BIOL 1104 UNIT 2

A single giant puffball mushroom may release ________ of barely visible spores when it bursts, making it more likely that some will land in an environment that will support growth.

Billions

Day 14 - Animals

DAY 14: ANIMALS · "Jellyfish" are the medusa phase of several distinct groups of phylum Cnidaria (corals, anemones, jellies, etc) · Almost all animals have distinct tissue types; Cnidaria have 2 (ectoderm outside, endoderm inside) · Sessile polyps/anemones and (usually) mobile medusae have similar body plan · Remember, there are entire subjects on botony, mycology, entomology (insects, a tiny subset of crustaceans, themselves a subset of the phylum Arthropoda), ichthyology (fish), herpetology (amphibians and reptiles), mammalogy · All we can do is look at the big picture · What distinguishes "major" groups like Protostome/Deuterostome? · How do tissues contribute to our understanding of complex structures and developmental changes? · Surface area/volume again important for circulation, respiration, nutrient exchange. · How have animals solved the challenge of reproduction on land, how is reproduction mode related to number of offspring and how they disperse? · Small changes in timing and location of expression of genes lead to massive diversity! · Much of what we know about the early radiation is from Burgess Shale fossils STAGES · Distinct event (DISTINCT FROM multicellular plants, multicellular fungi) - transition from unicellular organisms (protists: choanoflagellates) to multicellular (CELLS MUST COOPERATE!) · Cells take on particular jobs (RNA expression, cell signaling) and form developmental tissues - not all involved in reproduction. · Need OXYGEN to fuel those tissues, carbon to build - eating, waste removal, SOLVE the Surface Area/Volume (SA/V) problem... OXYGEN AND FOOD · Oxygen and food go in... Then, diffusion. DIFFUSION of nutrients, oxygen, and waste limited across cell layers. (Outside layers of cells will receive enough oxygen, but the inner layers will not). · When more surface area is exposed to environment (including the inner layers), the layers of cells will get what they need, and layers may specialize · DIFFUSION is the net movement of molecules or atoms from a region of high concentration (or high chemical potential) to a region of low concentration (or low chemical potential), as a result of random motion of the molecules or atoms. · Eventually this process led to the evolution of THE COMPLETE GUT · One key variation in animal development is how the embryo develops this gut. · At the blastula embryonic stage, when the ball of cells Invaginates to create that surface area, in PROTOSTOMES the "first pore" ends up as the mouth. · In DEUTEROSTOMES, it ends up as anus. TISSUE LAYERS · A key development in animals, though not all have distinct tissues. (Sponges). · ECTODERM - outer layer of developing cells, Creek ektos "outside" - nerves, tooth enamel, epidermis, lining of entry to gut · ENDODERM - gut, respiratory, endocrine glands, urinary system · MESODERM - the coelom (cavity), muscle, blood, part of gonads, connective tissue, kidneys ANIMAL PLAN AND SA/V · How to get nutrients and oxygen to organism of increasing size and complexity? · Pass-through gut (absorptive heterotrophy) · High SA/V tissues in lung · Circulatory system to transport nutrients/oxygen further into tissues when diffusion cannot reach · High SA/V tissues in excretory system as well. DEVELOPMENT, BODY PLANTS, AND LIMITATIONS · ACOELOMATE animals like flatworms (Platyhelminthes), oxygen/respiration entirely via diffusion, passive movement through cells and tissues. They must rely much more on diffusion. All their tissues are packed together, and there is no space within the body (Coelom). THE COELOM · Adding space within the body (the COELOM) allows for some independence among the functional organs and tissues, allows greater flexibility in how the body is arranged relative to its needs - requires more extensive circulatory system and/or use of the coelomic space to serve as circulatory system. Allows organisms to be larger, to be supported by internal skeletons, and more. -Our internal organs "hang" in diff locations. Not attached to lining. COELOM ALLOWS MORE FREEDOM IN HOW ANIMALS DEVELOP AND MOVE. AN ADDITIONAL COMPLEXITY: MOVEMENT · Most animals are FREE-LIVING: locomotion (multiple environments), finding food, avoidance of BEING food, led to dramatic diversification · The ability to incorporate CALCIUM and other minerals into body tissues leads to potential for protection, segmentation, independent movement of parts - new traits · HOW DID THESE TRAITS ORIGINATE? In part, a question of their origin, or HOMOLOGY... PHYLOGENY AS A MEANS OF STUDYING TRAITS: · As with BIOLUMINESCENCE, biologists generate phylogenies in part for resolving taxonomy, but primarily so we can answer questions about how traits have changed. · Traits can be gained, they can also be lost - or modified. · This is one reason PARSIMONY is sometimes not the best model, because there may be distinct rates of change, depending on the type of change. · Ex. In a phylogeny tree, other 4 limbed animals to ROOT phylogeny (at a point/node), assuming original tetrapod vertebrates were tetrapods · "Legless" not just in snakes. We know ancestors had legs, because some snakes have pelvises. · "Glass lizard: no legs, like snakes, but other traits that clearly put them among a different family of reptiles · In Phylogeny, note the large amount of DNA data, and almost all of the tree has high statistical support (2 types). Where it does not tend to have support places where groups radiated very quickly, so few changes define them (not a lot happened). (Use parsiomy when you don't have statistical support? HOMOPLASY · If HOMOLOGY is our assessment that a trait is derived from a single origin/change, HOMOPLASY (SAME TRAIT EVOLVES INDEPENDENTLY) is our assessment that a trait has EVOLVED MULTIPLE TIMES. THESE ARE CALLED PARALELLISMS, CONVERGENCES, REVERSALS. · Parallelisms: convergences (the same trait arises independently in 2 unrelated species), reversals - all can happen in part because the genetic machinery (DNA, RNA, proteins) influence the expression of certain traits. · Paradox: all vertebrate limbs have a homologous developmental origin, but the presence/absence/form/function of a limb ca represent homoplasy. 1. Vertebrate jaws are modified gills, but insect/arthropod mouths are modified limbs. 2. Dolphin flippers are modified front limbs, and vertebrate genitalia involve expression of "limb genes." (Homology of arms, legs, penises, etc.) 3. Flower petals are modified leaves, as are cactus needles. · BIOLOGISTS STUDY DIVERSE TRAITS, FROM NUCLEOTIDES TO FLIPPERS, TO UNDERSTAND HOW THAT TRAIT ORIGINATED AND IN WHAT ENVIRONMENT. · The blue whale Baloenapterus muscles also does not have hind legs; descended from terrestrial mammals (by all morphological and molecular assessments of phylogeny) WHY DO I CARE? · Understanding the embryological (developmental OVER TIME, OVER GENERATIONS) origin of a trait helps us diagnose where something "went wrong." (Medicine). · Understanding the origin of a trait helps us engineer alternate solutions to signal/reception. · Understanding the origins of nervous responses helps us identify model organisms for studying our own behaviors. · Ongoing "debate" how the non-bilateral phyla (Ctenophora, Porifera, Placozoa, Cnidaria) are related relative to the BILATERIA. · Current hypothesis includes molecular traits, including (Parahoxozoa) presence/absence of "Homeobox" genes that control METAMERIC development (regional, repeating patterns) · METAMERIC: SEGMENTATION AND SPECIALIZATION -repeating segments (like lines on a salmon, or a six pack) · Table in powerpoint shows some key moments in the history of Animalia, from structural compounds like chitin (shared with fungi) to gametogenesis, segmented development, cephalization (concentration of sense organs, nervous control, etc at the anterior -front- end of the body, forming a head and brain, both during evolution and in the course of embryo's development), and coelom, and so on! · IT IS BELIEVED THAT WE HAVE PROTIST ANCESTORS WHY FOCUS ON EXCRETION? · Autotrophs are collectors of diffuse resources (sunlight, chemicals, water, carbon); animals are scatterers, digesting food and releasing carbon and other compounds · Metabolic processes convert food to energy; convert food to lipids, nucleic acids, carbohydrates; use energy to eliminate wastes · AMMONIA (NH3) produced as oxygen added to amino groups (from breakdown of proteins) - VERY FOXIC TO ANIMAL TISSUES, soluble in water - affects the transport of potassium, needed to generate electrical potential for nerves, muscles, heart function · Excretory organs handle ammonia removal/reduction in different ways; marine animals release ammonia directly, terrestrial animals often as urea or uric acid GAIN AND LOSS OF TRAITS · How the "big 5" groups of taxa relate informs about origins of nervous system, origin of tissues/epitherlia · Complete guts can be lost. · In segmentation, gains and losses · Some things arose once (homologous) and define the group, e.g. mesoderm in all Bilateria (bilaterally symmetric organisms) REPRODUCTION AND DEVELOPMENT · EGGS (large gametes, less motile, energy resources for early development): higher survival but lower dispersal, and much smaller abundance than tiny low-resource SPERM · Many animals have BI-PHASIC LIFE CYCLE after egg hatch, metamorphose from young to adult phase, e.g. amphibians, many invertebrates · Larvae: animals that do not yet resemble parents. Haven't undergone metamorphosis yet. · Broadcast spawning (eggs and sperm into water), larval release, brooding (keep offspring in parental pouch) - many strategies balance ENERGY INPUT (how much energy you put into each offspring, giving them a good chance to survive) with FECUNDITY (number of offspring) and likely SURVIVAL · Single sea star may release 10 million eggs at once, offspring drift for weeks EGGS ARE ENERGY · Larger eggs often have greater survival, but limits to how many eggs · As fish (often non-deterministic growth) get larger, they allocate MORE energy per body weight toward reproduction · But, overfishing is SELECTING for smaller body sizes at maturity (we take the biggest fish out of their environment), and ocean acidification is reducing egg size. · So, animal size (as with plant size, kelp size, fungal size) often CORRELATES with fitness (survival and reproduction) · Human sex, gender, and sexuality are all spectrums (continuous, decided by several things). As with most other traits, sex isn't just determined by the shape of the chromosomes, and there is a spectrum of outcomes. SIZE MATTERS · The size of organisms harvested (oak trees, crabs, fish) has huge implications for the sustainability of that harvest. · Size of offspring influences how effective post-hatching movement will be: walking, swimming, flying, growth - how do small offspring use the environment (wind, rivers, currents) · Investment in offspring of course can also include parental care, additional resources/protection · Logarithmic (base 10) scale: each unit is an order of magnitude RANGE SIZE · The farther an organism can disperse, perhaps we would assume it would have a larger geographic range (and ability to change that range quickly). · Fly? Swim? Walk? (Larger organisms may be able to go farther: birds, whales, tuna, giraffes, zebras) · Wind? River? Currents? Many smaller organisms benefit from these: pollen, milkweed seeds, buoyant fish eggs, invertebrate larvae. · What else determines the spatial range of an organism? RESOURCES AVAILABLE, APPROPRIATE ENVIRONMENT. · (On graph, closer to the line, more likely to become extinct because large animals are in a small land area). · Large animals need larger distributions. BODY SIZE, RANGE SIZE · Larger organisms require more ENERGY to maintain health, continue growth, add to reproduction - and these budgets change over life span. · More energy means more resources - and since animals must find those resources, must search a larger area for grasses, berries, voles, nutrient sources. · So: will large organisms be more or less likely to shift their range through time with climate change? How do we explore that idea? This is a field of active research...

Journal Article

Dramatic Shifts in Benthic Microbial Eukaryotic Communities following the Deepwater Horizon Oil Spill · Benthic habitats have significant unexplored diversity of microscopic eukaryotic taxa, including metazoan phyla, protists, algae, fungi · These groups underpin ecosystem functioning across many marine environments · Look at eukaryotic microbial communities prior to and following oiling around heavily impacted shorelines · Results show significant changes in community structure, w/ pre-spill assemblages of diverse Metazoa giving way to dominant fungal communities in post-spill sediments · Post-spill fungal taxa exhibit low richness and are characterized by an abundance of known hydrocarbon-degrading genera, compared to prior communities that contained smaller and more diverse fungal assemblages · Comparative taxonomic data from nematodes suggests this too · Pre-spill samples exhibit high richness and evenness of genera · Post-spill communities contain mainly predatory and scavenger taxa alongside an abundance of juveniles · Based on community analysis, our data suggest considerable (hidden) initial impacts across Gulf beaches may be ongoing, despite the disappearance of visible surface oil in the region · Utilized marker gene and taxonomic approaches to characterize microbial eukaryotic communities inhabiting beach sediments prior to and after shoreline oiling · Pre-spill sediments contain high diversity of metazoan phyla, dominance of nematode taxa · Most post-spill sites dominated by fungi, show decreases in number of metazoan taxa recovered · Pre-spill sites: diverse and divergent community assemblages inhabiting beaches · Post-spill sites: converged into a single cluster, driven by a common set of putatively oil-tolerant eukaryotes that appear to subsequently dominate affected sites · Post-spill: and overall evenness in types of feeding strategies represented by genera present, · reduced nematode richness, a bias toward predatory species and scavengers, and resident pops showing atypical abundances of juvenile stages · There may be competitive advantage for predatory nematode species able to thrive by ingesting fungal prey or environmental carbon in oil-affected sediments · Oil-induced environmental stress may have favored the rise of resilient, opportunistic species (able to capitalize on large input of new resources) · Compared to many other fungi, marine Altenaria demonstrate increased activity of lignocellulose-degrading enzymes that have been implicated in breakdown of industrial toxins · Observed this and other fungi at post-spill sites. Rarely comprised a significant component of pre-spill fungal communities. Some of these groups also metabolize hydrocarbon compounds. · Ryan Court and Dauphin Bay showed distinct post-spill community compositions · Ryan Court dominated by nematode fauna (few taxa w/ a dominance of predators), drop in Metazoa, and low fungal abundances · Dauphin Bay: decrease in nematodes but retained high overall proportion of metazoan, as well as maintaining diverse fungal community · These shifts suggest disturbance resulting from hydrocarbon input and human-mediated beach cleaning activities, but indicate less dramatic community change compared to other nearby sites · FUNGAL DOMINANCE AT OTHER LOCATIONS · Little is known about seasonal community shifts in Gulf of Mexico · Implications for microbial eukaryote communities · Continued sampling will be critical · Findings indicate utility of these taxa (fungal) in biological and biochemical remediation, given the seemingly ubiquitous ability of environmental fungal isolates to utilize hydrocarbon compounds · Whether these shifts will be maintained over longer term is unclear · For nematodes, abundance of juvenile life stages in post-spill samples could suggest either some degree of community recovery or developmental hindrances that prevented individuals surviving to adulthood · Regardless, hydrocarbon-associated fungal communities dominated sediment eukaryote communities despite cessation of surface oil slicks by time of autumn sampling · Prolonged community biases across microbial eukaryote communities (due to SLOW recovery or persistent impacts of dispersed oil) could translate to long-term effects for higher level predators and food webs in gulf ecosystems · Raw sequence reads were processed: separated according to gene region and analyzed in parallel.

Haploid organisms are always microscopic.

False

One of several key traits that developed in the phylogenetic history of Animalia made it easier for these organisms to thrive on land.

The amniotic egg.

Kelp are a good example of diversity of protists. Also algae.

True

Cheese and yogurt are both thanks to prokaryotic diversity.

True.

As a human, you know that you produce haploid gametes (eggs or sperm). What is unusual about the reproductive lifestyle of plants?

Both haploid and diploid phases are multicellular.

Cats and dogs both share a denture trait (tooth trait) where a set of their molars are called carnassial, meant for shearing meat from bones and snapping thin bones. This is a defining characteristic of the lowest taxonomic level they are both defined to be in - what level is this?

Order Carnivora

Which of these statements is NOT true about protists?

They are all prokaryotic. What is true? Many of them have multiple nuclei performing different jobs Most can reproduce asexually or sexually Some of them are dangerous human pathogens.

When 2 haploid cells fuse in sexual reproduction, multi-cellular organism development begins from a single-celled:

Zygote

A mycelium is:

thread-like tubes of fungi you can find in soil.

Bacteria used in bioremediation can change toxic forms of mercury into nontoxic forms, and can even degrade oil into carbon dioxide. These highly specialized chemical reactions are just another example of:

Metabolism.

A pollen grain is:

A multicellular gametophyte

Huge "blooms" of phytoplankton would seem to be a good thing, because they are photosynthesizing and turn carbon to sugar. However, in some events, these blooms are deadly for other organisms because:

As individual cells die, bacteria eat them and use up most of the oxygen in the water.

"Budding" is when a part of a multicellular organism expands through cell growth to eventually split off and become a separate organism, this is a form of:

Asexual reproduction

When biologists refer to protists, are we talking about a monophyletic group? With a single origin, and all descendants of that event are called protists?

FALSE

In animals, after a sperm fertilizes an egg, the dividing cells begin to specialize and form distinct tissues that are involved in separate functions. The only members of Animalia that do not have tissues are:

Sponges

What we humans call a "mushroom" is actually:

The reproductive structure of a fungus.

When an organism dies, it is quickly broken down into basic molecules by organisms that are called:

SAPROPHYTES

Monophyly means:

Single origin.

A polysaccharide (carbohydrate) compound that is common to both fungi and animals is:

Chitin.

Why does section 15.3 focus on Platyhelminthes, Nematoda, and Arthropoda in same section (not closely related)?

Examples of coelomate, pseudocoelomate, and coelomate taxa.

Because prokaryotes reproduce asexually, the genetic material inside a species never changes other than by mutation.

False. (Also Horizontal Gene Transfer).

The fact that corals survive through photosynthesis is because of an endosymbiosis with photosynthetic algae entering their cells.

True.

Chapter 14

CHAPTER 14: DIVERSITY OF PLANTS · Plants shape physical terrain, influence climate, and maintain life as we know it · Nutrition and medical compounds · Current evolutionary thought holds that all plants are monophyletic: descendants of a single common ancestor · Evolutionary transition from water to land imposed severe constrains on ancestors of contemporary plants · Had to evolve strategies to avoid drying out, disperse reproductive cells in air, for structural support, and filter sunlight · While seed plants developed adaptations that allowed them to populate even the most arid habitats on Earth, full independence from water did not happen in all plants, and most seedless plants still require a moist environment!!! 14.1. Plant Kingdom. · Mosses, ferns, conifers, and flowering plants all belong to plant kingdom · Plant kingdom contains mostly photosynthetic organisms; a few parasitic forms have lost ability to photosynthesize · Photosynthesis uses chlorophyll, located in chloroplasts · Plants have cell walls with Cellulose · Most plants reproduce sexually, but also have diverse methods of asexual reproduction · Plants exhibit indeterminate growth: do not have a final body form, but continue to grow body mass until they die · Cell's interior (where majority of chem reactions of metabolism takes place) is watery · Desiccation (drying out) is constant danger for an organism exposed to air · Even when close to water, aerial structures likely to dry out · Water provides buoyancy to organisms living in aquatic habitats · On land, plants need to develop structural support in air - a medium that does not give same lift · Male gametes must reach female gametes w/ new strategy (swimming no longer possible) · Both gametes and zygotes must be protected from drying out · Life on land: several advantages: · Sunlight is abundant · Photosynthetic pigment, chlorophyll, is not filtered out by water or competing photosynthetic species in water column · Carbon dioxide more readily available because its concentration is higher in air than in water · Land plants evolved before land animals (no predators threatened their well-being on land until then) · Then, plants evolved strategies to deter predation: from spines and thorns to toxic chemicals · Early land plants didn't live far from source of water, developed survival strategies to combat dryness · One strategy: drought tolerance · Mosses can dry out to a brown and brittle mat, but when rain makes water available, mosses soak it up and regain healthy, green appearance · Strategy: colonize environments w/ high humidity where droughts are uncommon · Ferns thrive in damp and cool places (ex. understory of temperate forests) · Later plants moved away from aquatic environments using resistance to desiccation (drying out), rather than tolerance · These plants, like the cactus, minimize water loss to such an extent they can survive in driest env · 4 major adaptations are found in many terrestrial plants: alternation of generations, a sporangium in which spores are formed, a gametangium that produces haploid cells, and in vascular plants, apical meristem tissue in roots and shoots ALTERNATION OF GENERATIONS · Organism has both haploid and diploid multicellular stages · HAPLONTIC: life cycle in which there is a dominant haploid stage. · DIPLONTIC: life cycle in which diploid stage is the dominant stage, and the haploid chromosome number is only seen for a brief time in the life cycle during sexual reproduction. · Humans are diplontic · Most plants: alternation of generations: HAPLODIPLONTIC: haploid multicellular form known as GAMETOPHYTE is followed in development sequence by multicellular diploid organism, the SPOROPHYTE. · GAMETOPHYTE gives rise to gametes, or reproductive cells, by mitosis · Can be most obvious phase of life cycle of the plant (ex. mosses), or it can occur in a microscopic structure, such as pollen grain in the higher plants (collective term for vascular plants) · Sporophyte stage is barely noticeable in lower plants (collective term for plant group of mosses, liverworts, and hornworts). · Towering trees are the diplontic phase in in the lifecycles of plants such as sequoias and pines. (Vascular plant: any plant w/ specialized vascular tissue. 2 types of vascular tissue: xylem and phloem, move water and minerals, and products of photosynthesis through the plant. Vascular plants can grow larger). SPORANGIA IN SEEDLESS PLANTS · Sporophyte of seedless plants is diploid and results from SYNGAMY: fusion of 2 gametes · Sporophyte bears the SPORANGIA (singular sporangium): organs that first appeared in the land plants. "Spore in a vessel." Reproductive sac that contains spores. · Inside multicellular sporangia, the diploid sporocytes/mother cells produce haploid spores by meiosis, which reduces the 2n chromosome number to 1n. · These spores are later released by sporangia and disperse into environment · 2 types of spores produced in land plants, resulting in separation of sexes at diff points in life cycle · Seedless nonvascular plants with a dominant gametophyte phase produce only one kind of spore, so they are called HOMOSPOROUS. · After germinating from a spore, gametophyte produces both male and female GAMETANGIA (organ or cell in which gametes are formed), usually on the same individual. · In contrast, HETEROSPOROUS plants produce 2 morphologically different types of spores. · Male spore are called MICROSPORES because of smaller size. · Comparatively large MEGASPORES develop into female gametophyte. · Heterospory is observed in a few seedless vascular plants and in all seed plants. · When haploid spore germinates, it generates a multicellular gametophyte by mitosis. The gametophyte supports the zygote formed from the fusion of gametes and the resulting young sporophyte or vegetative form, and the cycle begins anew. · Spores of seedless plants and pollen of seed plants are surrounded by thick cell walls containing a tough polymer known as sporopollenin. · This substance characterized by long chains of organic molecules related to fatty acids and carotenoids, and gives most pollen its yellow color · Sporopollenin is unusually resistant to chemical and biological degradation · Its toughness explains existence of well-preserved fossils of pollen · Sporopollenin was once thought to be an innovation of land plants, but green algae Coleochaetes is now known to form spores w/ sporopollenin · Protection of embryo is major requirement for all plants · In both seedless and seed plants, female gametophyte provides nutrition, and in seed plants, the embryo is also protected as it develops into the new generation of sporophyte. · Gametangia are structures on the gametophytes of seedless plants in which gametes are produced by mitosis · The male gametangium, the ANTHERIDIUM, releases sperm · Many seedless plants produce sperm equipped with flagella that enable them to swim in a moist environment to the archegonia, the female gametangium · The embryo develops inside the archegonium as the sporophyte Apical Meristem · Shoots and roots of plants increase in length through rapid cell division within a tissue called APICAL MERISTEM: cap of cells at shoot tip or root tip made of undifferentiated cells that continue to proliferate through the life of the plant. · Meristematic cells give rise to the specialized tissues of the plant. · Elongation of the shoots and roots allows a plant to access additional space and resources: light in case of the shoot, and water and minerals in the case of roots. · Separate meristem (lateral meristem) produces cells that increase the diameter of stems and tree trunks · Apical meristems are an adaptation to allow vascular plants to grow in directions essential to their survival: upward to greater sunlight, and downward into soil to obtain water and minerals ADDITIONAL LAND PLANT ADAPTATIONS · Early land plants did not grow above a few inches off the ground, and on these low mats, they competed for light · By evolving shoot and growing taller, individual plants captured more light · Because air offers less support than water, land plants incorporated more rigid molecules in their stems (and later, tree trunks). · Evolution of these vascular tissue for distribution of water and solutes was a necessary prerequisite for plants to evolve larger larger bodies · Vascular system contains xylem and phloem tissues · Xylem conducts water and minerals taken from soil up to the shoot · Phloem transports food derived from photosynthesis toward the entire plant · Root system that evolved to take up water and minerals also anchored increasingly tall shoot in the soil · In large plants, waxy, waterproof cover called CUTICLE coats aerial parts of the plant: leaves and stems. Prevents desiccation. Also prevents intake of carbon dioxide needed for synthesis of carbohydrates through photosynthesis. Stomata/pores that open and close to regulate traffic of gases and vapor therefore appeared in plants as they moved into drier habitats. · Plants synthesize large range of poisonous secondary metabolites: complex organic molecules like alkaloids, whose noxious smells and unpleasant taste deter animals · These toxic compounds can cause disease and death · As plants coevolved w/ animals, sweet and nutritious metabolities were developed to lure animals into providing valuable assistance in dispersing pollen grains, fruit, or seeds · Plants have been coevolving w/ animal associates · Land plants classified into 2 major groups according to absence or presence of vascular tissue · Plants that lack vascular tissue of specialized cells for the transport of water and nutrients are referred to as NONVASCULAR PLANTS. Bryophytes, liverworts, mosses, and hornworts are seedless and nonvascular, and appeared early in land evolution · VASCULAR PLANTS developed network of cells that conduct water and solutes throughout the plant body. · First vascular plants were probably similar to lycophytes (ex. club mosses) and pterophytes (ferns, horsetails, whisk ferns). These are seedless vascular plants. Do not produce seeds, which are embryos w/ their stored food reserves protected by a hard casing. · Seed plants form largest group of all existing plants and dominate the landscape · Seed plants include gymnosperms (ex. conifers), which produce naked seeds, and are most successful · Also flowering plants/angiosperms, which protect seeds inside chambers at center of flower. Walls of these chambers later develop into fruits. 14.2. SEEDLESS PLANTS. · Incredible variety of seedless plants populates terrestrial landscape · Mosses · Horsetails display their jointed stems and spindly leaves on forest floor · Yet, seedless plants represent only small fraction of plants · Hundreds of millions of years ago, seedless plants dominated landscape and grew in enormous swampy forests of Carboniferous period · Their decomposing bodies created large deposits of coal we mine today · BRYOPHYTES, an informal grouping of nonvascular plants, are closest extant relative of early terrestrial plants. · First bryophytes probably appeared in Ordovician period, about 490 million years ago · Because of lack of lignin (tough polymer in cell walls in stems of vascular plants) and other resistant structures, likelihood of bryophytes forming fossils is small, though some spores made up of sporopollenin have been discovered that have been attributed to early bryophytes · By Silurian period, vascular plants had spread through continents. This is evidence that nonvascular plants must have preceded Silurian period. · Bryophytes thrive mostly in damp habitats, though some grow in deserts · Constitute major flora of inhospitable environments like tundra, where their small size and tolerance to desiccation offer distinct advantages · Do not have specialized cells that conduct fluids found in vascular plants, and lack lignin · In bryophytes, water and nutrients circulate inside specialized conducting cells · Although the name nontracheophyte is more accurate, bryophytes are commonly referred to as nonvascular · In bryophyte, all conspicuous vegetative organs belong to the haploid organism (gametophyte) · Diploid sporophyte is barely noticeable · Gametes formed by bryophytes swim using flagella · Sporangium, the multicellular sexual reproductive structure, is present · Embryo also remains attached to parent plant, which nourishes it · This is a characteristic of land plants · Bryophytes are divided into 3 divisions (in plants, taxonomic level "division" is used instead of "phylum"): liverworths (Marchantiophyta), hornworts (Anthocerotophyta), and mosses (true Bryophyta) LIVERWORTS · LIVERWORTS may be viewed as plants most closely related to ancestor that moved to and · Have colonized many habitats on Earth and diversified to more than 6,000 species · Some gametophytes form lobate green structures · The shape is similar to lobes of the liver, an provides origin of common name HORNWORTS - have colonized many land habitats, but are never far from a source of moisture. About 100 described species of hornworts. Dominant phase of life cycle of hornworts is short, blue-green gametophyte. Sporophyte is defining characteristic of the group. It is a long narrow pipe-like structure that emerges from parent gametophyte and maintains growth throughout life of plant. MOSSES - Habitats vary from tundra (where they are the main vegetation) to understory of tropical forests. In tundra, shallow rhizoids allow them to fasten to substrate without digging into frozen soil. They slow down erosion, store moisture and soil nutrients, and provide shelter for small animals and food for large herbivores, such as musk ox. Mosses are sensitive to air pollution and are used to monitor quality of air. Sensitivity of mosses to copper salts makes these salts a common ingredient of compounds marketed to eliminate mosses in lawns. VASCULAR PLANTS · Vascular plants are dominant and most conspicuous group of land plants · More than 90% of Earth's vegetation is vascular · Date to Silurian period · Simplest arrangement of conductive cells shows pattern of xylem at center surrounded by phlorem · XYLEM: tissue responsible for long-distance transport of water and minerals, transfer of water-soluble growth factors from the organs of synthesis to the target organs, and storage of water and nutrients · PHLOEM: transports sugars, proteins, and other sulutes throughout the plant. Phloem cells are divided into sieve elements/conducting cells, and supporting tissues. · Together, xylem and phloem tissues form vascular system · Roots are not well preserved in fossil record, but it seems they did appear later in evolution than vascular tissue · Development of extensive network of roots represented new feature of vascular plants · Thin rhizoids attached bryophytes to the substrate · Flimsy filaments did not provide a strong anchor for the plant; neither did they absorb water and nutrients · In contrast, roots, w/ prominent vascular tissue system, transport water and minerals from soil to rest of the plant · Extensive network of roots that penetrates deep in ground to reach sources of water also stabilizes trees by acting as ballast and an anchor · Majority of roots establish symbiotic relationship with fungi, forming mycorrihizae. · In mycorrhizae, fungal hyphae grow around the root and within the root around the cells, and in some instances, within the cells · Benefits plant by greatly increasing surface area for absorption · A third adaption marks seedless vascular plants. Accompanying sporophyte and development of vascular tissue, appearance of true leaves improved photosynthetic efficiency. · Leaves capture more sunlight w/ their increased surface area · In addition to photynthesis, leaves play another role. Pinecones, mature fronds of ferns, and flowers are all SPOROPHYLLS - leaves that were modified structurally to bear sporangia. · STROBILI - structures that contain the sporangia · They are prominent in conifers and are known commonly as cones. Ex. pine cones of pine trees. SEEDLESS VASCULAR PLANTS · By late Devonian period, plants had evolved vascular tissue, well-defined leaves, and root systems · With these advantages, increased in height and size · During Carboniferous period, swamp forests of club mosses and horsetails, w/ some specimens eaching 30 meters tall, covered most of land · These forests gave rise to extensive coal deposits that gave Carboniferous its name · In seedless vascular plants, sporophyte became dominant phase of the lifecycle · Water required for fertilization of seedless vascular plants, and most favor moist environment · Modern day seedless vascular plants include club mosses, horsetails, ferns, whisk ferns · CLUB MOSSES/LYCOPHYTA - earliest group of seedless vascular plants. Dominated landscape of Carboniferous period, growing into tall trees and forming large swamp forests. Today's club mosses are diminutive, evergreen plants w/ a stem (may be branched) and small leaves called microphylls. Division Lycophyta includes quillworts, club mosses, and spike mosses. None of which is a true moss. · Ferns and whisks belong to division Pterophyta. Third group of plants in Pterophyta, the horsetails, is sometimes classified separately. HORSETAILS have single genus, EQUISETUM. They are survivors of large group of plants, ARTHROPHYTA, which produced large trees and entire swamp forests in Carbonferous. The plants are usually ound in damp environments and marshes. Stem of horsetail is characterized by presence of joints, or nodes, hence the name Arthrophyta, which means "jointed plant." Leaves and branches come out of whorls from the evenly spaced rings. Needle-shaped leaves do not contribute greatly to photosynthesis, the majority of which takes place in green stem. · Ferns are most advanced seedless vascular plants, displays characteristics commonly observed in seed plants. Ferns form large leaves and branching roots. In contrast, WHISK FERNS (the psilophytes) lack both roots and leaves, which were probably lost by evolutionary reduction - natural selection reduces the size of a structure that is no longer favorable in a particular environment. Photosynethesis takes place in green stem of a whisk fern. Small yellow knobs form at tip of branch stem and contain sporangia. Whisk ferns have been classified outside the true ferns, but recent DNA suggests this group may have lost both vascular tissue and roots through evolution, and is actually closely related to ferns · FERNS are most readily recognizeable seedless vascular plants. Many environments. Most ferns are restricted to moist and shaded places. Made their appearance in fossil record during Devonian period and expanded during Carboniferous period. 14.3. SEED PLANTS: GYMNOSPERMS · First plants to colonize land were most likely closely related to modern day mosses and are thought to have appeared 500 million years ago · Followed by liverworts and primitive vascular plants, the pterophytes, from which modern ferns are derived · Life cycle of bryophytes (moss) and pterophytes characterized by alternation of generations · Completion of life cycle requires water, as male gametes must swim to female gemetes · Male gametophyte releases sperm, which must swim (propelled by flagella) to reach ferile female gamete or egg · After fertilization, the zygote matures and grows into a sporophyte, which in turn forms sporangia, or "spore vessels," in which mother cells undergo meiosis and produce haploid spores · Release of spores in suitable environment will lead to germination and new generation of gametophytes · In seed plants, evolutionary trend led to dominant sporophyte generation, in which larger and more ecologically significant generation for a species is the diploid plant · At same time, trend led to reduction in size of the gametophyte, from a conspicuous structure to a microscopic cluster of cells enclosed in the tissues of sporophyte · Lower vascular plants, such as club mosses and ferns, are mostly homosporous (produce only one type of spore) · In contrast, all seed plants/spermatophytes are heterosporous, forming 2 types of spore: megaspores (female) and microspores (male) · Megaspores develop into female gametophytes that produce eggs, and microspores mature into male gametophytes that generate sperm · Because gametophytes mature within spores, they are not free-living, as are the gametophytes of other seedless vascular plants · Heterosporous seedless plants are seen as the evolutionary forerunners of seed plants · Seeds and pollen (2 adaptations to drought) distinguish seed plants from other (seedless) vascular plants · Both adaptations critical to colonization of land · Fossils place earliest distinct seed plants 350 million years ago · Earliest reliable record of gymnosperms dates their appearance to Carboniferous period · Gymnosperms were preceded by progymnosperms (first naked seed plants) · This was transitional group of plants that resembled conifers ("cone bearers") because they produced ood from secondary growth of the vascular tissues · But they still reproduced like ferns, releasing spores to the environment · In Mesozoic era, gymnosperms dominated landscape · Angiosperms took over by middle of Cretaceous period in late Mesozoic era, and have since become the most abundant plant group in most terrestrial biomes · The 2 innovative structures of pollen and seed allowed seed plants to break their dependence on water for reproduction and development of the embryo, and to conquer dry land · The pollen grains carry the male gametes of the plant · The small haploid cells are encased in a protective coat that prevents desiccation (drying out) and mechanical damage · Pollen can travel far from sporophyte that bore it, spreading plant's genes and avoiding competition with other plants · The seed offers the embryo protection, nourishment and a mechanism to maintain dormancy for tens or even thousands of years, allowing it to survive in a hars environment and ensuring germination when growth conditions are optimal · Seeds allow plants to disperse the next generation through both space and time · With such evolutionary advantages, seed plants have become most successful and familiar group of plants · Spores are used by groups of ancient plants and fungi in one stage of their reproduction. ... Pollen is used by flowering plants to fertilize seeds. Fertilized seeds grow into adult plants, not intermediate gametophytes. GYMNOSPERMS - "naked seed" - diverse group of seed plants. PARAPHYLETIC. Paraphyletic groups do not include descendants of a single common ancestor. · Gymnosperm characteristics include naked seeds, separate female and male gametes, pollination by wind, and tracheids, which transport water and solutes in the vascular system LIFE CYCLE OF A CONIFER: · Pine trees are conifers and carry both male and female sporophylls on the same plant · Like all gymnosperms, pines are heterosporous and produce male microspores and female megaspores · In male cones/staminate cones, the MICROSPOROCYTES give rise to microspores by meiosis · Microspores then develop into pollen grains · Each pollen grain contains 2 cells: one generative cell that will divide into 2 sperm, and a second cell that will become the pollen tube cell · In spring, pine trees release large amounts of yellow pollen, carried by wind · Some gametophytes will land on a female cone · The pollen tube grows from the pollen grain slowly, and the generative cell in the pollen grain divides into 2 sperm cells by mitosis. · One of the sperm cells will finally unite its haploid nucleus with the haploid nucleus of an egg cell in process of fertilization · Female CONES/ovulate cones - contain 2 ovules per scale. · One MEGASPOROCYTE undergoes meiosis in each ovule · Only a single surviving haploid cell will develop into a female multicellular gametophyte that encloses an egg · On fertilization, zygote will give rise to the embryo, which is enclosed in seed coat of tissue from the parent plant · Fertilization and seed development is long process in pine trees - may take up 2 years after pollination · Seed that is formed contains 3 generations of tissues: the seed coat that originates from parent plant tissue, the gametophyte that will provide nutrients, and the embryo itself DIVERSITY OF GYMNOSPERMS · Modern gymnosperms are classified into 4 major divisions and comprise about 1,000 described species · Coniferophyta, Cycadophyta, and Ginkgophyta are similar in their production of secondary cambium (cells that generate the vascular system of the trunk or stem) and their pattern of seed development, but are not closely related phylogenetically to each other. · Gnetophyta are considered the closest group to angiosperms because they produce true xylem tissue that contain both tracheids and vessel elements CONIFERS - dominant phylum of gymnosperms, with the most variety of species. · Most are tall trees that usually bear scale-like or needle-like leaves · Thin shape of the needles and their waxy cuticle limits water loss through transpiration · Snow slides easily off needle shaped leaves, keeping the load light and decreasing breaking of branches · These adaptations to cold and dry weather explain the predominance of conifers at hgh altitudes and in cold climates · Conifers include evergreen trees (ex. pines, spruces, firs, cedars, sequoias, and yews). · A few species are deciduous and lose their leaves all at once in fall · European larch and tamarack are examples of deciduous conifer · Many coniferous trees are harvested for paper pulp and timber · Wood of confifers is more primitive than the wood of angiosperms; it contains tracheids, but no vessel elements. · Referred to as "soft wood" CYCADS · Thrive in mild climates and are often mistaken for palms because of the shape of their large, compound leaves · They bear large cones, and usually for gymnosperms, may be pollinated by beetles, rather than wind · They dominated the landscape during the age of dinosaurs in the Mesozoic era · Only a hundred or so cycad species persisted to modern times · Only a hundred or so cycad species persisted to modern times · Face possible extinction, and several species are protected through international conventions · Because of attractive shape, often used as ornamental plants in gardens GINGKOPHYTES · Single surviving species of GINKGOPHYTE · Fan shaped leaves, unique among seed plants because they feature a dichotomous venation pattern, turn yellow in autumn and fall from plant · Planted in public space because it is unusually resistant to pollution · Male and female organs found on separate plants · Usually, only male trees are planted by gardeners because the seeds produced by the female plant have an off-putting smel of rancid butter GNETOPHYTES - closest relatives to modern angiosperms, and include 3D genera of plants · Like angiosperms, have broad leaves · Gnetum species are mostly vines in tropical and subtropical zones · Welwitschia species is unusual, low growing plant in deserts. May live 2000 years · Genus Ephredia is represented in North America in dry areas of southwest US and Mexico · Ephreda's small, scale-like leaves are source of compound ephredine, used in medicine · Because ephedrine is similar to amphetamines, both in chem structure and neurological effect, use is restricted to prescription · Like angiosperms, but unlike other gymnosperms, all gnetophytes possess vessel elements in their xylem 14.4. SEED PLANTS: ANGIOSPERMS · Beginning during Jurassic period · Angiosperms/flowering plants have successfully evolved to dominate most terrestrial ecosystems · Angiosperms include a staggering number of genera and species; division is second only to insects in terms of diversification. (Over 260,000 species) · Angiosperm success is a result of 2 novel structures that ensure reproductive success: flowers and fruit · Flowers allowed plants to form cooperative evolutionary relationships with animals, in particular insects, to disperse their pollen to female gametophytes in a highly targeted way · Fruit protect the developing embryo and serve as an agent of dispersal · Diff structures on fruit reflect dispersal strategies that help with the spreading of seeds FLOWERS · Flowers are modified leaves or sporophylls organized around central stalk · Although they vary in appearance, all flowers contain same structures: sepals, petals, pistils, and stamens · A whorl of SEPALS (the CALYX) is located at the base of the penduncle/stem, and encloses the floral bud before it opens · Sepals are usually photosynthetic organs, although there are some exceptions · Ex. Corolla in lilies and tulips conists of 3 sepals and 3 petals that look virtually identical - this led botanists to coin the word "tepal" · PETALS (COLLECTIVELY, THE COROLLA) are located inside the whorl of sepals and usually display vivid colors to attract pollinators · Flowers pollinated by wind are usually small and dull · Sexual organs are located at center of the flower · STIGMA, STYLE, AND OVARY constitute female organ, the CARPEL/PISTIL/GYNOECIUM. A gynoecium may contain one or more carpels within a single flower. · Megaspores and the female gametophytes are produced and protected by the thick tissues of the carpel · Long, thin structure called a STYLE leads from the sticky STIGMA, where pollen is deposited, to the OVARY enclosed in the carpel. · Ovary houses one or more ovules that will each develop into a seed upon fertilization. · The male reproductive organs, the androecium or STAMENS, surround the central carpel. · Stamens are comprised of a thin stalk called a FILAMENT and a sac like structure, the ANTHER, in which microspores are produced by meiosis and develop into pollen grains. Filament supports the anther. FRUIT · Seed forms in an ovary, which enlarges as the seeds grow · As seed develops, walls of ovary also thicken and form fruit · In botany, a fruit is a fertilized and fully grown, ripened ovary · Many foods commonly called vegetables are actually fruit · Eggplants, zucchini, string beans, and bell peppers are all technically fruit because they contain seeds and derived from the thick ovary tissue · Acorns and winged maple keys, whose scientific name is samara, are also fruit · Mature fruits can be described as fleshy or dry · Fleshy fruit include familiar berries, peaches, etc · Rice, wheat, and nuts are examples of dry fruit · Another distingtion is that not all fruits are derived from ovary · Some fruits are derived from separate ovaries in a single flower, such as raspberry · Other fruits, such as the pineapple, form from clusters of flowers. · Additionally, some fruits, like watermelon and orange, have rinds · Regardless of how they are formed, fruits are an agent of dispersal · Variety of shapes and characteristics reflect mode of dispersal · The light, dry fruits of trees and dandelions are carried by the wind · Floating coconuts are transported by water · Some fruits are colored, perfumed, sweet, and nutritious to attract herbivores, which eat the fruit and disperse the touch undigested seeds in their feces · Other fruits have burs and hocks that cling to fur and hitch rides on animals LIFE CYCLE OF ANGIOSPERM · Adult/sporophyte phase is the main phase of the angiosperm's life cycle · Like gymnosperms, angiosperms are heterosporous · They produce microspores (develop into pollen grains, the male gametophytes) and megaspores (which form an ovule containing the female gametophytes). · Inside the anthers' microsporangia, male microsporocytes divide by meiosis, generating haploid microspores that undergo mitosis and give rise to pollen grains · Each pollen grain contains 2 cells: one generative cell that will divide into 2 sperm, and a second cell that will become the pollen tube cell · In the ovules, female gametophyte is produced when a megaspore undergoes meiosis to produce 4 haploid megaspores · One is larger than the others and undergoes mitosis to form the female gametophyte or embryo sac · 3 mitotic divisions produce 8 nuclei in 7 cells · The egg and 2 cells move to one end of the embryo sac (gametophyte) and 3 cells move to the other end · 2 of the nuclei remain in a single cell and fuse to form a 2n nucleus; this cell moves to the center of the embryo sac · When a pollen grain reaches the stigma, a pollen tube extends from the grain, grows down the style, and enters through an opening in the integuments of the ovule · The 2 sperm cells are deposited in the embryo sac · Double fertilization event occurs next. Unique to angiosperms · One sperm and the egg combine, forming a diploid zygote - the future embryo · The other sperm fuses with the diploid nucleus in the center of the embryo sac, forming a triploid cell that will develop into the endosperm: a tissue that serves as a food reserve · Zygote develops into an embryo with a radicle, or small root, and one or 2 leaf-like organs called COTYLEDONS · Seed food reserves are stored outside the embryo, and the cotyledons serve as conduits to transmit the broken-down food reserves to the developing embryo · Seed consists of a toughened layer of integuments forming the coat, the endosperm with food reserves and, at the center, the well-protected embryo · Most flowers carry both stamens and carpels; however, a few species self-polliate · These are known as "perfect" flowers because they contain both types of sex organs · Biochemical and anatomical barriers to self-pollination promote cross-pollination · Self-pollination is a severe form of inbreeding, and can increase number of genetic defects of offspring · A plant may have perfect flowers, and thus have both genders in each flower; or, it may have imperfect flowers of both kinds on one plant · In each case, such species are called monoecious plants, meaning "one house" · Some plants are dioecious, meaning "2 houses" and have male and female flowers ("imperfect flowers") on different plants · In these species, cross-pollination occurs all the time DIVERSITY OF ANGIOSPERMS · Angiosperms classified in a single division, the ANTHOPHYTA · Modern angiosperms are a monophyletic group, which means they originate from a single ancestor · Flowering plants are divided into 2 major groups, according to the structure of cotyledons, the pollen grains, and other features: · 2 groups: MONOCOTS, which include grasses and lilies, and EUDICOTS/DICOTS, a polyphyletic group · BASAL ANGIOSPERMS are a group of plants believed to have branched off before the separation into monocots and eudicots because they exhibit traits from both groups. Categorized separately in many classification schemes, and they correspond to a grouping known as the Magnoliidae. The Magnoliidae group is composed of magnolia trees, laurels, water lilies, and pepper family. BASIL ANGIOSPERMS · Magnoliidae are represented by the magnolias: tall trees that bear large, fragrant flowers with many parts, and are considered archaic · Laurel trees produce fragrant leaves and small inconspicuous flowers · Laurels are small trees and shrubs that grow mostly in warm climates · Familiar plants in this group include bay laurel, cinnamon, spice bush, and avocado tree · Nymphaeles are comprised of water lilies, lotus, and similar plants · All species of Nymphaeales thrive in freshwater biomes, and have leaves that float on the water surface or grow underwater · Water lilies are particularly prized by gardeners, and have graced ponds and pools since antiquity · Piperales are group of herbs, shrubs, and small trees in tropical climates. Have small flowers without petals tightly arranged in long spikes. · Many species are source of prized fragrances or spices MONOCOTS · Plants in monocot group have a single cotyledon in the seedling, and also share other anatomical features · Veins run parallel to the length of the leaves, and flower parts are arranged in a 3 or 6 fold symmetry · Pollen from the first angiosperms was monosculate (containing a single furrow or pore through the outer layer) · This feature is still seen in modern monocots · True woody tissue rarely found in monocots, and vascular tissue of the stem is not arranged in any particular pattern · Root system is mostly adventitious (unusually positioned) with no major taproot · Monocots include familiar plants like true lilies (not to be confused w/ water lilies), orchids, grasses, palms · Many important crops EUDICOTS · Eudicots, or true dicots, are characterized by presence of two cotyledons · Veins form a network in leaves · Flower parts come in 4, 5, or many whorls · Vascular tissue forms a ring in the stem. (In monocots, vascular tissue is scattered in the stem). · Eudicots can be HERBACEOUS (like dandelions or violets), or produce woody tissues. · Most eudicots produce pollen that is trisculate or triporate, with 3 furrows or pores · Root system is usually anchored by one main root developed from the embryonic radicle. · Eudicots comprise 2/3 of all the flowering plants · Mant species exhibit charatceristics that belong to either group, so classification of a plant as monocot or eudicot is not always clear · (See table for more info).

Chapter 12

CHAPT 12 · All life on Earth evolved from a common ancestor · Phylogenetic "tree of life" can be drawn to show when organisms evolved and the relationships among different organisms · PHYLOGENY: evolutionary history and relationships among a species or group of species. · SYSTEMATICS: study of organisms with the purpose of deriving their relationships · Many disciplines within bio contribute to understanding phylogeny · "Trees change as new data arrives." Scientists continue to discover new species · TAXONOMY ("arrangement law") - science of naming and grouping species to construct an internationally shared classification system. · Taxonomic/Linnaean System - uses hierarchical model. · Includes levels, and each group at one level includes groups at the next lowest level, so that at the lowest level, each member belongs to a series of nested groups. · In most inclusive grouping, organisms divided into 3 DOMAINS: BACTERIA, ARCHAEA, AND EUKARYA · Within each domain is a second level: KINGDOM · Then PHYLUM, CLASS, ORDER, FAMILY, GENUS, SPECIES · TAXON (plural: taxa): group at each level. (ex. For dogs, Carnivora is is the taxon at the order level). · Each taxon name is capitalized except for species, and genus and species names are italicized. · Scientific/Latin name: genus and species together. This 2 name system: BINOMIAL NOMENCLATURE. · Domestic dog is a subspecies of the wolf, not its own species, thus it is given an extra name to indicate its subspecies status: CANIS LUPUS FAMILIARIS. · At each sublevel, organisms become more similar because they are more closely related. · Before Darwin, naturalists sometimes classified organisms using arbitrary similarities, but since evolution theory 19th century, biologists made the system reflect evolutionary relationships · So, all members of a taxon should have a common ancestor and be more closely related to each other than to members of other taxa · Changes must be made as new discoveries take place · Ex. discovery of genetic differences separated prokaryotes into bacteria and archaea in 1970s · At each sublevel, organisms become more SIMILAR. · PHYLOGENETIC TREE: diagram to reflect evolutionary relationships among organisms or groups of organisms · Scientists consider these trees to be HYPOTHESIS of the evolutionary past · Unlike w/ taxonomic classification, a phylogenetic tree can be read like a map of evolutionary history!!!!!!!!!!!!!!!!!! · Shared characteristics are used to construct phylogenetic trees · The point where split occurs in a tree: BRANCH POINT: represents where a single lineage evolved into distinct new ones · Many have a single branch point at base representing a common ancestor · Scientists call these trees ROOTED: there is a single ancestral taxon at the base of phylogenetic tree to which all organisms represented in diagram descend from. · When 2 lineages stem from same branch point, they are called SISTER TAXA. (ex. 2 species of orangutans). · Branch point w/ more than 2 groups illustrates a situation for which scientists have not definitely determines relationships. · Ex. 3 branches leading to 3 gorilla subspecies (exact relationships are not yet understood). · Sister taxa share an ancestor, which does not mean that one taxon evolved from the other. Branch point/split represents common ancestor that existed in past but no longer exists. · Ex. Humans and chimpanzees both evolved from our closest living relatives. · Sometimes evolutionary character changes are identified by a branch or branch point. · Ex. Branch point that gives rise to mammal and reptile lineage from the frog lineage shows the origin of the amniotic egg character. Also, branch point that gives rise to organisms with legs is indicated at the common ancestor of mammals, retiles, amphibians, and jawed fishes. Limitations of Phylogenetic Trees · It is not always as simple as that the more organisms look alike, the more closely related they are · If 2 closely related lineages evolved under different surroundings or after the evolution of a major new adaptation, they may look very different · Also, unless otherwise indicated, branches DO NOT SHOW LENGTH OF TIME. THEY SHOW ONLY THE ORDER IN TIME OF EVOLUTIONARY EVENTS. · SHOWS ORDER IN TIME IN EVOLUTION OF DIFF TRAITS, NOT LENGTH OF TIME · Branches form in diff directions. (just because vertebrates evolved does not mean invertebrates stopped evolving). · Groups that are not closely related but evolve under similar conditions may appear more similar to each other than to a close relative 12.2 · 2 types of evidence: MORPHOLOGIC (FORM AND FUNCTION) AND GENETIC · Organisms that share similar features AND genetic sequences tend to be more closely related than those who do not · HOMOLOGOUS STRUCTURES: features that overlap both morphologically and genetically. Similarities stem from common evolutionary paths. · Ex. Wings of birds, arms of humans, and foreleg of a horse are homologous structures. Several bones arranged in similar ways, even though the elements of the structure have changed in shape and size. · Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look very different · Unrelated organisms may be distantly related but appear very alike, usually because common adaptations to similar environmental conditions evolved in both · Ex. Streamlines body shapes, shapes of fins and appendages, and shape of the tails in fishes and whales (mammals). Structures are similar because they are adaptations to moving in same environment - water. · When a characteristic that is similar occurs by ADAPTIVE CONVERGENCE/CONVERGENCE EVOLUTION, and not because of close evolutionary relationship, it is called an ANALOGOUS STRUCTURE. · Other example: insects have wings. So do birds and bats. Embryonic origin of the 2 wings is completely different. Difference in development/embryogenesis of wings in each case is a signal that insects and bats/birds do not share a common ancestor w/ wing. Wing structures evolved independently of 2 lineages. · HOMOLOGOUS TRAITS SHARE AN EVOLUTIONARY PATH · ANALOGOUS TRAITS DO NOT MOLECULAR COMPARISONS · With advancement of DNA technology, area of MOLECULAR SYSTEMATICS (describes use of information on molecular level including DNA sequencing) has blossomed. · Can include differences in amino acid sequence, nucleotide sequence, or different arrangement of genes · Similar sequences: more closely related organisms · Diff genes change evolutionarily at diff rates and this affects the level at which they are useful at identifying relationships · Rapidly evolving sequences are more useful for determining the relationships among closely related species · Slowly evolving sequnces are useful for determining relationships between distantly related species · Ex. to determine relationships between distant species (ex. a species within archaea and a species within eukarya), the genes used must be ancient and slowly evolving genes that are present in both groups (ex. genes for ribosomal RNA) · Sometimes 2 segments of DNA in distantly related organisms randomly share a high % of bases in the same locations, causing these organisms to appear closely related when they are not. · For this, computer statistical algorithms have been developed to identify actual relationships · Coupled use of morphologic and molecular info is MOST EFFECTIVE TO DETERMINE PHYLOGENY · 2 applications of understanding evolutionary history of species: understanding of evolution and transmission of disease AND making decisions about conservation efforts (preserving variation produced by evolution). Should focus on preserving a single species without sister species. BUILDING PHYLOGENETIC TREES · CLADISTICS: most accepted method for constructing phylogenetic trees · This method sorts organisms into CLADES, groups of organisms that are most closely related to each other and the ancestor from which they descended · A single clade: MONOPHYLETIC GROUP · Clades must include the ancestral species and all of the descendants from a branch point · Lizards, rabbits, and humans all belong to the clade AMNIOTA · Vertebrata is a larger clade that also includes fish and lamprey · Clades can vary in size depending on which branch point is being referenced · The important thing is that all the organisms in the clade/monophyletic group stem from a single point on the tree · 3 assumptions of Cladistics: · 1. Living things are related by descent from a common ancestor, which is a general assumption of evolution. · 2. Speciation occurs by splits of one species into 2, never more than 2 at a time, and essentially at one point in time. · 3. Traits change enough over time to be considered to be in a different state. Also, one can identify the actual direction of change for a state. So, we assume that an amniotic egg is a later character state than non-amniotic eggs. This is called POLARITY OF THE CHARACTER CHANGE. We know this by reference to a group outside the clade. · Cladistics compares ingroups and outgroups · An ingroup (lizard, rabbit, and human in our example) is the group of taxa being analyzed · An outgroup (ex. fish in our example) is a species or group of species that diverged before the lineage containing the group(s) of interest. · By comparing ingroup members to each other and to outgroup members, we can determine which characteristics are evolutionary modifications determining the branch points of the ingroup's phylogeny · If a characteristic is found in all members of a group/clade, it is a SHARED ANCESTRAL CHARACTER because there has been no change in the trait during the descent of each of the members of the clade. · In cladistic, these characters are not useful when we are trying to determine the relationships of the members of the clade because every member is the same · SHARED DERIVED CHARACTER: a trait that changed at some point during descent. Only some organisms in the group/clade have this trait. · This DOES tell us about relationships among the members of the clade; tells us that lizards, rabbits, and humans group more closely together than any of these organisms do with fish (and other organisms with no amniotic eggs) · The terms "ancestral" and "derived" are relative. The same trait could be either ancestral or deprived depending on the diagram being used and the organisms being compared. Scientists find these terms useful when distinguishing betweel clades during the building of phylogenetic trees, but important to remember their meaning depends on context. CHOOSING THE RIGHT RELATIONSHIP · Constructing a phylogenetic tree/cladogram from character data is a task usually left to computer · Computer draws a tree so that all the clades share the same list of derived characters · A CHARACTER STATE that appears in 2 clades must be assumed to have evolved independently in those clades. · Scientists often use a concept called MAXIMUM PARSIOMY: events occurred in the simplest, most obvious way. So, the "best tree" is the one with the fewest number of character reversals (a trait evolving and disappearing and reappearing, etc), fewest number of independent character changes, and fewest number of character changes throughout the tree. · Starting w/ all the homologous traits in a group of organisms, scientists can determine the order of evolutionary events of which those traits occurred that is the most obvious and simple. · People seem to be more closely related to fungi than fungi are to plants · DO PRACTICE PROBLEMS

Chapter 13

CHAPT 13 · Until late 20th century, 5 kingdoms: animals, plants, fungi, protists, bacteria · Carl Woese compared nucleotide sequences of subunit rRNA, resulted in 3 domains · Archaea and bacteria very different membrane structure and rRNA · Prokaryotes are ubiquitous - inhabit harsh and benign environments · Eukarya - animals, plants, fungi, protists 13.1: PROKARYOTIC DIVERSITY · Bacteria and archaea (w/ DNA sequencing) were shown to be as diff from each other as they are from eukaryotes · Prokaryotes: first forms of life on earth. Existed for billions of years before plants and animals · Earth: 4.54 billion years old · Based on dating of meteorite material · Other rocks have gone through geological changes to make them younger than the Earth · So, age of meteorites good indicator of formation of Earth · Estimate from Clare Patterson 1956 · For first 2 billion years, atmosphere was ANOXIC (NO OXYGEN) · Only ANAEROBIC ORGANISMS could live · PHOTOTROPHS: convert solar energy into chemical energy. Phototrophic organisms that required an organic source of carbon appeared within one billion years of formation of Earth. · Then, CYANOBACTERIA (AKA blue-green algae) evolved from these simple phototrophs 1 billion years later · Cyanobacteria can use CO2 as source of C · Increase in oxygen concentration allowed evolution of other life forms · Before atmosphere became oxygenated, STRONG RADIATION. So, first organisms flourished where they were protected (ex. ocean depths or beneath surface). · Strong volcanic activity was common, so first prokaryotes were adapted to high temperatures. · Microbial mats may represent earliest life forms. MICROBIAL MAT: large biofilm. A multi-layered sheet of prokaryotes, including mostly bacteria, but also archaea. A few centimeters thick. Grow on moist surfaces. Their diff types of prokaryotes carry out diff metabolic pathways, so reflect diff colors. Prokaryotes held together by a gummy-like substance they secrete. · First microbial mats obtained energy from HYDROTHERMAL VENTS: a fissure in Earth's surface that released geothermally heated water. W/ evolution of photosynthesis 3 billion years ago, some prokaryotes in microbial mats used a more widely available energy source - SUNLIGHT - whereas others were still dependent on chemicals from hydrothermal vents for food. · Fossilized microbial mats represent earliest record of life on Earth. · STROMATOLITE is a sedimentary structure formed when minerals are precipitated from water by prokaryotes in a microbial mat. · Stromatolites form layered rocks made of carbonate or silicate. · Although most stromatolites are artifacts from past, there are places where they still form. Ex. California. · Some prokaryotes can thrive and grow under conditions that would kill plants/animals. · Bacteria and archaea grow in extreme conditions called EXTREMOPHILES · Extremophiles found in depths of oceans, hot springs, Arctic and Antarctic, dry places, deep in Earth, harsh chem environments, high radiation environments · Give us understanding of prokaryotic diversity and open up possibility of discovery of new drugs or industrial applications, and finding life off Earth · Many extremophiles cannot survive in moderate environments BIOFILMS · Until recently, we thought prokaryotes were isolated entities living apart · This does not reflect true ecology of prokaryotes, most of which prefer to live in communities where they can interact · BIOFILM: microbial community held together in gummy-textured matrix, consisting primarily of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached to surfaces. Best studied ones are composed of prokaryotes, although fungal biofilms have been found. · Biofilms present almost everywhere. Cause clogging of pipes and readily colonize surfaces in industrial settings. Have been involved in outbreaks of bacterial contamination of food. Also colonize household surfaces. · These communities are more robust than are free-living/planktonic prokaryotes. · Biofilms are difficult to destroy, because they are resistant to common forms of sterilization. PROKARYOTE CHARACTERISTICS · All cells have 4 common structures: a plasma membrane that functions as a barrier for the cell and separates it from environment; cytoplasm (jelly-like substance inside cell); genetic material (DNA and RNA); and ribosomes (where protein synthesis takes place) · Prokaryotes come in diff shapes, fall into 3 categories: Cocci (sphere), Bacilli (rod), and Spirilla (Spiral) · Prokaryotes lack organelles surrounded by membranes · Do not have nucleus but instead have single chromosome (piece of circular DNA located in nucleoid) · Most have cell wall outside plasma membrane · Composition of cell wall differs between Bacteria and Archaea (also differs from cell wall in plants and fungi) · Cell wall: protective layer, responsible for organism shape · CAPSULE: found in some prokaryotic species: enables organism to attach to surfaces and protects it from dehydration. · Some species have FLAGELLA for locomotion and PILI for attachment to surfaces and to other bacteria for conjugation · PLASMIDS (small circle pieces of DNA outside main chromosome) also present in many species of bacteria · Bacteria and Archaea differ in cell wall and composition of cell membranes · Both have same basic structure, but built from diff chemical components: evidence of ANCIENT SEPARATION OF THEIR LINEAGE · Some archaeal membranes are lipid monolayers instead of phospholipid bilayers CELL WALL · Gives shape and rigidity to some prokaryotic cells · Prevents osmotic lysis (bursting caused by increasing volume) · Chem compositions of cell walls vary between archaea and bacteria, and among bacterial species · Bacterial cell walls have PEPTIDOGLYCAN (composed of polysaccharide chains cross-linked to peptides). · Bacteria divided into 2 groups: GRAM POSITIVE AND GRAM NEGATIVE: based on reaction to procedure called Gram staining · Diff responses to staining caused by cell wall structure · Gram positive: thick wall w/ many layers of peptidoglycan. · Gram negative: thin cell wall w/ few layers of peptidoglycan and additional structures, surrounded by outer membrane. · Archaeal cell walls DO NOT CONTAIN PEPTIDOGLYCAN. 3 diff types of archaeal cell walls. One is composed of PSEUDOPEPTIDOGLYCAN. The other 3 contain POLYSACCHARIDES, GLYCOPROTEINS, AND SURFACE LAYER PROTEINS (S-LAYERS). REPRODUCTION · Prokaryotes: primarily asexual and takes place by binary fission. · Prokaryotes do not undergo mitosis · Chromosome loop is replicated, and 2 resulting copies attached to the plasma membrane move apart as the cell grows in BINARY FISSION. · Prokaryote (now enlarged) is pinched inward at its equator, and 2 resulting cells (clones) separate · No opportunity for genetic recombination, but prokaryotes can alter their genetic makeup in 3 mechanisms of obtaining exogenous DNA · 1. TRANSFORMATION: cell takes in DNA found in environment that is shed by other prokaryotes, alive or dead. · -PATHOGEN: an organism that causes a disease. If a nonpathogenic bacterium takes up DNA from a pathogen and incorporates new DNA into chromosome, it may become pathogenic. · 2. TRANSDUCTION: bacteriophages (viruses that infect bacteria) move DNA from one bacterium to another. Archaea have diff set of viruses that infect them and translocate genetic material from one individual to another. · 3. CONJUGATION: DNA transferred from one prokaryote to another by means of a PILUS that brings organisms into contact with one another. Transferred DNA is usually a plasmid, but parts of chromosome can also be moved. · Cycles of binary fission can be rapid. Short generation time coupled w/ mechanisms of genetic recombination result in RAPID EVOLUTION OF PROKARYOTES, allowing them to respond to environmental changes (such as introduction of antibiotic) quickly · Prokaryotes: metabolically diverse organisms · Fill many niches on Earth · Involved in nitrogen and carbon cycles, decompose dead organisms, and grow and multiply inside living organisms · Diff prokaryotes can use diff sources of energy to assemble macromolecules from small molecules · Prokaryotes can be phototrophs or chemotrophs. Phototrophs obtain energy from sun. Chemotrophs obtain energy from chem compounds. · ALL PATHOGENIC PROKARYOTES ARE BACTERIA; there are no known pathogenic archaea in humans or other organisms · Pathogenic organisms evolved alongside humans Historical Perspective · Several PANDEMICS are caused by bacteria · Many were zoonses that appeared w/ domestication of animals (ex. tuberculosis) · Zoonosis: disease that infects animals but can be transmitted to humans · Infectious diseases: leading cause of death worldwide · Especially important in developing countries · Access to antibiotics is not universal, and overuse of antibiotics has led to development of resistant strains of bacteria · Sanitation efforts to dispose of sewage and provide clean water have done as much as medical advances to prevent deaths from bacterial infections · Bubonic plague decimated Europe more than once · BLACK DEATH: another outbreak of bubonic plague caused by bacterium YERSINIA PESTIS. Carried by fleas living on black rats. · It struck London again mid 1600s · Still, there are cases · Mortality rates now low because of antibiotics · European conquerers brought disease causing bacteria and viruses to west, triggering EPIDEMICS that devastated pops of Native Americans (no resistance) ANTIBIOTIC CRISIS · Antibiotic is organism-produced chemical that is hostile to growth of other organisms · One main reason for resistant bacteria is overuse and incorrect use of antibiotics (ex. not completing full course) · Also the excessive use of antibiotics in livestock · Used in animal feed to enhance production of products. Promotes resistance. · Staph is a common bacterium that can live in and on human body. Usually treatable with antibiotics. A dangerous strain in last few years: METHICILLIN-RESISTANT STAPH (MRSA), resistant to many common antibiotics. · Researchers are working on developing new antibiotics, but few are in drug development pipeline, and it takes many years to generate effective drug FOODBORNE DISEASES · Prokaryotes are everywhere · FOODBORNE DISEASE: illness from consumption of food contaminated with pathogenic bacteria, viruses, or other parasites · In past, it was common to hear about cases of BOTULISM, potentially fatal disease produced by a toxin from anaerobic bacterium CLOSTRIDIUM BOTULINUM. · Can, jar, or package made anaerobic environment for it to grow · Most foodborne illness linked to produce contaminated by animal waste · Not all prokaryotes are pathogenic · All life would not be possible without prokaryotes · Humans have used prokaryotes to create products before the term biotechnology was even coined. Ex. CHEESE, YOGURT HAVE BACTERIA AND ARCHAEA · Many foods contain both bacteria and archaea · Microbial BIOREMEDIATION: use of prokaryotes (or microbial metabolism) to remove pollutants. · Has been used to remove agricultural chemicals (pesticides and fertilizers) that leach from soil into groundwater · Toxic metals can also be removed from water · Ex. Mercury - highly toxic because it accumulates in living tissues. Several bacterial species can carry out biotransformation of toxic mercury into nontoxic forms. · Prokaryotes can also be used for the cleanup of oil spills · Bioremediation is promoted by adding inorganic nutrients that help bacteria already present in the environment to grow · Ex. Hydrocarbon-degrading bacteria feed on hydrocarbons in oil droplet, breaking them into inorganic compounds. · Some bacteria can solubilize the oil or degrade the oil into CO2 · For oil spills in ocean, natural bioremediation occurs. Oil-consuming bacteria in the ocean prior to the spill. · Other oil fractions w/ aromatic and highly branched hydrocarbon chains more difficult to remove · Researchers have genetically engineered other bacteria to consume petroleum products · First patent application for a bioremediation application in US was for genetically modified oil-eating bacterium · There are 10 to 100 times as many bacterial and archaeal cells inhabiting our bodies as we have cells in our bodies · Some of these are mutually beneficial relationships with us. Human is host. · Other relationships are classified as COMMENSALISM, a type of relaitionship in which bacterium benefits and human host is neither benefited nor harmed · Human gut flora live in large intestine, consist of hundreds of species of bacteria and archaea. Diff individuals contain diff species mixes. Term "flora" associated w/ plants, used because bacteria were once classified as plants. Primary function of these prokaryotes for humans is metabolism of food molecules we cannot break down, assistance w/ absorpotion of ions by colon, synthesis of vitamin K, training of infant immune system, maintenance of adult immune system, maintenance of epithelium of large intestine, and formation of protective barrier against pathogens. · Surface of skin also coated w/ prokaryotes · Diff surfaces of skin (ex. underarms, head, and hands) provide diff habitats for diff communities of prokaryotes · Some bacteria produce antimicrobial compounds as probably responsible for preventing infections by pathogenic bacteria 13.2. Eukaryotic Origins. · Prokaryotic cells were first organisms on Earth · Eukaryotic cells emerged about 2.1 billion years ago · During prokaryotic reign, photosynthetic prokaryotes evolved that were capable of applying energy from sunlight to synthesize organic materials (like carbohydrates) FROM CO2 AND AN ELECTRON SOURCE (LIKE HYDROGEN, HYDROGEN SULFIDE, OR WATER) · Functioning of photosynthetic bacteria over millions of years saturated Earth's water with oxygen and oxygenated the atmosphere, which previously contained much greater concentrations of carbon dioxide and lower concentrations of oxygen · Older anaerobic prokaryotes could not function in new aerobic environment. Some species perished, others survived in remaining anaerobic environments. · Other early prokaryotes evolved mechanisms (like aerobic respiration) to exploit oxygenated atmosphere by using oxygen to store energy contained within organic molecules · Aerobic respiration is more efficient way of obtaining energy from organic molecules, which contributed to success of these species (as evidenced by number and diversity of aerobic organisms on Earth today) · Evolution of aerobic prokaryotes: important step toward evolution of first Eukaryote ENDOSYMBIOSIS: THROUGH ENDOSYMBIOSIS, MANY PROKARYOTES EVOLVED INTO ORGANELLES INSIDE EUKARYOTES · 1960s Lynn Margulis developed ENDOSYMBIOTIC THEORY: eukaryotes are a product of one prokaryotic cell engulfing another, one living within another, and evolving together over time until the separate cells were no longer recognizable as such. · This is now widely accepted · Many nuclear eukaryotic genes and molecular machinery responsible for replicating and expressing those genes appear closely related to the Archaea. · On the other hand, metabolic organelles and the genes responsible for many energy-harvesting processes had origins in bacteria · Eukaryotic cells may contain anywhere from one to thousands of MITOCHONDRIA, depending on cell's level of energy consumption · Each mitochondria: moving, fusing, and dividing oblong spheroid · Mitochondria cannot survive outside the cell · As atmosphere was oxygenated, and as successful aerobic prokaryotes evolved, an ancestral cell engulfed and kept alive a free-living, aerobic prokaryote · This gave host cell ability to use oxygen to release energy stored in nutrients · Several lines of evidence support that mitochondria are derived from this endosymbiotic event. · Most mitochondria are shaped like a specific group of bateria and are surrounded by 2 membranes · Mitochondrial inner membrane involves infoldings or cristae that resemble textured outer surface of certain bacteria · MITOCHONDRIA ARE DERIVED FROM ENDOSYMBIOTIC EVENT · Mitochondria divide on their own by process that resembles binary fission in prokaryotes · Have their own circular DNA chromosomes that carries genes similar to those expressed by bacteria · Mitochondria also have special ribosomes and tRNAs that resemble these components in prokaryotes · These features all support that mitochondria were once free-living prokaryotes · CHLOROPLASTS are one type of PLASTID, a group of related organelles in plant cells that are involved in storage of starch, fat, protein, and pigments. Contain green pigment chlorophyll and play role in photosynthesis. · Genetic and morphological studies show that plastids EVOLVED FROM ENDOSYMBIOSIS of an ancestral cell that engulfed a photosynthetic cyanobacterium. · Plastids are similar in size and shape to cyanobacteria and are enveloped by 2 or more membranes, corresponding to inner and outer membranes of cyanobacteria. · Like mitochondria, plastids also contain circular genomes and divide by a process reminiscent of prokaryotic cell division. · Chloroplasts of red and green algae exhibit DNA sequences that are closely related to photosynthetic cyanobacteria, suggesting that red and green algae are direct descendants of this endosymbiotic event. · Mitochondria likely evolved before plastids, because all eukaryotes have either functional mitochondria or mitochondria-like organelles. · In contrast, plastids are only found in a subset of eukaryotes (terrestrial plants and algae) · Exact steps leading to first eukaryotic cell can only be hypothesized, and some controversy exists · Spirochete bacteria have been hypothesized to have given rise to microtubules, and flagellated prokaryote may have contributed raw materials for eukaryotic flagella and cilia · Other scientists suggest that membrane proliferation and compartmentalization (not endosymbiotic events) led to development of mitochondria and plastids. · However, vast majority of studies support endosymbiotic hypothesis · Early eukaryotes were unicellular like most protists are today, but as they became more complex, evolution of multicellularity allowed cells to remain small while still exhibiting specialized functions · Ancestors of today's multicellular eukaryotes are thought to have evolved about 1.5 billion years ago REMEMBER: KING, PHYLLUM, CLASS, ORDER, FAMILY, GENUS, SPECIES "KING PHYLLIP CAME OVER FROM GERMANY STONED." 13.3. PROTISTS. · Eukaryotic organisms that did not fir criteria for kingdoms Animalia, Fungi, or Plantae historically were called protists and were classified into kingdom Protista. · Protists include single-celled eukaryotes living in pond water, but many live in a variety of aquatic and terrestrial environments and niches · NOT ALL PROTISTS ARE MICROSCOPIC AND SINGLE-CELLED; there exist some very large multicellular species, such as KELPS · Molecular genetics has demonstrated that some protists are more related to animals, plants, or fungi than they are to other protists · So, protist linages originally classified into kingdom Protista have been reassigned into new kingdoms or other existing kingdoms · Evolutionary lineages of protists continue to be examined and debated · In meantime, term "protist" still used informally to describe this diverse group of eukaryotes · As a collective group, protists display astounding diversity of morphologies, physiologies, and ecologies · Many protists live in symbiotic relationships with other organisms, and these relationships are often species-specific, so there is huge potential for undescribed protist diversity that matches diversity of the hosts · Few characteristics are common to all protists · Nearly all protists exist in some type of aquatic environment, including freshwater and marine env, damp soil, and snow · Several protist species are PARASITES that infect animals or plants. Lives on another organism and feeds on it, often without killing it. A few protists live on dead organisms or their wastes, and contribute to their decay. · Cells of protists are among the most ELABORATE of all cells · Most protists are microscopic and unicellular · A few protists live as colonies that behave in some ways as a group of free-living cells and in other ways as a multicellular organism · Others are composed of enormous, multinucleate single cells that look like blobs or ferns · Many protist cells are multinucleated; in some species, nuclei are diff sizes and have distinct roles in protist cell division. · Single protist cells have a range of many diff sizes · Protist cells may be enveloped by animal-like cell membranes or plant-like cell walls · Others are encased in glassy silica-based shells or wound with PELLICLES of interlocking protein strips. · The pellicle functions like a flexible coat of armor, preventing protist from being torn or pierced without compromising its range of motion. · Majority of protists are motile, but diff types have evolved w/ diff modes of movement · Some have one or more flagella, which they rotate or whip · Others covered in rows or tifts of cilia that they beat in coordination to swim · Others send out lobe-like pseudopodia from anywhere on cell, anchor pseudopodium to substrate, and pull the rest of cell toward anchor point · Some can move toward light by coupling locomotion strategy with light-sensing organ · PROTISTS EXHIBIT MANY FORMS OF NUTRITION AND MAY BE AEROBIC OR ANAEROBIC. · Photosynthetic protists (photoautotrophs): presence of chloroplasts · Other protists are heterotrophs and consume organic materials to obtain nutrition · Amoebas and some other heterotrophic protist species ingest particles by a process called PHAGOCYTOSIS, in which cell membrane engulfs a food particle and brings it inward, pinching off an intracellular membranous sac, or vesicle, called a food vacuole · This vesicle fuses w/ lysosome, and food particle is broken down into small molecules that can diffuse into cytoplasm and be used in cellular metabolism. · Undigested remains ultimately are expelled from cell through exocytosis · Some heterotrophs absorb nutrients from dead organisms or their wastes, and others use photosynthesis or feed on organic matter, depending on conditions · Most protists are capable of some form of asexual reproduction, such as binary fission to produce 2 daughter cells, or multiple fission to divide simultaneously into many daughter cells · Others produce tiny buds that go on to divide and grow to size of parental protist · Sexual reproduction (involving meiosis and fertilization) common among protists · Many protist species can switch from asexual to sexual reproduction when necessary · Sexual reproduction often associated with periods when nutrients are depleted or environmental changes occur · Sexual reproduction may allow protist to recombine genes and produce new variations of progeny that are better suited to surviving in new env · But, sexual reproduction often associated with cysts that are a protective, resting stage · Depending on habitat, cysts may be particularly resistant to temperature extremes, desiccation, or low pH · This strategy also allows certain protists to "wait out" stressors until their environment becomes more favorable for survival or until they are carried (by wind, water, or transport on a larger organism) to a diff env because cysts exhibit virtually no cellular metabolism · Convergent evolution (diff types of protists exhibiting similar morphological features because theye volved analogous structures due to selective pressures, not due to recent common ancestory): one reason why protist classification is challenging · Emerging classificiation groups the entire domain Eukarryota into 6 supergroups that contain all protists, animals, plants, and fungi. 6 groups: EXCAVATA, CHROMALVEOLATA, EHIZARIA, ARCHAEPLASTIDA, AMOEBOZOA, AND OPISTHOKONTA. · Supergroups are believed to be monophyletic; all organisms within each supergroup evolved from a single common ancestor, and thus all members are most closelyr elated to each other than to organisms outside that group · Still, some evidence lacking for the monophyly of some groups · Many protists are PATHOGENIC PARASITES: must infect other organisms to survive and propagate. · Members of the genus PLASMODIUM must infect a mosquito and a vertebrate to complete their life cycle. · In vertebrates, parasite develops in liver cells and goes on to infect red blood cells, bursting from and destroying blood cells with each asexual replication cycle. · Of the 4 Plasmodium species known to infect humans, P Falciparum accounts for 50% of all malaria cases and it is primary cause of disease-related fatalities in tropical regions of the world. (MALARIA). · P Falciparum can infect and destroy more than one half of human's circulating blood cells, leading to severe anemia · In response to waste products released as parasites burst from infected blood cells, host immune system mounts a massive inflammatory response w/ delirium-inducing fever episodes, spilling parasite waste into blood stream · TRYPANOSOMES: · T. Brucei, parasite responsible for African sleeping sickness, confounds the human immune system by changing its thick layer of surface glycoproteins with each infectious sycle. Glycoproteins are identified by immune system as foreign matter, and a specific antibody defense is mounted against the parasite. · T. Brucei has thousands of possible antigens, though. With each subsequent generation, protist switches to a glycoprotein coating with a different molecular structure. · So, it is capable of replicating continuously without the immune system ever succeeding in clearing the parasite · Without treatment, African sleeping sickness leads invariably to death because of damage it does to the nervous system · In Latin America, another species in the genus, T. Cruzi, is responsible for Chagas disease. Mainly caused by a blood-sucking bug. · Parasite inhabits heart and digestive system tissues in chronic phase of infection, leading to malnutrition and heart failure · Protist parasites of terrestrial plants are agents that destroy food crops · Ex. Late Blight causing Irish Potato famine. Due to Phytophthora infestans. · PROTISTS ARE IMPORTANT ECOLOGICAL PRODUCERS, PARTICULARLY IN THE WORLD'S OCEANS. EQUALLY IMPORTANT AS DECOMPOSERS. · In some cases (ex. plankton) protists are consumed directly · Alternatively, photosynthetic protists serve as producers of nutrition for other organisms by carbon fixation · Ex. Symbiotic relationship between photosynthetic dinoflagellates (zooxanthellae) and coral polyps · In aquatic env, protists are primary producers (feed a large proportion of aquatic species) · On land, terrestrial plants are primary producers · ¼ of world's photosynthesis is conducted by protists (particularly dinoflagellates, diatoms, and multicellular algae) · Many fungus-like protists are SAPROBES, organisms that feed on dead organisms or the waste matter produced by organisms (saprophute is an equivalent term) and are specialized to absorb nutrients from nonliving organic matter. · Ex. Many types grow on dead animals or algae. · Saprobic protists have essential function of returning inorganic nutrients to the soil and water. · This process allows for new plant growth, which in turn generates sustenance for other organisms · Without saprobic species like protists, fungi, and bacteria, life would cease to exist. All organic carbon would be tied up in dead organisms. 13.4. FUNGI. · Kingdom fungi includes an enormous variety of living organisms collectively referred to as EUMYCOTA, or true fungi · Edible mushrooms, yeasts, black mold, and Penicillium notatum (producer of antibiotic penicillin) are all members · A typical fungal cell contains a true nucleus and many membrane-bound organelles · Fungi were once considered plant-like organisms; however, DNA comparisons have shown fungi more closely related to animals than plants · Fungi not capable of photosynthesis. Use complex organic compounds as sources of energy and carbon. · Some fungal organisms only multiply asexually, whereas others undergo both asexual reproduction and sexual. · Most fungi produce a large number of spores that are disseminated by the wind. · Like bacteria, fungi play an essential role in ecosystems, because they are decomposers and participate in cycling of nutrients by breaking down organic materials into simple molecules · Fungi often interact w/ other organisms, forming mutually beneficial or mutualistic associations · Fungi also cause serious infections in plants and animals · In humans, fungal infections are generally considered challenging to treat because, unlike bacteria, they do not respond to traditional antibiotic therapy since they are also eukaryotes · Fungi have many commercial applications. Ex. Yeasts in baking, brewing. Many industrial compounds are byproducts of fungal fermentation. Fungi are source of many commercial enzymes and antibiotics. · Fungi are eukaryotes and have a complex cellular organization · Contain a membrane-bound nucleus · Some types of fungi have structures comparable to the plasmids (loops of DNA) seen in bacteria · Fungal cells also have mitochondria and complex system of internal membranes, including endoplasmic reticulum and Golgi apparatus · Fungal cells DO NOT HAVE CHLOROPLASTS · Although the photosynthetic pigment chlorophyll is absent, many fungi display bright colors, ranging from red to green to black · Pigments in fungi are associated w/ cell wall and play protective role against UV radiation. Some pigments are toxic. · Like plant cells, fungal cells surrounded by THICK CELL WALL. However, rigid layers contain complex polysaccharides chitin and glucan and not cellulose that is used by plants. · Chitin, also found in exoskeleton of insects, gives structural strength to cell walls of fungi · Cell wall protects the cell from desiccation and predators · Fungi have plasma membranes similar to other eukaryotes, except that the structure is stabilized by ergosterol, a steroid molecule that functions like the cholesterol found in animal cell membranes · Most members of kingdom Fungi are NONMOTILE. · Flagella are produced only by the gametes in primary division CHYTRIDIOMYCOTA. · Vegetative body of a fungus is called THALLUS and can be unicellular or multicellular · Some fungi are dimorphic because they can go from being unicellular to multicellular depending on environmental conditions · Unicellular fungi are generally referred to as YEASTS · Saccharomyces cerevisiae (baker's yeast) and Candida species (agents of thrush, a common fungal infection) are examples · MOST FUNGI ARE MULTICELLULAR · They display 2 distinct morphological stages: vegetative and reproductive · Vegetative stage is characterized by a tangle of slender thread-like structures called HYPHAE, whereas reproductive stage can be more conspicuous (standing out, clearly visible) · A mass of hyphae is called MYCELIUM. It can grow on a surface, in soil or decaying material, in a liquid, or even in or on living tissue. (A hypha (plural hyphae, from Greek ὑφή, huphḗ, "web") is a long, branching filamentous structure of a fungus, oomycete, or actinobacterium) · Although individual hypha must be observed under microscope, mycelium of a fungus can be very large with some species truly being "the fungus humongous." · Giant Armillaria ostoyae (honey mushroom) is LARGEST ORGANISM ON EARTH · Most fungal hyphae are divided into separate cells by end walls called septa (singular: SEPTUM) · In most divisions (like plants, fungal phyla are called DIVISIONS by tradition) of fungi, tiny holes in the septa allow for rapid flow of nutrients and small molecules from cell to cell along the hyphae · They are described as perforated septa · Hyphae in bread MOLDS are not separated by septa. They are formed of large cells containing many nuclei, an arrangement described as COENOCYTIC HYPHAE. · Fungi thrive in environments that are MOIST AND SLIGHTLY ACIDIC, and can grow with or without light. · They vary in their oxygen requirements · Most fungi are obligate aerobes, requiring oxygen to survive · Other species, such as Chytridiomycota that reside in rumen of cattle, are obligate anaerobes, meaning they cannot grow and reproduce in environment with oxygen · Yeasts are intermediate: grow best in presence of oxygen but can use fermentation in absence of oxygen · Alcohol produced from yeast fermentation is used in wine and beer production, and CO2 they produce carbonates beer and sparkling wine, and makes bread rise · Reproductive stage could be sexual or asexual · In both sexual and asexual reproduction, fungi produce spres that disperse from parent organism by either floating in the wind or hitching a ride on an animal · Fungal spores are smaller and lighter than plant seeds, but they are not usually released as high in the air. · Giant puffball mushroom bursts open and releases trillions of spores: huge number of spores increases likelihood of spores landing in an environment that will support growth. · Like animals, fungi are heterotrophs: use complex organic compounds as a source of carbon. · Fungi do not fix nitrogen from the atmosphere. · Like animals, they must obtain it from their diet. · However, unlike most animals that ingest and digest food, fungi perform these steps in reverse order · First, exoenzymes (catalyze reactions on compounds outside the cell) are transported out of the hyphae where they break down nutrients in the environment. (Digestion). · Then, the smaller molecules produced by the external digestion are absorbed through the large surface areas of the mycelium. · As with animal cells, the fungal storage polysaccharide is glycogen rather than starch, as found in plants. · Fungi are mostly saprobes, organisms that derive nutrients from DECAYING ORGANIC MATTER, mainly plant material · Fungal exoenzymes break down polysaccharides, such as cellulose and lignin of dead wood, into readily absorbable glucose molecules · Because of their varied metabolic pathways, fungi fulfill an important ecological role and are being investigated as potential tools in bioremediation · Ex. Some species of fungi can break down diesel oil and polycyclic aromatic hydrocarbons. Other species take up heavy metals like cadmium and lead. · FUNGI KINGDOM CONTAINS 4 MAJOR DIVISIONS THAT WERE ESTABLISHED ACCORDING TO THEIR MODE OF SEXUAL REPRODUCTION. · Polyphyletic, unrelated fungi that reproduce without a sexual cycle, are placed for convenience in 5th division, and 6rg major fungal group that doesn't fit with any of the others has been described · Rapid advances in biology continue to reveal new diff relationships · Traditional division: CHYTRIDIOMYCOTA (chytrids), ZYGOMYCOTA (conjugated fungi), ASCOMYCOTA (sac fungi), and BASIDIOMYCOTA (club fungi). · An older classification scheme grouped fungi that strictly use asexual reproduction into Deutermycota, a group that is no longer in use. · GLOMEROMYCOTA belong to a newly described group. · FUNGI MAY BE PARASITES, PATHOGENS, AND IN VERY FEW CASES, PREDATORS · Most plant pathogens are fungi that cause tissue decay and eventual death of the host. · Some plant pathogens also spoil crops by producing potent toxins · Fungi responsible for food spoilage and rotting · Fungi attack animals directly by colonizing and destroying tissues · Individuals can eat poison mushrooms or develop allergies to molds · Difficult to treat fungi infections in humans because compounds that kill fungi also adversely affect the host (human) · Many fungal infections (MYCOSES) are superficial and termed cytaneous (meaning "skin") mycoses · Usually visible on skin of the animal · Rarely spread to underlying tissue · Secrete extracellular enzymes that break down keratin protein, causing conditions like athlete's foot · Systematic mycoses spread to internal organs, entering body through respiratory system · In soil env that is poor in nitrogen, some fungi resort to predation of nematodes (small roundworms). · Fungi prefer dark, moist ecosystems · Can thrive in hostile env like tundra, thanks to symbiosis with photosynthetic organisms, like lichens · Like bacteria, fungi are major decomposers of nature · W/ their versatile metabolism, fungi brea down organic matter · Fungi have evolved enzymes to break down cellulose and lignin, components of plant cell walls that few other organisms are able to digest, releasing their carbon content · FUNGI ARE ALSO INVOLVED IN ECOLOGICALLY IMPORTANT COEVOLVED SYMBIOSIS, BOTH MUTUALLY BENEFICIAL AND PATHOGENIC WITH ORGANISMS FROM OTHER KINGDOMS. · MYCORRHIZA: refers to association between vascular plant roots and their symbiotic fungi. Fungal mycelia use extensive network of hyphae and large surface area in contact with the soil to channel water and minerals from soil into the plant. In exchange, plant supplies products of photosynthesis to fuel metabolism of fungus. · LICHENS: blanket many rocks and tree bark, displaying range of colors and textures. Important pioneer organisms that colonize rock surfaces in otherwise lifeless env created by glacial recession. Can leach nutrients from rocks and break them down in first step to creating soil. Also present in mature habitats on rock surfaces or trunks of trees. Important food source for caribou. · Lichens are not a single organism, but a fungus living in close contact with a photosynthetic organism (an alga or cyanobacterium) · Body of lichen (THALLUS) is formed of hyphae wrapped around green partner. · Photosynthetic organism provides C and energy and receives protection from elements by thallus of fungal partner. · Some cyanobacteria fix nitrogen from atmosphere, contributing nitrogenous compounds to the association. In return, funfus supplies minerals and protection from excessive light. · As animal pathogens, fungi help control population of damaging pests · Potential to use fungal as microbial insecticides is being investigated · Without fungal partner in root systems, 90% of trees and grasses would not survive · Fermentation - wild yeasts are acquired from env and used to ferment sugars into CO2 and ethyl alcohol under anaerobic conditions. · Antibodies are naturally produced by fungi to kill or inhibit the growth of bacteria, and limit competition in the natural environment

Day 10

Day 10 Small stuff with big impacts (microbes) - Prokaryotes Plants get pathogens as well B. gladioli infects Gladiolus plants and lungs in humans. But also able to use petroleum oil as a Carbon resource for growth, metabolizing long hydrocarbon chains into less toxic molecules (BIODEGREDATION). Distinct from BIOREMEDIATION, an engineered attempt to clean a site - often uses organisms like bacteria and fungi that can BIODEGRADE oils, heavy metals, etc. Many natural microbes break down oils in the ocean. Viruses and replicating DNA within a genome are like TRANSPOSABLE ELEMENTS - cannot replicate on their own. Prokaryotes - packaged DNA self-replicates in appropriate environment, makes their own RNA, assembles their own proteins, interacts in diverse ways and some are photosynthetic. Origins of metabolic processes we have discussed are found in prokaryotes. A cell membrane (fats, proteins, sugars) selectively permeable to ions, organic molecules - and controls movement of some substances. Affects diffusion of rates of active transport of substances. Cell wall - proteins, sugars. Gives shape to the cell. CYTOPLASM contains "central dogma" - DNA, RNA, proteins interacting. "Eating" - active transport of molecules via engulfing - most important chemical compounds are large and cannot pass through the membrane passively. Reverse process to remove wastes, byproducts. So, METABOLISM AND EXCRETION in their environment. "Eating" Photoautotrophs photosynthesize - others are heterotrophs, ingesting particles or other organisms via phagocytosis. Endocytosis (Phagocytosis): Food particles ingested are digested by vacuoles (membrane bags) filled with enzymes that degrade organic matter. Undigested particles expelled through exocytosis. Overall, microbes fulfill the same functions, in the same ways, as larger plants, animals, fungi that we are more familiar with. Create and store energy, and break it down into simple molecules. REPRODUCTION IN PROKARYOTES: Primarily asexual - binary fission Diversity generated by MUTATION (no genetic recombination/shuffling like sexual) AND occasional ENDOCYTOSIS of DNA in environment incorporated into what gets replicated (TRANSFORMATION). Viruses (TRANSDUCTION) and active "DNA swaps" (CONJUGATION) can also transfer DNA. "HORIZONTAL GENE TRANSFER" (HGT) means that "species" identities are far more fluid in prokaryotes! Reproduction rates - not unusual for a population to DOUBLE EACH DAY UNDER GOOD CONDITIONS. Historically, prokaryotes classified by type of cell wall (shape) and substance they consume. DNA sequencing of shared genes (like ribosomes that assemble proteins) allowed recognition of 2 very different groups - bacteria and archaea. Archaea first recognized as organisms metabolizing in extreme environment - hot springs, salt lakes, or using anoxic metabolism to generate METHANE rather than CO2. Vast majority of prokaryotes cannot be cultured or grown in lab, so DNA sequencing has been key. Samples from environment can be sequenced for targeted, universal genes. Phylogeny then used to actually tell us what has been found and its relative abundance in that environment. Sequencing whole genome tells us what the FUNCTIONS are that a bacterium or Archaea tends to perform (reverse ecology) - e.g. certain genes involved in metabolizing lignin are required to break down wood. We're covered in bacteria (70% of cell count) Rapid replication - huge implications for immune system. Different diet or environment will lead to different bacteria. Mutations happen for a variety of reasons, at relatively constant rate. In multicellular organisms, only mutations in tissues that produce sperm, eggs, and spores are passed to the next generation. Mutational diversity is proportional to number of reproduction/replication events in a population. Small number of fish - low genetic diversity. Microbe (or virus) numbering in billions or more - very high genetic diversity. Mutations are not in response to antibiotic or other environment change, they happen spontaneously and are discovered because their tolerance allows them to spread - mutational diversity if very high and antibiotic resistance occurs naturally - and can be spread by horizontal gene transfer. Diversity arises spontaneously and constantly, and promotes resistance to medicines. 80% of antibiotics in US used on healthy livestock to promote growth. Non-therapeutic use of antibiotics expose many animals (therefore many bacteria) to low doses, helping resistant bacteria thrive. "Everything is everywhere, the environment selects." Anoxic (limited oxygen) environments - many OBLIGATE anaerobic bacteria/archaea - fermentation. Photoautotrophs - converting sunlight into chemical energy (cyanobacteria, blue-green algae are descendants of the first phototrophs - changed atmosphere on earth forever!) Chemoautotrophs - can metabolize directly from chemical compounds released (ex. from hot springs, hydrothermal vents). Microbes are everywhere. Metabolic processes are diverse! Many kinds! Microscopic size means movement difficult to track directly. Thus, environmental DNA sequencing! Movement of some bacteria through liquid possible with structures like FLAGELLA. Bacterial cell walls contain polysaccharides (carbohydrates, sugars) bonded to proteins. Together, peptidoglycan. This is the basis for Gram+ and Gram- Staining is how different cell walls absorb a stain. Specificity of these PEPTIDOGLYCANS is important for immune response. More easily a virus or pathogen kills a host, less easily it spreads to new host environment. -ex. Ebola. Less it affects the host, it may not replicate as much in that host, but spreads easily. -ex. Common cold. Carbohydrate structures on cell wall of bacteria (or capsid of virus) are species-specific TRAITS called ANTIGENS. Vertebrate adaptive immune system is able to respond quickly to antigens it has experienced before, less quickly to novel antigens - our immune cells then isolate and destroy the "marked cells." -Antibodies mark, immune cells attack. MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) "Self" vs "not self" recognition in vertebrate immune system. Series of gene regions with exceptionally high diversity in most animals, the more diverse the MHC is, the better it responds to diverse pathogens/parasites. If true, benefit to offspring to find a mate that is distinct (non random or disassortive mating) Olfaction (scent) used as a cue in fish, mice, humans, etc. Humans in different parts of the world have been exposed to different environments (and thus different pathogens) - there is greater dissimilarity between successful mates at MHC than other parts of the genome or "unsuccessful" mates. Your personal "microbiome" will vary depending on your diet, hygiene, sex, and more. OBLIGATE ANAEROBIC bacteria thrive as the disease initiates - suggesting that warm oceans and blooms of algae from human addition of nitrogen and phosphorus are leading to "subtopic" (low oxygen) sea water, and sea stars are unable to "breathe." BACTERIA IN FOOD: Lactobacillus converts sugars to lactic acid (fermentation) Common part of human microbiome, especially oral and urogenital areas - protects us from invasion by other microbes. Common use: yogurt, cheese, wine, sourdough, where production of lactic acid lowers pH and provides tart flavor. Protists, eukaryotic organisms that are often (typically) single-celled or very small multicellular organisms that are primary CONSUMERS of bacteria directly. As noted with termites, cows, camels, koalas - bacteria also assist in digestion for larger organisms.

Day 12 - Plants

Day 12 - Plants All flowers, on all flowering plants, produce a fruit. Cultivated roses are more effort for insects to pollinate, thus they have lower FITNESS than wild roses. Sharp objects on rose stem called thorns. Technically, PRICKLES - outgrowth of epidermis. PLANTS: ALTERNATION OF GENERATIONS - macroscopic diploid AND haploid phases, unlike other multicellular organisms - leads to variation in spore/gamete development. Important for understanding fertilization and DISPERSAL. MERISTEM tissue is TOTIPOTENT - can create all of the tissues of a plant as it grows. Land plants in particular have adaptations for obtaining and retaining water, growing against gravity to get more light, vasculature to carry water and nutrients throughout. Major division? Reproduction, from spores to flowers - a single pollen grain is itself a multicellular plant. All life requires 4 resources: carbon, energy, water, and mineral nutrients (nitrogen, phosphorus, potassium, calcium, etc). How do plants get these? Partly through photosynthesis, but from plant perspective, these resources are scarce/diffuse, not concentrated. Plants COLLECT scarce resources through surface area (leaves and root hairs) exposed to environment. Animals are chemoheterotrophs, move to find concentrated resources (food and water). Are INGESTIVE HETEROTROPHS (eat and drink). Fungi are heterotrophs (CHEMOHETEROTROPHS) -absorptive heterotrophs -internally, animals are also absorptive heterotrophs Heterotrophs are taking scarce materials necessary for life and recycling them, scattering them, returning them to the soil or water as products of waste and degradation. A key factor is SURFACE AREA (surface area / volume ratio) Animals have compact body plan (low SA/V ratio) to move through the environment to find resources, BUT absorption of oxygen and nutrients, excretion of wastes, all involve tissues with high SA/V ratio (lungs, kidneys, gut, etc.) -Resources must be distributed. First haploid. Then, when plants moved on to land, became alternation of generations. FUNGI below ground have high SA/V ratio that exposes lots of Surface Area to absorb resources, and the gill of a mushroom has a high SA/V ratio for spore release. Plants - almost entire body plan is focused on high SA/V ratio to absorb unconcentrated resources. AUTOTROPHS (plants, algae, some bacteria) - COLLECTORS - concentrate carbon, energy, and minerals in organic matter (food). HETEROTROPHS (animals, fungi, most bacteria) - SCATTERERS - digest food and release its C, minerals, and energy back to the soil. Plants "fix" C from the atmosphere. Increasing CO2 in atmosphere is reducing nutritive value of many plants we eat. WUE - Water use efficiency - how much water can be taken in for growth and photosynthesis - leads to more dilute soil resources and elements we need; increased sugar. Concerns that poorer countries will be affected by lower nutritive values from staples like rice. MODE OF NUTRITION - plants are unique among the 3 multicellular kingdoms, in being photosynthetic - PHOTOAUTOTROPHS are collectors and concentrators. BODY PLAN - photoautotrophs need a high SA/V ratio to collect diffuse, unconcentrated, and scarce resources. Leaves and roots in particular expose as much of the plant as possible to scarce resources. Leaves are thin and flat (high SA/V). Cell surfaces (cell walls) are wet: open space is filled with moist air. CO2 enters and water enters and oxygen leaves by diffusion (random molecular motion) through open pores (stomata). Leaves - thin and flat because: -Diffusion works well over short distances (mm). -Light would not penetrate thick leaves. -Thin structures radiate heat efficiently (prevents overheating). Root hairs are single cells. They develop near tip of roots but they are not lateral (branch) roots, which are organs. Root hairs absorb most of the water and minerals needed by the plant. Roots/root hairs alone aren't good enough: Plants and fungi establish mutualistic symbiosis called MYCORRHIZAE ("fungus roots"). Plants provide fungus with food, fungus provides additional water and mineral nutrients, especially PHOSPHORUS. Fungus acts as extensive network of root hairs. Not all plants photosynthesize... ex. Monotropa uniflora - how does it photosynthesize? MICORRHIZAE! These plants collect what they need to grow via underground root hairs and interactions through fungal filaments to other plants. They are PARASITES - but also used medicinally for nerve pain, muscle spasms, etc. HOW DO PLANTS GROW? Starting from seed, tissue is maintained that can generate multiple types of tissues - in a multicelled organism, not all cells get to reproduce, but of course they are "descendant cells" from the original fertilized egg. MERISTEM TISSUES retains this TOTIPOTENCY in plants. Plats grow from their tips (from apical meristems). Localized, intermediate growth. Growth from step apical meristems produces new stem tissues and new leaves. Growth from root apical meristems produces new root tissues, which develop root tips. near there, root hairs develop. This is REACHING GROWTH - plant is reaching into its environment to find scarce resources so it can grow. Animals have generalized, usually deterministic growth. On most types of plants, this area of growth (MERISTEM) is located at the tip (apical). On grasses (family poacaea), this growth point is located BELOW the tip (subapical). Location of meristem is important because, when only the tip of GRASS plant is cut away, and meristem remains, the grass can grow a new tip. Lawns are invention of the aristocracy in France and England. Trait variation among and within plants is natural! Gene flow through pollen. Reaching growth is mostly the result of enlargement of cell - the vacuole (a bag of water) -Vacuole enlargement is responsible for root hair elongation. -Large vacuole with a thin layer of cytoplasm around the periphery. -Vacuole enlargement is a cheap way to grow. -Fungi also have large vacuoles. Mode of nutrition linked to: BODY PLAN, characterized by: HIGH SA/V RATIO (leaves, root hairs), produced by: MERISTEM TISSUES, followed by CELL ELONGATION, followed by REACHING GROWTH, which is CONTINUOUS/SEASONAL GROWTH from meristems, which produces new SURFACE AREA mostly at the periphery. Reaching into the environment for resources. LEAVES AND ROOT HAIRS are short lived, delicate, expendable structures that need to be replaced. How do plants respond? Movement is not an option for plants. Is behavior an option? Plants respond in part through growth. Why does plants bending toward light happen in younger rather than older tissue? AUXIN is a growth HORMONE that degrades with UV exposure, so plant BENDS for maximum leaf exposure. Just like phototrophism, GEOTROPISM (growth of parts of plants with gravity upward (negative) and downward (positive)) is also caused by an unequal distribution of auxin. In a root placed horizontally, bottom side contains more auxin, and grows less - causing root to grow in the direction of the force of gravity. Positively geotrophic: downward Negatively geotrophic: upward Opposite happens in a stem. Tissues "know" what to do because of their environment. Can plants hear? A form of rapid acclimation - sound of a pollinator (vibrations captured by petal and leaf tissues) stimulates release of additional sugar into nectar. "Rewards" for pollination. An individual plant can grow toward resources, and can acclimate (ex. change chemistry and expression in the presence of competitors, predators). Over generations, dispersal and local population growth differences allow plant populations to "move." How do plants reproduce without moving to find mates? How do offspring move away from parents? Flowers - short branches with modified leaves - growth response for reproduction. Seeds - a cessation of growth (dormancy of the plant embryo) for survival and reproduction. Fruits are a growth response for seed dispersal. TRADE-OFFS IN DISPERSAL: Seeds may be so small they can't bee seen with naked eye. Or, the size of a coconut. Scientists "log transform" data (often satisfies statistical assumptions o normal distribution). In amazon river basin, some seeds are dispersed not just by gravity, not just by wind, not just by birds and land animals, but even by frugivorous fishes. POLLEN: Tiny multicellular organisms bearing the GAMETOPHYTE stage of plants (alternation of generations). Animal (pollinator) or wind-dispersed. Even sea grasses dispersed by small crustaceans and ocean currents. Huge potential for dispersal from parent-gene flow. Plants have been waging chemical warfare against their predators as long as animals have been eating plants. But animals continue to evolve countermeasures. Chemicals like nicotine, aspirin, morphine, H cyanide, tannins, and guinine taste bad, interfere with an herbivore's metabolism or digestion. In domesticating pants, we have bred out plants' natural chemical defenses so they taste better to us - and to herbivores. Plants respond to damage to neighboring plants by ramping up their own chemical defenses. Attacked plant releases volatile organic compounds (VOCs), neighboring plant senses them and increases production of chemical defenses to become resistant to predator attacks. ANTHOCYANINS: What makes flowers (and vegetables) pink and purple? A vascular pigment that attracts pollinators and herbivores (which scatter seeds) - seems to have protective role against cold. Fall color: ANTHOCYANINS get expressed late in year in many tree leaves as a compound from the breakdown of sugars in presence of light, as the level of phosphate in the leaf is reduced. Orange leaves result from combination of anthocyanins and CAROTENOIDS, which are present year-round to provide "photoprotection" for cells an some types of photosynthesis. Why change colors? -Chlorophyll breaks down and must be regenerated energetically all year long. As fall approaches, leaf veins start to close off prior to abcission (leaf fall). Chlorophyll disappears and hidden yellow and orange pigments are revealed. (So, color from disappearance of chlorophyll, reduced level of phosphate, and breakdown of sugars, which produces Anthocyanins). -Anthocyanins are produced from sugars of breakdown as chlorophyll degrades - much of the important amino acids and important nutrients are resorbed and stored in root system to be used next year. -Energy to grow, maintain, reproduce These pigments themselves are responding to the changing climate. Some pigments reflect UV light to attract pollinators and serve as "sunscreen." Study showed 2% increase in these pigments - changing temperatures, but many change how pollinators "see" flowers. Flower colors change in response to climate change!

Penicillin, a common antibiotic, was originally extracted from:

Fungal tissues.

When both eggs and sperm are released into the environment prior to fertilization (fusion to form zygotes), this is known as:

External Fertilization.

Though sometimes there are other popular terms used for examples of this, when offspring at first do not look much like adults and must go through metamorphosis to gain all of the adult traits, this stage is called:

Larvae

A fungus can dissolve stones.

Yes

Which of these common food items is not a fruit?

Carrot. Rice, tomato, and okra all are.

What is important about knowing whether the fruit trees or bushes in your yard are monoecious or dioecious?

That tells me whether I need to be sure and have both sexes to get fruit.

If researchers want to study an invertebrate "model system" that is as closely related to humans as possible, their best choice might be:

Sea stars (Asterias rubens)

Day 11

PROTISTS - DAY 11 · How are protists different from prokaryotes? How diverse is life and how do we study that? How has the invention of eukaryotes changed the world? · PROKARYOTES -DNA/chromosome(s) in same compartment with ribosomes, proteins often compartmentalized with membranes into vacuoles, etc. -Autotrophs and heterotrophs, all unicellular, asexual reproduction -Mutations add diversity, as do HORIZONTAL GENE TRANSFER (transformation, transduction, conjugation), because DNA not compartmentalized (no gene shuffling, like in sexual reproduction) CELLULAR SYMBIONTS: · Remember that dinoflagellates (related to brown algae) are absorbed by digestive cells of corals via PHAGOCYTOSIS, but they don't get digested - they gain calcium, potassium, etc from the coral diet, the coral gains sugars from their photynthate - and they can stay within the cell as long as this balance remains · And BURKHOLDERIA can be found in amoeba cells (protists) as well as human cellular infections · So, PHAGOCYTOSIS is how larger particles and whole cells are taken in by other cells (including those in our gut lining), and under the right conditions that symbiosis (or parasitism) persists... EUKARYOTES · NUCLEUS separates DNA replication (in nucleus) from metabolism (in mitochondria); mitochondria and chloroplasts replicate within cytoplasm · Greater diversity of cell structures, including the formation of tissues and multicellularity ENDOSYMBIOSIS · At least twice in evolutionary history - MITOCHONDRIA that generate ATP, CHLOROPLASTS that photosynthesize (this is how these organelles came about) - cells were engulfed by a larger cell and not digested, continued replicating inside via binary fission · Model of endosymbiotic origins accounts for unusual membrane layering of these organelles, which have lost many original genes DNA Sequence Data Again... · Sequencing the complete genomes of mitochondria suggest origin from bacteria like Rickettsia; chloroplasts originated from cyanobacteria (photoautotrophs) · Many lines of evidence - structural and genomic - and more examples: · Termite guts full of protists (Trichonympha) help termites eat wood; Trichonympha harbors bacterium Endomicrobia that metabolized cellulose; Burkholderia in eukaryotic cells... · A very thorough 2015 review of diverse theories of where, in fact, the NUCLEUS cane from (likely itself an absorbed prokaryote in an amoeba-like cell), as well as mitochondria, chloroplasts, and more. Much of this work suggests that the origin of Eukarya comes from Archaea (of course, our closer phylogenetic relative). · "The book of early evolution holds many exciting chapters, and the origin of eukaryotes is clearly one of the most crucial, because eukaryotes - and only eukaryotes, the cells that have mitochondria - brought forth genuinely complex life). · Adding complexity adds function and capability. Though bacteria and Archaea are EVERYWHERE, the efficiency of mobile hunters, further buffered from environmental change and additional capacity to combine autotrophy and heterotrophy, leads to a more STABLE lifespan across many diverse environmental niches of the planet! And, there are multiple ways to obtain that flexibility/efficiency. COMMON HUMAN PATHOGENS · Phylum Apicomplexa (within that TSAR clade at bottom left, containing coral symbionts and kelp) contains some nasty buggers like PLASMODIM that causes human malaria; GIARDIA which causes very bad diarrhea, TOXOPLASMA in undercooked meat (or in cat feces, and transferred mother-to-child in pregnancy), and more... · Many obligate parasitic organisms have highly reduced genomes (like VIRUSES) so that although they replicate their own DNA, they don't bother making a lot of other "necessary" things to live because they take it from their hosts! · Watermelon snow: Forms when photoautotrophic algae (Chlamydomonas) "swim" to surface of snow and photosynthesize, but produce other pigments like astaxanthin (carrots) as UV protection. Which, being darker, absorbs UV and warms the organisms, melts surrounding snow - production feedback loop to make more... The tiny tardigrade, an animal, grazes on this algae. · 50-75%: Well more than half of the oxygen produced by photosynthesis is produced by MARINE phytoplankton - diverse photosynthetic PROTISTS · Phytoplankton has so much to do with climate, harmful algal blooms, productivity, remote sensing, and more. · "BACI:" Before-After, Control-Impact. Two ways to study the effect of uncontrolled experimental change. KNOWNS AND UNKNOWNS · Particular regions of the genome from most organisms - such as the sequences that make RIBOSOMES (which make proteins) or are involved in ELECTRON TRANSPORT CHAIN will have very little diversity WITHIN groups of organisms, relative to BETWEEN groups of organisms · So, we can readily identify things that are different types of organisms, and often match to what is known in Genbank (database). Or, match to a higher taxon at least! · Set a threshold (here, 3%) to declare organisms "distinct" for analysis WHAT DO I WANT YOU TO TAKE FROM THE BIK PAPER? · DNA sequencing technology has told us so much about how diverse life is on this planet, among habits. · We use the same DNA sequence DISTANCE measures that we discussed earlier to discover new biodiversity. · The more we catalogue the biodiversity on this planet, the better we can understand how DISTINCT biodiversity RESPONDS TO ENVIRONMENTAL CHANGE. · Group exercise gives you experience w/ search engine GBIF to show how species change their distribution through time and space. · Often, people don't realize how many different "types" there are of the "types" they know! Not just sea turtles, but 7 species representing diverse POPULATIONS. Not just nematodes, but 1000s of species. · Thus, high-throughput sequencing of same gene, and use the gene "match" to reference data indicate. UniFrac is just phylogenetic distance. Same if you only focus on bacteria, or focus on recovering larvae from seawater, etc. · How do we look at "effects?" Before-after, control-impact. · How do we determine "different?" Many measures of similarity or dissimilarity, randomization, and so on. Teach unifrac that way. Now... How do we get to multicellularity? · Each cell has a genome that has a FITNESS (survival and reproduction) in that environment · Adding diverse functions to a cell can STABILIZE ITS FITNESS in its variable environment · Doing that by being MULTICELLULAR is a good idea.. BUT, which of you gets to pass along your genome? · MUST THE CELL NEXT DOOR BE IDENTICAL FOR YOU TO COOPERATE? · What jobs do you do to help for the common good? · How do you insure you don't get taken advantage of? Cyclic Amp (C AMP) - Remember Unit 1 to know what this compound is - Cooperative behavior of the slime mold (protist). Dictyostelium discoideum. These are single-celled, soil dwelling amoebae that transform into a motile "slug" and a "fruiting body" in their life cycle. Multicellular Diversity · Most of the diversity that we visually recognize has been through these struggles! A minority of cells are involved in reproduction. The cooperation among cells is based on signals of relatedness, on discriminating self from non-self. The success of the organism relies on cells taking cues from their neighbors to take on particular functions. · It is okay that there are multiple ways to end up being a combination of things, though as evolution progressed, many of these options have been lost, and so eg the chloroplasts of plants are homologous - single origin - thus can be directly compared phylogenetically. · Multicelled protists can be large - algae in particular well known. Life is crazy diverse, and it is everywhere. Watermelon snow is protistan; kelp forests.

What is an example of the earliest group of plants that produce seeds?

Pine tree.

Malaria is a very serious blood borne disease caused by infection of:

Plasmodium

Through photosynthesis, phytoplankton consume carbon dioxide on a scale equivalent to forests and other land plants.

True

Chapter 15. Animals.

· Kingdom Animalia is a group of multicellular Eukarya · Animal evolution began in ocean over 600 million years ago · Classification system characterizes animals based on anatomy, features of embryological development, and genetic makeup · Classification system is always changing 15.1. Features of the Animal Kingdom. · Almost all animals have specialized tissues · Most animals are motile, at least during certain life stages · Require a source of food to grow and develop · All are heterotrophing, ingesting living or dead organic matter · Distinguishes them from plants (photosynthesis) and fungi (digest food externally) · May be carnivores, herbivores, omnivores, or parasites · Most produce sexually · Offspring pass through a series of developmental stages that establish a determined body plan, unlike plants, for example, in which the exact shape of the body is INDETERMINATE. ANIMALS ARE DETERMINATE. · BODY PLAN refers to shape of an animal. · Most animals develop specialized cells that group together into tissues w/ specialized functions · A tissue is a collection of similar cells w/ a common embryonic origin · 4 major types of animal tissues: nervous, muscle, connective, and epithelial. · Nervous: neurons/nerve cells, which transit nerve impulses · Muscle: contracts to cause all types of body movement from locomotion to movement within body · Connective: many functions. Ex. transport and structural support. Ex. Blood and bone. Comprised of cells separated by extracellular material made of organic and inorganic materials, such as protein and mineral deposits of bone · Epithelial: covers internal and external surface of organs inside animal body, and the external surface of the body of an organism. · Most animals have diploid body (somatic) cells and a small number of haploid reproductive (gamete) cells produced through meiosis. Some exceptions: ex. bees, wasps, ants: male is haploid because it develops from an unfertilized egg. Most animals: sexual reproduction. Many also have mechanisms of asexual reproduction. · Sexual: male and female gametes combine in fertilization. · Sperm form is diverse and includes cells with flagella or amoeboid cells to facilitate motility. · Fertilization may be internal, especially in land animals, or external, as is common in many aquatic species · After fertilization, cells divide and differentiate · In many animals, like mammals, young resemble the adult · Other animals, such as some insects and amphibians, undergo complete metamorphosis in which individuals enter one or more larval stages. For these animals, young and adult have diff diets and sometimes habitats. · In other species, incomplete metamorphosis occurs in which the young somewhat resemble the adults and go through stages separated by molts (shedding of the skin) until they reach final adult form. · Some species (especially invertebrates - no backbone) are capable of asexual reproduction. Some fish, amphibians, reptiles. · Asexual absent in birds and mammals · Most common form of asexual reproduction for stationary aquatic animals is budding and fragmentation. A parent individual can separate and grow into a new individual. · In contrast, a form of asexual in some invertebrates and rare vertebrates is PARTHENOGENESIS (VIRGIN BEGINNING): unfertilized egg develops into new offspring. · Animals classified according to morphological and developmental characteristics, such as body plan · With exception of sponges, animal body plan is symmetrical · So, distribution of body parts is balanced along an axis · Additional characteristics that contribute to animal classification include number of tissue layers formed during development, presence or absence of an internal body cavity, and other features of embryonic development · Metazoa (animals) · Phylogenetic tree based on morphological, fossil, and genetic evidence · Animals may be asymmetrical, radial, or bilateral in form. · ASYMMETRICAL animals: no pattern or symmetry. Ex. a Sponge. · RADICAL SYMMETRY: longitudinal (up and down) orientation. Ex. Sea anemone. Any plane cut along this up-down axis produces roughly mirror image halves. · BILATERAL SYMMETRY: ex. goat. Has upper and lower sides to it, but they are not symmetrical. A vertical plane cut from front to back separates animal into roughly mirror-image right and left sides. Animals with bilateral symmetry also have a "head' and "tail" (anterior vs posterior) and a back and underside (dorsal versus ventral). · Most animal species undergo a layering of early tissues during embryonic development. These layers are called GERM LAYERS. · Each layer develops into a specific set of tissues and organs. · Animals develop either 2 or 3 embryonic germs layers. · The animals that display radial symmetry develop 2 germ layers, an inner layer (endoderm) and outer layer (ectoderm). These animals are called DIPLOBLASTS. · Animals with bilateral symmetry develop 3 germ layers: inner layer (endoderm), outer layer (ectoderm), and middle layer (mesoderm). Animals w/ 3 germ layers are called TRIPLOBLASTS. · Triploblasts may develop an internal body cavity derived from mesoderm, called a COELOM. This epithelial-lined cavity is a space, usually filled with fluid, which lies between the digestive system and the body wall. It houses organs such as kidneys and spleen, and contains the circulatory system. · Triploblasts that do not develop a coelom are called ACOELOMATES, and their mesoderm region is completely filled with tissue, although they have a gut cavity. · Examples of acoelomates include flatworms. Animals with a true coelom are called EUCOELOMATES (OR COELOMATES). · A true coelom arises entirely within the mesoderm germ layer · Animals like earthworms, snails, insects, starfish, and vertebrates are all eucoelomates. · A third group of triploblasts has a body cavity that is derived partly from mesoderm and partly from endoderm tissue. These animals are called PSEUDOCOELOMATES. Ex. Roundworms. · New data on relationships of pseudocoelomates suggests that these phyla are not closely related and so the evolution of the pseudocoelom must have occurred more than once. (Separate, analogous, convergent). · True coelomates can be further characterized based on features of their early embryological development. · Bilaterally symmetrical, triploblastic eucoelomates can be divided into 2 groups based on differences in their early embryonic development. · PROTOSTOMES include phyla such as arthropods, mollusks, and annelids. · DEUTEROSTOMES include chordates and echinoderms. · These 2 groups are named from which opening of the digestive cavity develops first: mouth or anus. · The word "protostome" comes from Greek words meaning "mouth first," and "deuterostome" originates from words meaning "mouth second," so anus first · This difference reflects the fate of a structure called the BLASTOPORE, which becomes the mouth in protostomes and the anus in deuterostomes. · Other developmental characteristics differ between protostomes and deuterostomes, including the mode of formation of the coelom and the early cell division of the embryo. 15.2. SPONGES AND CNIDARIANS. · Kingdom of animals is informally divided into invertebrate animals, those without a backbone, and vertebrate animals, those with a backbone · Vast majority (95%) are invertebrates · Sponges and cnidarians represent the simplest of animals. · Sponges appear to represent an early stage of multicellularity in the animal clade. · Although they have specialized cells for particular functions, they lack true tissues in which specialized cells are organized into functional groups · Sponges are similar to what might have been the ancestor of animals: colonial, flagellated protists · The cnidarians, or the jellyfish and their kin, are the simplest animal group that displays true tissues, although they possess only 2 tissue layers SPONGES · Animals in subkingdom PARAZOA represent the simplest animals and include the sponges, or phylum PORIFERA. · All sponges are aquatic and the majority of species are marine (saltwater) · Sponges live in intimate contact with water, which plays a role in their feeding, gas exchange, and excretion. · Much of the body structure of the sponge is dedicated to moving water through the body so it can filter out food, absorb dissolved oxygen, and eliminate wastes. · Body of the simplest sponges takes the shape of a xylinder with a large central cavity, the SPONGOCOEL. · Water enters the spongocoel from numerous pores in the body wall. · Water flows out through a large opening called the OSCULUM. · However, sponges exhibit a diversity of body forms, which vary in the size and branching of the spongocoel, the number of osculi, and where the cells that filter food from the water are located. · Sponges consist of an outer layer of flattened cells and an inner layer of cells called CHOANOCYTES separated by a jelly-like substance called MESOHYL. · The mesohyl contains embedded amoeboid cells that secrete tiny needles called SPICULES or protein fibers that help give the sponge is structural strength. · The cell body of the CHOANOCYTE is embedded in mesohyl, but protruding into the spongocoel is a mesh-like collar surrounding a single flagellum. · The beating of flagella from all choanocytes moves water through the sponge. · Food particles are trapped in mucus produced by the sieve-like collar of the choanocytes and are ingested by phagocytosis. · This process is called INTRACELLULAR DIGESTION · AMOEBOCYTES take up nutrients repackaged in food vacuoles of the choanocytes and deliver them to other cells within the sponge. · Despite their lack of complexity, sponges are clearly successful organisms, having persisted on Earth for more than half a billion years · Lacking a true digestive system, sponges depend on the intracellular digestive processes of their choanocytes for their energy intake · The limit of this type of digestion is that food particles must be smaller than individual cells · Gas exchange, circulation, and excretion occur by diffusion between cells and the water. · Sponges reproduce both sexually and asexually · Asexual reproduction is either by FRAGMENTATION (a piece of the sponge breaks off and develops into a new individual) or BUDDING (an outgrowth from the parent that eventually detaches). · A type of asexual reproduction found only in freshwater sponges occurs through the formation of GEMMULES, clusters of cells surrounded by a tough outer layer · Gemmules survive hostile environments and can attach to a substrate and grow into a new sponge. · Sponges are MONOECIOUS (or HERMAPHRODITIC), meaning one individual can produce both eggs and sperm. · Sponges may be sequentially hermaphroditic, producing eggs first and sperm later. · Eggs arise from amoebocytes and are retained within the spongocoel, whereas sperm arise from choanocytes and are ejected through the osculum. · Sperm carried by water currents fertilize the eggs of other sponges. · Early larval development occurs within the sponge, and free-swimming larvae are then released through the osculum. · This is the only time that sponges exhibit mobility. Sponges are sessile as adults and spend their lives attached to a fixed substrate. CNIDARIANS · The phylum CNIDARIA includes animals that show radial or biradial symmetry and are diploblastic. · Nearly all (about 99%) cnidarians are marine species · Cnidarians have specialized cells known as CNIDOCYTES (stinging cells) containing organelles called NEMATOCYSTS. · These cells are concentrated around the mouth and tentacles of the animal and can immobilize prey with toxins. · Nematocysts contain coiled threads that may bear barbs. · The outer wall of the cell has a hairlike projection that is sensitive to touch. · When touched, the cells fire the toxin-containing coiled threads that can penetrate and stun the predator or prey. · Cnidarians display 2 distinct body plans: POLYP (stalk) and MEDUSA (bell) · Examples of the polyp form: freshwater species of genus Hydra; perhaps best known medusoid animals are jellyfish · Polyps are sessile as adults, with a single opening to digestive system (the mouth) facing up with tenticles surrounding it · Medusae are motile, with mouth and tenticles hanging from bell-shaped body · In other cnidarians, both polyp and medusa form exist, and the life cycle alternates between these forms · All cnidarians have 2 tissue layers, with a jelly-like mesoglea between them · Outer layer: EPIDERMIS · Inner layer: GASTRODERMIS, and lines the digestive cavity · Between these layers: MESOGLEA · Differentiated cell types in each tissue layer, such as nerve cells, enzyme-secreting cells, and nutrient-absorbing cells, as well as intracellular connections between cells · But, organs and organ systems are not present in this phylum · Nervous system is primitive, with nerve cells scattered across the body in a network · The function of the nerve cells is to carry signals from sensory cells and to contractile cells · Groups of cells in nerve net form nerve cords that may be essential for more rapid transmission · Cnidarians perform EXTRACELLULAR DIGESTION, with digestion completed by intracellular digestive processes · Food is taken into the GASTROVASCULAR CAVITY, enzymes are secreted into the cavity, and the cells lining cavity absorb the nutrient products of the extracellular digestive process. · Gastrovascular cavity has only one opening that serves as both a mouth and an anus (an incomplete digestive system). Like sponges, Cnidarian cells exchange oxygen, carbon dioxide, and nitrogeneous wastes by diffusion between cells in the epidermis and gastrodermis with water. · Phylum Cnidaria contains 4 classes: Anthozoa, Scyphozoa, Cubozoa, and Hydrozoa · Class Arthozoa includes all cnidarians that exhibit a sessile polyp body plan only. No medusa stage within their life cycle. Ex. Sea anenomes, sea plants, corals. · Scypohozoans include all jellies and are motile and exclusively marine with 200 species · Medusa is dominant stage in this life cycle, although there is also a polyp stage. · Cubozoa include jellies that are square in cross-section: box jellyfish. Muscular pads called pedalia at corners of square bell canopy, with one or more tentacles attached to each pedalium. In some cases, digestive system may extend into pedalia. Exist in a polyp form that develops from a larva. Polyps may bud to form more polyps and then transform into the medusoid forms. · Hydrozoa: mostly marine, most have both polyp and medusa forms in life cycle. Many form colonies composed of branches of specialized polyps that share a gastrovasclar cavity. Colonies may also be free-floating and contain both medusa and polyp individuals. Other species are solitary polyps or solitary medusae. Characteristic shared by all these species is hat their gonads are derived from epidermal tissue, whereas in all other cnidarians, derived from gastrodermal tissue. 15.3. Flatworms, Nematodes, and Arthropods. · The animal phyla of this and subsequent modules are triploblastic and have an embryonic mesoderm sandwiched between the ectoderm and endoderm · These phyla are bilaterally symmetrical, so a longitudinal section will divide them into mirror right and left images · Associated with bilateralism is beginning of cephalization, the evolution of a concentration of nervous tissues and sensory organs in the head of an organism, which is where the organism first encounters its environment · Flatworms are acoelomate organisms that include free-living and parasitic forms · Nematodes, or roundworms, possess a pseudocoelom and consist of both free-living and parasitic forms · Arthropods, one of the most successful taxonomic groups on the planet, are coelomate organisms with a hard exoskeleton and jointed appendages · Nematodes and the arthropods belong to a clade with a common ancestor, called Ecdysozoa. Name comes from word ecdysis, which refers to periodic shredding, or molting, of exoskeleton. · Ecdysozoan phyla have a hard cuticle covering their bodies that must be periodically shred and replicated for them to increase in size FLATWORMS · Relationship among flatworms, or phylum Platyhelminthes, is being revised and the description here will follow traditional groupings · Most are parasitic, including parasites of humans · 3 embryonic germ layers that give rise to surfaces covering tissues, internal tissues, and digestive system lining · Epidermal tissue is a single layer of cells or a layer of fused cells covering a layer of circular muscle above a layer of longitudinal muscle · Mesodermal tissues include support cells and secretory cells that secrete mucus and other materials back to surface · Flatworms are acoelomate, so their bodies contain no cavities or spaces between outer surface and inner digestive tract · Free living species of flatworms are predators or scavengers, whereas parasitic forms feed from tissues of their hosts · Most flatworms have an incomplete digestive system with an opening, the "mouth," that is also used to expel digestive system wastes. · Some species also have an anal opening · Gut may be a simple sac or highly branched · Digestion is extracellular, with enzymes secreted into the space by cells lining the tract, and digested materials taken into the same cells by phagocytosis · One group, the cestodes, does not have a digestive system, because their parasitic lifestyle and the environment in which they live (suspended within the digestive cavity of their host) allows them to absorb nutrients directly across their body wall · Flatworms have an excretory system with a network of tubules throughout the body that open to the environment and nearby flame cells, whose cilia beat to direct waste fluids concentrated in the tubules out of the body · The system is responsible for regulation of dissolved salts and excreition of nitrogenous wastes · Nervous system consists of a pair of nerve cords running the length of the body with connections between them and a large ganglion or concentration of nerve cells at the anterior end of the worm; here, there may also be a concentration of photosensory and chemosensory cells. · Since there is no circulatory or respiratory system, gas and nutrient exchange is dependent on diffusion and intercellular junctions · This limits the thickness of the body in these organisms, constraining them to be "flat" worms · Most species are monoecious (hermaphroditic, processing both sets of sex organs), and fertilization is typically internal · Asexual reproduction common in some groups n which an entire organism can be regenerated from just a part of itself · Flatworms divided into 4 classes: Turbellaria, Monogenea, Trematoda, and Cestoda · Turbellarians include mainly free-living marine species, although some species live in freshwater or moist terrestrial environments · Simple planarians found in freshwater ponds and aquaria are examples · Epidermal layer of the underside of turbellarians is ciliated, and this helps them move · Some turbellarians are capable of remarkable feats of regeneration in which they may regrow the body, even from a small fragment · Monogeneans are external parasites mostly of fish with life cycles consisting of a free-swimming larva that attaches to a fish to begin transformation to the parasitic adult form · They have only one host during their life, typically of just one species · The worms may produce enzymes that digest the host tissues or graze on surface mucus and skin particles · Most monogeneans are hermaphroditic, but the sperm develop first, and it is typical for them to mate between individuals and not to self-fertilize · The trematodes, or flukes, are internal parasites of mollusks and many other groups, including humans · Trematodes have complex life cycles that involve a primary host in which sexual reproduction occurs and one or more secondary hosts in which asexual reproduction occurs · Primary host is almost always a mollusk · Trematodes are responsible for serious human diseases like schistosomiasis, caused by a blood fluke (SCHISTOSOMA). · Disease infects an estimated 200 million people in the tropics and leads to organ damage and chronic symptoms including fatigue. · Infection occurs when a human enters the water, and a larva, released from the primary snail host, locates and penetrates the skin · Parasite infects various organs in the body and feeds on red blood cells before reproducing · Msny eggs are released in feces and find their way into waterway where they are able to reinfect the primary snail host. · Cestodes, or tapeworms, are also internal parasites, mainly of vertebrates · Tapworms live in intestinal tract of primary host and remain fixed using a sucker on the anterior end, or scolex, of the tapeworm body · Remaining body of the tapeworm is made up of a long series of units called proglottids, each of which may contain an excretory system with flame cells, but will contain reproductive structures, both male and female. · Tapeworms do not have a digestive system, they absorb nutrients from the food matter passing them in the host's intestine · Proglottids are produced at the scolex and are pushed to the end of the tapeworm as new proglottids form, at which point, they are "mature" and all structures except fertilized eggs have degenerated · Most reproduction occurs by cross-fertilization · The proglottid detaches and is released in the feces of the host. · The fertilized eggs are eaten by an intermediate host. · The juvenile worms emerge and infect the intermediate host, taking up residence, usually in muscle tissue · When muscle tissue is eaten by the primary host, the cycle is completed · There are several tapeworm parasites of humans that are acquired by eating uncooked or poorly cooked pork, beef, fish NEMATODES · Phylum NEMATODA (roundworms) include many species. Many parasitic. · Name derived by "nemos:" thread · Present in all habitats. Very common. Usually not visible · Most nematodes look similar to each other: slender tubes, tapered at each end. · Nematodes are pseudocoelomates and have a COMPLEX DIGESTIVE SYSTEM with a distinct mouth and anus · Nematode body is encased in a cuticle, a flexible but tough exoskeleton, or external skeleton, which offers protection and support · Cuticle contains a carbohydrate-protein polymer called CHITIN. · Cuticle also lined the pharynx and rectum · Although the exoskeleton provides protection, it restricts growth, and therefore must be continually shed and replaced as the animal increases in size · Mouth opens at anterior end with 3 or 6 lips, and in some species, teeth in form of cuticular extensions · There may also be a sharp stylet that can protrude from the mouth to stab prey or pierce plant or animal cells · Mouth leads to a muscular pharynx and intestine, leading to the rectum and anal opening at the posterior end · In nematodes, excretory system is not specialized. Nitrogenous wastes are removed by diffusion. In marine nematodes, regulation of water and salt is achieved by specialized glands that remove unwanted ions while maintaining internal body fluid concentrations. · Most nematodes have 4 nerve cords running along length of body on top, bottom, and sides. · Nerve cords fuse in a ring around the pharynx, to form a head ganglion or "brain" of the worm, as well as the posterior end to form the tail ganglion. · Beneath the epidermis lies a layer of longitudinal muscles that permits only side-to-side, wave-like undulation of the body. · Employ a diversity of sexual reproductive strategies depending on the species; may be monoeious, DIOECIOUS (separate sexes), or may reproduce asexually by parthenogenesis. · Caenorhabditis elegans is nearly unique among animals in having both self-fertilizing hermaphrodites and a male sex that can mate with hermaphrodite. ARTHROPODA · Name means "jointed legs," which describes each of the enormous number of species belonging to this phylum · ARTHROPODA dominate animal kingdom with 85% of known species, with many still undiscovered or undescribed · Principle characteristic in this phylum are functional segmentation of the body and the presence of jointed appendages · As members of Ecdysozoa, also have an exoskeleton made mostly of chitin · Largest phylum in terms of numbers of species, and insects form the single largest group within this phylum · True coelomate animals and exhibit prostostomic development · Presence of segmented body with fusion of certain sets of segments to give rise to functional segments · Fused segments may form a head, thorax, abdomen, or cephalothorax and abdomen, or a head and trunk · Coelom takes form of a HEMOCOEL (blood cavity). The open circulatory system, in which blood bathes the internal organs rather than circulating in vessels, is regulated by a 2 chambered heart. · Respiratory systems vary, depending on group of arthropod: insects and myriapods use a series of tubes (TRACHEAE) that branch throughout the body, open to the outside through openings called SPIRACLES, and perform gas exchange directlu between the cells and air in the tracheae. · Aquatic crustaceans use gills, arachnids employ "book lungs," and aquatic chelicerates use "book gills." · Book lungs of arachnids are internal stacks of alternating air pockets and hemocoel tissue shaped like pages of a book · Book gills of crustaceans are external structures similar to book lungs w/ stacks of leaf like structures that exchange gases with surrounding water · Many habitats · Phylum classified into 5 subphyla: Trilobitomorpha (Trilobites), Hexapoda (insects and relatives), Myriapoda (millipedes, centipedes, and relatives), Crustacea (crabs, lobsters, crayfish, isopods, barnacles, and some zooplankton), and Chelicerata (horseshoe crabs, arachnids, scorpions, daddy longlegs) · Hexapoda have 6 legs. Segments are fused into head, thorax, and abdomen. Bears wings and 3 pairs of legs. The insects we encounter. · Crustaceans are the dominant aquatic arthropods · Although the basic body plan in crustaceans is similar to Hexapoda - head, thorax, and abdomen - head and thorax may be fused in some species to form a CEPHALOTHORAX, which is covered by a plate called the carapace · Exoskeleton of many species is also infused with calcium carbonate, which makes it even stronger than in other arthropods · Crustaceans have an open circulatory system in which blood is pumped into hemocoel by the dorsal heart · Most crustaceans typically have separate sexes, but some, like barnacles, may be hermaphroditic · Serial hermaphroditism, in which the gonad can switch from producing sperm to ova, is also found in some crustacean species · Larval stages are seen in early development of many crustaceans · Most crustaceans are carnivorous, but detrivores and filter feeders are also common · Subphylum Chelicerata includes animals like spiders, scorpions, horseshoe crabs, and sea spiders · Subphylum is predominantly terrestrial, although some marine species also exist. · An estimated 103,000 described species are included in subphylum Chelicerata · Body of chelicerates may be divided into 2 parts and a distinct "head" is not always discernible · Phylum derives its name from the first pair of appendages: the CHELICERAE, which are specialized mouthparts. · Chelicerae are mostly used for feeding, but in spiders, are typically modified to inject venom into their prey · As in other members of Arthropoda, chelicerates also utilize an open circulatory system, with a tube-like heart that pumps blood into large homocoel that bathes internal organs · Aquatic chelicerates utilize gill respiration, whereas terrestrial species use either tracheae or book lungs for gaseous exchange 15.4. MOLLUSKS AND ANNELIDS. · Mollusks are diverse group of mostly marine species · Have a variety of forms, ranging from large predatory solid and octopus, some of which show a high degree of intelligence, to small grazing forms with elaborately sculpted and colored shells · The annelids traditionally include the oligochaetes, which include the earthworms and leeches, the polychaetas, which are a marine group, and 2 other smaller classes · Phyla Mollusca and Annelida belong to a clade called the LOPHOTROPCHOZOA, which also includes the phylum Nemertea, or ribbon worms · They are distinct from the Ecdysozoa (nematodes and arthropods) based on evidence from analysis of their DNA, which has changed our views of the relationships among invertebrates PHYLUM MOLLUSCA · MOLLUSKA is predominant phylum in marine environment, where it is estimated that 23% of all known marine species belong to this phylum · 2nd most diverse phylum of animals · Name "molusca" signifies a soft body, as the earliest descriptions came from observations of unshelled, soft bodied cuttlefish (squid relatives) · Although body forms vary, they share key characteristics, such as a ventral, muscular foot that is typically used for locomotion; the visceral mass, which contains most internal organs; dorsal mantle, which is flap of tissue over the visceral mass that creates a space called mantle cavity · Mantle may or may not secrete a shell of calcium carbonate. In addition, many mollusks have a scraping structure at the mouth, called a RADULA. · Muscular foot varies in shape and function, depending on the type of mollusk · It is retractable as well as extendable organ, used for locomotion and anchorage · Mollusks are eucoelomates, but the coelomic cavity is restricted to a cavity around the heart of adult animals · Mantle cavity, formed inside the MANTLE, develops independently from coelomic cavity · It is a multi-purpose space, housing the gils, anus, organs for sensing food particles in water, and an outlet for gametes · Most mollusks have an open circulatory system with a heart that circulates the hemolymph in open space around the organs · Octopuses and squid are an exception to this and have a closed circulatory system with 2 hearts that move blood through gills and a third, systemtic heart that pumps blood through the rest of the body · Phylum is comprised of 7 classes: Aplacophora, Monoplacophora, Polyplacophora, Bivalvia, Gastropoda, Cephalopoda, and Scaphopoda · Class Aplacophora (bearing no plates) includes worm like animals living mostly on deep ocean bottoms · These animals lack a shell but have aragonite spicules on their skin · Members of class Monoplacophora (bearing one plate) have a single, cap-like shell enclosing the body · Monoplacophorans were believed extinct and only known as fossils until discovery of Neopilina galatheae in 1952 · Today, scientists have identified nearly 2 dozen living species · Animals in the class Polyplacophora (bearing many plates) are commonly known as "chitons" and bear an armor-like, 8 plated shell. These animals have a broad, ventral foot that is adapted for attachment to rocks and a mantle that extends beyond the shell in form of a girdle. They breathe with ctenidia (gills) present ventrally. These animals have a radula modified for scraping. Single pair of nephridia for excretion is present. · Class Bivalvia (2 shells) include clams, oysters, mussels, scallops, and geoducks. · Found in marine and freshwater habitats · As name suggests, bivalves are enclosed in a pair of shells (or valves) that are hinged at the dorsal sides · The body is flattened on the sides · They feed by filtering particles from water and a radula is absent · Exchange gases using a pair of ctenidia, and excretion and osmoregulation are carried out by a pair of nephridia · In some species, posterior edges of mantle may fuse to form 2 siphions that inhale and exhale water · Some bivales like yosters and mussels have unique ability to secrete and deposit a calcerous NACRE or "mother of pearl" around foreign particles that enter the mantle cavity · This property is commercially exploited to produce pearls · Gastropods (stomach food) include well known mollusks like snails, slugs, conchs, sea hares, sea butterflies · Gastropods include shell-bearing species as well as species w/ a reduced snell · These animals are asymmetrical and usually present a coiled shell · Visceral mass in shelled species is twisted and the foot is modified for crawling · Most gastropods bear a head w/ tentacles that support eyes · A complex radula is used to scrape food particles from substrate · Mantle cavity encloses ctenidia as well as a pair of nephridia · Class Cephalopoda (head food animals) includes octopuses, squids, cuttlefish, nautilus. Cephalopods include shelled and reduced-shell groups. Display vivid coloration, typically seen in squids and octupuses, used for camouflage. Ability of some octopuses to adjust their colors to mimic a background pattern or startle a predator. All animals in this class are predators and have beak-like jaws. All cephalopods have a well developed nervous system, complex eyes, and closed circulatory system. Foot is lobed and developed into tentacles and a funnel, used for locomotion. Suckers present on tentacles in octopus and squid. Ctenidia enclosed in large mantle cavity and are serviced by large blood vessels, each with its own heart. · Cephalopods can move quickly via jet propulsion by contracting the mantle cavity to forcefully eject a stream of water. Have separate sexes, and the females of some species care for the eggs for an extended period of time. Although the shell is much reduced and internal in squid and cuttlefish, and absent altogether in octopus, nautilus live inside a spiral, multi-chambered shell that is filled with gas or water to regulate buoyancy · Members of the class Scaphopoda (boat feet) are known colloquially as "tusk shells" or "tooth shells." Open at both ends and usually lie buried in sand with the front opening exposed to water and the reduced head end projecting from the back of the shell. Tooth shells have a radula and a foot modified into tentacles, each with a bulbous end that catches and manipulates prey. ANNELIDA · Phylum ANNELIDA are segmented worms found in marine, terrestrial, and freshwater habitats, but presence of water or humidity is a critical factor for their survival in terrestrial habitats · Name of the phylum is derived from the Latin word "annellus," which means a small ring · Phylum includes earthworms, polychaete worms, leeches · Luke mollusks, exhibit protostomic development · Bilaterally symmetrical and have worm-like appearance · Particularly segmented body plan results in repetition of internal and external features in each body segment · This type of body plan is called METAMERISM · EVOLUTIONARY BENEFIT OF SUCH A BODY PLAN IS THOUGHT TO BE the capacity it allows for evolution of independent modifications in different segments that perform different functions. · Overall body can then be divided into head, body, and tail · Skin is protected by cuticle that is thinner than the curicle of excdysozoans and does not need to be molted for growth · Chitinous hairlike extensions, anchored in skin and projecting from the cuticle, called CHAETAE, are present in every segment in most groups · The chaetae are a defining character of annelids. · Polychaete worms have paired, unjointed limbs called parapodia on each segment used for locomotion and breathing · Before the cuticle there are 2 layers of muscle, one running around its circumference (circular) and one running the length of the worm (longitudinal) · Annelids have a true coelom in which organs are distributed and bathed in coelomic fluid · Possess developed complex digestive system with specialized organs: mouth, muscular pharynx, esophagus, crop · Closed circulatory system w/ muscular pumping hearts in anterior system, dorsal and ventral blood vessels that run length of body with connections in each segment, and capillaries that service tissues · Gas exchange occurs across moist body surface · Excretion carried out by pairs of primitive "kidneys" called metanephridia that consit of a convoluted tubule and an open, ciliated funnel present in every segment · Annelids have well-developed nervous system w/ 2 ventral nerve cords and a nerve ring of fused ganglia present around the pharynx · May be monoecious with permanent gonads (like earthworms and leeches) or dioecious w/ temporary or seasonal gonads (as in polychaetes) · Phylum includes classes Polychaeta and Clitellata; latter contains subclasses Oligochaeta, Hirudinoidea, and Branchiodbdellida · Earthworms are most abundant members of subclass Oligochaeta, distinguished by presence of CLITELLUM, ring structure in skin that secretes mucus to bind mating inidviduals and forms a protective cocoon for eggs · Also have few, reduced chaetae · Number and size of chaetae diminished in oligochaetes as compared to the polychaetes · Chaetae of polychaetes are also arranged within fleshy, flat, paired appendages on each segment called parapodia · Subclass Hirundinoidea includes leeches · All species are obligate symbionts, meaning that they can only survive associated with their host, mainly with freshwater crayfish. · Feed on the algae that grows on the carapace of the crayfish. 15.2. ECHINODERMS AND CHORDATES. · Echinoderms named for their spiny skin · Phylum includes sea stars, sea cucumbers, sea urchins, brittle stars, etc. · ECHINODERMATA: Exclusively marine · Pentaradial symmetry and have a calcareous endoskeleton made of ossicles, although the early larval stages of all echinoderms have bilateral symmetry · Endoskeleton is developed by epidermal cells, which may also possess pigment cells, giving vivid colors to these animals, as well as cells laden with toxins · These animals have a true coelom, a portion of which is modified into a unique circulatory system called WATER VASCULAR SYSTEM · Power to regenerate when lots of body mass is lost · Unique system for gas exchange, nutrient circulation, and locomotion, called the water vascular system · System consists of a central ring canal and radial canals extending along each arm · Water circulates through these structures allowing for gas, nutrient, and waste exchange · Structure on top of the body, called the MADREPORITE, regulates the amount of water in the water vascular system. · Tube feet, which protrude through openings in endoskeleton, may be expanded or contracted using hydrostatic pressure in the system · The system allows for slow movement, but a great deal of power, as witnessed when the tube feet latch on to opposite halves of a bivalve mollusk, like a clam, and slowly but surely pulls the shells apart, exposing the flesh within · Echinoderm nervous system has a nerve ring at center and 5 radial nerves extending outward along the arms · No centralized nervous system · Echinoderms have separate sexes and release their gametes into the water where fertilization takes place · May also reproduce asexually through regeneration from body parts · Phylum divided into 5 classes: ASTEROIDEA (sea stars), OPHIURODIDEA (brittle stars), Echinoidea (sea urchins and sand dollars), Crinoidea (sea lilies or feather stars), and Holothuroidea (sea cucumbers) · Sea stars: thick arms that extend from central disk where organs penetrate into the arms · Use their tube feet not only for gripping surfaces but also for grasping prey · Have 2 stomachs, one of which they can evert through their mouths to secrete digestive juices into or onto prey before ingestion · Process can liquefy prey and make digestion easier · Brittle stars: long, thin arms that do not contain any organs · Sea urchins and sand dollars do not have arms but are hemispherical or flattened with 5 rows or tube feet · Sea lilies and feather stars: stalked suspension feeders · Sea cucumbers: soft-bodied and elongate with 5 rows of tube feet and series of tube feet around mouth that are modified into tentacles used in feeding CHORDATES · Majority of species in phylum CHORDATA are found in subphylum Vertebrata, which include many species with which we are familiar · Vertebrates contain many species, divided into major groupings of lampreys, fish, amphibians, reptiles, birds, and mammals · Animals in Chordata share 4 FEATURES that appear at some stage of their development: a notochord, a dorsal hollow nerve chord, pharyngeal slits, and a post-anal tail. · In certain groups, some of these traits are present only during embryonic development · Chordates are named for the NOTOCHORD, which is a flexible, rod-shaped structure found in embryonic stage of all chordates and in adult stage of some chordate species · It is located between the digestive tube and the nerve cord, and provides skeletal support through the length of the body · In some chordates, the notochord acts as the primary axial support of the body throughout the animal's lifetime · In vertebrates, the notochord is present during embryonic development, at which time it induces the development of the neural tube and serves as a support for the developing embryonic body · The notochord, however, is not found in the postnatal stage of vertebrates; at this point, it has been replaced by the VERTEBRAL COLUMN (the spine) · DORSAL HOLLOW NERVE CORD: derived from ectoderm that sinks below the surface of the skin and rolls into a hollow tube during development. In chordates, located dorsally to the notochord. In contrast, other animal phyla possess solid nerve cords that are located either ventrally or laterally. The nerve cord found in most chordate embryos develops into the brain and spinal cord, which compose the central nervous system · PHARYNGEAL SLITS are openings in the pharynx, the region just posterior to the mouth, that extend to the outside environment. In organisms that live in aquatic environments, pharyngeal slits allow for the exit of water that enters the mouth during feeding. Some invertebrate chordates use the pharyngeal slits to filter food from water that enters the mouth. In fishes, modified into gill supports, and in jawed fishes, jaw supports. In tetrapods, slits modified into components of ear and tonsils, since there is no longer any need for gill supports in these air-breathing animals. · TETRAPOD means "four footed" and this group includes amphibians, reptiles, birds, and mammals. (Birds because they evolved from tetrapod ancestors) · POST-ANAL TAIL: posterior elongation of the body extending beyond the anus. Tail contains skeletal elements and muscles, which provides a source of locomotion in aquatic species, such as fishes. In some terrestrial vertebrates, tail also functions in balance, locomotion, courting, and signalling when danger is near. In many species, tail is absent or reduced. Ex. In apes (including humans) present in embryo, but reduced in size and nonfunctional in adults INVERTEBRATE CHORDATES · In addition to vertebrates, phylum Chordata contains 2 clades of invertebrates: UROCHORDATA (tunicates) and CEPHALOCHORDATA (lancelets). · Members of these groups possess the 4 distinctive features of chordates at some point during their development. · TUNICATES are also called sea squirts. Name tunicate derives from the cellulose-like carbohydrate material, like the tunic, which covers the outer body. · Although the tunicates are classified as chordates, the adult forms are much modified in body plan and do not have a notochord, a dorsal hollow nerve cord, or a post-anal tail, although they do have pharyngeal slits. · Larval form possesses all 4 structures. Most tunicates are hermaphrodites. Tunicate larvae hatch from eggs inside the adult tunicate's body. After hatching, a tunicate larva swims for a few days until it finds suitable suface on which it can attach, usually in dark or shaded location · It then attaches by head to substrate and undergoes metamorphosis into adult form, at which point the notochord, nerve cord, and tail disappear · Most tunicates live a sessile existence in shallow ocean waters and are suspension feeders · The primary foods of tunicates are plankton and detritus · Seawater enters the tunicate's body through its incurrent siphon · Suspended material is filtered out of this water by a mucus net (pharyngeal slits) and is passed into intestine through action of cilia. The anus empties into the excurrent siphon, which expels wastes and water. · LANCELETS possess a notochord, dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail in the adult stage · Notochord extends into the head, which gives the subphylum its name · Extinct fossils of this subphylum date to the middle of the Cambrian period · The living forms, the lancelets, are named for their blade-like shape · Only a few centimeters long, usually buried in sand at bottom of warm temperate and tropical seas. Like tunicates, they are suspension feeders. 15.6. VERETEBRATES.

Day 13 - FUNGI

Day 13 - FUNGI Yeast (usually unicellular) - can be haploid, or diploid, or even multicellular. Lichen is 2 different fungi and one algae in symbiosis. Yeasts are everywhere, and produce useful products via RESPIRATION (with oxygen) and FERMENTATION (without). Role that fungi plays in ecosystem - ABSORPTIVE HETEROTROPHS (DECOMPOSERS) that concentrate nutrients and compounds in unusual ways. Medicinal, agricultural, cultural importance. Tell us about ecosystem health. Plants - AUTOTROPHS - photosynthesis collects diffuse resources (light, water, nutrients, carbon) and concentrates them. animals we know to be HETEROTROPHS - consumers, scatterers of seeds, nutrients, C, etc. FUNGI - heterotrophs/decomposers - return tissues of plants and animals to basic, useable components maintained in soil, shared via mycelia, concentrated in fruiting bodies. How do they eat? Just like us. Many food items are composed of macromolecules too large to move across integument (cell walls, digestive lining, etc). EXOENZYMES are secreted and function outside of cells - break macromolecules down to smaller compounds absorbed by phagocytosis. Your own mouth, stomach, gut full of exoenzymes - amylases for sugars, lipase for fatty tissues, etc. GROWTH - VACUOLES: As with plants, fungal fibers (HYPHAE) use vacuoles and water absorption to expand cells in MYCELIUM (collective for all hyphal cells in an organism). Cells use ENERGY (ENZYMATIC MOVEMENT) to carry VESICLES that release EXOENZYMES. As with other METABOLIC PROCESSES, burn some energy to find/extract new energy. Below-ground growth of fungi is far greater than what we see above-ground. Networks of fungal cells (HYPHAE) intertwine to make a network of MYCELIA, some of which interact directly with MYCORRHIZAE (plant cells). Many times, you see a lot of the same type of mushroom emerge - they may be the same organism. 1 hectare = 10,000 square meters. FUNGI ARE NON-DETERMINISTIC GROWERS. WE (HUMANS) are deterministic. Non-deterministic organisms can keep growing and surviving as long as water and nutrients are available! Multicellular/genetic tests - including if HYPHAE placed in dish and recognize self/non-self (will they fuse?) Multicellular cooperation tends to stop when individuals are distinct, with varying thresholds. CASE STUDY - ARMILLARIA Though some fungi are beneficial to plants, others are PARASITIC - derive nutrition from another, to that organism's detriment. Reproduces SEXUALLY, like most fungi - a mushroom is a fruiting body of the organism, not the organism itself. Mushroom releases SPORES dispersed by wind/animals. Fungal spores (HAPLOID) typically 2 mating types, A and a (but many exceptions) - so, 2 spores of different types must come into contact. Each type of spore releases PHEROMES (chemical communication), grow toward each other in some cases. Fuse to form DIPLOID ZYGOTE, new individual, new generation, new mycelium, eventually new mushroom. Very diverse types of reproduction for fungi. Some species vary in whether they require distinct mating types for successful reproduction. Microscopic spores are produced that can move very far, and then re-form a diploid organism when they encounter another spore of the same species (and typically of the other mating type). DIKARYON - cell of fungal hypha containing 2 haploid nuclei of different strains (different mating types). For many organisms, asking whether or not 2 types are unable to successfully reproduce is one way to ask if they are distinct SPECIES. Because fungi can be readily grown in labs, often have small genomes, and can even be convinced to stay in culture as haploid or diploid form (yeasts), many questions we can ask even about how GENOMIC DIVERGENCE correlates with REPRODUCTIVE ISOLATION, and "what is a species?" SPORES AND DISPERSAL A single puffball may produce 5 billion spores When a single haploid spore finds a good environment (moisture, nutrients, temperature, etc), may GERMINATE and form HAPLOID HYPHAE that grow outward - expanding circle of MYCELIUM ("fairy ring). LICHEN - holistic symbiosis between 2 types of fungi and an alga, often when the individual species do not exist without the others. The fungi degrade the stone/wood, the algae provide sugar. even the offspring are lichen-species-specific in many cases. Several major groups within the fungus, differ in: 1) MOTILITY (Chytrids are motile, with flagella). 2) REPRODUCTIVE STRUCTURES (only Ascomycota and Basidiomycota make "mushrooms." Most ascomycota don't make obvious fruiting bodies, but morels in this group). 3) Not all fungi build CHITIN WALLS (SEPTA) between cells. What if we don't have enough information to form a hypothesis? Some phylogeny trees/parts of trees will not have NODES resolved - this is called POLYTOMY Our assumption is that each node only branches once, but we cannot be sure of the order, so show as all branching from the same point. Another arrangement: what we feel good about is (B, A) and (G (B,A)). The rest is uncertain. Parenthesis indicate HIERARCHICAL RELATIONSHIP (who is more closely related to who). Like kingdom, phylum, class, order, family, genus, species. In PHYLOGENY, the probabilities associated with tree shape and order do not have standard distribution. Very complex. Not normal or chi squared. One way we ask whether MANY TRAITS SUPPORT A TREE is by random re-sample of data (performed thousands of times) to see whether most traits (morphology, DNA sequence, etc) support a particular tree relationship. Published tree should include this statistical justification about how their data support new hypothesis and how it changes taxonomy. Numbers at nodes indicate % of re-samples of data that support that node. 5 very distinct groups within Fungi. Basidio and Asco-mycota are most common species to see in the wild. With lichens, the "2 types of fungi" involved are one of each of these major types - diverged around 500 million years ago from many estimates - with an alga. So, kind of 3 way symbiosis (and bacteria, etc). Yeasts can be ascomycete or basidocyte. SYMBIOSIS AND ECOLOGICAL FUNCTION: Lichen - algae and fungi (usually asomycete) Until recently, biologists couldn't identify how to culture lichens - and some lichens with same alga and fungus have very different traits. In 2016, biologists found the skin of lichen has basidiomycete yeast cells embedded - requires all 3 members. Only because of symbiosis with algae (which have chloroplasts) are lichens photosynthetic autotrophs. Yeasts in particular have biology that benefits RAPID COLINIZATION OF RESOURCES - single celled, can grow quick, can grow aerobically or anaerobically. FERMENTATION - metabolic process that digests sugar in absence of oxygen (or, without using oxygen) - byproducts are acids, gases, or ethanol (ex. lactic acid in kimchi or yogurt, alcohol in beer). Breakdown of fruits (high sugar content) in particular involves yeast colonization - single celled organisms can be thought of as "everything is everywhere, the environment selects." When a resource becomes available, VERY RAPID growth/reproduction, ending in spore dispersal for the next resource. PATHOGENICITY: CHYTRIDS - a pathogen that has been implicated in wiping out many tropical frog populations. Ascomycote Pseudogymnoascus destructans causes white nose syndrome in bats in cold populations. YEASTS are single-celled fungi of Basidiomycota or ASCOMYCOTA (so, evolved from multicellular ancestors) that can colonize moist animal or plant tissues, ex. throast, GI tract, etc. Or, contribute to decaying fruits. Can be distinguished from molds (mostly Ascomycote or Zygomycota) that grow hyphae/mycelia. TOXICITY: Amanita phalloides - death cap, a basidiomycete. MYCORRHIZAL with trees. Has been introduced to new regions, looks like edible mushrooms. Toxins are not affected by heat. Cooking doesn't help. Amatoxins inhibit RNA from being formed - so, cell metabolism stops immediately and cell dies - liver goes first. Unique (to fungi) gene pathway that synthesizes these compounds. Other unique compounds (in different mushrooms) include a PSILOCYBIN, a compound that interacts with seratonin receptors in the brain. METABOLISM IS MORE THAN ENERGY-BUILDING PRODUCTS: Unique compounds that fungi create, and pathways they employ, of interest for: Agriculture: promoting/maintaining mycelial growth for organic crops. No-till farming to avoid disrupting mycelia. MEDICINE: some compounds help anxiety, depression, OCD, smoking cessation, etc. CUISINE - variety of edible fungi. BIOREMEDIATION - ability to uptake and metabolize radioactive and heavy metal compounds, speedy return of organic materials into soil. Some species vary in whether they require a distinct "mating type" allele between haploid spores. HOMOTHALLIC - mating occurs between spores of the same individual (or genotype). HETEROTHALLIC - hyphae from single individual are self-sterile. (Can only reproduce with other individuals of the same species and different mating type). The different mating types are typically controlled by 2 unlinked mating loci, each of which can have many alleles. Like MHC, reproductive diversity may be a benefit for evolution/fitness. Most mushrooms we see are Basidiomycetes, many known pathogens are Ascomycetes -like Candida Aspergillus.

Day 8

Day 8 Selection requires trait variation. In humans (and elephants), a POLYMORPHISM for lack of lateral incisors (2-4% lack these 2 lateral incisors). Tusks are overgrown upper lateral incisors (teeth between front teeth and canine teeth). MUTATION OR EXPRESSION of a single gene seems associated with expression of "teeth" phenotype - highly heritable. Background rate of "tuskless" for elephants was 2-4%, like humans. Now, some pops are 25% tuskles, due to poaching of tusked ones. Selection often involves trade-offs. There used to be elephants in North America - mammoths. 3 domains of life branch from a single point. Allele frequencies at each gene are controlled by drift, selection, migration, and mutation. Pops that are isolated enough have different allele and genotype frequencies. Hardy-Weinberg Equilibrium - we can objectively distinguish when 2 (or more) locations "make more sense" if they each fit HWE on their own rather than together. So, larger number of genotypes from many loci can tell us when individuals belong to distinct populations. We can distinguish populations of Painted Bunting in different parts of US based on genotype frequencies at 1000s of loci. When populations are isolated, new MUTATIONS, and the effects of DRIFT and SELECTION in distinct environments inevitably leads to distinct allele/genotype frequencies. GENE FLOW - consequence of migration and mating - will tend to suppress this divergence. More migrants that can mate, less divergence. Very few migrants, more isolation, unsuccessful mating between pops: MORE divergence of species. At some point, pops don't reproduce at same time, don't recognize each other, don't interact. Diverge and become different. GENETIC DISTANCE = (2 x Time) x Mutation Rate u With mutation rates (u), number of new mutations in a pop of size N every generation is PROPORTIONAL to Nxu. So, large pops: many mutations. Given many generations (time), many genes at which allele frequencies vary, as well as new mutations - pops diverge and become different. GENETIC DISTANCE - d - number of mutations we see among DNA sequences (very simple trait, just A/C/T/G). Sequence the DNA and count the differences. MUTATION RATE - u - mutations per site, per generation (time) TIME DIVERGED - t - both (so x2) populations have gained mutations since their ancestor. d = u x 2t GENOMIC SIMILARITY: The more similar genomic sequences (or trait data of other types) are, we can think: fewer mutations between them. So, not as far back in time since they had a common ancestor. So, we infer evolutionary history further back as we consider more dissimilar DNA, or traits. We get u from contrasting geologically-aged populations, or experiments with short lived organisms. Both work similarly. As does Distance between populations. Spatial distance AMONG humans predicts genetic distance. (Or, is it vice versa?) Less probability of encounter/mating, more genetic distance. Our diversity originates with distance. With time, isolation, mutation, drift, selection - populations change. They become distinct, and adapted to where we find them and the resources they need to survive. What becomes distinct? Nucleotides, expression of genes, traits, colors, size, what they eat. With enough time, they become less recognizable as being descended from the same ancestral population, and they spread and become isolated in new ways. PHYLOGENY: Diversity can be described hierarchically, but the names come from understanding of PHYLOGENY, not the other way around. Phylogenetic trees - a way to interpret massive genealogical relationships AMONG ALL LIFE. Difference between a genealogy and phylogeny is that we are inferring how ancestral populations have diverged, based on the traits we observe NOW. When populations no longe interact demographically (mating), their diversity starts to diverge. Phylogenetic trees are a way to interpret the massive genealogical relationships among all life. Branch points: nodes. Trees are not known, but inferred from available data. Typically evaluate traits and find the tree that requires the fewest number of changes across all traits (parsimony). So, might imagine that transition from tentacles to legs only happened once evolutionarily (might assume homology, not homoplasy). There are more mathematical ways though! Don't always use parsimony!

Day 9

Day 9 How did diverse traits arise throughout biodiversity? Phylogeny helps answer this. Do such traits arise once, or are they "invented" in multiple ways? Are traits associated with environment that organism lives in? HOMOLOGY - distinct traits may arise from structures that have a single origin. Birds and bats evolved wings in distinct events (analogous, parallel, convergent, homoplasy), but perhaps before that, homologous origin. Insect wings - different embryonic tissue entirely. DNA Sequences and Homology: With millions or billions of nucleotides in the genome - varying tremendously across the tree of life - how do we compare sequences? HOMOLOGOUS regions must be aligned to one another, to identify positions that are homologous. Homology isn't just about structures. It is also about genes and gene interactions that allow certain structures to form, such as eyes or pigments (form non-homologously, but due to the same genes). The code for necessary proteins is often older than the structures that use those proteins. Opsins: the proteins that change shape when they absorb a photon have existed for 700 million years. Protein in eyes, used in diff ways in diff animals. Homology means that our phylogenies help us organize biodiversity in terms of shared DERIVED TRAITS (current organism has it, previous ones didn't), more so than shared ancestral traits (both modern and ancestral organism have it). Birds and bats are homologous in terms of forelimb structure. BUT, still evolved in distinct events (parallel, analogous, convergence, homoplasy) independently after that. ex. WITHIN wings, further traits to be studies. Phylogenetic trees let these traits be understood in terms of TIME AND PLACE that they originated, and how they got modified afterward. BIOLUMINESCENCE - production and emission of light by a living organism - unlike simple traits, complex traits like this (also eyes, venom, etc) integrate many genes and their products... Bioluminescence excellent trait for studying multi-level CONVERGENT evolution of complex traits. Complex traits get separated into production of proteins, tissues/cells that these proteins are integrated into, and modification of organs and tissues for light emission. -One approach to learn about convergence - dissect a complete trait into functional modules, and examine convergence on all levels of life. Look at function, phenotype, organ, cellular, and biochemical. -84 independent ORIGINS of bioluminescence across all life. Photoproteins and luciferases (very heterogeneous) vary in amino acid length, protein domain architecture, and evolutionary history. Most are non-homologous, even in organisms that use the same lucifer in substrate (ex. ctenophores and sea pansies). As a result of this disparity, bioluminescence research proposed different hypothesis (Hy) for origins of these proteins. Phylogenetic tree is itself a hypothesis for how organisms are related based on traits they share. Traits like teeth shape, spatial and reproductive isolation, DNA. Classification (taxonomy) - a verbal way of communicating that hypothesis. A goal of modern systematics (phylogeny and taxonomy) is to improve phylogenies so that taxonomy doesn't conflict. e.g. So, definition of a group (family, genus, etc) only appears once. Enzymes may be homologous but then may go on to be used in different independent ways. TIPS are organisms BEING COMPARED. BRANCH POINTS/NODES are junctions of tree that link organisms (show common ancestor). BRANCHES indicate hypothesis of how distinct traits evolved. Branches can be rotated around a node with no change in meaning. Trees may have different shapes with the same meaning for how organisms are related. Branches may also represent the NUMBER of trait differences along a branch. (Also represent length of time that has passed?) Choose the more parsimonious tree (less evolutionary changes) when doubt, usually. Longer branch had lots of time/mutations/trait changes. More data, better answers! We can only recognize Archaea because of DNA sequencing. BRANCH LENGTHS: In addition to PARSIMONY, we can use the number of events (mutations, transition) to indicate evolutionary time. Proportion of mismatched/mutated DNA bases in a homologous gene region can estimate the DISTANCE between these organisms. (REMEMBER, HOMOLOGOUS GENE REGION DOES NOT MEAN THE NUCLEOTIDES ARE THE SAME. MEANS A REGION FROM THE SAME ANCESTOR, BUT NUCLEOTIDES HAVE SINCE CHANGED; AND THE MORE CHANGES, THE MORE EVOLUTIONARY TIME WE INDICATE HAS PASSED). 30 nucleotide differences out of 1000: distance: 3% Bacteria, Archaea, and Eukarya all replicate functions at different scales and in different habitats. Metabolism, energy, storage, photosynthesis, etc. Alignment of DNA/RNA sequences relies not only on MOST positions being invariant (we choose different genes for questions of different evolutionary depth), but also the sequence that "codes" for a protein with EVEN LESS VARIANT amino acid sequence, or secondary structure in ribosomal DNA (rDNA), and so on... Other than just parsimony, some trees use our understanding of how different mutations happen, and their probability over time, to improve approaches.

Which of these plants is considered a vascular plant?

Ferns

If you dig into moist loose soil and look closely you may find hundreds of thin pale thread-like structures weaving together and around plant roots, we refer to this as:

The mycelium.

When scientists talk about bacteria being divided into Gram positive and Gram negative, they are really talking about detection of a:

Trait

When 2 haploid cells fuse in sexual reproduction, multi-cellular organism development begins from a single celled:

Zygote

Does plant growth respond to vibrations?

Yes

What are Phytoplankton? Notes

· Phyto (plant) and plankton (made to wander or drift), phytoplankton are microscopic organisms that live in watery env, both salty and fresh · Some phytoplankton are bacteria, some are protists, and most are single-celled plants · Among common kinds are cyanobacteria (blue-green algae), diatoms, dinoflagellates, green algae, and chalk-coated coccolithophores · Extremely diverse, varying from photosynthesizing bacteria (cyanobacteria) to plant-like diatoms, to armor-plated coccolithophores. · Like land plants, phytoplankton have chlorophyll to capture sunlight, and use photosynthesis to turn it into chemical energy · Consume carbon dioxide, release oxygen · All phytoplankton photosynthesize, but some get additional energy by consuming other organisms · Phytoplankton growth depends on availability of carbon dioxide, sunlight, and nutrients · Phytoplankton, like land plants, require nutrients like nitrate, phosphate, and calcium at diff levels depending on species · Some phytoplankton can FIX NITROGEN and can grow in areas where nitrate concentrations are low · They also require trace amounts of iron which limits phytoplankton growth in large areas of the ocean because iron concentrations are very low. · Other factors influence phytoplankton growth rates, including water temperature and salinity, depth, wind, and what kinds of predators are grazing on them · When conditions are right, phytoplankton populations can grow explosively, a phenomenon known as a bloom · Blooms in the ocean may cover hundreds of square kilometers and are easily visible in satellite images · A bloom may last several weeks, but the life span of any individual phytoplankton is rarely more than a few days · Phytoplankton are the foundation of the AQUATIC FOOD WEB, the primary producers, feeding everything from microscopic, animal-like zooplankton to multi-ton whales. Small fish and invertebrates also graze on the plant-like organisms, and then those smaller animals eaten by bigger ones · Can also be harbingers of death or disease. May produce powerful biotoxins, making them responsible for red tides, harmful algal blooms. These blooms can kill marine life and people who eat contaminated sea food · Phytoplankton cause mass mortality in other ways. In aftermath of massive bloom, dead phytoplankton sink to ocean/lake floor. Bacteria that decompose the phytoplankton deplete the oxygen in the water, suffocating animal life. The result is the DEAD ZONE. · Through photosynthesis, phytoplankton consume carbon dioxide on a scale equivalent to forests and other land plants. · Some of this carbon is carried in the deep ocean when phytoplankton die, and some is transferred to different layers of the ocean as phytoplankton are eaten by other creatures, which themselves reproduce, generate waste, and die. · Phytoplankton responsible for most of the transfer of carbon dioxide from atmosphere to the ocean. Carbon dioxide is consumed during photosynthesis, and the carbon is incorporated in the phytoplankton, just as carbon is stored in the wood and leaves of a tree. Most of the carbon is returned to near-surface waters when phytoplankton are eaten or decompose, but some falls into the ocean depths. · Worldwide, this "biological carbon pump" transfers about 10 gigatonnes of carbon from the atmosphere to the deep ocean each year. Even small changes in the growth of phytoplankton may affect atmospheric carbon dioxide concentrations, which would feed back to global surface temperatures. · Phytoplankton samples can be taken directly from the water at permanent observation stations or from ships. Sampling devices include hoses and flasks to collect water samples, and sometimes, plankton are collected on filters dragged through the water behind a ship. · Samples may be sealed and put on ice and transported for laboratory analysis, where researchers may be able to identify the phytoplankton collected down to the genus or even species level through microscopic investigation or genetic analysis · Although samples taken from the ocean are necessary for some studies, satellites are pivotal for global-scale studies of phytoplankton and their role in climate change. · Individual phytoplankton are tiny, but when they bloom by the billions, high concentration of chlorophyll and other light-catching pigments change the way the surface reflects light · Water may turn greenish, reddish, or brownish. Chalky scales that cover coccolithopores color the water milky white or bright blue. Scientists use these changes in ocean color to estimate chlorophyll concentration and the biomass of phytoplankton in the ocean. · Phytoplankton thrive along coastlines and continental shelves, along the equator of the pacific and Atlantic, and in high-latitude areas · Winds play strong role in distribution of phytoplankton because they drive currents that cause deep water, loaded with nutrients, to be pulled up to the surface · These upwelling zones, including the one along the equator maintained by the convergence of the easterly trade winds, and others along the western coasts of several continents, are among the most productive ocean ecosystems. By contrast, phytoplankton are scarce in remote ocean gyres due to nutrient limitations. · Like plants on land, phytoplankton growth varies seasonally. In high latitudes, blooms peak in spring and summer, when sunlight increases and relentless mixing of water by winter storms subsides. Recent research suggests the vigorous winter mixing sets the stage for explosive spring growth by bringing nutrients up from deeper waters into the sunlit layers at the surface and separating phytoplankton from their zooplankton predators. · In subtropical oceans, by contrast, phytoplankton populations drop off in summer. · As surface waters warm up, through the summer, they become very buoyant. With warm, buoywant water on top and cold, dense water below, the water column doesn't mix easily. Phytoplankton use up the nutrients available, and growth falls off until winter storms kick-start mixing. · In lower latitude areas, including Arabian Sea and waters around Indonesia, seasonal blooms often linked to monsoon-related upwelling, which changes nutrient concentrations · In equatorial upwelling zone, very little seasonal change in phytoplankton productivity · Biggest influence on year-to-year differences in global phytoplankton productivity is the El Nino-Southern Oscillation ENSO climate pattern. ENSO cycles are significant changes from typical sea surface temperatures, wind patterns, and rainfall in Pacific Ocean along the equator. · During El Nino events, phytoplankton productivity in the equatorial Pacific declines dramatically as the easterly trade winds that normally drive upwelling grow still or even reverse direction. · Transition between El Nino and its counterpart, La Nina, is sometimes accompanied by dramatic surge in phytoplankton productivity as upwelling of nutrient-rich deep water is suddenly renewed · El Nino events influence weather patterns beyond the Pacific; in eastern Indian ocean around Indonesia, phytoplankton productivity increases during El Nino · Productivity in Gulf of Mexico and western subtropical Atlantic has increased during El nino events in past decade, probably because increased rainfall and runoff delivered more nutrients than usual · Compared to the ENSO-related changes in the productivity in the tropical Pacific, year-to-year differences in productivity in mid-and-high latitudes are small PRODUCTIVITY · Because phytoplankton are so crucial to ocean biology and climate, any change in their productivity could have a significant influence on biodiversity, fisheries and the human food supply, and the pace of global warming · Many models of ocean chemistry and biology predict that as the ocean surface warms in response to increasing atmospheric greenhouse gases, phytoplankton productivity will decline · Productivity is expected to drop because as the surface waters warm, the water column becomes increasingly STRATEFIED; there is less vertical mixing to recycle nutrients from deep waters back to the surface · About 70% of ocean is permanently stratified into 2 layers that don't mix well · Warmer than average temperatures led to below average chlorophyll concentrations in these areas · Over the past decade, scientists have begun looking for this trend in satellite observations, and early studies suggest there has been a small decrease in global phytoplankton productivity · Ex. Ocean scientists documented increase in area of subtropical ocean gyres - least productive ocean areas - over the past decade · These nutrient "marine deserts" appear to be expanding due to rising ocean surface temperatures SPECIES COMPOSITION · Hundreds of thousands of species of phytoplankton live in Earth's oceans, each adapted to particular water conditions. · Changes in water clarity, nutrient content, and salinity change the species that live in a given place. · Because larger plankton require more nutrients, they have greater need for verticle mixing of water column that restocks depleted nutrients. As ocean has warmed since 1950s, it has become more stratified, which cuts off nutrient recycling. · Continued warming due to the build up of carbon dioxide is predicts to reduce the amounts of larger phytoplankton (such as diatoms), compared to smaller types, like cyanobacteria · Shifts in relative abundance of larger versus smaller species of phytoplankton have been observed already in places around the world, but whether it will change productivity remains uncertain · These shifts in species composition may be benign, or they may result in a cascade of negative consequences throughout the marine food web · Accurate global mapping of phytoplankton taxonomic groups is one of the primary goals of proposed NASA missions