suited to suspension feeding. Mussels secrete strong threads that tether them to rocks, docks, boats, and the shells of other animals. However, clams can pull themselves into the sand or mud, using their muscular foot for an anchor, and scallops can skitter along the seafloor by flapping their shells, rather like the mechanical false teeth sold in novelty shops.

Figure 28.22 Examples of large chlorophytes. a) Zygnema, a common pond alga. This filamentous charophyte features two star-shaped chloroplasts in each cell. b)Ulva, or sea lettuce. This multicellular, edible chlorophyte has differentiated structures, such as its leaflike blades and a rootlike holdfast that anchors the alga c)Caulerpa, an intertidal chlorophyte. The branched filaments lack crosswalls and thus are multinucleate. In effect, the body of this alga is one huge "supercell."

Most chlorophytes have complex life cycles, with both sexual and asexual reproductive stages. Nearly all species of chlorophytes reproduce sexually by means of biflagellated gametes that have cup-shaped chloroplasts (Figure 28.23). Alternation of generations has evolved in some chlorophytes, including Ulva.

Phylum Coniferophyta: Phylum Coniferophyta, the largest gymnosperm phyla, consists of about 600 species of conifers (from the Latin conus, cone, and ferre, to carry), including many large trees. Most species have woody cones, but a few have fleshy cones. Some, such as pines, have needle-like leaves. Others, such as redwoods, have scale-like leaves. Some species dominate vast northern forests, whereas others are native to the Southern Hemisphere.

Most conifers are evergreens; they retain their leaves throughout the year. Even during winter, a limited amount of photosynthesis occurs on sunny days. When spring comes, conifers already have fully developed leaves that can take advantage of the sunnier, warmer days. Some conifers, such as the dawn redwood, tamarack, and larch, are deciduous trees that lose leaves each autumn.

One small group of cephalopods with external shells, the chambered nautiluses, survives today. Cephalopods are the only molluscs with a closed circulatory system, in which the blood remains separate from fluid in the body cavity. They also have well-developed sense organs and a complex brain. The ability to learn and behave in a complex manner is probably more critical to fast-moving predators than to sedentary animals such as clams. The ancestors of octopuses and squids were probably shelled molluscs that took up a predatory lifestyle; the shell was lost in later evolution. Shelled cephalopods called ammonites, some of them as large as truck tires, were the dominant invertebrate predators of the seas for hundreds of millions of years until their disappearance during the mass extinction at the end of the Cretaceous period, 65.5 million years ago.

Most species of squid are less than 75 cm long, but some are much larger. The giant squid (Architeuthis dux), for example, has an estimated maximum length of 13 m for females and 10 m for males. The colossal squid (Mesonychoteuthis hamiltoni), is even larger, with an estimated maximum length of 14 m. Unlike A. dux, which has large suckers and small teeth on its tentacles, M. hamiltoni has two rows of sharp hooks at the ends of its tentacles that can inflict deadly lacerations. It is likely that A. dux and M. hamiltoni spend most of their time in the deep ocean, where they may feed on large fishes. Remains of both giant squid species have been found in the stomachs of sperm whales, which are probably their only natural predator. Scientists first photographed A. dux in the wild in 2005 while it was attacking baited hooks at a depth of 900 m. M. hamiltoni has yet to be observed in nature. Overall, much remains to be learned about these marine giants.

Walled Spores Produced in Sporangia: Plant spores are haploid reproductive cells that can grow into multicellular haploid gametophytes by mitosis. The polymer sporopollenin makes the walls of plant spores tough and resistant to harsh environments. This chemical adaptation enables spores to be dispersed through dry air without harm. The sporophyte has multicellular organs called sporangia (singular, sporangium) that produce the spores. Within a sporangium, diploid cells called sporocytes, or spore mother cells, undergo meiosis and generate the haploid spores. The outer tissues of the sporangium protect the developing spores until they are released into the air. Multicellular sporangia that produce spores with sporopollenin-enriched walls are key terrestrial adaptations of plants. Although charophytes also produce spores, these algae lack multicellular sporangia, and their flagellated, water-dispersed spores lack sporopollenin.

Multicellular Gametangia: Another feature distinguishing early plants from their algal ancestors was the production of gametes within multicellular organs called gametangia. The female gametangia are called archegonia (singular, archegonium). Each archegonium is a pearshaped organ that produces a single nonmotile egg retained within the bulbous part of the organ (the top for the species shown here). The male gametangia, called antheridia (singular, antheridium), produce sperm and release them into the environment. In many groups of present-day plants, the sperm have flagella and swim to the eggs through water droplets or a film of water. Each egg is fertilized within an archegonium, where the zygote develops into an embryo. The gametophytes of seed plants are so reduced in size (as you will see in Chapter 30) that the archegonia and antheridia have been lost in many lineages.

The gametophyte produces haploid gametes by mitosis. Two gametes unite (fertilization) and form a diploid zygote The zygote develops into a multicellular diploid sporophyte. The sporophyte 3 produces unicellar haploid spores by meiosis The spores develop into multicellular haploid gametophytes

Multicellular, Dependent Embryos: As part of a life cycle with alternation of generations, multicellular plant embryos develop from zygotes that are retained within the tissues of the female parent (a gametophyte). The parental tissues protect the developing embryo from harsh environmental conditions and provide nutrients such as sugars and amino acids. The embryo has specialized placental transfer cells that enhance the transfer of nutrients to the embryo through elaborate ingrowths of the wall surface (plasma membrane and cell wall). The multicellular, dependent embryo of plants is such a significant derived trait that plants are also known as embryophytes.

Figure 33.27 A free-living nematode. (colorized SEM).

Multitudes of nematodes live in moist soil and in decomposing organic matter on the bottoms of lakes and oceans. While 25,000 species are known, perhaps 20 times that number actually exist. It has been said that if nothing of Earth or its organisms remained but nematodes, they would still preserve the outline of the planet and many of its features. These free-living worms play an important role in decomposition and nutrient cycling, but little is known about most species. One species of soil nematode, Caenorhabditis elegans, however, is very well studied and has become a model research organism in biology (see Concept 47.3). Ongoing studies of C. elegans are providing insight into mechanisms involved in aging in humans, as well as many other topics.

Pharyngeal Slits or Clefts: The digestive tube of chordates extends from the mouth to the anus. The region just posterior to the mouth is the pharynx. In all chordate embryos, a series of arches separated by grooves forms along the outer surface of the pharynx. In most chordates, these grooves (known as pharyngeal clefts) develop into slits that open into the pharynx. These pharyngeal slits allow water entering the mouth to exit the body without passing through the entire digestive tract. Pharyngeal slits function as suspension-feeding devices in many invertebrate chordates. In vertebrates (with the exception of vertebrates with limbs, the tetrapods), these slits and the pharyngeal arches that support them have been modified for gas exchange and are called gills. In tetrapods, the pharyngeal clefts do not develop into slits. Instead, the pharyngeal arches that surround the clefts develop into parts of the ear and other structures in the head and neck.

Muscular, Post-Anal Tail: Chordates have a tail that extends posterior to the anus, although in many species it is greatly reduced during embryonic development. In contrast, most nonchordates have a digestive tract that extends nearly the whole length of the body. The chordate tail contains skeletal elements and muscles, and it helps propel many aquatic species in the water.

There are two main types of mycorrhizal fungi (see Figure 37.15). Ectomycorrhizal fungi (from the Greek ektos, out) form sheaths of hyphae over the surface of a root and typically grow into the extracellular spaces of the root cortex. Arbuscular mycorrhizal fungi extend arbuscules through the root cell wall and into tubes formed by invagination (pushing inward, as in Figure 31.4b) of the root cell plasma membrane. In the Scientific Skills Exercise, you'll compare genomic data from fungi that form mycorrhizae and fungi that do not.

Mycorrhizae are enormously important both in natural ecosystems and in agriculture. Almost all vascular plants have mycorrhizae and rely on their fungal partners for essential nutrients. Many studies have shown the significance of mycorrhizae by comparing the growth of plants with and without them. Foresters commonly inoculate pine seedlings with mycorrhizal fungi to promote growth. In the absence of human intervention, mycorrhizal fungi colonize soils by dispersing haploid cells called spores that form new mycelia after germinating. Spore dispersal is a key component of how fungi reproduce and spread to new areas, as we discuss next.

Specialized Hyphae in Mycorrhizal Fungi: Some fungi have specialized hyphae that allow them to feed on living animals (Figure 31.4a), while others have modified hyphae called haustoria that enable them to extract nutrients from plants. Our focus here, however, will be on fungi that have specialized branching hyphae such as arbuscules (Figure 31.4b) that they use to exchange nutrients with their plant hosts. Such mutually beneficial relationships between fungi and plant roots are called mycorrhizae (the term means "fungus roots").

Mycorrhizal fungi (fungi that form mycorrhizae) can improve delivery of phosphate ions and other minerals to plants because the vast mycelial networks of the fungi are more efficient than the plants' roots at acquiring these minerals from the soil. In exchange, the plants supply the fungi with organic nutrients such as carbohydrates.

Figure 33.32 Horseshoe crabs (Limulus polyphemus). Common on the Atlantic and Gulf coasts of the United States, these "living fossils" have changed little in hundreds of millions of years. They are surviving members of a rich diversity of chelicerates that once filled the seas. Figure 33.34 Book lungs. Figure 33.35 Myriapods.: (a) Millipede, (b) Centipede

Myriapods: Millipedes and centipedes belong to the clade Myriapoda (Figure 33.35). All living myriapods are terrestrial. The myriapod head has a pair of antennae and three pairs of appendages modified as mouthparts, including the jaw-like mandibles. Millipedes have a large number of legs, though fewer than the thousand their name implies. Each trunk segment is formed from two fused segments and bears two pairs of legs (see Figure 33.35a). Millipedes eat decaying leaves and other plant matter. They may have been among the earliest animals on land, living on mosses and early vascular plants. Unlike millipedes, centipedes are carnivores. Each segment of a centipede's trunk region has one pair of legs (see Figure 33.35b). Centipedes have poison claws on their foremost trunk segment that paralyze prey and aid in defense.

Fossils now generally recognized as H. ergaster once were considered early members of another species, Homo erectus, and some paleoanthropologists still hold this position. Homo erectus originated in Africa and was the first hominin to migrate out of Africa. The oldest fossils of hominins outside Africa, dating back 1.8 million years, were discovered in the present-day country of Georgia. Homo erectus eventually migrated as far as the Indonesian archipelago. Fossil evidence indicates that H. erectus became extinct between 200,000 and 70,000 years ago.

Neanderthals: In 1856, miners discovered some mysterious human fossils in a cave in the Neander Valley in Germany. The 40,000-year-old fossils belonged to a thick-boned hominin with a prominent brow. The hominin was named Homo neanderthalensis and is commonly called a Neanderthal. Neanderthals were living in Europe by 350,000 years ago and later spread to the Near East, central Asia, and southern Siberia. They had a brain larger than that of present-day humans, buried their dead, and made hunting tools from stone and wood. But despite their adaptations and culture, Neanderthals became extinct at some point between 28,000 and 40,000 years ago.

Ecdysozoans are the most species-rich animal group: Although defined primarily by molecular evidence, the clade Ecdysozoa includes animals that shed a tough external coat (cuticle) as they grow; in fact, the group derives its name from this process, which is called ecdysis, or molting. Ecdysozoa includes about eight animal phyla and contains more known species than all other animal, protist, fungus, and plant groups combined. Here we'll focus on the two largest ecdysozoan phyla, the nematodes and arthropods, which are among the most successful and abundant of all animal groups.

Nematodes: Among the most ubiquitous of animals, nematodes (phylum Nematoda), or roundworms, are found in most aquatic habitats, in the soil, in the moist tissues of plants, and in the body fluids and tissues of animals. The cylindrical bodies of nematodes range from less than 1 mm to more than 1 m long, often tapering to a fine tip at the posterior end and to a blunter tip at the anterior end (Figure 33.27). A nematode's body is covered by a tough cuticle (a type of exoskeleton); as the worm grows, it periodically sheds its old cuticle and secretes a new, larger one. Nematodes have an alimentary canal, though they lack a circulatory system. Nutrients are transported throughout the body via fluid in the pseudocoelom. The body wall muscles are all longitudinal, and their contraction produces a thrashing motion.

Cycliophora (1 species): The only known cycliophoran species, Symbion pandora, was discovered in 1995 on the mouthparts of a lobster. This tiny, vase-shaped creature has a unique body plan and a particularly bizarre life cycle. Males impregnate females that are still developing in their mothers' bodies. The fertilized females then escape, settle elsewhere on the lobster, and release their offspring. The offspring apparently leave that lobster and search for another one to which they attach. A cycliophoran (colorized SEM)

Nemertea (900 species): Also called proboscis worms or ribbon worms, nemerteans swim through water or burrow in sand, extending a unique proboscis to capture prey. Like flatworms, they lack a true coelom. However, unlike flatworms, nemerteans have an alimentary canal and a closed circulatory system in which the blood is contained in vessels and hence is distinct from fluid in the body cavity. A ribbon worm Annelida (16,500 species): Annelids, or segmented worms, are distinguished from other worms by their body segmentation. Earthworms are the most familiar annelids, but the phylum consists primarily of marine and freshwater species (see Concept 33.3).

Figure 32.4 Cadherin proteins in choanoflagellates and animals. The ancestral cadherin-like protein of choanoflagellates has seven kinds of domains (regions), each represented here by a particular symbol. With the exception of the "CCD" domain, which is found only in animals, the domains of animal cadherin proteins are present in the choanoflagellate cadherin-like protein. The cadherin protein domains shown here were identified from whole-genome sequence data; evolutionary relationships are based on morphological and DNA sequence data.

Neoproterozoic Era (1 Billion-541 Million Years Ago): Although data from fossil steroids and molecular clocks indicate an earlier origin, the first generally accepted macroscopic fossils of animals date from about 560 million years ago. These fossils are members of an early group of softbodied multicellular eukaryotes, known collectively as the Ediacaran biota. The name comes from the Ediacara Hills of Australia, where fossils of these organisms were first discovered (Figure 32.5). Similar fossils have since been found on other continents. Among the oldest Ediacaran fossils that resemble animals, some have been classified as molluscs (snails and their relatives) or close relatives of the molluscs, while others are thought to be sponges or cnidarians (sea anemones and their relatives).

Let's take a closer look at the cadherin attachment proteins we just mentioned. DNA sequence analyses show that animal cadherin proteins are composed primarily of domains that are also found in a cadherin-like protein of choanoflagellates (Figure 32.4). However, animal cadherin proteins also contain a highly conserved region not found in the choanoflagellate protein (the "CCD" domain labeled in Figure 32.4). These data suggest that the cadherin attachment protein originated by the rearrangement of protein domains found in choanoflagellates plus the incorporation of a novel domain, the conserved CCD region. Overall, comparisons of choanoflagellate and animal genomes suggest that key steps in the transition to multicellularity in animals involved new ways of using proteins or parts of proteins that were encoded by genes found in choanoflagellates.

Next, we'll survey the fossil evidence for how animals evolved from their distant common ancestor over four geologic eras (see Table 25.1 to review the geologic time scale).

Fungi are heterotrophs that feed by absorption: Despite their vast diversity, all fungi share some key traits: most importantly, the way they derive nutrition. In addition, many fungi grow by forming multicellular filaments, a body structure that plays an important role in how they obtain food.

Nutrition and Ecology: Like animals, fungi are heterotrophs: They cannot make their own food as plants and algae can. But unlike animals, fungi do not ingest (eat) their food. Instead, a fungus absorbs nutrients from the environment outside of its body. Many fungi do this by secreting hydrolytic enzymes into their surroundings. These enzymes break down complex molecules to smaller organic compounds that the fungi can absorb into their cells and use. Other fungi use enzymes to penetrate the walls of cells, enabling the fungi to absorb nutrients from the cells. Collectively, the different enzymes found in various fungal species can digest compounds from a wide range of sources, living or dead.

Animals are multicellular, heterotrophic eukaryotes with tissues that develop from embryonic layers: Listing features shared by all animals is challenging, as there are exceptions to nearly every criterion we might select. When taken together, however, several characteristics of animals sufficiently describe the group for our discussion.

Nutritional Mode: Animals differ from both plants and fungi in their mode of nutrition. Plants are autotrophic eukaryotes capable of generating organic molecules through photosynthesis. Fungi are heterotrophs that grow on or near their food and that feed by absorption (often after they have released enzymes that digest the food outside their bodies). Unlike plants, animals cannot construct all of their own organic molecules, and so, in most cases, they ingest them—either by eating other living organisms or by eating nonliving organic material. But unlike fungi, most animals feed by ingesting their food and then using enzymes to digest it within their bodies.

The Significance of Seedless Vascular Plants: The ancestors of living lycophytes, horsetails, and ferns, along with their extinct seedless vascular relatives, grew to great heights during the Devonian and early Carboniferous, forming the first forests (Figure 29.15). How did their dramatic growth affect Earth and its other life?

One major effect was that early forests contributed to a large drop in CO2 levels during the Carboniferous period, causing global cooling that resulted in widespread glacier formation. The trees of early forests contributed to this drop in CO2 levels in part by the actions of their roots. The roots of vascular plants secrete acids that break down rocks, thereby increasing the rate at which calcium and magnesium are released from rocks into the soil. These chemicals react with carbon dioxide dissolved in rain water, forming compounds that ultimately wash into the oceans, where they are incorporated into rocks (calcium or magnesium carbonates). The net effect of these processes— which were accelerated by plants—is that CO2 removed from the air is stored in marine rocks. Although carbon stored in these rocks can be returned to the atmosphere, it typically takes millions of years for this to occur (as when geological uplift brings the rocks to the surface, exposing them to erosion).

Fossils of larger plant structures, such as the Cooksonia sporangium in Figure 29.5, date to 425 million years ago, which is 45 million years after the appearance of plant spores in the fossil record. While the precise age (and form) of the first plants has yet to be discovered, those ancestral species gave rise to the vast diversity of living plants. Table 29.1 summarizes the ten extant phyla in the taxonomic scheme used in this text. (Extant lineages are those that have surviving members.) As you read the rest of this section, look at Table 29.1 together with Figure 29.6, which reflects a view of plant phylogeny that is based on plant morphology, biochemistry, and genetics.

One way to distinguish groups of plants is whether or not they have an extensive system of vascular tissue, cells joined into tubes that transport water and nutrients throughout the plant body. Most present-day plants have a complex vascular tissue system and are therefore called vascular plants. Plants that do not have an extensive transport system—liverworts, mosses, and hornworts—are described as "nonvascular" plants, even though some mosses do have simple vascular tissue. Nonvascular plants are often informally called bryophytes (from the Greek bryon, moss, and phyton, plant). Although the term bryophyte is commonly used to refer to all nonvascular plants, molecular studies and morphological analyses of sperm structure have concluded that bryophytes do not form a monophyletic group (a clade).

In northern coniferous forests, species such as the feather moss Pleurozium harbor nitrogen-fixing cyanobacteria that increase the availability of nitrogen in the ecosystem. Other mosses inhabit such extreme environments as mountaintops, tundra, and deserts. Many mosses are able to live in very cold or dry habitats because they can survive the loss of most of their body water, then rehydrate when moisture is available. Few vascular plants can survive the same degree of desiccation. Moreover, phenolic compounds in moss cell walls absorb damaging levels of UV radiation present in deserts or at high altitudes.

One wetland moss genus, Sphagnum, or peat moss, is often a major component of deposits of partially decayed organic material known as peat (Figure 29.10a). Boggy regions with thick layers of peat are called peatlands. Sphagnum does not decay readily, in part because of phenolic compounds embedded in its cell walls. The low temperature, pH, and oxygen level of peatlands also inhibit decay of moss and other organisms in these boggy wetlands. As a result, some peatlands have preserved corpses for thousands of years (Figure 29.10b).

Sea stars and some other echinoderms have considerable powers of regeneration. Sea stars can regrow lost arms, and members of one genus can even regrow an entire body from a single arm if part of the central disk remains attached. The clade Asteroidea, to which sea stars belong, also includes a small group of armless species, the sea daisies. Only three species of sea daisies are known, all of which live on submerged wood. A sea daisy's body is typically disk-shaped; it has a five-sided organization and measures less than a centimeter in diameter (Figure 33.45). The edge of the body is ringed with small spines. Sea daisies absorb nutrients through a membrane that surrounds their body.

Ophiuroidea: Brittle Stars: Brittle stars have a distinct central disk and long, flexible arms (Figure 33.46). They move primarily by lashing their arms in serpentine movements. The base of a brittle star tube foot lacks the flattened disk found in sea stars but does secrete adhesive chemicals. Hence, like sea stars and other echinoderms, brittle stars can use their tube feet to grip substrates. Some species are suspension feeders; others are predators or scavengers.

Ferns and other seedless vascular plants were the first plants to grow tall During the first 100 million years of plant evolution, bryophytes were prominent types of vegetation. But it is vascular plants that dominate most landscapes today. The earliest fossils of vascular plants date to 425 million years ago. These plants lacked seeds but had well-developed vascular systems, an evolutionary novelty that set the stage for vascular plants to grow taller than their bryophyte counterparts. As in bryophytes, however, the sperm of ferns and all other seedless vascular plants are flagellated and swim through a film of water to reach eggs. In part because of these swimming sperm, seedless vascular plants today are most common in damp environments.

Origins and Traits of Vascular Plants: Unlike the nonvascular plants, ancient relatives of vascular plants had branched sporophytes that were not dependent on gametophytes for nutrition (Figure 29.11). Although these early plants were less than 20 cm tall, their branching enabled their bodies to become more complex and to have multiple sporangia. As plant bodies became more complex over time, competition for space and sunlight probably increased. As we'll see, that competition may have stimulated still more evolution in vascular plants, eventually leading to the formation of the first forests.

Figure 31.6 Penicillium, a mold commonly encountered as a decomposer of food. The bead-like clusters in the colorized SEM are conidia, structures involved in asexual reproduction. Figure 31.7 The yeast Saccharomyces cerevisiae in several stages of budding (SEM).

Other fungi reproduce asexually by growing as single-celled yeasts. Instead of producing spores, asexual reproduction in yeasts occurs by ordinary cell division or by the pinching of small "bud cells" off a parent cell (Figure 31.7). As already mentioned, some fungi that grow as yeasts can also grow as filamentous mycelia

Phylogenetic analyses indicate that liverworts, mosses, and hornworts diverged from other plant lineages early in the history of plant evolution (see Figure 29.6). Fossil evidence provides some support for this idea: The earliest spores of plants (dating from 450 to 470 million years ago) have structural features found only in the spores of liverworts, and by 430 million years ago spores similar to those of mosses and hornworts also occur in the fossil record. The earliest fossils of vascular plants date to about 425 million years ago.

Over the long course of their evolution, liverworts, mosses, and hornworts have acquired many unique adaptations. Next, we'll examine some of those features.

The earliest gnathostomes include extinct lineages of armored vertebrates known collectively as placoderms, which means "plate-skinned." Most placoderms were less than a meter long, though some giants measured more than 10 m (Figure 34.14). Other jawed vertebrates, called acanthodians, emerged at roughly the same time and radiated during the Silurian and Devonian periods (444-359 million years ago). Placoderms had disappeared by 359 million years ago, and acanthodians became extinct about 70 million years later

Overall, a series of recent fossil discoveries have revealed that 440-420 million years ago was a period of tumultuous evolutionary change. Gnathostomes that lived during this period had highly variable forms, and by 420 million years ago, they had diverged into the three lineages of jawed vertebrates that survive today: chondrichthyans, ray-finned fishes, and lobe-fins.

Pollen cones have a relatively simple structure: Their scales are modified leaves (microsporophylls) that bear microsporangia. Within each microsporangium, cells called microsporocytes undergo meiosis, producing haploid microspores. Each microspore develops into a pollen grain containing a male gametophyte. In conifers, the yellow pollen is released in large amounts and carried by the wind, dusting everything in its path.

Ovulate cones are more complex: their scales are compound structures composed of both modified leaves (megasporophylls bearing megasporangia) and modified stem tissue. Within the each megasporangium, megasporocytes undergo meiosis and produce haploid megaspores inside the ovule. Surviving megaspores develop into female gametophytes, which are retained within the sporangia.

Heterospory: The Rule Among Seed Plants You read in Concept 29.3 that most seedless plants are homosporous—they produce one kind of spore, which usually gives rise to a bisexual gametophyte. Ferns and other close relatives of seed plants are homosporous, suggesting that seed plants had homosporous ancestors. At some point, seed plants or their ancestors became heterosporous, producing two kinds of spores: Megasporangia on modified leaves called megasporophylls produce megaspores that give rise to female gametophytes, and microsporangia on modified leaves called microsporophylls produce microspores that give rise to male gametophytes. Each megasporangium has one megaspore, whereas each microsporangium has many microspores. As noted previously, the miniaturization of seed plant gametophytes probably contributed to the great success of this clade. Next, we'll look at the development of the female gametophyte within an ovule and the development of the male gametophyte in a pollen grain. Then we'll follow the transformation of a fertilized ovule into a seed.

Ovules and Production of Eggs: Although a few species of seedless plants are heterosporous, seed plants are unique in retaining the megasporangium within the parent sporophyte. A layer of sporophyte tissue called integument envelops and protects the megasporangium. Gymnosperm megasporangia are surrounded by one integument, whereas those in angiosperms usually have two integuments. The whole structure—megasporangium, megaspore, and their integument(s)—is called an ovule (Figure 30.3a). Inside each ovule (from the Latin ovulum, little egg), a female gametophyte develops from a megaspore and produces one or more eggs.

Figure 32.6 Early evidence of predation. This 550-millionyear-old fossil of the animal Cloudina shows evidence of having been attacked by a predator that bored through its shell. Figure 32.5 Ediacaran fossil animals. Fossils dating to 560 million years ago document the earliest known macroscopic animals, including these two species. (a) Dickinsonia costata (taxonomic affiliation unknown) (b) Kimberella, a mollusc (or close relative)

Paleozoic Era (541-252 Million Years Ago): Another wave of animal diversification occurred 535-525 million years ago, during the Cambrian period of the Paleozoic era—a phenomenon referred to as the Cambrian explosion (see Concept 25.3). In strata formed before the Cambrian explosion, only a few animal phyla have been observed. But in strata that are 535-525 million years old, paleontologists have found the oldest fossils of about half of all extant animal phyla, including the first arthropods, chordates, and echinoderms. Many of these fossils, which include the first large animals with hard, mineralized skeletons, look very different from most living animals (Figure 32.7). Even so, paleontologists have established that these Cambrian fossils are members of extant animal phyla, or at least are close relatives. In particular, most of the fossils from the Cambrian explosion are of bilaterians, an enormous clade whose members (unlike sponges and cnidarians) typically have a two-sided or bilaterally symmetric form and a complete digestive tract, an efficient digestive system that has a mouth at one end and an anus at the other. As we'll discuss later in the chapter, bilaterians include molluscs, arthropods, chordates, and most other living animal phyla.

Phylum Nematoda includes many species that parasitize plants, and some are major agricultural pests that attack the roots of crops. Other nematodes parasitize animals. Some of these species benefit humans by attacking insects such as cutworms that feed on the roots of crop plants. On the other hand, humans are hosts to at least 50 nematode species, including various pinworms and hookworms. One notorious nematode is Trichinella spiralis, the worm that causes trichinosis (Figure 33.28). Humans acquire this nematode by eating raw or undercooked pork or other meat (including wild game such as bear or walrus) that has juvenile worms encysted in the muscle tissue. Within the human intestines, the juveniles develop into sexually mature adults. Females burrow into the intestinal muscles and produce more juveniles, which bore through the body or travel in lymphatic vessels to other organs, including skeletal muscles, where they encyst.

Parasitic nematodes have an extraordinary molecular toolkit that enables them to redirect some of the cellular functions of their hosts. Some species inject their plant hosts with molecules that induce the development of root cells, which then supply nutrients to the parasites. When Trichinella parasitizes animals, it regulates the expression of specific muscle cell genes encoding proteins that make the cell elastic enough to house the nematode. Additionally, the infected muscle cell releases signals that promote the growth of new blood vessels, which then supply the nematode with nutrients.

Mutualistic Bacteria: As is true for many other eukaryotes, human well-being can depend on mutualistic prokaryotes. For example, our intestines are home to an estimated 500-1,000 species of bacteria; their cells outnumber all human cells in the body by a factor of ten. Different species live in different portions of the intestines, and they vary in their ability to process different foods. Many of these species are mutualists, digesting food that our own intestines cannot break down. The genome of one of these gut mutualists, Bacteroides thetaiotaomicron, includes a large array of genes involved in synthesizing carbohydrates, vitamins, and other nutrients needed by humans. Signals from the bacterium activate human genes that build the network of intestinal blood vessels necessary to absorb nutrient molecules. Other signals induce human cells to produce antimicrobial compounds to which B. thetaiotaomicron is not susceptible. This action may reduce the population sizes of other, competing species, thus potentially benefiting both B. thetaiotaomicron and its human host.

Pathogenic Bacteria: All the pathogenic prokaryotes known to date are bacteria, and they deserve their negative reputation. Bacteria cause about half of all human diseases. For example, more than 1 million people die each year of the lung disease tuberculosis, caused by Mycobacterium tuberculosis. And another 2 million people die each year from diarrheal diseases caused by various bacteria

Some bacterial diseases are transmitted by other species, such as fleas or ticks. In the United States, the most widespread pest-carried disease is Lyme disease, which infects 15,000 to 20,000 people each year (Figure 27.20). Caused by a bacterium carried by ticks that live on deer and field mice, Lyme disease can result in debilitating arthritis, heart disease, nervous disorders, and death if untreated.

Pathogenic prokaryotes usually cause illness by producing poisons, which are classified as exotoxins or endotoxins. Exotoxins are proteins secreted by certain bacteria and other organisms. Cholera, a dangerous diarrheal disease, is caused by an exotoxin secreted by the proteobacterium Vibrio cholerae. The exotoxin stimulates intestinal cells to release chloride ions into the gut, and water follows by osmosis. In another example, the potentially fatal disease botulism is caused by botulinum toxin, an exotoxin secreted by the gram-positive bacterium Clostridium botulinum as it ferments various foods, including improperly canned meat, seafood, and vegetables. Like other exotoxins, the botulinum toxin can produce disease even if the bacteria that manufacture it are no longer present when the food is eaten. Another species in the same genus, C. difficile, produces exotoxins that cause severe diarrhea, resulting in more than 12,000 deaths per year in the United States alone.

Dinoflagellates: The cells of many dinoflagellates are reinforced by cellulose plates. Two flagella located in grooves in this "armor" make dinoflagellates (from the Greek dinos, whirling) spin as they move through the waters of their marine and freshwater communities (Figure 28.15a). Although their ancestors may have originated by secondary endosymbiosis (see Figure 28.3), roughly half of all dinoflagellates are now purely heterotrophic. Others are important species of phytoplankton (photosynthetic plankton, which include photosynthetic bacteria as well as algae); many photosynthetic dinoflagellates are mixotrophic

Periods of explosive population growth (blooms) in dinoflagellates sometimes cause a phenomenon called "red tide"(Figure 28.15b). The blooms make coastal waters appear brownish red or pink because of the presence of carotenoids, the most common pigments in dinoflagellate plastids. Toxins produced by certain dinoflagellates have caused massive kills of invertebrates and fishes. Humans who eat molluscs that have accumulated the toxins are affected as well, sometimes fatally.

Unicellular protists carry out the same essential functions, but they do so using subcellular organelles, not multicellular organs. The organelles that protists use are mostly those discussed in Figure 6.8, including the nucleus, endoplasmic reticulum, Golgi apparatus, and lysosomes. Certain protists also rely on organelles not found in most other eukaryotic cells, such as contractile vacuoles that pump excess water from the protistan cell (see Figure 7.13). Protists are also very diverse in their nutrition. Some protists are photoautotrophs and contain chloroplasts. Some are heterotrophs, absorbing organic molecules or ingesting larger food particles. Still other protists, called mixotrophs, combine photosynthesis and heterotrophic nutrition.

Photoautotrophy, heterotrophy, and mixotrophy have all arisen independently in many different protist lineages. Reproduction and life cycles also are highly varied among protists. Some protists are only known to reproduce asexually; others can also reproduce sexually or at least employ the sexual processes of meiosis and fertilization. All three basic types of sexual life cycles (see Figure 13.6) are represented among protists, along with some variations that do not quite fit any of these types. We will examine the life cycles of several protist groups later in this chapter.

Phylum Ginkgophyta: Ginkgo biloba is the only surviving species of this phylum; like cycads, ginkgos have flagellated sperm. Also known as the maidenhair tree, Ginkgo biloba has deciduous fanlike leaves that turn gold in autumn. It is a popular ornamental tree in cities because it tolerates air pollution well. Landscapers often plant only pollenproducing trees because the fleshy seeds smell rancid as they decay.

Phylum Gnetophyta: Phylum Gnetophyta includes plants in three genera: Gnetum, Ephedra, and Welwitschia. Some species are tropical, whereas others live in deserts. Although very different in appearance, the genera are grouped together based on molecular data. ◀ Gnetum. This genus includes about 35 species of tropical trees, shrubs, and vines, mainly native to Africa and Asia. Their leaves look similar to those of flowering plants, and their seeds look somewhat like fruits. ▶ Welwitschia. This genus consists of one species, Welwitschia mirabilis, a plant that can live for thousands of years and is found only in the deserts of southwestern Africa. Its straplike leaves are among the largest leaves known. ▶ Ephedra. This genus includes about 40 species that inhabit arid regions worldwide. These desert shrubs, commonly called "Mormon tea", produce the compound ephedrine, which is used medicinally as a decongestant.

Whisk Ferns and Relatives: Like primitive vascular plant fossils, the sporophytes of whisk ferns (genus Psilotum) have dichotomously branching stems but no roots. Stems have scalelike outgrowths that lack vascular tissue and may have resulted from the evolutionary reduction of leaves. Each yellow knob on a stem consists of three fused sporangia. Species of the genus Tmesipteris closely related to whisk ferns and found only in the South Pacific, also lack roots but have small, leaflike outgrowths in their stems, giving them a vine-like appearance. Both genera are homosporous, with spores giving rise to bisexual gametophytes that grow underground and are only about a centimeter long.

Phylum Lycophyta: Club Mosses, Spikemosses, and Quillworts Present-day species of lycophytes are relicts of a far more impressive past. By the Carboniferous period (359-299 million years ago), the lycophyte evolutionary lineage included small herbaceous plants and giant trees with diameters of more than 2 m and heights of more than 40 m. The giant lycophyte trees thrived for millions of years in moist swamps, but their diversity declined when Earth's climate became drier during the Permian period (299-252 million years ago). The small lycophytes survived, represented today by about 1,200 species. Though some are commonly called club mosses and spikemosses, they are not true mosses (which, as discussed earlier, are nonvascular plants).

Evolutionary Links with Animals: Plants and animals have interacted for hundreds of millions of years, and those interactions have led to evolutionary change. For example, herbivores can reduce a plant's reproductive success by eating its roots, leaves, or seeds. As a result, if an effective defense against herbivores originates in a group of plants, those plants may be favored by natural selection—as will herbivores that overcome this new defense. Plant-pollinator and other mutually beneficial interactions also can have such reciprocal evolutionary effects.

Plant-pollinator interactions also may have affected the rates at which new species form. Consider the impact of a flower's symmetry (see Figure 30.9). On a flower with bilateral symmetry, an insect pollinator can obtain nectar only when approaching from a certain direction (Figure 30.15). This constraint makes it more likely that pollen is placed on a part of the insect's body that will come into contact with the stigma of a flower of the same species. Such specificity of pollen transfer reduces gene flow between diverging populations and could lead to increased rates of speciation in plants with bilateral symmetry. This hypothesis can be tested using the approach illustrated in this diagram: A key step in this approach is to identify cases in which a clade with bilaterally symmetric flowers shares an immediate common ancestor with a clade whose members have radially symmetric flowers. One recent study identified 19 pairs of closely related "bilateral" and "radial" clades. On average, the clade with bilaterally symmetric flowers had nearly 2,400 more species than did the related clade with radial symmetry. This result suggests that flower shape can affect the rate at which new species form, perhaps by affecting the behavior of insect pollinators. Overall, plant-pollinator interactions may have contributed to the increasing dominance of flowering plants in the Cretaceous period, helping to make angiosperms of central importance in ecological communities.

Looking at a lush landscape, such as that shown in Figure 29.1, it is hard to imagine the land without plants or other organisms. Yet for much of Earth's history, the land was largely lifeless. Geochemical analysis and fossil evidence suggest that thin coatings of cyanobacteria and protists existed on land by 1.2 billion years ago. But it was only within the last 500 million years that small plants, fungi, and animals joined them ashore. Finally, by about 385 million years ago, tall plants appeared, leading to the first forests (which consisted of very different species than those in Figure 29.1). Today, there are more than 290,000 known plant species. Plants inhabit all but the harshest environments, such as some mountaintop and desert areas and the polar ice sheets. Although a few plant species, such as sea grasses, returned to aquatic habitats during their evolution, most present-day plants live on land. In this text, we distinguish plants from algae, which are photosynthetic protists.

Plants enabled other life-forms to survive on land. For example, plants supply oxygen and are a key source of food for terrestrial animals. Also, by their very presence, plants such as the trees of a forest physically create the habitats required by animals and many other organisms. This chapter traces the first 100 million years of plant evolution, including the emergence of seedless plants such as mosses and ferns. Chapter 30 examines the later evolution of seed plants.

Tapeworms: The tapeworms are a second large and diverse group of parasitic rhabditophorans (Figure 33.12). The adults live mostly inside vertebrates, including humans. In many tapeworms, the anterior end, or scolex, is armed with suckers and often hooks that the worm uses to attach itself to the intestinal lining of its host. Tapeworms lack a mouth and gastrovascular cavity; they simply absorb nutrients released by digestion in the host's intestine. Absorption occurs across the tapeworm's body surface.

Posterior to the scolex is a long ribbon of units called proglottids, which are little more than sacs of sex organs. After sexual reproduction, proglottids loaded with thousands of fertilized eggs are released from the posterior end of a tapeworm and leave the host's body in feces. In one type of life cycle, feces carrying the eggs contaminate the food or water of intermediate hosts, such as pigs or cattle, and the tapeworm eggs develop into larvae that encyst in muscles of these animals. A human acquires the larvae by eating undercooked meat containing the cysts, and the worms develop into mature adults within the human. Large tapeworms can block the intestines and rob enough nutrients from the human host to cause nutritional deficiencies. Several different oral medications can kill the adult worms.

Human welfare depends on seed plants: In forests and on farms, seed plants are key sources of food, fuel, wood products, and medicine. Our reliance on them makes the preservation of plant diversity critical.

Products from Seed Plants: Most of our food comes from angiosperms. Just six crops— maize, rice, wheat, potatoes, cassava, and sweet potatoes— yield 80% of all the calories consumed by humans. We also depend on angiosperms to feed livestock: It takes 5-7 kg of grain to produce 1 kg of grain-fed beef.

Branching: Water uptake relies on passive diffusion. The highly branched filaments of a fungal mycelium increase the surface area across which water and minerals can be absorbed from the environment. (See Figure 31.2.)

Projections: In vertebrates, the small intestine is lined with finger-like projections called villi that absorb nutrients released by the digestion of food. Each of the villi shown here is covered with large numbers of microscopic projections called microvilli, resulting in a total surface area of about 300 m2 in humans, as large as a tennis court. (See Figure 41.12.).

figure 27.20 Lyme disease. Ticks in the genus Ixodes spread the disease by transmitting the spirochete Borrelia burgdorferi (colorized SEM). A rash may develop at the site of the tick's bite; the rash may be large and ring-shaped (as shown) or much less distinctive

Prokaryotes in Research and Technology: On a positive note, we reap many benefits from the metabolic capabilities of both bacteria and archaea. For example, people have long used bacteria to convert milk to cheese and yogurt. Bacteria are also used in the production of beer and wine, pepperoni, fermented cabbage (sauerkraut), and soy sauce. In recent decades, our greater understanding of prokaryotes has led to an explosion of new applications in biotechnology. Examples include the use of E. coli in gene cloning (see Figure 20.4) and the use of DNA polymerase from Pyrococcus furiosus in the PCR technique (see Figure 20.8). Through genetic engineering, we can modify bacteria to produce vitamins, antibiotics, hormones, and other products (see Concept 20.1). In addition, naturally occurring soil bacteria have potential as sources of new antibiotics, as you can explore in the Scientific Skills Exercise.

The Origin and Evolutionary Radiation of Reptiles: Fossil evidence indicates that the earliest reptiles lived about 310 million years ago and resembled lizards. Like all reptiles today, these early reptiles were diapsids. A key derived character of diapsids is a pair of holes on each side of the skull, behind the eye sockets; muscles pass through these holes and attach to the jaw, controlling jaw movement. The diapsids are composed of two main lineages. One lineage gave rise to the lepidosaurs, which include tuataras, lizards, and snakes. This lineage also produced some marine reptiles, including the giant mososaurs. Some of these marine species rivaled today's whales in length; all of them are extinct. The other main diapsid lineage, the archosaurs, produced the turtles, crocodilians, pterosaurs, and dinosaurs. Our focus here will be on extinct lineages of archosaurs; we'll discuss living reptiles shortly.

Pterosaurs, which originated in the late Triassic, were the first tetrapods to exhibit flapping flight. The pterosaur wing was completely different from the wings of birds and bats. It consisted of a collagen-strengthened membrane that stretched between the trunk or hind leg and a very long digit on the foreleg. The smallest pterosaurs were no bigger than a sparrow, and the largest had a wingspan of nearly 11 m. They appear to have converged on many of the ecological roles later played by birds; some were insect-eaters, others grabbed fish out of the ocean, and still others filtered small animals through thousands of fine needlelike teeth. But by 66 million years ago, pterosaurs had become extinct. On land, the dinosaurs diversified into a vast range of shapes and sizes, from bipeds the size of a pigeon to 45-m-long quadrupeds with necks long enough to let them browse the tops of trees. One lineage of dinosaurs, the ornithischians, were herbivores; they included many species with elaborate defenses against predators, such as tail clubs and horned crests. The other main lineage of dinosaurs, the saurischians, included the long-necked giants and a group called the theropods, which were bipedal carnivores. Theropods included the famous Tyrannosaurus rex as well as the ancestors of birds.

Figure 33.17 A chiton. Note the eight-plate shell characteristic of molluscs in the clade Polyplacophora. Figure 33.16 The basic body plan of a mollusc. Metanephridium. Excretory organs called metanephridia remove metabolic wastes from the hemolymph. Heart. Most molluscs have an open circulatory system. The dorsally located heart pumps circulatory fluid called hemolymph through arteries into sinuses (body spaces). The organs of the mollusc are thus continually bathed in hemolymph. The long digestive tract is coiled in the visceral mass.

Radula. The mouth region in many mollusc species contains a rasp-like feeding organ called a radula. This belt of backwardcurved teeth repeatedly thrusts outward and then retracts into the mouth, scraping and scooping like a backhoe. The nervous system consists of a nerve ring around the esophagus, from which nerve cords extend.

Ray-Finned Fishes: Nearly all the aquatic osteichthyans familiar to us are among the over 27,000 species of ray-finned fishes (Actinopterygii) (Figure 34.17). Named for the bony rays that support their fins, the ray-finned fishes originated during the Silurian period (444-419 million years ago). The group has diversified greatly since that time, resulting in numerous species and many modifications in body form and fin structure that affect maneuvering, defense, and other functions.

Ray-finned fishes serve as a major source of protein for humans, who have harvested them for thousands of years. However, industrial-scale fishing operations appear to have driven some of the world's biggest fisheries to collapse. For example, after decades of abundant harvests, in the 1990s the catch of cod (Gadus morhua) in the northwest Atlantic plummeted to just 5% of its historic maximum, bringing cod fishing there to a near halt. Despite ongoing restrictions on the fishery, cod populations have yet to recover to sustainable levels. Ray-finned fishes also face other pressures from humans, such as the diversion of rivers by dams. Changing water flow patterns can hamper the fishes' ability to obtain food and interferes with migratory pathways and spawning grounds.

Red algae and green algae are the closest relatives of plants: As described earlier, morphological and molecular evidence indicates that plastids arose when a heterotrophic protist acquired a cyanobacterial endosymbiont. Later, photosynthetic descendants of this ancient protist evolved into red algae and green algae (see Figure 28.3), and the lineage that produced green algae then gave rise to plants. Together, red algae, green algae, and plants make up our third eukaryotic supergroup, which is called Archaeplastida. Archaeplastida is a monophyletic group that descended from the ancient protist that engulfed a cyanobacterium. We will examine plants in Chapters 29 and 30; here we will look at the diversity of their closest algal relatives, red algae and green algae.

Red Algae: Many of the 6,000 known species of red algae (rhodophytes, from the Greek rhodos, red) are reddish, owing to the photosynthetic pigment phycoerythrin, which masks the green of chlorophyll (Figure 28.21). However, other species (those adapted to shallow water) have less phycoerythrin. As a result, red algal species may be greenish red in very shallow water, bright red at moderate depths, and almost black in deep water. Some species lack pigmentation altogether and live as heteroptrophic parasites on other red algae. Red algae are abundant in the warm coastal waters of tropical oceans. Some of their photosynthetic pigments, including phycoerythrin, allow them to absorb blue and green light, which penetrate relatively far into the water. A species of red alga has been discovered near the Bahamas at a depth of more than 260 m. There are also a small number of freshwater and terrestrial species.

Early Amniotes: The most recent common ancestor of living amphibians and amniotes lived 350 million years ago. No fossils of amniotic eggs have been found from that time, which is not surprising given how delicate they are. Thus, it is not yet possible to say when the amniotic egg evolved, although it must have existed in the last common ancestor of living amniotes, which all have amniotic eggs. Based on where their fossils have been found, the earliest amniotes lived in warm, moist areas, as did the first tetrapods. Over time, early amniotes expanded into a wide range of new environments, including dry and high-latitude regions. Fossil evidence shows that the earliest amniotes resembled small lizards with sharp teeth, a sign that they were predators (Figure 34.27). Later groups of amniotes also included herbivores, as evidenced by their grinding teeth and other features.

Reptiles: The reptile clade includes tuataras, lizards, snakes, turtles, crocodilians, and birds, along with a number of extinct groups, such as plesiosaurs and ichthyosaurs (see Figure 34.25). As a group, the reptiles share several derived characters that distinguish them from other tetrapods. For example, unlike amphibians, reptiles have scales that contain the protein keratin (as does a human nail). Scales help protect the animal's skin from desiccation and abrasion. In addition, most reptiles lay their shelled eggs on land; the shell protects the egg from drying out (Figure 34.28). Fertilization occurs internally, before the eggshell is secreted. Reptiles such as lizards and snakes are sometimes described as "cold-blooded" because they do not use their metabolism extensively to control their body temperature. However, they do regulate their body temperature by using behavioral adaptations. For example, many lizards bask in the sun when the air is cool and seek shade when the air is too warm. A more accurate description of these reptiles is to say that they are ectothermic, which means that they absorb external heat as their main source of body heat. By warming themselves directly with solar energy rather than through the metabolic breakdown of food, an ectothermic reptile can survive on less than 10% of the food energy required by a mammal of the same size. But the reptile clade is not entirely ectothermic; birds are endothermic, capable of maintaining body temperature through metabolic activity.

Early Chordate Evolution: Although lancelets and tunicates are relatively obscure animals, they occupy key positions in the history of life and can provide clues about the evolutionary origin of vertebrates. For example, as you have read, lancelets display key chordate characters as adults, and their lineage branches from the base of the chordate phylogenetic tree. These findings suggest that the ancestral chordate may have looked something like a lancelet—that is, it had an anterior end with a mouth; a notochord; a dorsal, hollow nerve cord; pharyngeal slits; and a post-anal tail.

Research on lancelets has also revealed important clues about the evolution of the chordate brain. Rather than a fullfledged brain, lancelets have only a slightly swollen tip on the anterior end of their dorsal nerve cord (Figure 34.6). But the same Hox genes that organize major regions of the forebrain, midbrain, and hindbrain of vertebrates express themselves in a corresponding pattern in this small cluster of cells in the lancelet's nerve cord. This suggests that the vertebrate brain is an elaboration of an ancestral structure similar to the lancelet's simple nerve cord tip.

Figure 27.21 CRISPR: Opening new avenues of research for treating HIV infection. (a) In laboratory experiments, untreated (control) human cells were susceptible to infection by HIV, the virus that causes AIDS. (b) In contrast, cells treated with a CRISPR-Cas9 system that targets HIV were resistant to viral infection. The CRISPRCas9 system was also able to remove HIV proviruses (see Figure 19.8) that had become incorporated into the DNA of human cells. (a) Control cells. The green color indicates infection by HIV. (b) Experimental cells. These cells were treated with a CRISPR-Cas9 system that targets HIV.

Researchers are also seeking to reduce the use of petroleum and other fossil fuels by engineering bacteria that can produce ethanol from various forms of biomass, including agricultural waste, switchgrass, and corn.

Evolution of Roots: Vascular tissue also provides benefits below ground. Instead of the rhizoids seen in bryophytes, roots evolved in the sporophytes of almost all vascular plants. Roots are organs that absorb water and nutrients from the soil. Roots also anchor vascular plants to the ground, hence allowing the shoot system to grow taller.

Root tissues of living plants closely resemble stem tissues of early vascular plants preserved in fossils. This suggests that roots may have evolved from the lowest belowground portions of stems in ancient vascular plants. It is unclear whether roots evolved only once in the common ancestor of all vascular plants or independently in different lineages. Although the roots of living members of these lineages of vascular plants share many similarities, fossil evidence hints at convergent evolution. The oldest fossils of lycophytes, for example, already displayed simple roots 400 million years ago, when the ancestors of ferns and seed plants still had none. Studying genes that control root development in different vascular plant species may help resolve this question.

The word rotifer is derived from the Latin meaning "wheelbearer," a reference to the crown of cilia that draws a vortex of water into the mouth. Posterior to the mouth, rotifers have jaws called trophi that grind up food, mostly microorganisms suspended in the water. Digestion is then completed farther along the alimentary canal. Most other bilaterians also have an alimentary canal, which enables the stepwise digestion of a wide range of food particles.

Rotifers exhibit some unusual forms of reproduction. Some species consist only of females that produce more females from unfertilized eggs, a type of asexual reproduction called parthenogenesis. Some other invertebrates (for example, aphids and some bees) and even some vertebrates (for example, some lizards and some fishes) can also reproduce in this way. In addition to being able to produce females by parthenogenesis, some rotifers can also reproduce sexually under certain conditions, such as high levels of crowding. The resulting embryos can remain dormant for years. Once they break dormancy, the embryos develop into another generation of females that reproduce asexually.

Rotifers and Acanthocephalans: Recent phylogenetic analyses have shown that two traditional animal phyla, the rotifers (former phylum Rotifera) and the acanthocephalans (former phylum Acanthocephala), should be combined into a single phylum, Syndermata. Each of the two groups has distinctive characteristics.

Rotifers: There are roughly 1,800 species of rotifers, tiny animals that inhabit freshwater, marine, and damp soil habitats. Ranging in size from about 50 µm to 2 mm, rotifers are smaller than many protists but nevertheless are multicellular and have specialized organ systems (Figure 33.13). In contrast to cnidarians and flatworms, which have a gastrovascular cavity, rotifers have an alimentary canal, a digestive tube with two openings, a mouth and an anus. Internal organs lie within the pseudocoelom, a body cavity that is not completely lined by mesoderm (see Figure 32.9b). Fluid in the pseudocoelom serves as a hydrostatic skeleton. Movement of a rotifer's body distributes the fluid throughout the body, circulating nutrients.

Euglenids: A euglenid has a pocket at one end of the cell from which one or two flagella emerge (Figure 28.8). Some euglenids are mixotrophs: They perform photosynthesis when sunlight is available, but when it is not, they can become heterotrophic, absorbing organic nutrients from their environment. Many other euglenids engulf prey by phagocytosis.

SAR is a highly diverse group of protists defined by DNA similarities: Our second supergroup, referred to as SAR, was proposed recently based on whole-genome DNA sequence analyses. These studies have found that three major clades of protists— the stramenopiles, alveolates, and rhizarians—form a monophyletic supergroup. This supergroup contains a large, extremely diverse collection of protists. To date, this supergroup has not received a formal name but is instead known by the first letters of its major clades: SAR.

The Earliest Hominins: The study of human origins is known as paleoanthropology. Paleoanthropologists have unearthed fossils of approximately 20 extinct species that are more closely related to humans than to chimpanzees. These species are known as hominins (Figure 34.47). Since 1994, fossils of four hominin species dating to more than 4 million years ago have been discovered. The oldest of these hominins, Sahelanthropus tchadensis, lived about 6.5 million years ago.

Sahelanthropus and other early hominins shared some of the derived characters of humans. For example, they had reduced canine teeth, and some fossils suggest that they had relatively flat faces. They also show signs of having been more upright and bipedal than other apes. One clue to their upright stance can be found in the foramen magnum, the hole at the base of the skull through which the spinal cord passes. In chimpanzees, the foramen magnum is relatively far back on the skull, while in early hominins (and in humans), it is located underneath the skull. This position allows us to hold our head directly over our body, as early hominins apparently did as well. The pelvis, leg bones, and feet of the 4.4-millionyear-old Ardipithecus ramidus also suggest that early hominins were increasingly bipedal (Figure 34.48). (We will return to the subject of bipedalism later in the chapter.)

Steps in the Origin of Multicellular Animals: One way to gather information about the origin of animals is to identify protist groups that are closely related to animals. As shown in Figure 32.3, a combination of morphological and molecular evidence points to choanoflagellates as the closest living relatives of animals. Based on such evidence, researchers have hypothesized that the common ancestor of choanoflagellates and living animals may have been a suspension feeder similar to present-day choanoflagellates.

Scientists exploring how animals may have arisen from their single-celled ancestors have noted that the origin of multicellularity requires the evolution of new ways for cells to adhere (attach) and signal (communicate) to each other. In an effort to learn more about such mechanisms, researchers compared the genome of the unicellular choanoflagellate Monosiga brevicollis with those of representative animals. This analysis uncovered 78 protein domains in M. brevicollis that were otherwise only known to occur in animals. (A domain is a key structural or functional region of a protein.) For example, M. brevicollis has genes that encode domains of certain proteins (known as cadherins) that play key roles in how animal cells attach to one another, as well as genes that encode protein domains that animals (and only animals) use in cell-signaling pathways.

Asteroidea: Sea Stars and Sea Daisies: Sea stars have arms radiating from a central disk; the undersurfaces of the arms bear tube feet. By a combination of muscular and chemical actions, the tube feet can attach to or detach from a substrate. The sea star adheres firmly to rocks or creeps along slowly as its tube feet extend, grip, release, extend, and grip again. Although the base of the tube foot has a flattened disk that resembles a suction cup, the gripping action results from adhesive chemicals, not suction (see Figure 33.44).

Sea stars also use their tube feet to grasp prey, such as clams and oysters. The arms of the sea star embrace the closed bivalve, clinging tightly with their tube feet. The sea star then turns part of its stomach inside out, everting it through its mouth and into the narrow opening between the halves of the bivalve's shell. Next, the digestive system of the sea star secretes juices that begin digesting the mollusc within its own shell. The sea star then brings its stomach back inside its body, where digestion of the mollusc's (now liquefied) body is completed. The ability to begin the digestive process outside of its body allows a sea star to consume bivalves and other prey species that are much larger than its mouth.

It is puzzling that many rotifer species persist without males. The vast majority of animals and plants reproduce sexually at least some of the time, and sexual reproduction has certain advantages over asexual reproduction (see Concept 46.1). For example, species that reproduce asexually tend to accumulate harmful mutations in their genomes faster than sexually reproducing species. As a result, asexual species should experience higher rates of extinction.

Seeking to understand how they persist without males, researchers have been studying a clade of asexual rotifers named Bdelloidea. Some 360 species of bdelloid rotifers are known, and all of them reproduce by parthenogenesis without any males. Paleontologists have discovered bdelloid rotifers preserved in 35-million-year-old amber, and the morphology of these fossils resembles only the female form, with no evidence of males. Molecular clock analyses indicate that bdelloids have been asexual for over 50 million years. While it appears that they do not reproduce sexually, bdelloid rotifers may be able to generate genetic diversity in other ways. For example, bdelloids can tolerate very high levels of desiccation. When conditions improve and their cells rehydrate, DNA from other species enters their cells through cracks in the plasma membrane. Recent evidence suggests that this foreign DNA can be incorporated into the bdelloids' genome, thereby leading to increased genetic diversity.

Figure 31.5 generalizes the many different life cycles that can produce fungal spores. In this section, we will survey the main aspects of sexual and asexual reproduction in fungi. Figure 31.5 Generalized life cycle of fungi. Many fungi reproduce both sexually and asexually, as shown here; others, however, reproduce only sexually or asexually.

Sexual Reproduction: The nuclei of fungal hyphae and the spores of most fungi are haploid, although many species have transient diploid stages that form during sexual life cycles. Sexual reproduction often begins when hyphae from two mycelia release sexual signaling molecules called pheromones. If the mycelia are of different mating types, the pheromones from each partner bind to receptors on the other, and the hyphae extend toward the source of the pheromones. When the hyphae meet, they fuse. In species with such a "compatibility test," this process contributes to genetic variation by preventing hyphae from fusing with other hyphae from the same mycelium or another genetically identical mycelium.

Endotoxins are lipopolysaccharide components of the outer membrane of gram-negative bacteria. In contrast to exotoxins, endotoxins are released only when the bacteria die and their cell walls break down. Endotoxin-producing bacteria include species in the genus Salmonella, such as Salmonella typhi, which causes typhoid fever. You might have heard of food poisoning caused by other Salmonella species that can be found in poultry and some fruits and vegetables.

Since the 19th century, improved sanitation systems in the industrialized world have greatly reduced the threat of pathogenic bacteria. Antibiotics have saved a great many lives and reduced the incidence of disease. However, resistance to antibiotics is currently evolving in many bacterial strains. As you read earlier, the rapid reproduction of bacteria enables cells carrying resistance genes to quickly give rise to large populations as a result of natural selection, and these genes can also spread to other species by horizontal gene transfer.

Amoebozoans: The amoebozoan clade includes many species of amoebas that have lobe- or tube-shaped pseudopodia rather than the threadlike pseudopodia found in rhizarians. Amoebozoans include slime molds, tubulinids, and entamoebas.

Slime Molds: Slime molds, or mycetozoans (from the Latin, meaning "fungus animals"), once were thought to be fungi because, like fungi, they produce fruiting bodies that aid in spore dispersal. However, DNA sequence analyses indicate that the resemblance between slime molds and fungi is a case of evolutionary convergence. DNA sequence analyses also show that slime molds descended from unicellular ancestors—an example of the independent origin of multicellularity in eukaryotes. Slime molds have diverged into two main branches, plasmodial slime molds and cellular slime molds. We'll compare their characteristics and life cycles.

Figure 33.36 The phylogenetic position of the insects. Recent results have shown that the insects are nested within lineages of aquatic crustaceans. The remipedians are one of several groups of aquatic crustaceans that may be the sister group to the insects.

Small crustaceans exchange gases across thin areas of the cuticle; larger species have gills. Nitrogenous wastes also diffuse through thin areas of the cuticle, but a pair of glands regulates the salt balance of the hemolymph. Sexes are separate in most crustaceans. In the case of lobsters and crayfishes, the male uses a specialized pair of abdominal appendages to transfer sperm to the reproductive pore of the female during copulation. Most aquatic crustaceans go through one or more swimming larval stages. One of the largest groups of crustaceans (numbering over 11,000 species) is the isopods, which include terrestrial, freshwater, and marine species. Some isopod species are abundant in habitats at the bottom of the deep ocean. Among the terrestrial isopods are the pill bugs, or wood lice, common on the undersides of moist logs and leaves.

Fungi as Parasites: Like mutualistic fungi, parasitic fungi absorb nutrients from the cells of living hosts, but they provide no benefits in return. About 30% of the 100,000 known species of fungi make a living as parasites or pathogens, mostly of plants (Figure 31.24). An example of a plant pathogen is Cryphonectria parasitica, the ascomycete fungus that causes chestnut blight, which dramatically changed the landscape of the northeastern United States. Accidentally introduced via trees imported from Asia in the early 1900s, spores of the fungus entered cracks in the bark of American chestnut trees and produced hyphae, killing many trees. The oncecommon chestnuts now survive mainly as sprouts from the stumps of former trees. Another ascomycete, Fusarium circinatum, causes pine pitch canker, a disease that threatens pines throughout the world. Between 10% and 50% of the world's fruit harvest is lost annually due to fungi, and grain crops also suffer major losses each year.

Some fungi that attack food crops produce compounds that are toxic to humans. One example is the ascomycete Claviceps purpurea, which grows on rye plants, forming purple structures called ergots (see Figure 31.24c). If infected rye is milled into flour, toxins from the ergots can cause ergotism, characterized by gangrene, nervous spasms, burning sensations, hallucinations, and temporary insanity. An epidemic of ergotism around 944 ce killed up to 40,000 people in France. One compound that has been isolated from ergots is lysergic acid, the raw material from which the hallucinogen LSD is made.

Systemic mycoses, by contrast, spread through the body and usually cause very serious illnesses. They are typically caused by inhaled spores. For example, coccidioidomycosis is a systemic mycosis that produces tuberculosis-like symptoms in the lungs. Each year, hundreds of cases in North America require treatment with antifungal drugs, without which the disease could be fatal.

Some mycoses are opportunistic, occurring only when a change in the body's microorganisms, chemical environment, or immune system allows fungi to grow unchecked. Candida albicans, for example, is one of the normal inhabitants of moist epithelia, such as the vaginal lining. Under certain circumstances, Candida can grow too rapidly and become pathogenic, leading to so-called "yeast infections." Many other opportunistic mycoses in humans have become more common in recent decades, due in part to AIDS, which compromises the immune system.

Body Cavities: Most triploblastic animals have a body cavity, a fluid- or airfilled space located between the digestive tract and the outer body wall. This body cavity is also called a coelom (from the Greek koilos, hollow). A so-called "true" coelom forms from tissue derived from mesoderm. The inner and outer layers of tissue that surround the cavity connect and form structures that suspend the internal organs. Animals with a true coelom are known as coelomates (Figure 32.9a).

Some triploblastic animals have a body cavity that is formed from mesoderm and endoderm (Figure 32.9b). Such a cavity is called a "pseudocoelom" (from the Greek pseudo, false), and the animals that have one are called pseudocoelomates. Despite its name, however, a pseudocoelom is not false; it is a fully functional body cavity. Finally, some triploblastic animals lack a body cavity altogether (Figure 32.9c). They are known collectively as acoelomates (from the Greek a-, without).

All turtles have a boxlike shell made of upper and lower shields that are fused to the vertebrae, clavicles (collarbones), and ribs (Figure 34.29d). Most of the 307 known species of turtles have a hard shell, providing excellent defense against predators. Fossil evidence shows that Pappochelys, a turtle that lived 240 million years ago, had a series of hard, shelllike bones along its belly. By 220 million years ago, another early turtle had a complete lower shell but an incomplete upper shell, suggesting that turtles acquired full shells in stages. The earliest turtles could not retract their head into their shell, but mechanisms for doing so evolved independently in two separate branches of turtles. The side-necked turtles fold their neck horizontally, while the vertical-necked turtles fold their neck vertically.

Some turtles have adapted to deserts, and others live almost entirely in ponds and rivers. Still others live in the sea. Sea turtles have a reduced shell and enlarged forelimbs that function as flippers. They include the largest living turtles, the deep-diving leatherbacks, which can exceed a mass of 1,500 kg and feed on jellies. Leatherbacks and other sea turtles are endangered by being caught in fishing nets, as well as by the residential and commercial development of the beaches where the turtles lay their eggs.

Echinodermata (7,000 species): Echinoderms, such as sand dollars, sea stars, and sea urchins, are marine animals in the deuterostome clade that are bilaterally symmetrical as larvae but not as adults. They move and feed by using a network of internal canals to pump water to different parts of their body (see Concept 33.5). A sea urchin.

Sponges are basal animals that lack tissues: Animals in the phylum Porifera are known informally as sponges. (Recent molecular studies indicate that sponges are monophyletic, and that is the phylogeny we present here; this remains under debate, however, as some studies suggest that sponges are paraphyletic.) Among the simplest of animals, sponges are sedentary and were mistaken for plants by the ancient Greeks. Most species are marine, and they range in size from a few millimeters to a few meters. Sponges are filter feeders: They filter out food particles suspended in the surrounding water as they draw it through their body, which in some species resembles a sac perforated with pores. Water is drawn through the pores into a central cavity, the spongocoel, and then flows out of the sponge through a larger opening called the osculum (Figure 33.4). More complex sponges have folded body walls, and many contain branched water canals and several oscula.

Most sponges are hermaphrodites, meaning that each individual functions as both male and female in sexual reproduction by producing sperm and eggs. Almost all sponges exhibit sequential hermaphroditism: They function first as one sex and then as the other. Cross-fertilization can result when sperm released into the water current by an individual functioning as a male is drawn into a neighboring individual that is functioning as a female. The resulting zygotes develop into flagellated, swimming larvae that disperse from the parent sponge. After settling on a suitable substrate, a larva develops into a sessile adult.

Sponges produce a variety of antibiotics and other defensive compounds, which hold promise for fighting human diseases. For example, a compound called cribrostatin isolated from marine sponges can kill both cancer cells and penicillin-resistant strains of the bacterium Streptococcus. Other sponge-derived compounds are also being tested as possible anticancer agents.

All animals have developmental genes that regulate the expression of other genes, and many of these regulatory genes contain sets of DNA sequences called homeoboxes (see Concept 21.6). In particular, most animals share a unique homeobox-containing family of genes, known as Hox genes. Hox genes play important roles in the development of animal embryos, controlling the expression of many other genes that influence morphology.

Sponges, which are among the simplest extant (living) animals, lack Hox genes. However, they have other homeobox genes that influence their shape, such as those that regulate the formation of water channels in the body wall, a key feature of sponge morphology (see Figure 33.4). In the ancestors of more complex animals, the Hox gene family arose via the duplication of earlier homeobox genes. Over time, the Hox gene family underwent a series of duplications, yielding a versatile "toolkit" for regulating development. In most animals, Hox genes regulate the formation of the anterior-posterior (front-to-back) axis, as well as other aspects of development. Similar sets of conserved genes govern the development of both flies and humans, despite their obvious differences and hundreds of millions of years of divergent evolution.

Evolution of Leaves: Leaves are structures that serve as the primary photosynthetic organ of vascular plants. In terms of size and complexity, leaves can be classified as either microphylls or megaphylls (Figure 29.13). All of the lycophytes—and only the lycophytes—have microphylls, small, often spineshaped leaves supported by a single strand of vascular tissue. Almost all other vascular plants have megaphylls, leaves with a highly branched vascular system; a few species have reduced leaves that appear to have evolved from megaphylls. Megaphylls are typically larger than microphylls and therefore support greater photosynthetic productivity than microphylls. Microphylls first appear in the fossil record 410 million years ago, but megaphylls do not emerge until about 370 million years ago, toward the end of the Devonian period.

Sporophylls and Spore Variations: One milestone in the evolution of plants was the emergence of sporophylls, modified leaves that bear sporangia. Sporophylls vary greatly in structure. For example, fern sporophylls produce clusters of sporangia known as sori (singular, sorus), usually on the undersides of the sporophylls (see Figure 29.12). In many lycophytes and in most gymnosperms, groups of sporophylls form cone-like structures called strobili. The sporophylls of angiosperms are called carpels and stamens (see Figure 30.8).

Figure 29.13 Microphyll and megaphyll leaves. Microphyll leaves: Selaginella kraussiana (Krauss's spikemoss) Megaphyll leaves: Hymenophyllum tunbrigense (Tunbridge filmy fern) Lycophytes (Phylum Lycophyta): Many lycophytes grow on tropical trees as epiphytes, plants that use other plants as a substrate but are not parasites. Other species grow on temperate forest floors. In some species, the tiny gametophytes live above ground and are photosynthetic. Others live below ground, nurtured by symbiotic fungi.

Sporophytes have upright stems with many small leaves, as well as groundhugging stems that produce dichotomously branching roots. Spike mosses are usually relatively small and often grow horizontally. In many club mosses and spike mosses, sporophylls are clustered into clubshaped cones (strobili). Quillworts, named for their leaf shape, form a single genus whose members live in marshy areas or as submerged aquatic plants. Club mosses are all homosporous, whereas spike mosses and quillworts are all heterosporous. The spores of club mosses are released in clouds and are so rich in oil that magicians and photographers once ignited them to create smoke or flashes of light.

3. Are acoelomate flatworms basal bilaterians? A series of recent molecular papers have indicated that acoelomate flatworms (phylum Acoela) are basal bilaterians, as shown in Figure 32.11. A different conclusion was supported by a 2011 analysis, which placed acoelomates within Deuterostomia. Researchers are currently sequencing the genomes of several acoelomates and species from closely related groups to provide a more definitive test of the hypothesis that acoelomate flatworms are basal bilaterians. If further evidence supports this hypothesis, this would suggest that the bilaterians may have descended from a common ancestor that resembled living acoelomate flatworms—that is, from an ancestor that had a simple nervous system, a saclike gut with a single opening (the "mouth"), and no excretory system.

Starting with its striking colors and surreal shape, the blue dragon (Glaucus atlanticus) in Figure 33.1 is full of surprises. Its thin, finger-like structures increase the surface area of its body, aiding in respiration and helping it to float (upside down) on the sea's surface. This small sea slug also packs a powerful punch: It eats Portuguese men-of-war and absorbs their stinging cells, which the blue dragon then uses to deliver a deadly sting of its own.

We'll survey the diversity of eukaryotes throughout the rest of this unit, beginning in this chapter with the protists. As you explore this material, bear in mind that the organisms in most eukaryotic lineages are protists, and most protists are unicellular.Thus, life differs greatly from how most of us commonly think of it. The large, multicellular organisms that we know best (plants, animals, and fungi) are the tips of just a few branches on the great tree of life (see Figure 26.21).

Structural and Functional Diversity in Protists: Given that they are classified in a number of different groups, it isn't surprising that few general characteristics of protists can be cited without exceptions. In fact, protists exhibit more structural and functional diversity than the eukaryotes with which we are most familiar—plants, animals, and fungi. For example, most protists are unicellular, although there are some colonial and multicellular species. Single-celled protists are justifiably considered the simplest eukaryotes, but at the cellular level, many protists are very complex—the most elaborate of all cells. In multicellular organisms, essential biological functions are carried out by organs.

However, the charophytes are the only present-day algae that share the following distinctive traits with plants, suggesting that they are the closest living relatives of plants: Rings of cellulose-synthesizing proteins. The cells of both plants and charophytes have distinctive circular rings of proteins (small photo) embedded in the plasma membrane. These protein rings synthesize the cellulose microfibrils of the cell wall. In contrast, noncharophyte algae have linear sets of proteins that synthesize cellulose.

Structure of flagellated sperm. In species of plants that have flagellated sperm, the structure of the sperm closely resembles that of charophyte sperm.

Formation of a phragmoplast. Particular details of cell division occur only in plants and certain charophytes. For example, a group of microtubules known as the phragmoplast forms between the daughter nuclei of a dividing cell. A cell plate then develops in the middle of the phragmoplast, across the midline of the dividing cell (see Figure 12.10). The cell plate, in turn, gives rise to a new cross wall that separates the daughter cells.

Studies of nuclear, chloroplast, and mitochondrial DNA from a wide range of plants and algae indicate that certain groups of charophytes—such as Zygnema (see Figure 28.22a) and Coleochaete—are the closest living relatives of plants. Although this evidence shows that plants arose from within a group of charophyte algae, it does not mean that plants are descended from these living algae. Even so, present-day charophytes may tell us something about the algal ancestors of plants.

Once on land, some fungi formed symbiotic associations with early plants. For example, 405-million-year-old fossils of the early plant Aglaophyton contain evidence of mycorrhizal relationships between plants and fungi (see Figure 25.12). This evidence includes fossils of hyphae that have penetrated within plant cells and formed structures that resemble the arbuscules formed today by arbuscular mycorrhizae. Similar structures have been found in a variety of other early plants, suggesting that plants probably existed in beneficial relationships with fungi from the earliest periods of colonization of land. The earliest plants lacked roots, limiting their ability to extract nutrients from the soil. As occurs in mycorrhizal associations today, it is likely that soil nutrients were transferred to early plants via the extensive mycelia formed by their symbiotic fungal partners.

Support for the antiquity of mycorrhizal associations has also come from recent molecular studies. For a mycorrhizal fungus and its plant partner to establish a symbiotic relationship, certain genes must be expressed by the fungus and other genes must be expressed by the plant. Researchers focused on three plant genes (called sym genes) whose expression is required for the formation of mycorrhizae in flowering plants. They found that these genes were present in all major plant lineages, including basal lineages such as liverworts (see Figure 29.7). Furthermore, after they transferred a liverwort sym gene to a flowering plant mutant that could not form mycorrhizae, the mutant recovered its ability to form mycorrhizae. These results suggest that mycorrhizal sym genes were present in early plants—and that the function of these genes has been conserved for hundreds of millions of years as plants continued to adapt to life on land.

Protists play key roles in ecological communities: Most protists are aquatic, and they are found almost anywhere there is water, including moist terrestrial habitats such as damp soil and leaf litter. In oceans, ponds, and lakes, many protists are bottom-dwellers that attach to rocks and other substrates or creep through the sand and silt. As we've seen, other protists are important constituents of plankton. We'll focus here on two key roles that protists play in the varied habitats in which they live: that of symbiont and that of producer.

Symbiotic Protists: Many protists form symbiotic associations with other species. For example, photosynthetic dinoflagellates are food-providing symbiotic partners of the animals (coral polyps) that build coral reefs. Coral reefs are highly diverse ecological communities. That diversity ultimately depends on corals—and on the mutualistic protists that nourish them. Corals support reef diversity by providing food to some species and habitat to many others.

Like all features of organisms, animal body plans have evolved over time. In some cases, including key stages in gastrulation, novel body plans emerged early in the history of animal life and have not changed since. As we'll discuss, however, other aspects of animal body plans have changed multiple times over the course of evolution. As we explore the major features of animal body plans, bear in mind that similar body forms may have evolved independently in different lineages. In addition, body features can be lost over the course of evolution, causing some closely related species to look very different from one another.

Symmetry: A basic feature of animal bodies is their type of symmetry—or absence of symmetry. (Many sponges, for example, lack symmetry altogether.) Some animals exhibit radial symmetry, the type of symmetry found in a flowerpot (Figure 32.8a). Sea anemones, for example, have a top side (where the mouth is located) and a bottom side. But they have no front and back ends and no left and right sides.

For centuries, humans have also depended on seed plants for medicines. Many cultures use herbal remedies, and scientists have extracted and identified medicinally active compounds from many of these plants and later synthesized them. Willow leaves and bark have long been used in painrelieving remedies, including prescriptions by the Greek physician Hippocrates. In the 1800s, scientists traced the willow's medicinal property to the chemical salicin. A synthesized derivative, acetylsalicylic acid, is what we call aspirin. Plants are also a direct source of medicinal compounds (Table 30.1). In the United States, about 25% of prescription drugs contain an active ingredient from plants, usually seed plants.

Table 30.1 Examples of Plant-Derived Medicines

As described in Figure 17.2, biologists in the 1930s used Neurospora in research that led to the one gene-one enzyme hypothesis. Today, this ascomycete continues to serve as a model research organism. In 2003, its entire genome was published. This tiny fungus has about three-fourths as many genes as the fruit fly Drosophila and about half as many as a human (Table 31.1). The Neurospora genome is relatively compact, having few of the stretches of noncoding DNA that occupy so much space in the genomes of humans and many other eukaryotes. In fact, there is evidence that Neurospora has a genomic defense system that prevents noncoding DNA such as transposons from accumulating.

Table 31.1 Comparison of Gene Density in Neurospora, Drosophila, and Homo sapiens Figure 31.16 The life cycle of Neurospora crassa, an ascomycete. Neurospora is a bread mold and research organism that also grows in the wild on burned vegetation. Ascomycete mycelia can reproduce asexually by producing pigmented haploid spores (conidia). Neurospora can also reproduce sexually by producing specialized hyphae. Conidia of the opposite mating type fuse to these hyphae. The dikaryotic hyphae that result from plasmogamy produce many dikaryotic asci, two of which are shown here.Karyogamy occurs within each ascus, producing a diploid nucleus. Each diploid nucleus divides by meiosis, yielding four haploid nuclei. Each haploid nucleus divides once by mitosis, yielding eight nuclei. Cell walls and plasma membranes develop around the nuclei, forming ascospores (LM). The ascospores are discharged forcibly from the asci through an opening in the ascocarp. Germinating ascospores give rise to new mycelia.

Figure 26.15 Research Method Applying Parsimony to a Problem in Molecular Systematics Application In considering possible phylogenies for a group of species, systematists compare molecular data for the species. An efficient way to begin is by identifying the most parsimonious hypothesis—the one that requires the fewest evolutionary events (molecular changes) to have occurred. Technique Follow the numbered steps as we apply the principle of parsimony to a hypothetical phylogenetic problem involving three closely related beetle species. 1) First, draw the three possible trees for the species. (Although only 3 trees are possible when ordering 3 species, the number of possible trees increases rapidly with the number of species: There are 15 trees for 4 species and 34,459,425 trees for 10 species.)

Tabulate the molecular data for the species. In this simplified example, the data represent a DNA sequence consisting of just four nucleotide bases. Data from several outgroup species (not shown) were used to infer the ancestral DNA sequence. 3 Now focus on site 1 in the DNA sequence. In the tree on the left, a single base-change event, represented by the purple hatch mark on the branch leading to species I and II (and labeled 1/C, indicating a change at site 1 to nucleotide C), is sufficient to account for the site 1 data. In the other two trees, two base-change events are necessary. 4 Continuing the comparison of bases at sites 2, 3, and 4 reveals that each of the three trees requires a total of five additional basechange events (purple hatch marks). Results To identify the most parsimonious tree, we total all of the base-change events noted in steps 3 and 4. We conclude that the first tree is the most parsimonious of the three possible phylogenies. (In a real example, many more sites would be analyzed. Hence, the trees would often differ by more than one base-change event.)

Onychophora (110 species): Onychophorans, also called velvet worms, originated during the Cambrian explosion (see Chapter 32). Originally, they thrived in the ocean, but at some point they succeeded in colonizing land. Today they live only in humid forests. Onychophorans have fleshy antennae and several dozen pairs of saclike legs. An onychophoran.

Tardigrada (800 species): Tardigrades (from the Latin tardus, slow, and gradus, step) are sometimes called water bears for their overall shape and lumbering, bearlike gait. Most tardigrades are less than 0.5 mm in length. Some live in oceans or fresh water, while others live on plants or animals. Harsh conditions may cause tardigrades to enter a state of dormancy; while dormant, they can survive for days at temperatures as low as -200°C! A 2015 phylogenomic study found that over 15% of tardigrade genes entered their genome by horizontal gene transfer, the largest fraction known for any animal. Tardigrades (colorized SEM)

A body cavity has many functions. Its fluid cushions the suspended organs, helping to prevent internal injury. In softbodied coelomates, such as earthworms, the coelom contains noncompressible fluid that acts like a skeleton against which muscles can work. The cavity also enables the internal organs to grow and move independently of the outer body wall. If it were not for your coelom, for example, every beat of your heart or ripple of your intestine would warp your body's surface.

Terms such as coelomates and pseudocoelomates refer to organisms that have a similar body plan and hence belong to the same grade (a group whose members share key biological features). However, phylogenetic studies show that true coeloms and pseudocoeloms have been independently gained or lost multiple times in the course of animal evolution. As shown by this example, a grade is not necessarily equivalent to a clade (a group that includes an ancestral species and all of its descendants). Thus, while terms such as coelomate or pseudocoelomate can be helpful in describing an organism's features, these terms must be interpreted with caution when seeking to understand evolutionary history

Figure 34.16 Anatomy of a trout, a ray-finned fish

Tetrapods are gnathostomes that have limbs: One of the most significant events in vertebrate history took place 365 million years ago, when the fins of a lineage of lobefins gradually evolved into the limbs and feet of tetrapods. Until then, all vertebrates had shared the same basic fishlike anatomy. After the colonization of land, tetrapods diversified greatly and gave rise to many new forms, from leaping frogs to flying eagles to bipedal humans.

Views of animal phylogeny continue to be shaped by new molecular and morphological data: As animals with diverse body plans radiated during the early Cambrian, some lineages arose, thrived for a period of time, and then became extinct, leaving no descendants. However, by 500 million years ago, most animal phyla with members alive today were established. Next, we'll examine relationships among these taxa along with some remaining questions that are currently being addressed using genomic data.

The Diversification of Animals: Zoologists currently recognize about three dozen phyla of extant animals, 15 of which are shown in Figure 32.11. Researchers infer evolutionary relationships among these phyla by analyzing whole genomes, as well as morphological traits, ribosomal RNA (rRNA) genes, Hox genes, proteincoding nuclear genes, and mitochondrial genes. Notice how the following points are reflected in Figure 32.11.

Homo sapiens: Evidence from fossils, archaeology, and DNA studies has improved our understanding about how our own species, Homo sapiens, emerged and spread around the world. Fossil evidence indicates that the ancestors of humans originated in Africa. Older species (perhaps H. ergaster or H. erectus) gave rise to later species, ultimately including H. sapiens. Furthermore, the oldest known fossils of our own species have been found at two different sites in Ethiopia and include specimens that are 195,000 and 160,000 years old. These early humans had less pronounced browridges than those found in H. erectus and Neanderthals, and they were more slender than other recent hominins.

The Ethiopian fossils support inferences about the origin of humans from molecular evidence. DNA analyses show that Europeans and Asians share a relatively recent common ancestor and that many African lineages branched off more basal positions on the human family tree. These findings suggest that all living humans have ancestors that originated as H. sapiens in Africa. The oldest fossils of H. sapiens outside Africa are from the Middle East and date back about 115,000 years. Fossil evidence and genetic analyses suggest that humans spread beyond Africa in one or more waves, first into Asia and then to Europe and Australia. The date of the first arrival of humans in the New World is uncertain, although the oldest generally accepted evidence puts that date at about 15,000 years ago.

Gymnosperms bear "naked" seeds, typically on cones: Extant seed plants form two sister clades: gymnosperms and angiosperms. Recall that gymnosperms have "naked" seeds exposed on sporophylls that usually form cones. (Angiosperm seeds are enclosed in chambers that mature into fruits.) Most gymnosperms are cone-bearing plants called conifers, such as pines, firs, and redwoods.

The Life Cycle of a Pine: As you read earlier, seed plant evolution has included three key reproductive adaptations: the miniaturization of their gametophytes; the advent of the seed as a resistant, dispersible stage in the life cycle; and the appearance of pollen as an airborne agent that brings gametes together. Figure 30.4 shows how these adaptations come into play during the life cycle of a pine, a familiar conifer. The pine tree is the sporophyte; its sporangia are located on scalelike structures packed densely in cones. Like all seed plants, conifers are heterosporous. As such, they have two types of sporangia that produce two types of spores: microsporangia that produce microspores, and megasporangia that produce megaspores. In conifers, the two types of spores are produced by separate cones: small pollen cones and large ovulate cones.

Basal Fungal Groups: Insights into the nature of basal fungal groups have begun to emerge from recent genomic studies. For example, several studies have identified chytrids in the genus Rozella as having diverged from other fungi early in the history of the group. Furthermore, one metagenomics study placed Rozella within a large, previously unknown clade of unicellular fungi, tentatively called "cryptomycota." Like Rozella (and chytrids in general), fungi in the cryptomycota clade have flagellated spores. Current evidence also indicates that Rozella and other members of the cryptomycota are unique among fungi in that they do not synthesize a chitin-rich cell wall during any of their life cycle stages. This suggests that a cell wall strengthened by chitin—a key structural feature found in most fungi—may have arisen after the cryptomycota diverged from other fungi.

The Move to Land: Plants colonized land about 470 million years ago (see Concept 29.1), and fungi may well have colonized land before plants. Indeed, some researchers have described life on land before the arrival of plants as a "green slime" that consisted of cyanobacteria, algae, and a variety of small, heterotrophic species, including fungi. With their capacity for extracellular digestion, fungi would have been well suited for feeding on other early terrestrial organisms (or their remains).

Flight also requires both acute vision and fine muscle control. Birds have color vision and excellent eyesight. The visual and motor areas of the brain are well developed, and the brain is proportionately larger than those of amphibians and nonbird reptiles. Birds generally display very complex behaviors, particularly during breeding season, when they engage in elaborate courtship rituals. Because eggs have shells by the time they are laid, fertilization must be internal. Copulation usually involves contact between the openings to the birds' cloacas. After eggs are laid, the avian embryo must be kept warm through brooding by the mother, the father, or both, depending on the species.

The Origin of Birds Cladistic analyses of birds and reptilian fossils indicate that birds belong to the group of bipedal saurischian dinosaurs called theropods. Since the late 1990s, Chinese paleontologists have unearthed a spectacular trove of feathered theropod fossils that are shedding light on the origin of birds. Several species of dinosaurs closely related to birds had feathers with vanes, and a wider range of species had filamentous feathers. Such findings imply that feathers evolved long before powered flight. Among the possible functions of these early feathers were insulation, camouflage, and courtship display.

Adaptations Enabling the Move to Land: Many species of charophyte algae inhabit shallow waters around the edges of ponds and lakes, where they are subject to occasional drying. In such environments, natural selection favors individual algae that can survive periods when they are not submerged. In charophytes, a layer of a durable polymer called sporopollenin prevents exposed zygotes from drying out. A similar chemical adaptation is found in the tough sporopollenin walls that encase plant spores.

The accumulation of such traits by at least one population of charophyte algae (now extinct) probably enabled their descendants—the first plants—to live permanently above the waterline. This ability opened a new frontier: a terrestrial habitat that offered enormous benefits. The bright sunlight was unfiltered by water and plankton; the atmosphere offered more plentiful carbon dioxide than did water; and the soil by the water's edge was rich in some mineral nutrients. But these benefits were accompanied by challenges: a relative scarcity of water and a lack of structural support against gravity. (To appreciate why such support is important, picture how the soft body of a jellyfish sags when taken out of water.) Plants diversified as new adaptations arose that enabled them to thrive despite these challenges.

Many yeasts and filamentous fungi have no known sexual stage in their life cycle. Since early mycologists (biologists who study fungi) classified fungi based mainly on their type of sexual structure, this posed a problem. Mycologists have traditionally lumped all fungi lacking sexual reproduction into a group called deuteromycetes (from the Greek deutero, second, and mycete, fungus). Whenever a sexual stage is discovered for a so-called deuteromycete, the species is reclassified in a particular phylum, depending on the type of sexual structures it forms. In addition to searching for sexual stages of such unassigned fungi, mycologists can now use genomic techniques to classify them.

The ancestor of fungi was an aquatic, single-celled, flagellated protist: Data from both paleontology and molecular systematics offer insights into the early evolution of fungi. As a result, systematists now recognize that fungi and animals are more closely related to each other than either group is to plants or to most other eukaryotes. Figure 31.8 Fungi and their close relatives. Molecular evidence indicates that the nucleariids, a group of single-celled protists, are the closest living relatives of fungi. The three parallel lines leading to the chytrids indicate that this group is paraphyletic.

Sponges represent a lineage that diverged from other animals early in the history of the group; thus, they are said to be basal animals. Unlike nearly all other animals, sponges lack tissues, groups of similar cells that act as a functional unit as in muscle tissue and nervous tissue. However, the sponge body does contain several different cell types. For example, lining the interior of the spongocoel are flagellated choanocytes, or collar cells (named for the finger-like projections that form a "collar" around the flagellum). These cells engulf bacteria and other food particles by phagocytosis. The similarity between choanocytes and the cells of choanoflagellates supports molecular evidence suggesting that animals evolved from a choanoflagellate-like ancestor (see Figure 32.3).

The body of a sponge consists of two layers of cells separated by a gelatinous region called the mesohyl. Because both cell layers are in contact with water, processes such as gas exchange and waste removal can occur by diffusion across the membranes of these cells. Other tasks are performed by cells called amoebocytes, named for their use of pseudopodia. These cells move through the mesohyl and have many functions. For example, they take up food from the surrounding water and from choanocytes, digest it, and carry nutrients to other cells. Amoebocytes also manufacture tough skeletal fibers within the mesohyl. In some sponges, these fibers are sharp spicules made from calcium carbonate or silica. Other sponges produce more flexible fibers composed of a protein called spongin; you may have seen these pliant skeletons being sold as brown bath sponges. Finally, and perhaps most importantly, amoebocytes are totipotent (capable of becoming other types of sponge cells). This gives the sponge body remarkable flexibility, enabling it to adjust its shape in response to changes in its physical environment (such as the direction of water currents).

General Characteristics of Arthropods: Over the course of evolution, the appendages of some arthropods have become modified, specializing in functions such as walking, feeding, sensory reception, reproduction, and defense. Like the appendages from which they were derived, these modified structures are jointed and come in pairs. Figure 33.31 illustrates the diverse appendages and other arthropod characteristics of a lobster.

The body of an arthropod is completely covered by the cuticle, an exoskeleton constructed from layers of protein and the polysaccharide chitin. As you know if you've ever eaten a crab or lobster, the cuticle can be thick and hard over some parts of the body and thin and flexible over others, such as the joints. The rigid exoskeleton protects the animal and provides points of attachment for the muscles that move the appendages. But it also prevents the arthropod from growing, unless it occasionally sheds its exoskeleton and produces a larger one. This molting process is energetically expensive, and it leaves the arthropod vulnerable to predation and other dangers until its new, soft exoskeleton hardens.

Chelicerates: Chelicerates (clade Chelicerata) are named for clawlike feeding appendages called chelicerae, which serve as pincers or fangs. Chelicerates lack antennae, and most have simple eyes (eyes with a single lens). The earliest chelicerates were eurypterids, or water scorpions. These marine and freshwater predators grew up to 3 m long; it is thought that some species could have walked on land, much as land crabs do today. Most of the marine chelicerates, including all of the eurypterids, are extinct. Among the marine chelicerates that survive today are the sea spiders (pycnogonids) and horseshoe crabs (Figure 33.32).

The bulk of modern chelicerates are arachnids, a group that includes scorpions, spiders, ticks, and mites (Figure 33.33). Nearly all ticks are bloodsucking parasites that live on the body surfaces of reptiles or mammals. Parasitic mites live on or in a wide variety of vertebrates, invertebrates, and plants. Arachnids have six pairs of appendages: the chelicerae; a pair of appendages called pedipalps that function in sensing, feeding, defense, or reproduction; and four pairs of walking legs. Spiders use their fang-like chelicerae, which are equipped with poison glands, to attack prey. As the chelicerae pierce the prey, the spider secretes digestive juices onto the prey's torn tissues. The food softens, and the spider sucks up the liquid meal. In most spiders, gas exchange is carried out by book lungs, stacked platelike structures contained in an internal chamber (Figure 33.34). The extensive surface area of these respiratory organs enhances the exchange of O2 and CO2 between the hemolymph and air.

Cell Structure and Specialization: Animals are eukaryotes, and like plants and most fungi, animals are multicellular. In contrast to plants and fungi, however, animals lack the structural support of cell walls. Instead, proteins external to the cell membrane provide structural support to animal cells and connect them to one another (see Figure 6.28). The most abundant of these proteins is collagen, which is not found in plants or fungi.

The cells of most animals are organized into tissues, groups of similar cells that act as a functional unit. For example, muscle tissue and nervous tissue are responsible for moving the body and conducting nerve impulses, respectively. The ability to move and conduct nerve impulses underlies many of the adaptations that differentiate animals from plants and fungi (which lack muscle and nerve cells). For this reason, muscle and nerve cells are central to the animal lifestyle.

Arthropod Origins: Biologists hypothesize that the diversity and success of arthropods are related to their body plan—their segmented body, hard exoskeleton, and jointed appendages. How did this body plan arise and what advantages did it provide?

The earliest fossils of arthropods are from the Cambrian explosion (535-525 million years ago), indicating that the arthropods are at least that old. The fossil record of the Cambrian explosion also contains many species of lobopods, a group from which arthropods may have evolved. Lobopods such as Hallucigenia (see Figure 32.7) had segmented bodies, but most of their body segments were identical to one another. Early arthropods, such as the trilobites, also showed little variation from segment to segment (Figure 33.29). As arthropods continued to evolve, groups of segments tended to become functionally united into "body regions" specialized for tasks such as feeding, walking, or swimming. These evolutionary changes resulted not only in great diversification but also in efficient body plans that permit the division of labor among different body regions.

Early signs of a skull can be seen in Myllokunmingia (see Figure 34.1). About the same size as Haikouella, Myllokunmingia had ear capsules and eye capsules, parts of the skull that surround these organs. Based on these and other characters, Myllokunmingia is considered the first chordate to have a head. The origin of a head—consisting of a brain at the anterior end of the dorsal nerve cord, eyes and other sensory organs, and a skull—enabled chordates to coordinate more complex movement and feeding behaviors. Although it had a head, Myllokunmingia lacked vertebrae and hence is not classified as a vertebrate.

The earliest fossils of vertebrates date to 500 million years ago and include those of conodonts, a group of slender, soft-bodied vertebrates that lacked jaws and whose internal skeleton was composed of cartilage. Conodonts had large eyes, which they may have used in locating prey that were then impaled on a set of barbed hooks at the anterior end of their mouth (Figure 34.11). These hooks were made of dental tissues that were mineralized—hardened by the incorporation of minerals such as calcium. The food was then passed back to the pharynx, where a different set of dental elements sliced and crushed the food.

Derived Characters of Primates: Most primates have hands and feet adapted for grasping, and their digits have flat nails instead of the narrow claws of other mammals. There are other characteristic features of the hands and feet, too, such as skin ridges on the fingers (which account for human fingerprints). Relative to other mammals, primates have a large brain and short jaws, giving them a flat face. Their forward-looking eyes are close together on the front of the face. Primates also exhibit relatively well-developed parental care and complex social behavior.

The earliest known primates were tree-dwellers, and many of the characteristics of primates are adaptations to the demands of living in the trees. Grasping hands and feet allow primates to hang onto tree branches. All living primates except humans have a big toe that is widely separated from the other toes, enabling them to grasp branches with their feet. All primates also have a thumb that is relatively movable and separate from the fingers, but monkeys and apes have a fully opposable thumb; that is, they can touch the ventral surface (fingerprint side) of the tip of all four fingers with the ventral surface of the thumb of the same hand. In monkeys and apes other than humans, the opposable thumb functions in a grasping "power grip." In humans, a distinctive bone structure at the base of the thumb allows it to be used for more precise manipulation. The unique dexterity of humans represents descent with modification from our tree-dwelling ancestors. Arboreal maneuvering also requires excellent eye-hand coordination. The overlapping visual fields of the two forward-facing eyes enhance depth perception, an obvious advantage when brachiating (traveling by swinging from branch to branch in trees).

Fungus-Animal Mutualisms: As mentioned earlier, some fungi share their digestive services with animals, helping break down plant material in the guts of cattle and other grazing mammals. Many species of ants take advantage of the digestive power of fungi by raising them in "farms." Leaf-cutter ants, for example, scour tropical forests in search of leaves, which they cannot digest on their own but carry back to their nests and feed to the fungi (Figure 31.21). As the fungi grow, their hyphae develop specialized swollen tips that are rich in proteins and carbohydrates. The ants feed primarily on these nutrient-rich tips. Not only do the fungi break down plant leaves into substances the insects can digest, but they also detoxify plant defensive compounds that would otherwise kill or harm the ants. In some tropical forests, the fungi have helped these insects become the major consumers of leaves.

The evolution of such farmer ants and that of their fungal "crops" have been tightly linked for over 50 million years. The fungi have become so dependent on their caretakers that in many cases they can no longer survive without the ants, and vice versa.

. Still others have proved difficult to classify, as they do not seem to be closely related to any living animal or algal groups. In addition to these macroscopic fossils, Neoproterozoic rocks have also yielded what may be microscopic fossils of early animal embryos. Although these microfossils appear to exhibit the basic structural organization of present-day animal embryos, debate continues about whether these fossils are indeed of animals.

The fossil record from the Ediacaran period (635-541 million years ago) also provides early evidence of predation. Consider Cloudina, a small animal whose body was protected by a shell resembling a series of nested cones (Figure 32.6). Some Cloudina fossils show signs of attack: round "bore holes" that resemble those formed today by predators that drill through the shells of their prey to gain access to the soft-bodied organisms lying within. Like Cloudina, some other small Ediacaran animals had shells or other defensive structures that may have been selected for by predators. Overall, the fossil evidence indicates that the Ediacaran was a time of increasing animal diversity—a trend that continued in the Paleozoic.

Although animals are less susceptible to parasitic fungi than are plants, about 500 fungi are known to parasitize animals. One such parasite, the chytrid Batrachochytrium dendrobatidis, has been implicated in the recent decline or extinction of about 200 species of frogs and other amphibians (Figure 31.25). This chytrid can cause severe skin infections, leading to massive die-offs. Field observations and studies of museum specimens indicate that B. dendrobatidis first appeared in frog populations shortly before their declines in Australia, Costa Rica, the United States, and other countries. In addition, in regions where it infects frogs, this chytrid has very low levels of genetic diversity. These findings are consistent with the hypothesis that B. dendrobatidis has emerged recently and spread rapidly across the globe, decimating many amphibian populations.

The general term for an infection in an animal by a fungal parasite is mycosis. In humans, skin mycoses include the disease ringworm, so named because it appears as circular red areas on the skin. Most commonly, the ascomycetes that cause ringworm grow on the feet, causing the intense itching and blisters known as athlete's foot. Though highly contagious, athlete's foot and other ringworm infections can be treated with fungicidal lotions and powders.

Figure 32.2 Early embryonic development in animals. The zygote of an animal undergoes a series of mitotic cell divisions called cleavage. An eight-cell embryo is formed by three rounds of cell division. In most animals, cleavage produces a multicellular stage called a blastula. The blastula is typically a hollow ball of cells that surround a cavity called the blastocoel. Most animals also undergo gastrulation, a process in which one end of the embryo folds inward, expands, and eventually fills the blastocoel, producing layers of embryonic tissues: the ectoderm (outer layer) and the endoderm (inner layer). The pouch formed by gastrulation, called the archenteron, opens to the outside via the blastopore. The endoderm of the archenteron develops into the tissue lining the animal's digestive tract.

The history of animals spans more than half a billion years: To date, biologists have identified 1.3 million extant species of animals, and estimates of the actual number run far higher. This vast diversity encompasses a spectacular range of morphological variation, from corals to cockroaches to crocodiles. Various studies suggest that this great diversity originated during the last billion years. For example, researchers have unearthed 710-million-year-old sediments containing chemical evidence of steroids that today are primarily produced by a particular group of sponges. Since sponges are animals, these "fossil steroids" suggest that animals had arisen by 710 million years ago.

Consider the bacterium Escherichia coli as it reproduces by binary fission in a human intestine, one of its natural environments. After repeated rounds of division, most of the offspring cells are genetically identical to the original parent cell. However, if errors occur during DNA replication, some of the offspring cells may differ genetically. The probability of such a mutation occurring in a given E. coli gene is about one in 10 million (1 * 10-7 ) per cell division. But among the 2 * 1010 new E. coli cells that arise each day in a person's intestine, there will be approximately (2 * 1010) * (1 * 10-7 ) = 2,000 bacteria that have a mutation in that gene. The total number of new mutations when all 4,300 E. coli genes are considered is about 4,300 * 2,000—more than 8 million per day per human host.

The key point is that new mutations, though rare on a per gene basis, can increase genetic diversity quickly in species with short generation times and large populations. This diversity, in turn, can lead to rapid evolution (Figure 27.10): Individuals that are genetically better equipped for their environment tend to survive and reproduce at higher rates than other individuals. The ability of prokaryotes to adapt rapidly to new conditions highlights the point that although the structure of their cells is simpler than that of eukaryotic cells, prokaryotes are not "primitive" or "inferior" in an evolutionary sense. They are, in fact, highly evolved: For 3.5 billion years, prokaryotic populations have responded successfully to many types of environmental challenges.

Once a tunicate has settled on a substrate, it undergoes a radical metamorphosis in which many of its chordate characters disappear. Its tail and notochord are resorbed; its nervous system degenerates; and its remaining organs rotate 90°. As an adult, a tunicate draws in water through an incurrent siphon; the water then passes through the pharyngeal slits into a chamber called the atrium and exits through an excurrent siphon (Figure 34.5b and c). Food particles are filtered from the water by a mucous net and transported by cilia to the esophagus. The anus empties into the excurrent siphon. Some tunicate species shoot a jet of water through their excurrent siphon when attacked, earning them the informal name of "sea squirts."

The loss of chordate characters in the adult stage of tunicates appears to have occurred after the tunicate lineage branched off from other chordates. Even the tunicate larva appears to be highly derived. For example, tunicates have nine Hox genes, whereas all other chordates studied to date—including the early-diverging lancelets—share a set of 13 Hox genes. The apparent loss of four Hox genes indicates that the chordate body plan of a tunicate larva is built using a different set of genetic controls than other chordates.

Threats to Plant Diversity: Although plants may be a renewable resource, plant diversity is not. The exploding human population and its demand for space and resources are threatening plant species across the globe. The problem is especially severe in the tropics, where more than two-thirds of the human population live and where population growth is fastest. About 63,000 km2 (15 million acres) of tropical rain forest are cleared each year (Figure 30.18), a rate that would completely eliminate the remaining 11 million km2 of tropical forests in 175 years. The loss of forests reduces the absorption of atmospheric carbon dioxide (CO2) that occurs during photosynthesis, potentially contributing to global warming. Also, as forests disappear, so do large numbers of plant species. Of course, once a species becomes extinct, it can never return.

The loss of plant species is often accompanied by the loss of insects and other rain forest animals. Scientists estimate that if current rates of loss in the tropics and elsewhere continue, 50% or more of Earth's species will become extinct within the next few centuries. Such losses would constitute a global mass extinction, rivaling the Permian and Cretaceous mass extinctions and forever changing the evolutionary history of plants (and many other organisms).

Conjugation and transfer of an F plasmid: In an Hfr cell, the F factor (dark blue) is integrated into the bacterial chromosome. Since an Hfr cell has all of the F factor genes, it can form a mating bridge with an F- cell and transfer DNA. A single strand of the F factor breaks and begins to move through the bridge. DNA replication occurs in both donor and recipient cells, resulting in double-stranded DNA (daughter strands shown in lighter color).

The mating bridge usually breaks before the entire chromosome is transferred. Crossing over at two sites (dotted lines) can result in the exchange of homologous genes (here, A+ and A-) between the transferred DNA (brown) and the recipient's chromosome (green). Cellular enzymes degrade any linear DNA not incorporated into the chromosome. The recipient cell, with a new combination of genes but no F factor, is now a recombinant F- cell. (b) Conjugation and transfer of part of an Hfr bacterial chromosome, resulting in recombination. A+/A- and B+/B- indicate alleles for gene A and gene B, respectively.

Figure 30.4 The life cycle of a pine. In most conifer species, each tree has both ovulate and pollen cones. Microsporocytes divide by meiosis, producing haploid microspores. A microspore develops into a pollen grain (a male gametophyte enclosed within the pollen wall). An ovulate cone scale has two ovules, each containing a megasporangium. Only one ovule is shown. Pollination occurs when a pollen grain reaches the ovule. The pollen grain then germinates, forming a pollen tube that slowly digests its way through the megasporangium. While the pollen tube develops, the megasporocyte undergoes meiosis, producing four haploid cells. One survives as a megaspore.

The megaspore develops into a female gametophyte that contains two or three archegonia, each of which will form an egg. By the time the eggs are mature, sperm cells have developed in the pollen tube, which extends to the female gametophyte. Fertilization occurs when sperm and egg nuclei unite. Fertilization usually occurs more than a year after pollination. All eggs may be fertilized, but usually only one zygote develops into an embryo. The ovule becomes a seed, consisting of an embryo, food supply, and seed coat.

Lichens: A lichen is a symbiotic association between a photosynthetic microorganism and a fungus in which millions of photosynthetic cells are held in a mass of fungal hyphae. Lichens grow on the surfaces of rocks, rotting logs, trees, and roofs in various forms (Figure 31.22). The photosynthetic partners are unicellular or filamentous green algae or cyanobacteria. The fungal component is most often an ascomycete, but one glomeromycete and 75 basidiomycete lichens are known. The fungus usually gives a lichen its overall shape and structure, and tissues formed by hyphae account for most of the lichen's mass. The cells of the alga or cyanobacterium generally occupy an inner layer below the lichen surface (Figure 31.23).

The merger of fungus and alga or cyanobacterium is so complete that lichens are given scientific names as though they were single organisms; to date, 17,000 lichen species have been described. As might be expected of such "dual organisms," asexual reproduction as a symbiotic unit is common. This can occur either by fragmentation of the parental lichen or by the formation of soredia (singular, soredium), small clusters of hyphae with embedded algae (see Figure 31.23). The fungi of many lichens also reproduce sexually.

Body Structure: The most common fungal body structures are multicellular filaments and single cells (yeasts). Many fungal species can grow as both filaments and yeasts, but even more grow only as filaments; relatively few species grow only as single-celled yeasts. Yeasts often inhabit moist environments, including plant sap and animal tissues, where there is a ready supply of soluble nutrients, such as sugars and amino acids.

The morphology of multicellular fungi enhances their ability to grow into and absorb nutrients from their surroundings (Figure 31.2). The bodies of these fungi typically form a network of tiny filaments called hyphae (singular, hypha). Hyphae consist of tubular cell walls surrounding the plasma membrane and cytoplasm of the cells. The cell walls are strengthened by chitin, a strong but flexible polysaccharide. Chitin-rich walls can enhance feeding by absorption. As a fungus absorbs nutrients from its environment, the concentrations of those nutrients in its cells increases, causing water to move into the cells by osmosis. The movement of water into fungal cells creates pressure that could cause them to burst if they were not surrounded by a rigid cell wall.

Applying a Molecular Clock: Dating the Origin of HIV:Researchers have used a molecular clock to date the origin of HIV infection in humans. Phylogenetic analysis shows that HIV, the virus that causes AIDS, is descended from viruses that infect chimpanzees and other primates. (Most of these viruses do not cause AIDS-like diseases in their native hosts.) When did HIV jump to humans? There is no simple answer because the virus has spread to humans more than once. The multiple origins of HIV are reflected in the variety of strains (genetic types) of the virus. HIV's genetic material is made of RNA, and like other RNA viruses, it evolves quickly.

The most widespread strain in humans is HIV-1 M. To pinpoint the earliest HIV-1 M infection, researchers compared samples of the virus from various times during the epidemic, including a sample from 1959. A comparison of gene sequences showed that the virus has evolved in a clocklike fashion. Extrapolating backward in time using the molecular clock indicates that the HIV-1 M strain first spread to humans around 1930 (Figure 26.20). A later study, which dated the origin of HIV using a more advanced molecular clock approach than that covered in this book, estimated that the HIV-1 M strain first spread to humans around 1910.

Tool Use: As you read earlier, the manufacture and use of complex tools are derived behavioral characters of humans. Determining the origin of tool use in hominin evolution is very difficult. Other apes are capable of surprisingly sophisticated tool use. Orangutans, for example, can fashion sticks into probes for retrieving insects from their nests. Chimpanzees are even more adept, using rocks to smash open food and putting leaves on their feet to walk over thorns. It's likely that early hominins were capable of this sort of simple tool use, but finding fossils of modified sticks or leaves that were used as shoes is practically impossible.

The oldest generally accepted evidence of tool use by hominins is 2.5-million-year-old cut marks on animal bones found in Ethiopia. These marks suggest that hominins cut flesh from the bones of animals using stone tools. Interestingly, the hominins whose fossils were found near the site where the bones were discovered had a relatively small brain. If these hominins, which have been named Australopithecus garhi, were in fact the creators of the stone tools used on the bones, that would suggest that stone tool use originated before the evolution of large brains in hominins.

Four Supergroups of Eukaryotes: Our understanding of the evolutionary history of eukaryotic diversity has been in flux in recent years. Not only has kingdom Protista been abandoned, but other hypotheses have been discarded as well. For example, many biologists once thought that the first lineage to have diverged from all other eukaryotes was the amitochondriate protists, organisms without conventional mitochondria and with fewer membrane-enclosed organelles than other protist groups. But recent structural and DNA data have undermined this hypothesis. Many of the so-called amitochondriate protists have been shown to have mitochondria—though reduced ones—and some of these organisms are now classified in distantly related groups

The ongoing changes in our understanding of the phylogeny of protists pose challenges to students and instructors alike. Hypotheses about these relationships are a focus of scientific activity, changing rapidly as new data cause previous ideas to be modified or discarded. We'll focus here on one current hypothesis: the four supergroups of eukaryotes shown in Figure 28.2. Because the root of the eukaryotic tree is not known, all four supergroups are shown as diverging simultaneously from a common ancestor. We know that this is not correct, but we do not know which supergroup was the first to diverge from the others. In addition, while some of the groups in Figure 28.2 are well supported by morphological and DNA data, others are more controversial. As you read this chapter, it may be helpful to focus less on the specific names of groups of organisms and more on why the organisms are important and how ongoing research is elucidating their evolutionary relationships.

Lepidosaurs: One surviving lineage of lepidosaurs is represented by two species of lizard-like reptiles called tuataras (Figure 34.29a). Fossil evidence indicates that tuatara ancestors lived at least 220 million years ago. These organisms thrived on many continents well into the Cretaceous period and reached up to a meter in length. Today, however, tuataras are found only on 30 islands off the coast of New Zealand. When humans arrived in New Zealand 750 years ago, the rats that accompanied them devoured tuatara eggs, eventually eliminating the reptiles on the main islands. The tuataras that remain on the outlying islands are about 50 cm long and feed on insects, small lizards, and bird eggs and chicks. They can live to be over 100 years old. Their future survival depends on whether their remaining habitats are kept rat-free.

The other major living lineage of lepidosaurs consists of the lizards and snakes, or squamates, which number about 7,900 species (Figure 34.29b and c). Many squamates are small; the Jaragua lizard, discovered recently in the Dominican Republic, is only 16 mm long—small enough to fit comfortably on a dime. In contrast, the Komodo dragon of Indonesia is a lizard that can reach a length of 3 m. It hunts deer and other large prey, delivering venom with its bite. Snakes descended from lizards with legs—hence they are classified as legless lizards (see the opening paragraphs of Chapter 26). Today, some species of snakes retain vestigial pelvic and limb bones, providing evidence of their ancestry. Despite their lack of legs, snakes are quite proficient at moving on land, most often by producing waves of lateral bending that pass from head to tail. Force exerted by the bends against solid objects pushes the snake forward. Snakes can also move by gripping the ground with their belly scales at several points along the body while the scales at intervening points are lifted slightly off the ground and pulled forward.

The Origin of Tetrapods: As you have read, the Devonian coastal wetlands were home to a wide range of lobe-fins. Those that entered shallow, oxygen-poor water could have used their lungs to breathe air. Some species probably used their stout fins to swim and "walk" underwater across the bottom (moving their fins in an alternating gait, as do some living lobe-fins). This suggests that the tetrapod body plan did not evolve "out of nowhere" but was simply a modification of a preexisting body plan.

The recent discovery of a fossil called Tiktaalik provided new details on how this process of modification occurred (Figure 34.20). Like a fish, this species had fins, gills, and lungs, and its body was covered in scales. But unlike a fish, Tiktaalik had a full set of ribs that would have helped it breathe air and support its body. Also unlike a fish, Tiktaalik had a neck and shoulders, allowing it to move its head about. In addition, the bones of Tiktaalik's front fin have the same basic pattern found in all limbed animals: one bone (the humerus), followed by two bones (the radius and ulna), followed by a group of small bones that comprise the wrist.

Homo ergaster marks an important shift in the relative sizes of the sexes. In primates, a size difference between males and females is a major component of sexual dimorphism (see Concept 23.4). On average, male gorillas and orangutans weigh about twice as much as females of their species. In Australopithecus afarensis, males were 1.5 times as heavy as females. The extent of sexual dimorphism decreased further in early Homo, a trend that continues through our own species: Human males weigh only about 1.2 times as much as females

The reduced sexual dimorphism may offer some clues to the social systems of extinct hominins. In extant primates, extreme sexual dimorphism is associated with intense malemale competition for multiple females. In species that undergo more pair-bonding (including our own), sexual dimorphism is less dramatic. In H. ergaster, therefore, males and females may have engaged in more pair-bonding than earlier hominins did.

Most apicomplexans have intricate life cycles with both sexual and asexual stages. Those life cycles often require two or more host species for completion. For example, Plasmodium, the parasite that causes malaria, lives in both mosquitoes and humans (Figure 28.16). Historically, malaria has rivaled tuberculosis as the leading cause of human death by infectious disease. The incidence of malaria was diminished in the 1960s by insecticides that reduced carrier populations of Anopheles mosquitoes and by drugs that killed Plasmodium in humans. But the emergence of resistant varieties of both Anopheles and Plasmodium has led to a resurgence of malaria. About 200 million people in the tropics are currently infected, and 600,000 die each year. In regions where malaria is common, the lethal effects of this disease have resulted in the evolution of high frequencies ofthe sickle-cell allele; for an explanation of this connection, see Figure 23.18.

The search for malarial vaccines has been hampered by the fact that Plasmodium lives mainly inside cells, hidden from the host's immune system. And, like trypanosomes, Plasmodium continually changes its surface proteins. Even so, significant progress was made in 2015, when European regulators approved the world's first licensed malarial vaccine. However, this vaccine, which targets a protein on the surface of sporozoites, provides only partial protection against malaria. As a result, researchers continue to study other potential vaccine targets, including the apicoplast. This approach may be effective because the apicoplast is a modified plastid; as such, it descended from a cyanobacterium and hence has different metabolic pathways from those in the human patients.

Flatworms: Flatworms (phylum Platyhelminthes) live in marine, freshwater, and damp terrestrial habitats. In addition to free-living species, flatworms include many parasitic species, such as flukes and tapeworms. Flatworms are so named because they have thin bodies that are flattened dorsoventrally (between the dorsal and ventral surfaces); the word platyhelminth means "flat worm." (Note that worm is not a formal taxonomic name but rather refers to a grade of animals with long, thin bodies.)

The smallest flatworms are nearly microscopic free-living species, while some tapeworms are more than 20 m long. Although flatworms undergo triploblastic development, they are acoelomates (animals that lack a body cavity). Their flat shape increases their surface area, placing all their cells close to water in the surrounding environment or in their gut. Because of this proximity to water, gas exchange and the elimination of nitrogenous waste (ammonia) can occur by diffusion across the body surface. As shown in Figure 33.9, a flat shape is one of several structural features that maximize surface area and have arisen (by convergent evolution) in different groups of animals and other organisms.

The two-sided symmetry of a shovel is an example of bilateral symmetry (Figure 32.8b). A bilateral animal has two axes of orientation: front to back and top to bottom. Such animals have a dorsal (top) side and a ventral (bottom) side, a left side and a right side, and an anterior (front) end and a posterior (back) end. Nearly all animals with a bilaterally symmetrical body plan (such as arthropods and mammals) have sensory equipment concentrated at their anterior end, including a central nervous system ("brain") in the head.

The symmetry of an animal generally fits its lifestyle. Many radial animals are sessile (living attached to a substrate) or planktonic (drifting or weakly swimming, such as jellies, commonly called jellyfishes). Their symmetry equips them to meet the environment equally well from all sides. In contrast, bilateral animals typically move actively from place to place. Most bilateral animals have a central nervous system that enables them to coordinate the complex movements involved in crawling, burrowing, flying, or swimming. Fossil evidence indicates that these two fundamentally different kinds of symmetry have existed for at least 550 million years.

Our discussion of humans brings this unit on biological diversity to an end. But keep in mind that our sequence of topics isn't meant to imply that life consists of a ladder leading from lowly microorganisms to lofty humanity. Biological diversity is the product of branching phylogeny, not ladderlike "progress." The fact that there are almost as many species of ray-finned fishes alive today as in all other vertebrate groups combined shows that our finned relatives are not outmoded underachievers that failed to leave the water.

The tetrapods—amphibians, reptiles, and mammals—are derived from one lineage of lobe-finned vertebrates. As tetrapods diversified on land, fishes continued their branching evolution in the greatest portion of the biosphere's volume. Similarly, the ubiquity of diverse prokaryotes throughout the biosphere today is a reminder of the enduring ability of these relatively simple organisms to keep up with the times through adaptive evolution. Biology exalts life's diversity, past and present.

The second lineage of living lobe-fins, the lungfishes (Dipnoi), is represented today by six species in three genera, all of which are found in the Southern Hemisphere. Lungfishes arose in the ocean but today are found only in fresh water, generally in stagnant ponds and swamps. They surface to gulp air into lungs connected to their pharynx. Lungfishes also have gills, which are the main organs for gas exchange in Australian lungfishes. When ponds shrink during the dry season, some lungfishes can burrow into the mud and estivate (wait in a state of torpor; see Concept 40.4).

The third lineage of lobe-fins that survives today is far more diverse than the coelacanths or the lungfishes. During the mid-Devonian, these organisms adapted to life on land and gave rise to vertebrates with limbs and feet, called tetrapods—a lineage that includes humans.

Another way to harness prokaryotes is bioremediation, the use of organisms to remove pollutants from soil, air, or water. For example, anaerobic bacteria and archaea decompose the organic matter in sewage, converting it to material that can be used as landfill or fertilizer after chemical sterilization. Other bioremediation applications include cleaning up oil spills (Figure 27.23) and precipitating radioactive material (such as uranium) out of groundwater.

The usefulness of prokaryotes largely derives from their diverse forms of nutrition and metabolism. All this metabolic versatility evolved prior to the appearance of the structural novelties that heralded the evolution of eukaryotic organisms, discussed in the rest of this unit.

When the name Chondrichthyes was first coined in the 1800s, scientists thought that chondrichthyans represented an early stage in the evolution of the vertebrate skeleton and that mineralization had evolved only in more derived lineages (such as "bony fishes"). However, as armored jawless vertebrates demonstrate, the mineralization of the vertebrate skeleton had already begun before the chondrichthyan lineage branched off from other vertebrates. Moreover, bone-like tissues have been found in early chondrichthyans, such as the fin skeleton of a shark that lived in the Carboniferous period. Traces of bone can also be found in living chondrichthyans—in their scales, at the base of their teeth, and, in some sharks, in a thin layer on the surface of their vertebrae. Such findings indicate that the restricted distribution of bone in the chondrichthyan body is a derived condition, emerging after chondrichthyans diverged from other gnathostomes.

There are about 1,000 species of living chondrichthyans. The largest and most diverse group consists of the sharks, rays, and skates (Figure 34.15a and b). A second group is composed of a few dozen species of ratfishes, also called chimaeras (Figure 34.15c). Most sharks have a streamlined body and are swift swimmers, but they do not maneuver very well. Powerful movements of the trunk and the tail fin propel them forward. The dorsal fins function mainly as stabilizers, and the paired pectoral (fore) and pelvic (hind) fins are important for maneuvering. Although a shark gains buoyancy by storing a large amount of oil in its huge liver, the animal is still more dense than water, and if it stops swimming it sinks. Continual swimming also ensures that water flows into the shark's mouth and out through the gills, where gas exchange occurs. However, some sharks and many skates and rays spend a good deal of time resting on the seafloor. When resting, they use muscles of their jaws and pharynx to pump water over the gills.

Ray-Finned Fishes and Lobe-Fins: The vast majority of vertebrates belong to the clade of gnathostomes called Osteichthyes. Unlike chondrichthyans, nearly all living osteichthyans have an ossified (bony) endoskeleton with a hard matrix of calcium phosphate. Like many other taxonomic names, the name Osteichthyes ("bony fish") was coined long before the advent of phylogenetic systematics. When it was originally defined, the group excluded tetrapods, but we now know that such a taxon would be paraphyletic (see Figure 34.2). Therefore, systematists today include tetrapods along with bony fishes in the clade Osteichthyes. Clearly, the name of the group does not accurately describe all of its members.

This section discusses the aquatic osteichthyans known informally as fishes. Most fishes breathe by drawing water over four or five pairs of gills located in chambers covered by a protective bony flap called the operculum (Figure 34.16). Water is drawn into the mouth, through the pharynx, and out between the gills by movement of the operculum and contraction of muscles surrounding the gill chambers.

Protecting Freshwater and Terrestrial Molluscs: Species extinction rates have increased dramatically in the last 400 years, raising concern that a sixth, human-caused mass extinction may be under way (see Concept 25.4). Among the many taxa under threat, molluscs have the dubious distinction of being the animal group with the largest number of documented extinctions (Figure 33.22).

Threats to molluscs are especially severe in two groups, freshwater bivalves and terrestrial gastropods. For example, the pearl mussels, a group of freshwater bivalves that can make natural pearls (gems that form when a mussel or oyster secretes layers of a lustrous coating around a grain of sand or other small irritant), are among the world's most endangered animals. Roughly 10% of the 300 pearl mussel species that once lived in North America have become extinct in the last 100 years, and over two-thirds of those that remain are threatened by extinction. Terrestrial gastropods, such as the snail in Figure 33.22, are faring no better. Hundreds of Pacific island land snails have disappeared since 1800. Overall, more than 50% of the Pacific island land snails are extinct or under imminent threat of extinction.

Finally, a 2014 study found that Tiktaalik's pelvis and rear fin were larger and more robust than those of a fish; the pelvis is the bony structure to which hind limbs are attached in tetrapods. Although it is unlikely that Tiktaalik could walk on land, the skeletal structure of its fins and pelvis suggests that it could prop itself up and walk in water on its fins. Since Tiktaalik predates the oldest known tetrapod, its features suggest that key "tetrapod" traits, such as a wrist, ribs, and a neck, were in fact ancestral to the tetrapod lineage.

Tiktaalik and other extraordinary fossil discoveries have allowed paleontologists to reconstruct how fins became progressively more limb-like over time, culminating in the appearance in the fossil record of the first tetrapods 365 million years ago (Figure 34.21). Over the next 60 million years, a great diversity of tetrapods arose. Some of these species retained functional gills and had weak limbs, while others had lost their gills and had stronger limbs that facilitated walking on land. Overall, judging from the morphology and locations of their fossils, most of these early tetrapods probably remained tied to water, a characteristic they share with some members of the most basal group of living tetrapods, the amphibians.

Endosymbiosis in Eukaryotic Evolution: What gave rise to the enormous diversity of protists that exist today? There is abundant evidence that much of protistan diversity has its origins in endosymbiosis, a relationship between two species in which one organism lives inside the cell or cells of another organism (the host). In particular, as we discussed in Concept 25.3, structural, biochemical,and DNA sequence data indicate that mitochondria and plastids are derived from prokaryotes that were engulfed by the ancestors of early eukaryotic cells. The evidence also suggests that mitochondria evolved before plastids. Thus, a defining moment in the origin of eukaryotes occurred when a host cell engulfed a bacterium that would later become an organelle found in all eukaryotes—the mitochondrion.

To determine which prokaryotic lineage gave rise to mitochondria, researchers have compared the DNA sequences of mitochondrial genes (mtDNA) to those found in major clades of bacteria and archaea. In the Scientific Skills Exercise, you will interpret one such set of DNA sequence comparisons.

Life Cycles with Dominant Sporophytes: As mentioned earlier, mosses and other bryophytes have life cycles dominated by gametophytes (see Figure 29.7). Fossil evidence suggests that a change began to develop in some of the earliest vascular plants, whose gametophytes and sporophytes were about equal in size. Further reductions in gametophyte size occurred among extant vascular plants; in these groups, the sporophyte generation is the larger and more complex form in the alternation of generations (Figure 29.12). In ferns, for example, the familiar leafy plants are the sporophytes. You would have to get down on your hands and knees and search the ground carefully to find fern gametophytes, which are tiny structures that often grow on or just below the soil surface.

Transport in Xylem and Phloem: Vascular plants have two types of vascular tissue: xylem and phloem. Xylem conducts most of the water and minerals. The xylem of most vascular plants includes tracheids, tubeshaped cells that carry water and minerals up from the roots (see Figure 35.10). The water-conducting cells in vascular plants are lignified; that is, their cell walls are strengthened by the polymer lignin. The tissue called phloem has cells arranged into tubes that distribute sugars, amino acids, and other organic products (see Figure 35.10).

Parasitic Species: More than half of the known species of rhabditophorans live as parasites in or on other animals. Many have suckers that attach to the internal organs or outer surfaces of the host animal. In most species, a tough covering helps protect the parasites within their hosts. We'll discuss two ecologically and economically important subgroups of parasitic rhabditophorans, the trematodes and the tapeworms.

Trematodes: As a group, trematodes parasitize a wide range of hosts, and most species have complex life cycles with alternating sexual and asexual stages. Many trematodes require an intermediate host in which larvae develop before infecting the final host (usually a vertebrate), where the adult worms live. For example, various trematodes that parasitize humans spend part of their lives in snail hosts (Figure 33.11). Around the world, about 200 million people are infected with trematodes called blood flukes (Schistosoma) and suffer from schistosomiasis, a disease whose symptoms include pain, anemia, and diarrhea. Living within more than one kind of host puts demands on trematodes that free-living animals don't face. A blood fluke, for instance, must evade the immune systems of both snails and humans. By mimicking the surface proteins of its hosts, the blood fluke creates a partial immunological camouflage for itself. It also releases molecules that manipulate the hosts' immune systems into tolerating the parasite's existence. These defenses are so effective that individual blood flukes can survive in humans for more than 40 years.

Figure 34.6 Expression of developmental genes in lancelets and vertebrates. Hox genes (including BF1, Otx, and Hox3) control the development of major regions of the vertebrate brain. These genes are expressed in the same anterior-to-posterior order in lancelets and vertebrates. Each colored bar is positioned above the portion of the brain whose development that gene controls.

Tunicates: Recent molecular studies indicate that the tunicates (Urochordata) are more closely related to other chordates than are lancelets. The chordate characters of tunicates are most apparent during their larval stage, which may be as brief as a few minutes (Figure 34.5a). In many species, the larva uses its tail muscles and notochord to swim through water in search of a suitable substrate on which it can settle, guided by cues it receives from light- and gravity-sensitive cells.

Snakes are carnivorous, and a number of adaptations aid them in hunting and eating prey. They have acute chemical sensors, and though they lack eardrums, they are sensitive to ground vibrations, which helps them detect the movements of prey. Heat-detecting organs between the eyes and nostrils of pit vipers, including rattlesnakes, are sensitive to minute temperature changes, enabling these night hunters to locate warm animals. Venomous snakes inject their toxin through a pair of sharp teeth that may be hollow or grooved. The flicking tongue is not venomous but helps fan odors toward olfactory (smell) organs on the roof of the mouth. Loosely articulated jawbones and elastic skin enable most snakes to swallow prey larger than the diameter of the snake's head (see Figure 23.14). We'll conclude our survey of the reptiles by discussing the three clades of archosaurs with living members: The turtles, the crocodilians, and the birds.

Turtles: Turtles are one of the most distinctive groups of reptiles alive today. For example, turtles do not have any holes in their skull behind the eye sockets, whereas other reptiles have two holes behind each eye socket. Recall that such skull holes are a key derived trait of the diapsids. Thus, until recently it was not clear whether turtles—like all other living reptiles— should be classified within the diapsid clade. However, in 2015, new fossil discoveries showed that early turtles had the skull openings found in other diapsids. This suggests that turtles are diapsids that have lost the holes in their skull over the course of evolution. The diapsid affinity of turtles was also confirmed by recent phylogenomic studies showing that turtles are archosaurs, more closely related to crocodilians and birds than to other reptiles (see Figure 34.25).

As for tunicates, several of their genomes have been completely sequenced and can be used to identify genes likely to have been present in early chordates. Researchers have suggested that ancestral chordates had genes associated with vertebrate organs such as the heart and thyroid gland. These genes are found in tunicates and vertebrates but are absent from nonchordate invertebrates. In another example, a 2015 study found that tunicates (but not lancelets) have embryonic cells that have some of the characteristics of the neural crest, a derived trait found in all vertebrates (see Figure 34.7). This suggests that embryonic cells similar to those in tunicates may represent an intermediate cell population from which the vertebrate neural crest evolved.

Vertebrates are chordates that have a backbone: During the Cambrian period, half a billion years ago, a lineage of chordates gave rise to vertebrates. With a skeletal system and a more complex nervous system than that of their ancestors, vertebrates became more efficient at two essential tasks: capturing food and avoiding being eaten.

Conodonts were extremely abundant for 300 million years. Their fossilized dental elements are so plentiful that they have been used for decades by petroleum geologists as guides to the age of rock layers in which they search for oil.

Vertebrates with additional innovations emerged during the Ordovician, Silurian, and Devonian periods (485-359 million years ago). These vertebrates had paired fins and, as in lampreys, an inner ear with two semicircular canals that provided a sense of balance. Like conodonts, these vertebrates lacked jaws, but they had a muscular pharynx, which they may have used to suck in bottom-dwelling organisms or detritus. They were also armored with mineralized bone, which covered varying amounts of their body and may have offered protection from predators (Figure 34.12). There were many species of these jawless, armored swimming vertebrates, but they all became extinct by the end of the Devonian.

Figure 30.15 A bee pollinating a bilaterally symmetrical flower. To harvest nectar (a sugary solution secreted by flower glands) from this Scottish broom flower, a honeybee must land as shown. This releases a tripping mechanism that arches the flower's stamens over the bee and dusts it with pollen. Later, some of this pollen may rub off onto the stigma of the next flower of this species that the bee visits.

Walking through a pine forest in Switzerland, you might spot some small reddish mushrooms in the genus Russula scattered here and there beneath the towering trees (Figure 31.1). These little mushrooms are just the aboveground portion of a vast network of filaments located beneath the forest floor. As they grow, these fungal filaments absorb nutrients, some of which they transfer to the roots of trees. In turn, the trees provide the fungi with sugars produced in photosynthesis. A 2016 study found that these fungal filaments can even transfer sugars between the trees of different species. Thus, sugars produced by one tree might actually nourish the cells of nearby trees—adding a new level of complexity to our understanding of life in a forest.

The Origin and Diversification of Plants: The algae most closely related to plants include many unicellular species and small colonial species. Since it is likely that the first plants were similarly small, the search for the earliest fossils of plants has focused on the microscopic world. As mentioned earlier, microorganisms colonized land as early as 1.2 billion years ago. But the microscopic fossils that document life on land changed dramatically 470 million years ago with the appearance of spores from early plants.

What distinguishes these spores from those of algae or fungi? One clue comes from their chemical composition, which matches the composition of plant spores today but differs from that of the spores of other organisms. In addition, the walls of these ancient spores have structural features that today are found only in the spores of certain plants (liverworts). And in rocks dating to 450 million years ago, researchers have discovered similar spores embedded in plant cuticle material that resembles spore-bearing tissue in living plants (Figure 29.4).

Fossil Angiosperms: Angiosperms are now thought to have originated in the early Cretaceous period, about 140 million years ago. By the mid-Cretaceous (100 million years ago), angiosperms began to dominate some terrestrial ecosystems. Landscapes changed dramatically as conifers and other gymnosperms gave way to flowering plants in many parts of the world. The Cretaceous ended 66 million years ago with mass extinctions of dinosaurs and many other animal groups and with further increases in the diversity and importance of angiosperms.

What evidence suggests that angiosperms arose 140 million years ago? First, although pollen grains are common in rocks from the Jurassic period (201 to 145 million years ago), none of these pollen fossils have features characteristic of angiosperms, suggesting that angiosperms may have originated after the Jurassic. Indeed, the earliest fossils with distinctive angiosperm features are of 130-million-year-old pollen grains discovered in China, Israel, and England. Early fossils of larger flowering plant structures include those of Archaefructus (Figure 30.13) and Leefructus, both of which were discovered in China in rocks that are about 125 million years old. Overall, early angiosperm fossils indicate that the group arose and began to diversify over a 20- to 30-million-year period—a less sudden event than was suggested by the fossils known during Darwin's lifetime.

About ten years before the discovery of H. naledi, researchers reported another astonishing find: skeletal remains of adult hominins dating from just 18,000 years ago and representing a previously unknown species, Homo floresiensis. Discovered in a limestone cave on the Indonesian island of Flores, the individuals were much shorter and had a much smaller brain volume than H. sapiens—more similar, in fact, to an australopith. The researchers who discovered these fossils argue that certain features of the skeletons, such as the shape of the teeth and the thickness and proportions of the skull, suggest that H. floresiensis descended from the larger H. erectus. Not convinced, some researchers have argued that the fossils represent small H. sapiens individuals with a disorder such as Down syndrome or microcephaly (a condition in which a person has a deformed, miniature brain).

While the issue remains controversial, most studies have supported the designation of H. floresiensis as a new hominin. One such study found that the wrist bones of the Flores fossils are similar in shape to those of nonhuman apes and early hominins, but different from those of Neanderthals and H. sapiens. These researchers concluded that the Flores fossils represent a species whose lineage branched off before the origin of the clade that includes Neanderthals and humans. A different study comparing the foot bones of the Flores fossils with those of other hominins also concluded that H. floresiensis arose before H. sapiens; in fact, these researchers suggested that H. floresiensis may have descended from an as-yet-unidentified hominin that lived even earlier than H. erectus. Finally, in a 2015 paper that analyzed hominin tooth morphologies, other researchers argued that H. floresiensis was a distinct species that was closely related to H. erectus. Compelling questions that may yet be answered from the anthropological and archaeological finds on Flores include how H. floresiensis originated and whether it encountered H. sapiens, which also was living in Indonesia 18,000 years ago.

The rapid expansion of our species may have been spurred by changes in human cognition as H. sapiens evolved in Africa. Evidence of sophisticated thought in H. sapiens includes the recent discovery in South Africa of 77,000-year-old art— geometric markings made on pieces of ochre (Figure 34.54). Similarly, archaeologists working in southern and eastern Africa recently found 75,000-year-old ostrich eggs and snail shells with holes neatly drilled through them. By 30,000 years ago, humans were producing spectacular cave paintings.

While these developments can help us understand the spread of H. sapiens, it is not clear whether they played a role in the extinction of other hominins. Neanderthals, for example, also made complex tools and showed a capacity for symbolic thought. As a result, while some scientists have suggested that Neanderthals were driven to extinction by competition with H. sapiens, others question that idea.

Diatoms: A key group of photosynthetic protists, diatoms are unicellular algae that have a unique glass-like wall made of silicon dioxide embedded in an organic matrix (Figure 28.10). The wall consists of two parts that overlap like a shoe box and its lid. These walls provide effective protection from the crushing jaws of predators: Live diatoms can withstand pressures as great as 1.4 million kg/m2 , equal to the pressure under each leg of a table supporting an elephant!

With an estimated 100,000 living species, diatoms are a highly diverse group of protists (see Figure 28.2). They are among the most abundant photosynthetic organisms both in the ocean and in lakes: One bucket of water scooped from the surface of the sea may contain millions of these microscopic algae. The abundance of diatoms in the past is also evident in the fossil record, where massive accumulations of fossilized diatom walls are major constituents of sediments known as diatomaceous earth. These sediments are mined for their quality as a filtering medium and for many other uses.

Diatoms are so widespread and abundant that their photosynthetic activity affects global carbon dioxide (CO2) levels. Diatoms have this effect in part because of events that occur during episodes of rapid population growth, or blooms, when ample nutrients are available. Typically, diatoms are eaten by a variety of protists and invertebrates, but during a bloom, many escape this fate. When these uneaten diatoms die, their bodies sink to the ocean floor. It takes decades, or even centuries, for diatoms that sink to the ocean floor to be broken down by bacteria and other decomposers. As a result, the carbon in their bodies remains there for some time, rather than being released immediately as CO2 as the decomposers respire. The overall effect of these events is that CO2 absorbed by diatoms during photosynthesis is transported, or "pumped," to the ocean floor.

With an eye toward reducing global warming by lowering atmospheric CO2 levels, some scientists advocate promoting diatom blooms by fertilizing the ocean with essential nutrients such as iron. In a 2012 study, researchers found that CO2 was indeed pumped to the ocean floor after iron was added to a small region of the ocean. Further tests are planned to examine whether iron fertilization has undesirable side effects (such as oxygen depletion or the production of nitrous oxide, a more potent greenhouse gas than CO2).

Figure 34.19 A coelacanth (Latimeria). These lobe-fins were found living off the coasts of southern Africa and Indonesia. Figure 34.18 A reconstruction of an ancient lobe-fin. Discovered in 2009, Guiyu oneiros is the earliest known lobe-fin, dating to 420 million years ago. The fossil of this species was nearly complete, allowing for an accurate reconstruction; regions shown in gray were missing from the fossil.

Yellowfin tuna (Thunnus albacares) is a fast-swimming, schooling fish that is commercially important worldwide. ▶ Native to coral reefs of the Pacific Ocean, the brightly colored red lionfish (Pterois volitans) can inject venom through its spines, causing a severe and painful reaction in humans. ▲ The sea horse has a highly modified body form, as exemplified by Hippocampus ramulosus, shown above. Sea horses are unusual among animals in that the male carries the young during their embryonic development. ▲ The fine-spotted moray eel (Gymnothorax dovii) is a predator that ambushes prey from crevices in its coral reef habitat Figure 34.17 Ray-finned fishes (Actinopterygii).

Living Primates: There are three main groups of living primates: (1) the lemurs of Madagascar (Figure 34.43) and the lorises and bush babies of tropical Africa and southern Asia; (2) the tarsiers, which live in southeastern Asia; and (3) the anthropoids, which include monkeys and apes and are found worldwide. The first group—lemurs, lorises, and bush babies— probably resemble early arboreal primates. The oldest known tarsier fossils date to 55 million years ago; along with DNA evidence, these fossils indicate that tarsiers are more closely related to anthropoids than to the lemur group (Figure 34.44).

You can see in Figure 34.44 that monkeys do not form a clade but rather consist of two groups, the New and Old World monkeys. Both of these groups are thought to have originated in Africa or Asia. The fossil record indicates that New World monkeys first colonized South America roughly 25 million years ago. By that time, South America and Africa had drifted apart, and monkeys may have reached South America from Africa by rafting on logs or other debris. What is certain is that New World monkeys and Old World monkeys underwent separate adaptive radiations during their many millions of years of separation (Figure 34.45). All species of New World monkeys are arboreal, whereas Old World monkeys include ground-dwelling as well as arboreal species. Most monkeys in both groups are diurnal (active during the day) and usually live in bands held together by social behavior.

As discussed earlier, molecular evidence indicates that some chytrid lineages diverged early in fungal evolution. The fact that chytrids are unique among fungi in having flagellated spores, called zoospores (Figure 31.11), supports this hypothesis. Like other fungi, chytrids (other than those in the recently discovered cryptomycota clade) have cell walls made of chitin, and they also share certain key enzymes and metabolic pathways with other fungal groups. Some chytrids form colonies with hyphae, while others exist as single spherical cells.

Zygomycetes: There are approximately 1,000 known species of zygomycetes, fungi in the phylum Zygomycota. This diverse phylum includes species of fast-growing molds responsible for causing foods such as bread, peaches, strawberries, and sweet potatoes to rot during storage. Other zygomycetes live as parasites or as commensal (neutral) symbionts of animals. The life cycle of Rhizopus stolonifer (black bread mold) is fairly typical of zygomycete species (Figure 31.12). Its hyphae spread out over the food surface, penetrate it, and absorb nutrients. The hyphae are coenocytic, with septa found only where reproductive cells are formed. In the asexual phase, bulbous black sporangia develop at the tips of upright hyphae. Within each sporangium, hundreds of genetically identical haploid spores develop and are dispersed through the air. Spores that happen to land on moist food germinate, growing into new mycelia.

If environmental conditions deteriorate—for instance, if the mold consumes all its food—Rhizopus may reproduce sexually. The parents in a sexual union are mycelia of different mating types, which possess different chemical markers but may appear identical. Plasmogamy produces a sturdy structure called a zygosporangium (plural, zygosporangia), in which karyogamy and then meiosis occur. Note that while a zygosporangium represents the zygote (2n) stage in the life cycle, it is not a zygote in the usual sense (that is, a cell with one diploid nucleus). Rather, a zygosporangium is a multinucleate structure, first heterokaryotic with many haploid nuclei from the two parents, then with many diploid nuclei after karyogamy.

Zygosporangia are resistant to freezing and drying and are metabolically inactive. When conditions improve, the nuclei of the zygosporangium undergo meiosis, the zygosporangium germinates into a sporangium, and the sporangium releases genetically diverse haploid spores that may colonize a new substrate. Some zygomycetes, such as Pilobolus, can actually "aim" and then shoot their sporangia toward bright light (Figure 31.13).

Bacteria: As surveyed in Figure 27.16, bacteria include the vast majority of prokaryotic species familiar to most people, from the pathogenic species that cause strep throat and tuberculosis to the beneficial species used to make Swiss cheese and yogurt. Every major mode of nutrition and metabolism is represented among bacteria, and even a small taxonomic group of bacteria may contain species exhibiting many different nutritional modes. As we'll see, the diverse nutritional and metabolic capabilities of bacteria—and archaea—are behind the great impact these organisms have on Earth and its life.

figure 27.16 Exploring Selected Major Groups of Bacteria Proteobacteria: This large and diverse clade of gram-negative bacteria includes photoautotrophs, chemoautotrophs, and heterotrophs. Some are anaerobic, while others are aerobic. Molecular systematists currently recognize five subgroups of proteobacteria; the phylogenetic tree at right shows their relationships based on molecular data.

Figure 33.4 Anatomy of a sponge. In the main diagram, portions of the front and back wall are cut away to show the sponge's internal structure.: Mesohyl. The wall of this sponge consists of two layers of cells separated by a gelatinous matrix, the mesohyl ("middle matter"). Epidermis. The outer layer consists of tightly packed epidermal cells. Pores. Water enters the sponge through pores formed by doughnutshaped cells that span the body wall. Spongocoel. Water passing through pores enters a cavity called the spongocoel. Choanocytes. The spongocoel is lined with flagellated cells called choanocytes. By beating flagella, the choanocytes create a current that draws water in through the pores and out through the osculum.

the movement of a choanocyte's flagellum also draws water through its collar of finger-like projections. Food particles are trapped in the mucus that coats the projections, engulfed by phagocytosis, and either digested or transferred to amoebocytes. Amoebocytes. These cells can transport nutrients to other cells of the sponge body, produce materials for skeletal fibers (spicules), or become any type of sponge cell as needed.

A unique adaptation of many spiders is the ability to catch insects by constructing webs of silk, a liquid protein produced by specialized abdominal glands. The silk is spun by organs called spinnerets into fibers that then solidify. Each spider engineers a web characteristic of its species and builds it perfectly on the first try, indicating that this complex behavior is inherited. Various spiders also use silk in other ways: as droplines for rapid escape, as a cover for eggs, and even as "gift wrap" for food that males offer females during courtship. Many small spiders also extrude silk into the air and let themselves be transported by wind, a behavior known as "ballooning."

▲ Scorpions have pedipalps that are pincers special- ized for defense and the capture of food. The tip of the tail bears a poisonous stinger. ▲ Dust mites are ubiquitous scavengers in human dwellings but are harmless except to those people who are allergic to them (colorized SEM). ◀ Web-building spiders are generally most active during the daytime. Figure 33.33 Arachnids.

Eudicots: More than two-thirds of angiosperm species are eudicots —roughly 170,000 species. The largest group is the legume family, which includes such crops as peas and beans. Also important economically is the rose family, which includes many plants with ornamental flowers as well as some species with edible fruits, such as strawberry plants and apple and pear trees. Most of the familiar flowering trees are eudicots, such as oak, walnut, maple, willow, and birch.

◀ Snow pea (Pisum sativum), a legume ◀ Pyrenean oak (Quercus pyrenaica) Dog rose (Rosa canina), a wild rose

▶ Douglas fir. This evergreen tree (Pseudotduga menziesii) provides more timber than any other North American tree species. Some uses include house framing, plywood, pulpwood for paper, railroad ties, and boxes and crates. ▶ Common juniper. The "berries" of the common juniper (Juniperus communis) are actually ovuleproducing cones consisting of fleshy sporophylls. ◀ European larch. The needle-like leaves of this deciduous conifer (Larix decidua) turn yellow before they are shed in autumn. Native to the mountains of central Europe, including Switzerland's Matterhorn, depicted here, this species is extremely cold-tolerant, able to survive winter temperatures that plunge to -50°C.

◀ Wollemi pine. Survivors of a conifer group once known only from fossils, living Wollemi pines (Wollemia nobilis) were discovered in 1994 in a national park near Sydney, Australia. At that time, the species consisted of 40 known trees. As a result of conservation efforts, it is now widely propagated. The inset photo compares the leaves of this "living fossil" with actual fossils. ▶ Sequoia. This giant sequoia (Sequoiadendron giganteum) in California's Sequoia National Park weighs about 2,500 metric tons, equivalent to about 24 blue whales (the largest animals) or 40,000 people. The giant sequoia is one of the largest living organisms and also among the most ancient, with some individuals estimated to be between 1,800 and 2,700 years old. Their cousins, the coast redwoods (Sequoia sempervirens), grow to heights of more than 110 m (taller than the Statue of Liberty) and are found only in a narrow coastal strip of northern California and southern Oregon. ▶ Bristlecone pine. This species (Pinus longaeva), which is found in the White Mountains of California, includes some of the oldest living organisms, reaching ages of more than 4,600 years. One tree (not shown here) is called Methuselah because it may be the word's oldest living tree. To protect the tree, scientists keep its location a secret.

Figure 26.14 Branch lengths can indicate time. This tree is based on the same DNA data as that in Figure 26.13, but here the branch points are dated based on fossil evidence. Thus, the branch lengths are proportional to time. Each lineage has the same total length from the base of the tree to the branch tip, indicating that all the lineages have diverged from the common ancestor for equal amounts of time.

A maximum likelihood approach identifies the tree most likely to have produced a given set of DNA data, based on certain probability rules about how DNA sequences change over time. For example, the underlying probability rules could be based on the assumption that all nucleotide substitutions are equally likely. However, if evidence suggests that this assumption is not correct, more complex rules could be devised to account for different rates of change among different nucleotides or at different positions in a gene. Scientists have developed many computer programs to search for trees that are parsimonious and likely. When a large amount of accurate data is available, the methods used in these programs usually yield similar trees. As an example of one method, Figure 26.15 walks you through the process of identifying the most parsimonious molecular tree for a three-species problem. Computer programs use the principle of parsimony to estimate phylogenies in a similar way: They examine large numbers of possible trees and identify those that require the fewest evolutionary changes.

Figure 27.11 Transduction. Phages may carry pieces of a bacterial chromosome from one cell (the donor) to another (the recipient). If crossing over occurs after the transfer, genes from the donor may be incorporated into the recipient's genome.

A phage infects a bacterial cell that carries the A+ and B+ alleles on its chromosome (brown). This bacterium will be the "donor" cell. The phage DNA is replicated, and the cell makes many copies of phage proteins (represented as purple dots). Certain phage proteins halt the synthesis of proteins encoded by the host cell's DNA, and the host cell's DNA may be fragmented, as shown here. As new phage particles assemble, a fragment of bacterial DNA carrying the A+ allele happens to be packaged in a phage capsid. The phage carrying the A+ allele from the donor cell infects a recipient cell with alleles A- and B-. Crossing over at two sites (dotted lines) allows donor DNA (brown) to be incorporated into recipient DNA (green) The genotype of the resulting recombinant cell (A+B-) differs from the genotypes of both the donor (A+B+) and the recipient (A-B-).

Maximum Parsimony and Maximum Likelihood: As the database of DNA sequences that enables us to study more species grows, the difficulty of building the phylogenetic tree that best describes their evolutionary history also grows. What if you are analyzing data for 50 species? There are 3 * 1076 different ways to arrange 50 species into a tree! And which tree in this huge forest reflects the true phylogeny? Systematists can never be sure of finding the most accurate tree in such a large data set, but they can narrow the possibilities by applying the principles of maximum parsimony and maximum likelihood.

According to the principle of maximum parsimony, we should first investigate the simplest explanation that is consistent with the facts. (The parsimony principle is also called "Occam's razor" after William of Occam, a 14th-century English philosopher who advocated this minimalist problem-solving approach of "shaving away" unnecessary complications.) In the case of trees based on morphology, the most parsimonious tree requires the fewest evolutionary events, as measured by the origin of sharedderived morphological characters. For phylogenies based on DNA, the most parsimonious tree requires the fewest base changes.

Gene Duplications and Gene Families: What do molecular data reveal about the evolutionary history of genome change? Consider gene duplication, which plays a particularly important role in evolution because it increases the number of genes in the genome, providing more opportunities for further evolutionary changes. Molecular techniques now allow us to trace the phylogenies of gene duplications. These molecular phylogenies must account for repeated duplications that have resulted in gene families, groups of related genes within an organism's genome (see Figure 21.11).

Accounting for such duplications leads us to distinguish two types of homologous genes (Figure 26.18): orthologous genes and paralogous genes. In orthologous genes (from the Greek orthos, exact), the homology is the result of a speciation event and hence occurs between genes found in different species (see Figure 26.18a). For example, the genes that code for cytochrome c (a protein that functions in electron transport chains) in humans and dogs are orthologous. In paralogous genes (from the Greek para, in parallel), the homology results from gene duplication; hence, multiple copies of these genes have diverged from one another within a species (see Figure 26.18b). In Concept 23.1, you encountered the example of olfactory receptor genes, which have undergone many gene duplications in vertebrates; humans have 380 functional copies of these paralogous genes, while mice have 1,200.

The genome of a prokaryote is structurally different from a eukaryotic genome and in most cases has considerably less DNA. Prokaryotes generally have circular chromosomes (Figure 27.9), whereas eukaryotes have linear chromosomes. In addition, in prokaryotes the chromosome is associated with many fewer proteins than are the chromosomes of eukaryotes. Also unlike eukaryotes, prokaryotes lack a nucleus; their chromosome is located in the nucleoid, a region of cytoplasm that is not enclosed by a membrane. In addition to its single chromosome, a typical prokaryotic cell may also have much smaller rings of independently replicating DNA molecules called plasmids (see Figure 27.9), most carrying only a few genes.

Although DNA replication, transcription, and translation are fundamentally similar processes in prokaryotes and eukaryotes, some of the details are different (see Chapter 17). For example, prokaryotic ribosomes are slightly smaller than eukaryotic ribosomes and differ in their protein and RNA content. These differences allow certain antibiotics, such as erythromycin and tetracycline, to bind to ribosomes and block protein synthesis in prokaryotes but not in eukaryotes. As a result, people can use these antibiotics to kill or inhibit the growth of bacteria without harming themselves.

Figure 26.16 A phylogenetic tree of birds and their close relatives. († indicates extinct lineages.) Figure 26.17 Fossil support for a phylogenetic prediction: Dinosaurs built nests and brooded their eggs. (a)Fossil remains of Oviraptor and eggs. The orientation of the bones, which surround and cover the eggs, suggests that the dinosaur died while incubating or protecting its eggs. (b) ) Artist's reconstruction of the dinosaur's posture based on the fossil findings.

An organism's evolutionary history is documented in its genome: As you have seen in this chapter, comparisons of nucleic acids or other molecules can be used to deduce relatedness. In some cases, such comparisons can reveal phylogenetic relationships that cannot be determined by nonmolecular methods such as comparative anatomy. For example, the analysis of molecular data helps us uncover evolutionary relationships between groups that have little common ground for morphological comparison, such as animals and fungi. And molecular methods allow us to reconstruct phylogenies among groups of present-day organisms for which the fossil record is poor or lacking entirely.

Look closely at the organism in Figure 26.1. Although it resembles a snake, this animal is actually a legless lizard known as the European glass lizard (Ophisaurus apodus). Why isn't this glass lizard considered a snake? More generally, how do biologists distinguish and categorize the millions of species on Earth?

An understanding of evolutionary relationships suggests one way to address these questions: We can decide in which category to place a species by comparing its traits with those of potential close relatives. For example, the glass lizard does not have a highly mobile jaw, a large number of vertebrae, or a short tail located behind the anus, three traits shared by all snakes. These and other characteristics suggest that despite a superficial resemblance, the glass lizard is not a snake.

Evolutionary Origins of Bacterial Flagella: The bacterial flagellum shown in Figure 27.7 has three main parts (the motor, hook, and filament) that are themselves composed of 42 different kinds of proteins. How could such a complex structure evolve? In fact, much evidence indicates that bacterial flagella originated as simpler structures that were modified in a stepwise fashion over time. As in the case of the human eye (see Concept 25.6), biologists asked whether a less complex version of the flagellum could still benefit its owner.

Analyses of hundreds of bacterial genomes indicate that only half of the flagellum's protein components appear to be necessary for it to function; the others are inessential or not encoded in the genomes of some species. Of the 21 proteins required by all species studied to date, 19 are modified versions of proteins that perform other tasks in bacteria. For example, a set of 10 proteins in the motor is homologous to 10 similar proteins in a secretory system found in bacteria. (A secretory system is a protein complex that enables a cell to produce and release certain macromolecules.) Two other proteins in the motor are homologous to proteins that function in ion transport. The proteins that comprise the rod, hook, and filament are all related to each other and are descended from an ancestral protein that formed a piluslike tube. These findings suggest that the bacterial flagellum evolved as other proteins were added to an ancestral secretory system. This is an example of exaptation, the process in which structures originally adapted for one function take on new functions through descent with modification.

Potential Problems with Molecular Clocks: As we've seen, molecular clocks do not run as smoothly as would be expected if the underlying mutations were selectively neutral. Many irregularities are likely to be the result of natural selection in which certain DNA changes are favored over others. Indeed, evidence suggests that almost half the amino acid differences in proteins of two Drosophila species, D. simulans and D. yakuba, are not neutral but have resulted from natural selection. But because the direction of natural selection may change repeatedly over long periods of time (and hence may average out), some genes experiencing selection can nevertheless serve as approximate markers of elapsed time.

Another question arises when researchers attempt to extend molecular clocks beyond the time span documented by the fossil record. Although an abundant fossil record extends back only about 550 million years, molecular clocks have been used to date evolutionary divergences that occurred a billion or more years ago. These estimates assume that the clocks have been constant for all that time. Such estimates are highly uncertain.

Phylogenies show evolutionary relationships: Organisms share many characteristics because of common ancestry (see Concept 22.3). As a result, we can learn a great deal about a species if we know its evolutionary history. For example, an organism is likely to share many of its genes, metabolic pathways, and structural proteins with its close relatives. We'll consider practical applications of such information later in this section, but first we'll examine how organisms are named and classified, the scientific discipline of taxonomy. We'll also look at how we can interpret and use diagrams that represent evolutionary history.

Binomial Nomenclature: Common names for organisms—such as monkey, finch, and lilac—convey meaning in casual usage, but they can also cause confusion. Each of these names, for example, refers to more than one species. Moreover, some common names do not accurately reflect the kind of organism they signify. Consider these three "fishes": jellyfish (a cnidarian), crayfish (a small, lobsterlike crustacean), and silverfish (an insect). And, of course, a given organism has different names in different languages

In our analysis, a character found in both the outgroup and the ingroup is assumed to be ancestral. We'll also assume that each derived character in Figure 26.12a arose only once in the ingroup. Thus, for a character that only occurs in a subset of the ingroup, we'll assume that the character arose in the lineage leading to those members of the ingroup.

By comparing members of the ingroup with each other and with the outgroup, we can determine which characters were derived at the various branch points of vertebrate evolution. In our example, all of the vertebrates in the ingroup have backbones: This character was present in the ancestral vertebrate, but not in the outgroup. Now note that hinged jaws are absent in the outgroup and in lampreys, but present in all other members of the ingroup. This indicates that hinged jaws arose in a lineage leading to all members of the ingroup except lampreys. Hence, we can conclude that lampreys are the sister taxon to the other vertebrates in the ingroup. Proceeding in this way, we can translate the data in our table of characters into a phylogenetic tree that places all the ingroup taxa into a hierarchy based on their shared derived characters (Figure 26.12b).

Figure 27.2 The most common shapes of prokaryotes. (a) Cocci (singular, coccus) are spherical prokaryotes. They occur singly, in pairs (diplococci), in chains of many cells (streptococci), and in clusters resembling bunches of grapes (staphylococci). (b) Bacilli (singular, bacillus) are rod-shaped prokaryotes. They are usually solitary, but in some forms the rods are arranged in chains (streptobacilli). (c) Spiral prokaryotes include spirilla, which range from comma-like shapes to loose coils, and spirochetes (shown here), which are corkscrew-shaped (colorized SEMs).

Cell-Surface Structures: A key feature of nearly all prokaryotic cells is the cell wall, which maintains cell shape, protects the cell, and prevents it from bursting in a hypotonic environment (see Figure 7.12). In a hypertonic environment, most prokaryotes lose water and shrink away from their wall (plasmolyze). Such water losses can inhibit cell reproduction. Thus, salt can be used to preserve foods because it causes food-spoiling prokaryotes to lose water, preventing them from rapidly multiplying.

Prokaryotes play crucial roles in the biosphere: If people were to disappear from the planet tomorrow, life on Earth would change for many species, but few would be driven to extinction. In contrast, prokaryotes are so important to the biosphere that if they were to disappear, the prospects of survival for many other species would be dim..

Chemical Recycling: The atoms that make up the organic molecules in all living things were at one time part of inorganic substances in the soil, air, and water. Sooner or later, those atoms will return to the nonliving environment. Ecosystems depend on the continual recycling of chemical elements between the living and nonliving components of the environment, and prokaryotes play a major role in this process. For example, some chemoheterotrophic prokaryotes function as decomposers, breaking down dead organisms as well as waste products and thereby unlocking supplies of carbon, nitrogen, and other elements. Without the actions of prokaryotes and other decomposers such as fungi, life as we know it would cease. (See Concept 55.4 for a detailed discussion of chemical cycles.)

Subgroup: Epsilon Proteobacteria: Most species in this subgroup are pathogenic to humans or other animals. Epsilon proteobacteria include Campylobacter, which causes blood poisoning and intestinal inflammation, and Helicobacter pylori, which causes stomach ulcers. Helicobacter pylori (colorized TEM)

Chlamydias: These parasites can survive only within animal cells, depending on their hosts for resources as basic as ATP. The gram-negative walls of chlamydias are unusual in that they lack peptidoglycan. One species, Chlamydia trachomatis, is the most common cause of blindness in the world and also causes nongonococcal urethritis, the most common sexually transmitted disease in the United States. Chlamydia (arrows) inside an animal cell (colorized TEM)

Shared characters are used to construct phylogenetic trees: As we've discussed, a key step in reconstructing phylogenies is to distinguish homologous features from analogous ones (since only homology reflects evolutionary history). Next, we'll describe cladistics, a widely used set of methods for inferring phylogeny from homologous characters.

Cladistics: In the approach to systematics called cladistics, common ancestry is the primary criterion used to classify organisms. Using this methodology, biologists attempt to place species into groups called clades, each of which includes an ancestral species and all of its descendants. Clades, like taxonomic categories of the Linnaean system, are nested within larger clades. In Figure 26.4, for example, the cat group (Felidae) represents a clade within a larger clade (Carnivora) that also includes the dog group (Canidae).

Spirochetes: These helical gram-negative heterotrophs spiral through their environment by means of rotating, internal, flagellum-like filaments. Many spirochetes are free-living, but others are notorious pathogenic parasites: Treponema pallidum causes syphilis, and Borrelia burgdorferi causes Lyme disease.Leptospira, a spirochete (colorized TEM)

Cyanobacteria: These gram-negative photoautotrophs are the only prokaryotes with plantlike, oxygen-generating photosynthesis. (In fact, chloroplasts are thought to have evolved from an endosymbiotic cyanobacterium.) Both solitary and filamentous cyanobacteria are abundant components of freshwater and marine phytoplankton, the collection of photosynthetic organisms that drift near the water's surface. Some filaments have cells specialized for nitrogen fixation, the process that incorporates atmospheric N2 into inorganic compounds that can be used in the synthesis of amino acids and other organic molecules. Oscillatoria, a filamentous cyanobacterium

Figure 26.19 A molecular clock for mammals. The number of accumulated mutations in seven proteins has increased over time in a consistent manner for most mammal species. The three green data points represent primate species, whose proteins appear to have evolved more slowly than those of other mammals. The divergence time for each data point was based on fossil evidence.

Differences in Clock Speed: What causes such differences in the speed at which clocklike genes evolve? The answer stems from the fact that some mutations are selectively neutral—neither beneficial nor detrimental. Of course, many new mutations are harmful and are removed quickly by selection. But if most of the rest are neutral and have little or no effect on fitness, then the rate of evolution of those neutral mutations should indeed be regular, like a clock. Differences in the clock rate for different genes are related to how important a gene is. If the exact sequence of amino acids that a gene specifies is essential to survival, most of the mutational changes will be harmful and only a few will be neutral. As a result, such genes change only slowly. But if the exact sequence of amino acids is less critical, fewer of the new mutations will be harmful and more will be neutral. Such genes change more quickly.

Figure 26.7 Convergent evolution in burrowers. A long body, large front paws, small eyes, and a pad of thick skin that protects the nose all evolved independently in these species

Evaluating Molecular Homologies: Comparing DNA molecules often poses technical challenges for researchers. The first step after sequencing the molecules is to align comparable sequences from the species being studied. If the species are very closely related, the sequences probably differ at only one or a few sites. In contrast, comparable nucleic acid sequences in distantly related species usually have different bases at many sites and may have different lengths. This is because insertions and deletions accumulate over long periods of time.

R Plasmids and Antibiotic Resistance :During the 1950sin Japan, physicians started noticing that some hospital patients with bacterial dysentery, which produces severe diarrhea, did not respond to antibiotics that had been effective in the past. Apparently, resistance to these antibiotics had evolved in some strains of Shigella, the bacterium that causes the disease. Eventually, researchers began to identify the specific genes that confer antibiotic resistance in Shigella and other pathogenic bacteria. Sometimes mutation in a chromosomal gene of the pathogen can confer resistance. For example, a mutation in one gene may make it less likely that the pathogen will transport a particular antibiotic into its cell. Mutation in a different gene may alter the intracellular target protein for an antibiotic molecule, reducing its inhibitory effect. In other cases, bacteria have "resistance genes," which code for enzymes that specifically destroy or otherwise hinder the effectiveness of certain antibiotics, such as tetracycline or ampicillin. Such resistance genes are often carried by plasmids known as R plasmids (R for resistance).

Exposing a bacterial population to a specific antibiotic will kill antibiotic-sensitive bacteria but not those that happen to have R plasmids with genes that counter the antibiotic. Under these circumstances, we would predict that natural selection would cause the fraction of the bacterial population carrying genes for antibiotic resistance to increase, and that is exactly what happens. The medical consequences are also predictable: Resistant strains of pathogens are becoming more common, making the treatment of certain bacterial infections more difficult. The problem is compounded by the fact that many R plasmids, like F plasmids, have genes that encode pili and enable DNA transfer from one bacterial cell to another by conjugation. Making the problem still worse, some R plasmids carry genes for resistance to as many as ten antibiotics.

Figure 27.17 Extreme thermophiles. Orange and yellow colonies of thermophilic prokaryotes grow in the hot water of Yellowstone National Park's Grand Prismatic Spring.

Extreme thermophiles (from the Greek thermos, hot) thrive in very hot environments (Figure 27.17). For example, archaea in the genus Sulfolobus live in sulfur-rich volcanic springs as hot as 90°C. At temperatures this high, the cells of most organisms die because their DNA does not remain in a double helix and many of their proteins denature. Sulfolobus and other extreme thermophiles avoid this fate because they have structural and biochemical adaptations that make their DNA and proteins stable at high temperatures. One extreme thermophile that lives near deep-sea hot springs called hydrothermal vents is informally known as "strain 121," since it can reproduce even at 121°C. Another extreme thermophile, Pyrococcus furiosus, is used in biotechnology as a source of DNA polymerase for the PCR technique (see Figure 20.8).

Shared Ancestral and Shared Derived Characters: As a result of descent with modification, organisms have characters they share with their ancestors, and they also have characters that differ from those of their ancestors. For example, all mammals have backbones, but a backbone does not distinguish mammals from other vertebrates because all vertebrates have backbones. The backbone predates the branching of mammals from other vertebrates. Thus for mammals, the backbone is a shared ancestral character, a character that originated in an ancestor of the taxon. In contrast, hair is a character shared by all mammals but not found in their ancestors. Thus, in mammals, hair is considered a shared derived character, an evolutionary novelty unique to a clade.

Figure 26.11 Examples of a paraphyletic and a polyphyletic group. This group is paraphyletic because it does not include all the descendants of the common ancestor (it excludes cetaceans). This group is polyphyletic because it does not include the most recent common ancestor of its members.

Phylogenetic Trees with Proportional Branch Lengths: In the phylogenetic trees we have presented so far, the lengths of the tree's branches do not indicate the degree of evolutionary change in each lineage. Furthermore, the chronology represented by the branching pattern of the tree is relative (earlier versus later) rather than absolute (how many millions of years ago). But in some tree diagrams, branch lengths are proportional to amount of evolutionary change or to the times at which particular events occurred.

Figure 26.12 Using derived characters to infer phylogeny. The derived characters used here include the amnion, a membrane that encloses the embryo inside a fluid-filled sac (see Figure 34.26). Note that a different set of characters could lead us to infer a different phylogenetic tree.

Different genes can evolve at different rates, even in the same evolutionary lineage. As a result, molecular trees can represent short or long periods of time, depending on which genes are used. For example, the DNA that codes for ribosomal RNA (rRNA) changes relatively slowly. Therefore, comparisons of DNA sequences in these genes are useful for investigating relationships between taxa that diverged hundreds of millions of years ago. Studies of rRNA sequences indicate, for instance, that fungi are more closely related to animals than to plants. In contrast, mitochondrial DNA (mtDNA) evolves relatively rapidly and can be used to explore recent evolutionary events. One research team has traced the relationships among Native American groups through their mtDNA sequences. The molecular findings corroborate other evidence that the Pima of Arizona, the Maya of Mexico, and the Yanomami of Venezuela are closely related, probably descending from the first of three waves of immigrants that crossed the Bering Land Bridge from Asia to the Americas about 15,000 years ago.

Figure 26.18 Two types of homologous genes. Colored bands mark regions of the genes where differences in base sequences have accumulated. (a) Formation of orthologous genes: a product of speciation b) Formation of paralogous genes: within a species

To avoid ambiguity when communicating about their research, biologists refer to organisms by Latin scientific names. The two-part format of the scientific name, commonly called a binomial, was instituted in the 18th century by Carolus Linnaeus (see Concept 22.1). The first part of a binomial is the name of the genus (plural, genera) to which the species belongs. The second part, called the specific epithet, is unique for each species within the genus. An example of a binomial is Panthera pardus, the scientific name for the leopard. Notice that the first letter of the genus is capitalized and the entire binomial is italicized. (Newly created scientific names are also "latinized": You can name an insect you discover after a friend, but you must add a Latin ending.) Many of the more than 11,000 binomials assigned by Linnaeus are still used today, including the optimistic name he gave our own species—Homo sapiens, meaning "wise man."

Figure 26.2 Convergent evolution of limbless bodies. A phylogeny based on DNA sequence data reveals that a legless body form evolved independently from legged ancestors in the lineages leading to the glass lizard and to snakes.

Our understanding of the tree of life continues to change based on new data : The discovery that the glass lizard in Figure 26.1 evolved from a different lineage of legless lizards than did snakes is one example of how our understanding of life's diversity is informed by systematics. Indeed, in recent decades, systematists have gained insight into even the very deepest branches of the tree of life by analyzing DNA sequence data.

Figure 26.20 Dating the origin of HIV-1 M. The black data points are based on DNA sequences of an HIV gene in patients' blood samples. (The dates when these individual HIV gene sequences arose are not certain because a person can harbor the virus for years before symptoms occur.) Projecting the gene's rate of change backward in time by this method suggests that the virus originated in the 1930s

Figure 26.23 A tangled web of life. Horizontal gene transfer may have been so common in the early history of life that the base of a "tree of life" might be more accurately portrayed as a tangled web. Figure 26.22 A recipient of transferred genes: the alga Galdieria sulphuraria. Genes received from prokaryotes enable G. sulphuraria (inset) to grow in extreme environments, including on sulfur-encrusted rocks around volcanic hot springs similar to this one in Yellowstone National Park.

Figure 26.21 The three domains of life. This phylogenetic tree is based on sequence data for rRNA and other genes. For simplicity, only some of the major branches in each domain are shown. Lineages within Eukarya that are dominated by multicellular organisms (plants, fungi, and animals) are in red type, while the two lineages denoted by an asterisk are based on DNA from cellular organelles. All other lineages consist solely or mainly of single-celled organisms. Note: A branch point leading to multiple lineages is called a polytomy, an unresolved pattern of divergence. COMMON ANCESTOR OF ALL LIFE

Classifying species is a way to structure our human view of the world. We lump together various species of trees to which we give the common name of pines and distinguish them from other trees that we call firs. Taxonomists have decided that pines and firs are different enough to be placed in separate genera, yet similar enough to be grouped into the same family, Pinaceae. As with pines and firs, higher levels of classification are usually defined by particular characters chosen by taxonomists. However, characters that are useful for classifying one group of organisms may not be appropriate for other organisms. For this reason, the larger categories often are not comparable between lineages; that is, an order of snails does not exhibit the same degree of morphological or genetic diversity as an order of mammals. As we'll see, the placement of species into orders, classes, and so on also does not necessarily reflect evolutionary history.

Figure 26.3 Linnaean classification. At each level, or "rank," species are placed in groups within more inclusive groups. Figure 26.4 The connection between classification and phylogeny. Hierarchical classification can reflect the branching patterns of phylogenetic trees. This tree shows evolutionary relationships between some of the taxa within order Carnivora, itself a branch of class Mammalia.

Figure 26.6 Inquiry What is the species identity of food being sold as whale meat? Experiment C. S. Baker and S. R. Palumbi purchased 13 samples of "whale meat" from Japanese fish markets. They sequenced part of the mitochondrial DNA (mtDNA) from each sample and compared their results with the comparable mtDNA sequence from known whale species. To infer the species identity of each sample, the team constructed a gene tree, a phylogenetic tree that shows patterns of relatedness among DNA sequences rather than among taxa. Results Of the species in the resulting gene tree, only Minke whales caught in the Southern Hemisphere can be sold legally in Japan. Conclusion This analysis indicated that mtDNA sequences of six of the unknown samples (in red) were most closely related to mtDNA sequences of whales that are not legal to harvest.

Figure 26.5 Visualizing Phylogenetic Relationships Memorize this figure.

Just as with morphological characters, it is necessary to distinguish homology from analogy in evaluating molecular similarities for evolutionary studies. Two sequences that resemble each other at many points along their length most likely are homologous (see Figure 26.8). But in organisms that do not appear to be closely related, the bases that their otherwise very different sequences happen to share may simply be coincidental matches, called molecular homoplasies. For example, if the two DNA sequences in Figure 26.9 were from distantly related organisms, the fact that they share 23% of their bases would be coincidental. Statistical tools have been developed to determine whether DNA sequences that share more than 25% of their bases do so because they are homologous.

Figure 26.8 Aligning segments of DNA. Systematists search for similar sequences along DNA segments from two species (only one DNA strand is shown for each species). In this example, 11 of the original 12 bases have not changed since the species diverged. Hence, those portions of the sequences still align once the length is adjusted. These homologous DNA sequences are identical as species 1 and species 2 begin to diverge from their common ancestor. Deletion and insertion mutations shift what had been matching sequences in the two species. Of the regions of the species 2 sequence that match the species 1 sequence, those shaded orange no longer align because of these mutations. The matching regions realign after a computer program adds gaps in sequence 1.

Figure 27.12 Bacterial conjugation. The E. coli donor cell (left) extends a pilus that attaches to a recipient cell, a key first step in the transfer of DNA. The pilus is a flexible tube of protein subunits (TEM)

Figure 27.13 Conjugation and recombination in E. coli. The DNA replication that accompanies transfer of an F plasmid or part of an Hfr bacterial chromosome is called rolling circle replication. In effect, the intact circular parental DNA strand "rolls" as its other strand peels off and a new complementary strand is synthesized. 1)A cell carrying an F plasmid (an F+ cell) forms a mating bridge with an F- cell. One strand of the plasmid's DNA breaks at the point marked by the arrowhead. 2) Using the unbroken strand as a template, the cell synthesizes a new strand (light blue). Meanwhile, the broken strand peels off (red arrow), and one end enters the F- cell. There synthesis of its complementary strand begins. 3) DNA replication continues in both the donor and recipient cells, as the transferred plasmid strand moves farther into the recipient cell. 4)Once DNA transfer and synthesis are completed, the plasmid in the recipient cell circularizes. The recipient cell is now a recombinant F+ cell. (a)Conjugation and transfer of an F plasmid

Another important lesson from molecular systematics is that horizontal gene transfer has played a key role in the evolution of prokaryotes. Over hundreds of millions of years, prokaryotes have acquired genes from even distantly related species, and they continue to do so today. As a result, significant portions of the genomes of many prokaryotes are actually mosaics of genes imported from other species. For example, a study of 329 sequenced bacterial genomes found that an average of 75% of the genes in each genome had been transferred horizontally at some point in their evolutionary history. As we saw in Concept 26.6, such gene transfers can make it difficult to determine phylogenetic relationships. Still, it is clear that for billions of years, the prokaryotes have evolved in two separate lineages, the bacteria and the archaea (see Figure 27.15).

Figure 27.15 A simplified phylogeny of prokaryotes. This tree shows relationships among major prokaryotic groups based on molecular data; some of these relationships are shown as polytomies to reflect their uncertain order of divergence. Recent studies indicate that within Archaea, the thaumarchaeotes, aigarchaeotes, crenarchaeotes, and korarchaeotes are closely related; systematists have placed them in a supergroup called "TACK" in reference to the first letters of their names.

Figure 27.18 Impact of bacteria on soil nutrient availability. Pine seedlings grown in sterile soils to which one of three strains of the bacterium Burkholderia glathei had been added absorbed more potassium (K+ ) than did seedlings grown in soil without any bacteria. Other results (not shown) demonstrated that strain 3 increased the amount of K+ released from mineral crystals to the soil.

Figure 27.19 Mutualism: bacterial "headlights." The glowing oval below the eye of the flashlight fish (Photoblepharon palpebratus) is an organ harboring bioluminescent bacteria. The fish uses the light to attract prey and to signal potential mates. The bacteria receive nutrients from the fish.

Finally, some prokaryotes stick to their substrate or to one another by means of hairlike appendages called fimbriae (singular, fimbria) (Figure 27.6). For example, the bacterium that causes gonorrhea, Neisseria gonorrhoeae, uses fimbriae to fasten itself to the mucous membranes of its host. Fimbriae are usually shorter and more numerous than pili (singular, pilus), appendages that pull two cells together prior to DNA transfer from one cell to the other (see Figure 27.12); pili are sometimes referred to as sex pili.

Figure 27.4 Capsule. The polysaccharide capsule around this Streptococcus bacterium enables the prokaryote to attach to cells in the respiratory tract—in this colorized TEM, a tonsil cell. Figure 27.5 An endospore. Bacillus anthracis, the bacterium that causes the disease anthrax, produces endospores (TEM). An endospore's protective, multilayered coat helps it survive in the soil for years. Figure 27.6 Fimbriae. These numerous protein-containing appendages enable some prokaryotes to attach to surfaces or to other cells (colorized TEM).

Figure 27.7 A prokaryotic flagellum. The motor of a prokaryotic flagellum consists of a system of rings embedded in the cell wall and plasma membrane (TEM). The electron transport chain pumps protons out of the cell. The diffusion of protons back into the cell provides the force that turns a curved hook and thereby causes the attached filament to rotate and propel the cell. (This diagram shows flagellar structures characteristic of gram-negative bacteria.)

Figure 27.9 A prokaryotic chromosome and plasmids. The thin, tangled loops surrounding this ruptured Escherichia coli cell are parts of the cell's large, circular chromosome (colorized TEM). Three of the cell's plasmids, the much smaller rings of DNA, are also shown

Ecological Interactions: Prokaryotes play a central role in many ecological interactions. Consider symbiosis (from a Greek word meaning "living together"), an ecological relationship in which two species live in close contact with each other. Prokaryotes often form symbiotic associations with much larger organisms. In general, the larger organism in a symbiotic relationship is known as the host, and the smaller is known as the symbiont. There are many cases in which a prokaryote and its host participate in mutualism, an ecological interaction between two species in which both benefit (Figure 27.19). Other interactions take the form of commensalism, an ecological relationship in which one species benefits while the other is not harmed or helped in any significant way.

For example, more than 150 bacterial species live on the outer surface of your body, covering portions of your skin with up to 10 million cells per square centimeter. Some of these species are commensalists: You provide them with food, such as the oils that exude from your pores, and a place to live, while they neither harm nor benefit you. Finally, some prokaryotes engage in parasitism, an ecological relationship in which a parasite eats the cell contents, tissues, or body fluids of its host. As a group, parasites harm but usually do not kill their host, at least not immediately (unlike a predator). Parasites that cause disease are known as pathogens, many of which are prokaryotic. (We'll discuss mutualism, commensalism, and parasitism in greater detail in Concept 54.1.)

In some cases, problems may be avoided by calibrating molecular clocks with data on the rates at which genes have evolved in different taxa. In other cases, problems may be avoided by using many genes rather than just using one or a few genes. By using many genes, fluctuations in evolutionary rate due to natural selection or other factors that vary over time may average out.

For example, one group of researchers constructed molecular clocks of vertebrate evolution from published sequence data for 658 nuclear genes. Despite the broad period of time covered (nearly 600 million years) and the fact that natural selection probably affected some of these genes, their estimates of divergence times agreed closely with fossil-based estimates. As this example suggests, if used with care, molecular clocks can aid our understanding of evolutionary relationships.

Sorting Homology from Analogy: A potential source of confusion in constructing a phylogeny is similarity between organisms that is due to convergent evolution— called analogy—rather than to shared ancestry (homology). Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages.

For example, the two mole-like animals shown in Figure 26.7 look very similar. However, their internal anatomy, physiology, and reproductive systems are very dissimilar. Indeed, genetic and fossil evidence indicate that the common ancestor of these animals lived 140 million years ago. This common ancestor and most of its descendants were not mole-like. It appears that analogous characteristics evolved independently in these two lineages as they became adapted to similar lifestyles—hence, the similar features of these animals should not be considered when reconstructing their phylogeny.

Note that orthologous genes can only diverge after speciation has taken place, that is, after the genes are found in separate gene pools. For example, although the cytochrome c genes in humans and dogs serve the same function, the gene's sequence in humans has diverged from that in dogs in the time since these species last shared a common ancestor. Paralogous genes, on the other hand, can diverge within a species because they are present in more than one copy in the genome. The paralogous genes that make up the olfactory receptor gene family in humans have diverged from each other during our long evolutionary history. They now specify proteins that confer sensitivity to a wide variety of molecules, ranging from food odors to sex pheromones.

Genome Evolution: Now that we can compare the entire genomes of different organisms, including our own, two patterns have emerged. First, lineages that diverged long ago often share many orthologous genes. For example, though the human and mouse lineages diverged about 65 million years ago, 99% of the genes of humans and mice are orthologous. And 50% of human genes are orthologous with those of yeast, despite 1 billion years of divergent evolution. Such commonalities explain why disparate organisms nevertheless share many biochemical and developmental pathways. As a result of these shared pathways, the functioning of genes linked to diseases in humans can often be investigated by studying yeast and other organisms distantly related to humans.

What causes trees based on data from different genes to yield such different results? Comparisons of complete genomes from the three domains show that there have been substantial movements of genes between organisms in the different domains. These took place through horizontal gene transfer, a process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids, viral infection (see Concept 19.2), and perhaps fusions of organisms (as when a host and its endosymbiont become a single organism). Recent research reinforces the view that horizontal gene transfer is important. For example, one study found that on average, 80% of the genes in 181 prokaryotic genomes had moved between species at some point during the course of evolution. Because phylogenetic trees are based on the assumption that genes are passed vertically from one generation to the next, the occurrence of such horizontal transfer events helps to explain why trees built using different genes can give inconsistent results.

Horizontal gene transfer can also occur between eukaryotes. For example, over 200 cases of the horizontal transfer of transposons have been reported in eukaryotes, including humans and other primates, plants, birds, and lizards. Nuclear genes have also been transferred horizontally from one eukaryote to another. The Scientific Skills Exercise describes one such example, giving you the opportunity to interpret data collected by Nancy Moran on the transfer of a pigment gene to an aphid from another species.

From Two Kingdoms to Three Domains: Taxonomists once classified all known species into two kingdoms: plants and animals. Classification schemes with more than two kingdoms gained broad acceptance in the late 1960s, when many biologists recognized five kingdoms: Monera (prokaryotes), Protista (a diverse kingdom consisting mostly of unicellular organisms), Plantae, Fungi, and Animalia. This system highlighted the two fundamentally different types of cells, prokaryotic and eukaryotic, and set the prokaryotes apart from all eukaryotes by placing them in their own kingdom, Monera.

However, phylogenies based on genetic data soon revealed a problem with this system: Some prokaryotes differ as much from each other as they do from eukaryotes. Such difficulties led biologists to adopt a three-domain system. The three domains— Bacteria, Archaea, and Eukarya—are a taxonomic level higher than the kingdom level. The validity of these domains has been supported by many studies, including a recent study that analyzed nearly 100 completely sequenced genomes.

What We Can and Cannot Learn from Phylogenetic Trees: Regardless of how groups are named, a phylogenetic tree represents a hypothesis about evolutionary relationships (Figure 26.5). These relationships often are depicted as a series of dichotomies, or two-way branch points. Each branch point represents the common ancestor of the two evolutionary lineages diverging from it.

In Figure 26.5, each tree has a branch point that represents the common ancestor of the lineages leading to chimpanzees and humans. Chimps and humans are considered sister taxa, groups of organisms that share an immediate common ancestor that is not shared by any other group. The members of a sister group are each other's closest relatives, making sister groups a useful way to describe the evolutionary relationships shown in a tree. For example, in Figure 26.5, the evolutionary lineage leading to lizards shares an immediate common ancestor with the lineage leading to chimpanzees and humans. Thus, we can describe this portion of the tree by saying that of the groups shown here, lizards are the sister taxon to a group consisting of chimpanzees and humans. As also shown in Figure 26.5, the branches of a tree can be rotated around branch points without changing the relationships shown in the tree. That is, the order in which the taxa appear at the right side of the tree does not represent a sequence of evolution—in this case, it does not imply a sequence leading from fishes to humans.

The cell wall of many prokaryotes is surrounded by a sticky layer of polysaccharide or protein. This layer is called a capsule if it is dense and well-defined (Figure 27.4) or a slime layer if it is not as well organized. Both kinds of sticky outer layers enable prokaryotes to adhere to their substrate or to other individuals in a colony. Some capsules and slime layers protect against dehydration, and some shield pathogenic prokaryotes from attacks by their host's immune system.

In another way of withstanding harsh conditions, certain bacteria develop resistant cells called endospores when they lack water or essential nutrients (Figure 27.5). The original cell produces a copy of its chromosome and surrounds that copy with a multilayered structure, forming the endospore. Water is removed from the endospore, and its metabolism halts. The original cell then lyses, releasing the endospore. Most endospores are so durable that they can survive in boiling water; killing them requires heating lab equipment to 121°C under high pressure. In less hostile environments, endospores can remain dormant but viable for centuries, able to rehydrate and resume metabolism when their environment improves.

Morphological and Molecular Homologies: Recall that phenotypic and genetic similarities due to shared ancestry are called homologies. For example, the similarity in the number and arrangement of bones in the forelimbs of mammals is due to their descent from a common ancestor with the same bone structure; this is an example of a morphological homology (see Figure 22.15). In the same way, genes or other DNA sequences are homologous if they are descended from sequences carried by a common ancestor.

In general, organisms that share very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences. In some cases, however, the morphological divergence between related species can be great and their genetic divergence small (or vice versa). Consider the Hawaiian silversword plants: some of these species are tall, twiggy trees, while others are dense, ground-hugging shrubs (see Figure 25.22). But despite these striking phenotypic differences, the silverswords' genes are very similar. Based on these small molecular divergences, scientists estimate that the silversword group began to diverge 5 million years ago. We'll discuss how scientists use molecular data to estimate such divergence times later in this chapter.

Reproduction: Many prokaryotes can reproduce quickly in favorable environments. By binary fission (see Figure 12.12), a single prokaryotic cell divides into 2 cells, which then divide into 4, 8, 16, and so on. Under optimal conditions, many prokaryotes can divide every 1-3 hours; some species can produce a new generation in only 20 minutes. At this rate, a single prokaryotic cell could give rise to a colony outweighing Earth in only two days!

In reality, of course, this does not occur. The cells eventually exhaust their nutrient supply, poison themselves with metabolic wastes, face competition from other microorganisms, or are consumed by other organisms. Still, many prokaryotic species' potential for rapid population growth emphasizes three key features of their biology: They are small, they reproduce by binary fission, and they often have short generation times. As a result, prokaryotic populations can consist of many trillions of individuals—far more than populations of multicellular eukaryotes, such as plants or animals.

For many years after transformation was discovered in laboratory cultures, most biologists thought it was too rare and haphazard to play an important role in natural bacterial populations. But researchers have since learned that many bacteria have cell-surface proteins that recognize DNA from closely related species and transport it into the cell. Once inside the cell, the foreign DNA can be incorporated into the genome by homologous DNA exchange.

In transduction, phages (from "bacteriophages," the viruses that infect bacteria) carry prokaryotic genes from one host cell to another. In most cases, transduction results from accidents that occur during the phage replicative cycle (Figure 27.11). A virus that carries prokaryotic DNA may not be able to replicate because it lacks some or all of its own genetic material. However, the virus can attach to another prokaryotic cell (a recipient) and inject prokaryotic DNA acquired from the first cell (the donor). If some of this DNA is then incorporated into the recipient cell's chromosome by crossing over, a recombinant cell is formed.

Note that a shared derived character can refer to the loss of a feature, such as the loss of limbs in snakes or whales. In addition, it is a relative matter whether a character is considered ancestral or derived. A backbone can also qualify as a shared derived character, but only at a deeper branch point that distinguishes all vertebrates from other animals.

Inferring Phylogenies Using Derived Characters: Shared derived characters are unique to particular clades. Because all features of organisms arose at some point in the history of life, it should be possible to determine the clade in which each shared derived character first appeared and to use that information to infer evolutionary relationships. To give an example of this approach, consider the set of characters shown in Figure 26.12a for each of five vertebrates—a leopard, turtle, frog, bass, and lamprey (a jawless aquatic vertebrate). As a basis of comparison, we need to select an outgroup. An outgroup is a species or group of species from an evolutionary lineage that is closely related to but not part of the group of species that we are studying (the ingroup). A suitable outgroup can be determined based on evidence from morphology, paleontology, embryonic development, and gene sequences. An appropriate outgroup for our example is the lancelet, a small animal that lives in mudflats and (like vertebrates) is a member of the more inclusive group called the chordates. Unlike the vertebrates, however, the lancelet does not have a backbone.

Figure 27.8 Specialized membranes of prokaryotes. (a) Infoldings of the plasma membrane, reminiscent of the cristae of mitochondria, function in cellular respiration in some aerobic prokaryotes (TEM). (b) Photosynthetic prokaryotes called cyanobacteria have thylakoid membranes, much like those in chloroplasts (TEM)

Internal Organization and DNA: The cells of prokaryotes are simpler than those of eukaryotes in both their internal structure and the physical arrangement of their DNA (see Figure 6.5). Prokaryotic cells lack the complex compartmentalization associated with the membraneenclosed organelles found in eukaryotic cells. However, some prokaryotic cells do have specialized membranes that perform metabolic functions (Figure 27.8). These membranes are usually infoldings of the plasma membrane. Recent discoveries also indicate that some prokaryotes can store metabolic by-products in simple compartments that are made out of proteins; these compartments do not have a membrane.

This approach has been used to make novel predictions about dinosaurs. For example, there is evidence that birds descended from the theropods, a group of bipedal saurischian dinosaurs. As seen in Figure 26.16, the closest living relatives of birds are crocodiles. Birds and crocodiles share numerous features: They have four-chambered hearts, they "sing" to defend territories and attract mates (although a crocodile's "song" is more like a bellow), and they build nests. Both birds and crocodiles also care for their eggs by brooding, a behavior in which a parent warms the eggs with its body. Birds brood by sitting on their eggs, whereas crocodiles cover their eggs with their neck. Reasoning that any feature shared by birds and crocodiles is likely to have been present in their common ancestor (denoted by the blue dot in Figure 26.16) and all of its descendants, biologists predicted that dinosaurs had fourchambered hearts, sang, built nests, and exhibited brooding.

Internal organs, such as the heart, rarely fossilize, and it is, of course, difficult to test whether dinosaurs sang to defend territories and attract mates. However, fossilized dinosaur eggs and nests have provided evidence supporting the prediction of brooding in dinosaurs. First, a fossil embryo of an Oviraptor dinosaur was found, still inside its egg. This egg was identical to those found in another fossil, one that showed an Oviraptor crouching over a group of eggs in a posture similar to that seen in brooding birds today (Figure 26.17). Researchers suggested that the Oviraptor dinosaur preserved in this second fossil died while incubating or protecting its eggs. The broader conclusion that emerged from this work—that dinosaurs built nests and exhibited brooding—has since been strengthened by additional fossil discoveries that show that other species of dinosaurs built nests and sat on their eggs. Finally, by supporting predictions based on the phylogenetic hypothesis shown in Figure 26.16, fossil discoveries of nests and brooding in dinosaurs provide independent data that suggest that the hypothesis is correct.

Many other archaea live in more moderate environments. Consider the methanogens, archaea that release methane as a by-product of their unique ways of obtaining energy. Many methanogens use CO2 to oxidize H2, a process that produces both energy and methane waste. Among the strictest of anaerobes, methanogens are poisoned by O2. Although some methanogens live in extreme environments, such as under kilometers of ice in Greenland, others live in swamps and marshes where other microorganisms have consumed all the O2. The "marsh gas" found in such environments is the methane released by these archaea. Other species inhabit the anaerobic guts of cattle, termites, and other herbivores, playing an essential role in the nutrition of these animals. Methanogens are also useful to humans as decomposers in sewage treatment facilities.

Many extreme halophiles and all known methanogens are archaea in the clade Euryarchaeota (from the Greek eurys, broad, a reference to their wide habitat range). The euryarchaeotes also include some extreme thermophiles, though most thermophilic species belong to a second clade, Crenarchaeota (cren means "spring," such as a hydrothermal spring). Metagenomic studies have identified many species of euryarchaeotes and crenarchaeotes that are not extremophiles. These archaea exist in habitats ranging from farm soils to lake sediments to the surface of the open ocean.

Metabolic Cooperation: Cooperation between prokaryotic cells allows them to use environmental resources they could not use as individual cells. In some cases, this cooperation takes place between specialized cells of a filament. For instance, the cyanobacterium Anabaena has genes that encode proteins for photosynthesis and for nitrogen fixation. However, a single cell cannot carry out both processes at the same time because photosynthesis produces O2, which inactivates the enzymes involved in nitrogen fixation. Instead of living as isolated cells, Anabaena forms filamentous chains (Figure 27.14). Most cells in a filament carry out only photosynthesis, while a few specialized cells called heterocysts (sometimes called heterocytes) carry out only nitrogen fixation. Each heterocyst is surrounded by a thickened cell wall that restricts entry of O2 produced by neighboring photosynthetic cells. Intercellular connections allow heterocysts to transport fixed nitrogen to neighboring cells and to receive carbohydrates.

Metabolic cooperation between different prokaryotic species often occurs in surface-coating colonies known as biofilms. Cells in a biofilm secrete signaling molecules that recruit nearby cells, causing the colonies to grow. The cells also produce polysaccharides and proteins that stick the cells to the substrate and to one another; these polysaccharides and proteins form the capsule, or slime layer, mentioned earlier in the chapter. Channels in the biofilm allow nutrients to reach cells in the interior and wastes to be expelled. Biofilms are common in nature, but they can cause problems by contaminating industrial products and medical equipment and contributing to tooth decay and more serious health problems. Altogether, damage caused by biofilms costs billions of dollars annually.

Second, the number of genes a species has doesn't seem to increase through duplication at the same rate as perceived phenotypic complexity. Humans have only about four times as many genes as yeast, a single-celled eukaryote, even though—unlike yeast—we have a large, complex brain and a body with more than 200 different types of tissues. Evidence is emerging that many human genes are more versatile than those of yeast: A single human gene can encode multiple proteins that perform different tasks in various body tissues. Unraveling the mechanisms that cause this genomic versatility and phenotypic variation is an exciting challenge.

Molecular clocks help track evolutionary time: One goal of evolutionary biology is to understand the relationships among all organisms. It is also helpful to know when lineages diverged from one another, including those for which there is no fossil record. But how can we determine the timing of phylogenies that extend beyond the fossil record?

The Role of Oxygen in Metabolism: Prokaryotic metabolism also varies with respect to oxygen (O2). Obligate aerobes must use O2 for cellular respiration and cannot grow without it. Obligate anaerobes, on the other hand, are poisoned by O2. Some obligate anaerobes live exclusively by fermentation; others extract chemical energy by anaerobic respiration, in which substances other than O2, such as nitrate ions (NO3 -) or sulfate ions (SO4 2-), accept electrons at the "downhill" end of electron transport chains. Facultative anaerobes use O2 if it is present but can also carry out fermentation or anaerobic respiration in an anaerobic environment.

Nitrogen Metabolism: Nitrogen is essential for the production of amino acids and nucleic acids in all organisms. Whereas eukaryotes can obtain nitrogen only from a limited group of nitrogen compounds, prokaryotes can metabolize nitrogen in many forms. For example, some cyanobacteria and some methanogens (a group of archaea) convert atmospheric nitrogen (N2) to ammonia (NH3), a process called nitrogen fixation. The cells can then incorporate this "fixed" nitrogen into amino acids and other organic molecules. In terms of nutrition, nitrogen-fixing cyanobacteria are some of the most self-sufficient organisms, since they need only light, CO2, N2, water, and some minerals to grow.

However, a taxon is equivalent to a clade only if it is monophyletic (from the Greek, meaning "single tribe"), signifying that it consists of an ancestral species and all of its descendants (Figure 26.10a). Contrast this with a paraphyletic ("beside the tribe") group, which consists of an ancestral species and some, but not all, of its descendants (Figure 26.10b), or a polyphyletic ("many tribes") group, which includes distantly related species but does not include their most recent common ancestor (Figure 26.10c).

Note that in a paraphyletic group, the most recent common ancestor of all members of the group is part of the group, whereas in a polyphyletic group the most recent common ancestor is not part of the group. For example, a group consisting of even-toed ungulates (hippopotamuses, deer, and their relatives) and their common ancestor is paraphyletic because it does not include cetaceans (whales, dolphins, and porpoises), which descended from that ancestor (Figure 26.11). In contrast, a group consisting of seals and cetaceans (based on their similar body forms) is polyphyletic because it does not include the common ancestor of seals and cetaceans. Biologists avoid defining such polyphyletic groups; if new evidence indicates that an existing group is polyphyletic, its members are reclassified.

Motility: About half of all prokaryotes are capable of taxis, a directed movement toward or away from a stimulus (from the Greek taxis, to arrange). For example, prokaryotes that exhibit chemotaxis change their movement pattern in response to chemicals. They may move toward nutrients or oxygen (positive chemotaxis) or away from a toxic substance (negative chemotaxis). Some species can move at velocities exceeding 50 µm/sec—up to 50 times their body length per second. For perspective, consider that a person 1.7 m tall moving that fast would be running 306 km (190 miles) per hour!

Of the various structures that enable prokaryotes to move, the most common are flagella (Figure 27.7). Flagella (singular, flagellum) may be scattered over the entire surface of the cell or concentrated at one or both ends. Prokaryotic flagella differ greatly from eukaryotic flagella: They are one-tenth the width and typically are not covered by an extension of the plasma membrane (see Figure 6.24). The flagella of prokaryotes and eukaryotes also differ in their molecular composition and their mechanism of propulsion. Among prokaryotes, bacterial and archaeal flagella are similar in size and rotational mechanism, but they are composed of entirely different and unrelated proteins. Overall, these structural and molecular comparisons indicate that the flagella of bacteria, archaea, and eukaryotes arose independently. Since current evidence shows that the flagella of organisms in the three domains perform similar functions but are not related by common descent, they are described as analogous, not homologous, structures (see Concept 22.2).

An Overview of Prokaryotic Diversity: In the 1970s, microbiologists began using small-subunit ribosomal RNA as a marker for evolutionary relationships. Their results indicated that many prokaryotes once classified as bacteria are actually more closely related to eukaryotes and belong in a domain of their own: Archaea. Microbiologists have since analyzed larger amounts of genetic data—including more than 1,700 entire genomes—and have concluded that a few traditional taxonomic groups, such as cyanobacteria, are monophyletic. However, other traditional groups, such as gram-negative bacteria, are scattered throughout several lineages. Figure 27.15 shows one phylogenetic hypothesis for some of the major taxa of prokaryotes based on molecular systematics.

One lesson from studying prokaryotic phylogeny is that the genetic diversity of prokaryotes is immense. When researchers began to sequence the genes of prokaryotes, they could investigate only the small fraction of species that could be cultured in the laboratory. In the 1980s, researchers began using the polymerase chain reaction (PCR; see Figure 20.8) to analyze the genes of prokaryotes collected from the environment (such as from soil or water samples). Such "genetic prospecting" is now widely used; in fact, today entire prokaryotic genomes can be obtained from environmental samples using metagenomics (see Concept 21.1). Each year these techniques add new branches to the tree of life. While only about 10,600 prokaryotic species worldwide have been assigned scientific names, a single handful of soil could contain 10,000 prokaryotic species by some estimates. Taking full stock of this diversity will require many years of research.

Diverse nutritional and metabolic adaptations have evolved in prokaryotes: The extensive genetic variation found in prokaryotes is reflected in their diverse nutritional adaptations. Like all organisms, prokaryotes can be categorized by how they obtain energy and the carbon used in building the organic molecules that make up cells. Every type of nutrition observed in eukaryotes is represented among prokaryotes, along with some nutritional modes unique to prokaryotes. In fact, prokaryotes have an astounding range of metabolic adaptations, much broader than that found in eukaryotes.

Organisms that obtain energy from light are called phototrophs, and those that obtain energy from chemicals are called chemotrophs. Organisms that need only CO2 or related compounds as a carbon source are called autotrophs. In contrast, heterotrophs require at least one organic nutrient, such as glucose, to make other organic compounds. Combining possible energy sources and carbon sources results in four major modes of nutrition, summarized in Table 27.1.

Recent evidence indicates that eukaryotes can even acquire nuclear genes from bacteria and archaea. For example, a 2013 genomic analysis showed that the alga Galdieria sulphuraria (Figure 26.22) acquired about 5% of its genes from various bacterial and archaeal species. Unlike most eukaryotes, this alga can survive in environments that are highly acidic or extremely hot, as well as those with high concentrations of heavy metals. The researchers identified specific genes transferred from prokaryotes that have enabled G. sulphuraria to thrive in such extreme habitats.

Overall, horizontal gene transfer has played a key role throughout the evolutionary history of life, and it continues to occur today. Some biologists have argued that horizontal gene transfer was so common that the early history of life should be represented not as a dichotomously branching tree like that in Figure 26.21, but rather as a tangled network of connected branches (Figure 26.23). Although scientists continue to debate how best to portray the earliest steps in the history of life, in recent decades there have been many exciting discoveries about evolutionary events that occurred over time. We'll explore such discoveries in the rest of this unit, beginning with Earth's earliest inhabitants, the prokaryotes.

Prokaryotes also convert some molecules to forms that can be taken up by other organisms. Cyanobacteria and other autotrophic prokaryotes use CO2 to make organic compounds such as sugars, which are then passed up through food chains. Cyanobacteria also produce atmospheric O2, and a variety of prokaryotes fix atmospheric nitrogen (N2) into forms that other organisms can use to make the building blocks of proteins and nucleic acids. Under some conditions, prokaryotes can increase the availability of nutrients that plants require for growth, such as nitrogen, phosphorus, and potassium (Figure 27.18).

Prokaryotes can also decrease the availability of key plant nutrients; this occurs when prokaryotes "immobilize" nutrients by using them to synthesize molecules that remain within their cells. Thus, prokaryotes can have complex effects on soil nutrient concentrations. In marine environments, an archaean from the clade Crenarchaeota can perform nitrification, a key step in the nitrogen cycle (see Figure 55.14). Crenarchaeotes dominate the oceans by numbers, comprising an estimated 1028 cells. The sheer abundance of these organisms suggests that they may have a large impact on the global nitrogen cycle.

The very existence of an ecosystem can depend on prokaryotes. For example, consider the diverse ecological communities found at hydrothermal vents. These communities are densely populated by many different kinds of animals, including worms, clams, crabs, and fishes. But since sunlight does not penetrate to the deep ocean floor, the community does not include photosynthetic organisms. Instead, the energy that supports the community is derived from the metabolic activities of chemoautotrophic bacteria. These bacteria harvest chemical energy from compounds such as hydrogen sulfide (H2S) that are released from the vent. An active hydrothermal vent may support hundreds of eukaryotic species, but when the vent stops releasing chemicals, the chemoautotrophic bacteria cannot survive. As a result, the entire vent community collapses.

Prokaryotes have both beneficial and harmful impacts on humans: Although the best-known prokaryotes tend to be the bacteria that cause human illness, these pathogens represent only a small fraction of prokaryotic species. Many other prokaryotes have positive interactions with people, and some play essential roles in agriculture and industry..

In another example of cooperation between prokaryotes, sulfate-consuming bacteria coexist with methane-consuming archaea in ball-shaped aggregates on the ocean floor. The bacteria appear to use the archaea's waste products, such as organic compounds and hydrogen. In turn, the bacteria produce sulfur compounds that the archaea use as oxidizing agents when they consume methane in the absence of oxygen. This partnership has global ramifications: Each year, these archaea consume an estimated 300 billion kg of methane, a major greenhouse gas (see Concept 56.4).

Prokaryotes have radiated into a diverse set of lineages: Since their origin 3.5 billion years ago, prokaryotic populations have radiated extensively as a wide range of structural and metabolic adaptations have evolved in them. Collectively, these adaptations have enabled prokaryotes to inhabit every environment known to support life—if there are organisms in a particular place, some of those organisms are prokaryotes. Yet despite their obvious success, it is only in recent decades that advances in genomics have begun to reveal the full extent of prokaryotic diversity.

Like Halobacterium, many other prokaryotes can tolerate extreme conditions. Examples include Deinococcus radiodurans, which can survive 3 million rads of radiation (3,000 times the dose fatal to humans), and Picrophilus oshimae, which can grow at a pH of 0.03 (acidic enough to dissolve metal). Other prokaryotes live in environments that are too cold or too hot for most other organisms, and some have even been found living in rocks 3.2 km (2 miles) below Earth's surface.

Prokaryotic species are also very well adapted to more "normal" habitats—the lands and waters in which most other species are found. Their ability to adapt to a broad range of habitats helps explain why prokaryotes are the most abundant organisms on Earth. Indeed, the number of prokaryotes in a handful of fertile soil is greater than the number of people who have ever lived. In this chapter, we'll examine the adaptations, diversity, and enormous ecological impact of these remarkable organisms.

Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes: As we discussed in Unit Four, evolution cannot occur without genetic variation. The diverse adaptations exhibited by prokaryotes suggest that their populations must have considerable genetic variation—and they do. In this section, we'll examine three factors that give rise to high levels of genetic diversity in prokaryotes: rapid reproduction, mutation, and genetic recombination.

Rapid Reproduction and Mutation: In sexually reproducing species, the generation of a novel allele by a new mutation is rare for any particular gene. Instead, most of the genetic variation in sexual populations results from the way existing alleles are arranged in new combinations during meiosis and fertilization (see Concept 13.4). Prokaryotes do not reproduce sexually, so at first glance their extensive genetic variation may seem puzzling. But in many species, this variation can result from a combination of rapid reproduction and mutation.

Figure 27.10 Inquiry Can prokaryotes evolve rapidly in response to environmental change? Experiment Vaughn Cooper and Richard Lenski tested the ability of E. coli populations to adapt to a new environment. They established 12 populations, each founded by a single cell from an E. coli strain, and followed these populations for 20,000 generations (3,000 days). To maintain a continual supply of resources, each day the researchers performed a serial transfer: They transferred 0.1 mL of each population to a new tube containing 9.9 mL of fresh growth medium. The growth medium used throughout the experiment provided a challenging environment that contained only low levels of glucose and other resources needed for growth. Samples were periodically removed from the 12 populations and grown in competition with the common ancestral strain in the experimental (low glucose) environment.

Results The fitness of the experimental populations, as measured by the growth rate of each population, increased rapidly for the first 5,000 generations (2 years) and more slowly for the next 15,000 generations. The graph shows the averages for the 12 populations. Conclusion Populations of E. coli continued to accumulate beneficial mutations for 20,000 generations, allowing rapid evolution of increased population growth rates in their new environment.

Archaea: Archaea share certain traits with bacteria and other traits with eukaryotes (Table 27.2). However, archaea also have many unique characteristics, as we would expect in a taxon that has followed a separate evolutionary path for so long. The first prokaryotes assigned to domain Archaea live in environments so extreme that few other organisms can survive there. Such organisms are called extremophiles, meaning "lovers" of extreme conditions (from the Greek philos, lover), and include extreme halophiles and extreme thermophiles. Extreme halophiles (from the Greek halo, salt) live in highly saline environments, such as the Great Salt Lake in Utah, the Dead Sea in Israel, and the Spanish lake shown in Figure 27.1.

Some species merely tolerate salinity, while others require an environment that is several times saltier than seawater (which has a salinity of 3.5%). For example, the proteins and cell wall of Halobacterium have unusual features that improve function in extremely salty environments but render these organisms incapable of survival if the salinity drops below 9%.

Gram-Positive Bacteria: Gram-positive bacteria rival the proteobacteria in diversity. Species in one subgroup, the actinomycetes (from the Greek mykes, fungus, for which these bacteria were once mistaken), form colonies containing branched chains of cells. Two species of actinomycetes cause tuberculosis and leprosy. However, most actinomycetes are free-living species that help decompose the organic matter in soil; their secretions are partly responsible for the "earthy" odor of rich soil. Soil-dwelling species in the genus Streptomyces (top) are cultured by pharmaceutical companies as a source of many antibiotics, including streptomycin. Gram-positive bacteria include many solitary species, such as Bacillus anthracis, which causes anthrax, and Clostridium botulinum, which causes botulism. The various species of Staphylococcus and Streptococcus are also gram-positive bacteria. Mycoplasmas (bottom) are the only bacteria known to lack cell walls. They are also the tiniest known cells, with diameters as small as 0.1 μm, only about five times as large as a ribosome. Mycoplasmas have small genomes—Mycoplasma genitalium has only 517 genes, for example. Many mycoplasmas are free-living soil bacteria, but others are pathogens.

Streptomyces, the source of many antibiotics (SEM) Hundreds of mycoplasmas covering a human fibroblast cell (colorized SEM)

Subgroup: Alpha Proteobacteria: Many of the species in this subgroup are closely associated with eukaryotic hosts. For example, Rhizobium species live in nodules within the roots of legumes (plants of the pea/bean family), where the bacteria convert atmospheric N2 to compounds the host plant can use to make proteins. Species in the genus Agrobacterium produce tumors in plants; genetic engineers use these bacteria to carry foreign DNA into the genomes of crop plants. Scientists hypothesize that mitochochondria evolved from aerobic alpha proteobacteria through endosymbiosis.Rhizobium (arrows) inside a root cell of a legume (TEM)

Subgroup: Beta Proteobacteria: This nutritionally diverse subgroup includes Nitrosomonas, a genus of soil bacteria that play an important role in nitrogen recycling by oxidizing ammonium (NH4 +), producing nitrite (NO2 -) as a waste product. Other members of this subgroup include a wide range of aquatic species, such as the photoheterotroph Rubrivivax, along with pathogens such as the species that causes the sexually transmitted disease gonorrhea, Neisseria gonorrhoeae. Nitrosomonas (colorized TEM)

Subgroup: Gamma Proteobacteria: This subgroup's autotrophic members include sulfur bacteria, such as Thiomargarita namibiensis, which obtain energy by oxidizing H2S, producing sulfur as a waste product (the small globules in the photograph at right). Some heterotrophic gamma proteobacteria are pathogens; for example, Legionella causes Legionnaires' disease, Salmonella is responsible for some cases of food poisoning, and Vibrio cholerae causes cholera. Escherichia coli, a common resident of the intestines of humans and other mammals, normally is not pathogenic.Thiomargarita namibiensis containing sulfur wastes (LM)

Subgroup: Delta Proteobacteria: This subgroup includes the slime-secreting myxobacteria. When the soil dries out or food is scarce, the cells congregate into a fruiting body that releases resistant "myxospores." These cells found new colonies in favorable environments. Another group of delta proteobacteria, the bdellovibrios, attack other bacteria, charging at up to 100 μm/sec (comparable to a human running 240 km/hr). The attack begins when a bdellovibrio attaches to specific molecules found on the outer covering of some bacterial species. The bdellovibrio then drills into its prey by using digestive enzymes and spinning at 100 revolutions per second. Fruiting bodies of Chondromyces crocatus, a myxobacterium (SEM)

Linking Classification and Phylogeny: The evolutionary history of a group of organisms can be represented in a branching diagram called a phylogenetic tree. As in Figure 26.4, the branching pattern often matches how taxonomists have classified groups of organisms nested within more inclusive groups. Sometimes, however, taxonomists have placed a species within a genus (or other group) to which it is not most closely related. One reason for such a mistake might be that over the course of evolution, a species has lost a key feature shared by its close relatives. If DNA or other new evidence indicates that an organism has been misclassified, the organism may be reclassified to accurately reflect its evolutionary history. Another issue is that while the Linnaean system may distinguish groups, such as amphibians, mammals, reptiles, and other classes of vertebrates, it tells us nothing about these groups' evolutionary relationships to one another.

Such difficulties in aligning Linnaean classification with phylogeny have led some systematists to propose that classification be based entirely on evolutionary relationships. In such systems, names are only assigned to groups that include a common ancestor and all of its descendants. As a consequence of this approach, some commonly recognized groups would become part of other groups previously at the same level of the Linnaean system. For example, because birds evolved from a group of reptiles, Aves (the Linnaean class to which birds are assigned) would be considered a subgroup of Reptilia (also a class in the Linnaean system).

Suppose, for example, that certain noncoding DNA sequences near a particular gene are very similar in two species, except that the first base of the sequence has been deleted in one of the species. The effect is that the remaining sequence shifts back one notch. A comparison of the two sequences that does not take this deletion into account would overlook what in fact is a very good match. To address such problems, researchers have developed computer programs that estimate the best way to align comparable DNA segments of differing lengths (Figure 26.8).

Such molecular comparisons reveal that many base substitutions and other differences have accumulated in the comparable genes of an Australian "mole" and a golden mole. The many differences indicate that their lineages have diverged greatly since their common ancestor; thus, we say that the living species are not closely related. In contrast, the high degree of gene sequence similarity among the silversword plants indicates that they are all very closely related, in spite of their considerable morphological differences.

Nitrogen fixation has a large impact on other organisms. For example, nitrogen-fixing prokaryotes can increase the nitrogen available to plants, which cannot use atmospheric nitrogen but can use the nitrogen compounds that the prokaryotes produce from ammonia. Concept 55.4 discusses this and other essential roles that prokaryotes play in the nitrogen cycles of ecosystems.

Table 27.1 Major Nutritional Modes Figure 27.14 Metabolic cooperation in a prokaryote. In the filamentous freshwater cyanobacterium Anabaena, heterocysts fix nitrogen, while the other cells carry out photosynthesis (LM).

The F Factor as a Plasmid The F factor in its plasmid form is called the F plasmid. Cells containing the F plasmid, designated F + cells, function as DNA donors during conjugation (Figure 27.13a). Cells lacking the F factor, designated F - , function as DNA recipients during conjugation. The F + condition is transferable in the sense that an F+ cell converts an F- cell to F+ if a copy of the entire F plasmid is transferred. Even if this does not occur, as long as some of the F plasmid's DNA is transferred successfully to the recipient cell, that cell is now a recombinant cell.

The F Factor in the Chromosome Chromosomal genes can be transferred during conjugation when the donor cell's F factor is integrated into the chromosome. A cell with the F factor built into its chromosome is called an Hfr cell (for high frequency of recombination). Like an F + cell, an Hfr cell functions as a donor during conjugation with an F - cell (Figure 27.13b). When chromosomal DNA from an Hfr cell enters an F - cell, homologous regions of the Hfr and F - chromosomes may align, allowing segments of their DNA to be exchanged. As a result, the recipient cell becomes a recombinant bacterium that has genes derived from the chromosomes of two different cells— a new genetic variant on which evolution can act.

Conjugation and Plasmids: In a process called conjugation, DNA is transferred between two prokaryotic cells (usually of the same species) that are temporarily joined. In bacteria, the DNA transfer is always one-way: One cell donates the DNA, and the other receives it. We'll focus here on the mechanism used by E. coli. First, a pilus of the donor cell attaches to the recipient (Figure 27.12). The pilus then retracts, pulling the two cells together, like a grappling hook. The next step is thought to be the formation of a temporary structure between the two cells, a "mating bridge" through which the donor may transfer DNA to the recipient. However, the mechanism by which DNA transfer occurs is unclear; indeed, recent evidence indicates that DNA may pass directly through the hollow pilus.

The ability to form pili and donate DNA during conjugation results from the presence of a particular piece of DNA called the F factor (F for fertility). The F factor of E. coli consists of about 25 genes, most required for the production of pili. As shown in Figure 27.13, the F factor can exist either as a plasmid or as a segment of DNA within the bacterial chromosome.

Gram staining is a valuable tool in medicine for quickly determining if a patient's infection is due to gram-negative or to gram-positive bacteria. This information has treatment implications. The lipid portions of the lipopolysaccharides in the walls of many gram-negative bacteria are toxic, causing fever or shock. Furthermore, the outer membrane of a gramnegative bacterium helps protect it from the body's defenses. Gram-negative bacteria also tend to be more resistant than gram-positive species to antibiotics because the outer membrane impedes entry of the drugs. However, certain grampositive species have virulent strains that are resistant to one or more antibiotics. (Figure 22.14 discusses one example: methicillin-resistant Staphylococcus aureus, or MRSA, which can cause lethal skin infections.)

The effectiveness of certain antibiotics, such as penicillin, derives from their inhibition of peptidoglycan cross-linking. The resulting cell wall may not be functional, particularly in gram-positive bacteria. Such drugs destroy many species of pathogenic bacteria without adversely affecting human cells, which do not have peptidoglycan.

At certain times of year, the Laguna Salada de Torrevieja in Spain (the "Salty Lagoon") appears pink (Figure 27.1), a sign that its waters are many times saltier than seawater. Yet despite these harsh conditions, the dramatic color is caused not by minerals or other nonliving sources, but by living things. What organisms can live in such an inhospitable environment, and how do they do it?

The pink color in the Laguna Salada de Torrevieja comes from trillions of prokaryotes in the domains Archaea and Bacteria, including archaea in the genus Halobacterium. These archaea have red membrane pigments, some of which capture light energy that is used to drive ATP synthesis. Halobacterium species are among the most salt-tolerant organisms on Earth; they thrive in salinities that dehydrate and kill other cells. A Halobacterium cell compensates for water lost through osmosis by pumping potassium ions (K+ ) into the cell until the ionic concentration inside the cell matches the concentration outside.

Hierarchical Classification: In addition to naming species, Linnaeus also grouped them into a hierarchy of increasingly inclusive categories. The first grouping is built into the binomial: Species that appear to be closely related are grouped into the same genus. For example, the leopard (Panthera pardus) belongs to a genus that also includes the African lion (Panthera leo), the tiger (Panthera tigris), and the jaguar (Panthera onca). Beyond genera, taxonomists employ progressively more comprehensive categories of classification. The taxonomic system named after Linnaeus, the Linnaean system, places related genera in the same family, families into orders, orders into classes, classes into phyla (singular, phylum), phyla into kingdoms, and, more recently, kingdoms into domains (Figure 26.3).

The resulting biological classification of a particular organism is somewhat like a postal address identifying a person in a particular apartment, in a building with many apartments, on a street with many apartment buildings, in a city with many streets, and so on. The named taxonomic unit at any level of the hierarchy is called a taxon (plural, taxa). In the leopard example, Panthera is a taxon at the genus level, and Mammalia is a taxon at the class level that includes all the many orders of mammals. Note that in the Linnaean system, taxa broader than the genus are not italicized, though they are capitalized.

Another clue to distinguishing between homology and analogy is the complexity of the characters being compared. The more elements that are similar in two complex structures, the more likely it is that the structures evolved from a common ancestor. For instance, the skulls of an adult human and an adult chimpanzee both consist of many bones fused together. The compositions of the skulls match almost perfectly, bone for bone. It is highly improbable that such complex structures, matching in so many details, have separate origins. More likely, the genes involved in the development of both skulls were inherited from a common ancestor

The same argument applies to comparisons at the gene level. Genes are sequences of thousands of nucleotides, each of which represents an inherited character in the form of one of the four DNA bases: A (adenine), G (guanine), C (cytosine), or T (thymine). If genes in two organisms share many portions of their nucleotide sequences, it is likely that the genes are homologous.

The domain Bacteria contains most of the currently known prokaryotes, while the domain Archaea consists of a diverse group of prokaryotic organisms that inhabit a wide variety of environments. The domain Eukarya consists of all the organisms that have cells containing true nuclei. This domain includes many groups of single-celled organisms as well as multicellular plants, fungi, and animals. Figure 26.21 represents one possible phylogenetic tree for the three domains and some of the many lineages they encompass.

The three-domain system highlights the fact that much of the history of life has been about single-celled organisms. The two prokaryotic domains consist entirely of single-celled organisms, and even in Eukarya, only the branches labeled in red type (plants, fungi, and animals) are dominated by multicellular organisms. Of the five kingdoms previously recognized by taxonomists, most biologists continue to recognize Plantae, Fungi, and Animalia, but not Monera and Protista. The kingdom Monera is obsolete because it would have members in two different domains. The kingdom Protista has also crumbled because it includes members that are more closely related to plants, fungi, or animals than to other protists (see Figure 28.2). New research continues to change our understanding of the tree of life. For example, in the past decade, metagenomic studies have uncovered the genomes of many new species of archaea, leading to discovery of the Thaumarchaeota and other previously unknown phyla of archaea (see Concept 27.4).

Even though the branches of a phylogenetic tree may have different lengths, among organisms alive today, all the different lineages that descend from a common ancestor have survived for the same number of years. To take an extreme example, humans and bacteria had a common ancestor that lived over 3 billion years ago. Fossils and genetic evidence indicate that this ancestor was a singlecelled prokaryote. Even though bacteria have apparently changed little in their morphology since that common ancestor, there have nonetheless been 3 billion years of evolution in the bacterial lineage, just as there have been 3 billion years of evolution in the lineage that ultimately gave rise to humans.

These equal spans of chronological time can be represented in a phylogenetic tree whose branch lengths are proportional to time (Figure 26.14). Such a tree draws on fossil data to place branch points in the context of geologic time. Additionally, it is possible to combine these two types of trees by labeling branch points with information about rates of genetic change or dates of divergence.

Phylogenetic Trees as Hypotheses: This is a good place to reiterate that any phylogenetic tree represents a hypothesis about how the organisms in the tree are related to one another. The best hypothesis is the one that best fits all the available data. A phylogenetic hypothesis may be modified when new evidence compels systematists to revise their trees. Indeed, while many older phylogenetic hypotheses have been supported by new morphological and molecular data, others have been changed or rejected.

Thinking of phylogenies as hypotheses also allows us to use them in a powerful way: We can make and test predictions based on the assumption that a particular phylogeny— our hypothesis—is correct. For example, in an approach known as phylogenetic bracketing, we can predict (by parsimony) that features shared by two groups of closely related organisms are present in their common ancestor and all of its descendants unless independent data indicate otherwise. (Note that "prediction" can refer to unknown past events as well as to evolutionary changes yet to occur.)

Second, we cannot necessarily infer the ages of the taxa or branch points shown in a tree. For example, the tree in Figure 26.5 does not indicate that chimpanzees evolved before humans. Rather, the tree shows only that chimpanzees and humans share a recent common ancestor, but we cannot tell when that ancestor lived or when the first chimpanzees or humans arose. Generally, unless given specific information about what the branch lengths in a tree mean—for example, that they are proportional to time—we should interpret the diagram solely in terms of patterns of descent. No assumptions should be made about when particular species evolved or how much change occurred in each lineage.

Third, we should not assume that a taxon on a phylogenetic tree evolved from the taxon next to it. Figure 26.5 does not indicate that humans evolved from chimpanzees or vice versa. We can infer only that the lineage leading to humans and the lineage leading to chimpanzees both evolved from a recent common ancestor. That ancestor, which is now extinct, was neither a human nor a chimpanzee.

The Important Role of Horizontal Gene Transfer: In the phylogeny shown in Figure 26.21, the first major split in the history of life occurred when bacteria diverged from other organisms. If this tree is correct, eukaryotes and archaea are more closely related to each other than either is to bacteria.

This reconstruction of the tree of life is based in part on sequence comparisons of rRNA genes, which code for the RNA components of ribosomes. However, some other genes reveal a different set of relationships. For example, researchers have found that many of the genes that influence metabolism in yeast (a unicellular eukaryote) are more similar to genes in the domain Bacteria than they are to genes in the domain Archaea— a finding that suggests that the eukaryotes may share a more recent common ancestor with bacteria than with archaea.

New findings continue to inform our understanding of archaeal phylogeny. For example, recent metagenomic studies have uncovered the genomes of many species that are not members of Euryarchaeota or Crenarchaeota. Moreover, phylogenomic analyses show that three of these newly discovered groups—the Thaumarchaeota, Aigarchaeota, and Korarchaeota—are more closely related to the Crenarchaeota than they are to the Euryarchaeota. These findings have led to the identification of a "supergroup" that contains the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (see Figure 27.15).

This supergroup is referred to as "TACK" based on the names of the groups it includes. In 2015, the importance of the TACK supergroup was highlighted by the discovery of the lokiarchaeotes, a group that is closely related to TACK archaea and that could possibly represent the long sought-after sister group of the eukaryotes. As such, the characteristics of lokiarchaeotes may shed light on one of the major puzzles of biology today—how eukaryotes arose from their prokaryotic ancestors. The pace of these and other recent discoveries suggests that as metagenomic prospecting continues, the tree in Figure 27.15 will likely undergo further changes.

Phylogenies are inferred from morphological and molecular data:

To infer phylogeny, systematists must gather as much information as possible about the morphology, genes, and biochemistry of the relevant organisms. It is important to focus on features that result from common ancestry because only those features reflect evolutionary relationships.

Snakes and lizards are part of the continuum of life extending from the earliest organisms to the great variety of species alive today. In this unit, we will survey this diversity and describe hypotheses regarding how it evolved. As we do so, our emphasis will shift from the process of evolution (the evolutionary mechanisms described in Unit Four) to its pattern (observations of evolution's products over time).

To set the stage for surveying life's diversity, in this chapter we consider how biologists trace phylogeny, the evolutionary history of a species or group of species. A phylogeny of lizards and snakes, for example, indicates that both the eastern glass lizard and snakes evolved from lizards with legs—but they evolved from different lineages of legged lizards (Figure 26.2). Thus, it appears that their legless conditions evolved independently. As we'll see, biologists reconstruct phylogenies like that in Figure 26.2 using systematics, a discipline focused on classifying organisms and determining their evolutionary relationships.

Genetic Recombination: Although new mutations are a major source of variation in prokaryotic populations, additional diversity arises from genetic recombination, the combining of DNA from two sources. In eukaryotes, the sexual processes of meiosis and fertilization combine DNA from two individuals in a single zygote. But meiosis and fertilization do not occur in prokaryotes. Instead, three other mechanisms—transformation, transduction, and conjugation—can bring together prokaryotic DNA from different individuals (that is, different cells). When the individuals are members of different species, this movement of genes from one organism to another is called horizontal gene transfer. Although scientists have found evidence that each of these mechanisms can transfer DNA within and between species in both domain Bacteria and domain Archaea, to date most of our knowledge comes from research on bacteria.

Transformation and Transduction: In transformation, the genotype and possibly phenotype of a prokaryotic cell are altered by the uptake of foreign DNA from its surroundings. For example, a harmless strain of Streptococcus pneumoniae can be transformed into pneumoniacausing cells if the cells are exposed to DNA from a pathogenic strain (see Concept 16.1). This transformation occurs when a nonpathogenic cell takes up a piece of DNA carrying the allele for pathogenicity and replaces its own allele with the foreign allele, an exchange of homologous DNA segments. The cell is now a recombinant: Its chromosome contains DNA derived from two different cells.

The cell walls of prokaryotes differ in structure from those of eukaryotes. In eukaryotes that have cell walls, such as plants and fungi, the walls are usually made of cellulose or chitin (see Concept 5.2). In contrast, most bacterial cell walls contain peptidoglycan, a polymer composed of modified sugars cross-linked by short polypeptides. This molecular fabric encloses the entire bacterium and anchors other molecules that extend from its surface. Archaeal cell walls contain a variety of polysaccharides and proteins but lack peptidoglycan.

Using a technique called the Gram stain, developed by the 19th-century Danish physician Hans Christian Gram, scientists can categorize many bacterial species according to differences in cell wall composition. To do this, samples are first stained with crystal violet dye and iodine, then rinsed in alcohol, and finally stained with a red dye such as safranin that enters the cell and binds to its DNA. The structure of a bacterium's cell wall determines the staining response (Figure 27.3). Gram-positive bacteria have relatively simple walls composed of a thick layer of peptidoglycan. The walls of gram-negative bacteria have less peptidoglycan and are structurally more complex, with an outer membrane that contains lipopolysaccharides (carbohydrates bonded to lipids).

Molecular Clocks: We stated earlier that researchers have estimated that the common ancestor of Hawaiian silversword plants lived about 5 million years ago. How did they make this estimate? They relied on the concept of a molecular clock, an approach for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates. An assumption underlying the molecular clock is that the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the genes branched from their common ancestor. In the case of paralogous genes, the number of substitutions is proportional to the time since the ancestral gene was duplicated

We can calibrate the molecular clock of a gene that has a reliable average rate of evolution by graphing the number of genetic differences—for example, nucleotide, codon, or amino acid differences—against the dates of evolutionary branch points that are known from the fossil record (Figure 26.19). The average rates of genetic change inferred from such graphs can then be used to estimate the dates of events that cannot be discerned from the fossil record, such as the origin of the silverswords discussed earlier. Of course, no gene marks time with complete precision. In fact, some portions of the genome appear to have evolved in irregular bursts that are not at all clocklike. And even those genes that seem to act as reliable molecular clocks are accurate only in the statistical sense of showing a fairly smooth average rate of change. Over time, there may still be deviations from that average rate. Furthermore, the same gene may evolve at different rates in different groups of organisms. Finally, when comparing genes that are clocklike, the rate of the clock may vary greatly from one gene to another; some genes evolve a million times faster than others.

Structural and functional adaptations contribute to prokaryotic success: The first organisms to inhabit Earth were prokaryotes that lived 3.5 billion years ago (see Concept 25.3). Throughout their long evolutionary history, prokaryotic populations have been (and continue to be) subjected to natural selection in all kinds of environments, resulting in their enormous diversity today.

We'll begin by describing prokaryotes. Most prokaryotes are unicellular, although the cells of some species remain attached to each other after cell division. Prokaryotic cells typically have diameters of 0.5-5 µm, much smaller than the 10- to 100-µm diameter of many eukaryotic cells. (One notable exception, Thiomargarita namibiensis, can be as large as 750 µm in diameter—bigger than a poppy seed.) Prokaryotic cells have a variety of shapes (Figure 27.2). Finally, although they are unicellular and small, prokaryotes are well organized, achieving all of an organism's life functions within a single cell.

This tree, like all of the phylogenetic trees in this book, is rooted, which means that a branch point within the tree (often drawn farthest to the left) represents the most recent common ancestor of all taxa in the tree. A lineage that diverges from all other members of its group early in the history of the group is called a basal taxon. Hence, like the fishes in Figure 26.5, a basal taxon lies on a branch that diverges near the common ancestor of the group.

What other key points do we need to keep in mind when interpreting phylogenetic trees? First, they are intended to show patterns of descent, not phenotypic similarity. Although closely related organisms often resemble one another due to their common ancestry, they may not if their lineages have evolved at different rates or faced very different environmental conditions. For example, even though crocodiles are more closely related to birds than to lizards (see Figure 22.17), they look more like lizards because morphology has changed dramatically in the bird lineage.