Lecture 14: Macroevolution: Evidence for evolution (Major Concepts)

Summary of Chapter 15

* The theory of evolution—what Darwin called "descent with modification"—draws two main conclusions about life: that all living things are related, sharing a common ancestor in the distant past; and that the species we see today are the result of natural selection operating over millions of years. * The theory of evolution is supported by a wealth of evidence, including fossil, anatomical, and DNA evidence. * Fossils are the preserved remains or impressions of once-living organisms that provide a record of past life on Earth. Not all organisms are equally likely to form fossils. * Fossils can be dated directly or indirectly: on the basis of the age of the rocks they are found in, or on their position relative to rocks or fossils of known ages. * When fossils are dated and placed in sequence, they show how life on Earth has changed over time. * As predicted by descent with modification, the fossil record shows the same overall pattern for all lines of descent: younger fossils are more similar to modern organisms than are older fossils. * Descent with modification also predicts the existence of intermediate organisms, such as Tiktaalik, that possess mixtures of "old" and "new" traits. Tiktaalik has features of both fish and tetrapods (four-limbed vertebrates). * An organism's anatomy reflects adaptation to its ecological environment. Changed ecological circumstances provide opportunities for new adaptations to evolve by natural selection. * Homology—the anatomical, developmental, or genetic similarities shared among groups of related organisms—is strong evidence that those groups descend from a common ancestor. * Homology can be seen in the common bone structure of the forelimbs of tetrapods, the similar embryonic development of all vertebrate animals, and the universal genetic code. * Many genes, including those controlling limb development, are shared among distantly related species, an example of molecular homology owing to common ancestry. * DNA can be used as a molecular clock: more-closely related species show greater DNA sequence homology than do more-distantly related species.

Vestigial structure

A structure inherited from an ancestor that no longer serves a clear function in the organism that possesses it (homologous structure) * Development helps us solve other evolutionary conundrums as well, such as why reptiles like snakes don't have limbs like other tetrapods. In fact, snake embryos do possess the beginnings of limbs, but these limb buds remain rudimentary and do not develop into full-fledged limbs (although you can still see stubby hindlimbs in some species of snake today). Such vestigial structures, which serve no apparent function in a modern organism, are strong evidence for evolution: these now apparently useless features are inherited from an ancestor in whom they did serve a function. Other examples of vestigial structures include the human tailbone and the phenomenon of "goose pimples" (technically called erector pili), which in fur-covered animals help to puff fur up to better maintain heat.

Continental drift and plate tectonics

Continental: The movement of the continents relative to one another over time. Plate: The movement of Earth's upper mantle and crust, which influences the geographical distribution of landmasses and organisms. * Tectonic plates continue to move, occasionally causing dramatic events such as earthquakes and volcanic eruptions. GPS measurements, used to track the direction and velocity of plate movement, show that some are moving at about 2 to 5 cm per year—about as fast as your fingernails grow.

Punctuated equilibrium

Periodic bursts of species change as a result of sudden environmental change. * With the extinction of the dinosaurs, it was mammals' chance to spread and diversify on land and thus give rise to many of the species of organisms we see on the planet today. This pattern of sudden change—extinctions followed by adaptive radiations—is seen in the fossil record multiple times. It is an example of punctuated equilibrium, in which most evolutionary change occurs in sudden bursts related to environmental change rather than taking place gradually.

Fossils and the fossil record

The preserved remains or impressions of once-living organisms. * Fossils are formed in a number of ways: an animal or plant may be frozen in ice, trapped in amber (hardened tree sap), or buried in a thick layer of mud. The entombed organism is thereby protected from being eaten by scavengers or rapidly decomposed by bacteria. Over time, if conditions are right—for example, if the mud encasing the specimen remains undisturbed long enough for hardening to occur—the organism's shape is preserved. Not all organisms are equally likely to form fossils, however: animals with bones or shells are more likely to be preserved than animals without such hard parts (think earthworms or jellyfish) that decay quickly. And conditions permitting fossilization are rare: the organism has to be in just the right place at just the right time (INFOGRAPHIC 15.1). An assemblage of fossils arranged in order of age, providing evidence of changes in species over time. * Because not all organisms are preserved, the fossil record is not a complete record of past life. Nevertheless, the existing fossil record is remarkably rich and offers a revealing window into the past. Paleontologists, scientists who study ancient life, have uncovered hundreds of thousands of fossils throughout the world, from many evolutionary time periods. When fossils are arranged in order of age, they provide a tangible history of life on Earth. The fossil record also allows biologists to test certain tenets of Darwin's theory. * For example, if all organisms have descended from a single common ancestor that lived billions of years ago, as the theory of evolution concludes they did, then we would expect the fossil record to show an ordered succession of evolutionary stages as organisms evolved and diversified. And, indeed, that is exactly what we see: prokaryotes appear before eukaryotes, single-celled organisms before multicellular ones, water-dwelling organisms before land-dwelling ones, fish before amphibians, reptiles before birds, and so on.

Fossils

The remains or impression of a prehistoric organism preserved in petrified form or as a mold or cast in rock; including volcanic ashes, amber, floods, etc. * Patterns in the Fossil Record: - Oldest fossils are simple organisms; complex taxa appear later - Oldest fossils are most different from living species - Chronologically adjacent forms show greatest physical similarity * The Fossil Record reveals the great age of life on earth and a persistent pattern of change among all living things

Adaptive radiation

The spreading and diversification of organisms that occur when the organisms colonize a new habitat. * Where similar selection pressures lead to similar forms in distantly related taxa

comparative anatomy

The study of similarities and differences in the anatomy/structures of various species * Fossil species show combinations of traits not found in descendants * Descendants retain traits found in ancestors (Homologies) Embryology and anatomy reveal traits found in early ancestors

Biogeography

The study of the distribution of organisms in geographical space. * Biogeography reveals a constant process of speciation and diversification of life on earth.

Transitional / intermediate fossils

And that's what makes Tiktaalik such an important find: it occupies a midpoint between fish and tetrapods. "It very much fits in that gray area between things we typically call fish and things we typically call limbed animals," says Daeschler. Such intermediate, or transitional, fossils document important steps in the evolution of life on Earth. They help biologists understand how groups of organisms evolved, through natural selection, from one form into another. And they confirm that Darwin's theory of descent with modification—which predicts such intermediate forms—is correct. * Another famous transitional fossil is Pakicetus, an early whale. Unlike tetrapods, which evolved first in water and then spread to land, some land-dwelling creatures eventually made their way back to the sea, adapting to an aquatic life once more. That group includes cetaceans—whales, porpoises, and dolphins. The ancestor of cetaceans was a wolf-size land-dwelling mammal that lived 50 million years ago. Although this animal, Pakicetus, had the body of a land animal, including four legs and paws, its head had the long skull shape reminiscent of a whale's. Fossils dating from the period since the time that Pakicetus lived show how whales became increasingly adapted to an aquatic existence.

Convergent evolution / trait analogy

Convergent evolution is the process in which organisms that are not closely related independently evolve similar features. Adaptions may take the form of similar body forms, colors, organs and other adaptions which make up the organism's phenotype. Convergent evolution creates analogous structures or 'homoplasies', those which have similar forms or functions between diverged species, but were not present in the common ancestor of the two. On the other hand, homologous structures, i.e., a specific organ or bone which appears throughout many different organisms, albeit often in a slightly different form or shape, can indicate a divergence from a common ancestor. There are several circumstances that can result in convergent evolution. Often, convergence occurs when organisms are required to adapt to similar environmental conditions, such as in the evolution of thick water-retaining leaves and spines on cacti and Euphorbia species, which are adapted to tolerate conditions of extreme drought but are native to separate continents. It may also occur when two different organisms occupy a similar niche, for example, the cryptic green coloration of Emerald Tree Boas (Corallus caninus) from South America and Green Tree Pythons (Chondropython viridis) from Australia, both of which live high up in the canopy of similar rainforests and occupy a niche predating upon birds. Convergence of life cycle and behavioral traits, such as the similar social colony structures between Naked Mole-rats (Heterocephalus glaber) and many species of social bees and ants, can also take place in order to maximize breeding success of individuals and within colonies. On a molecular level, the independent evolution of proteins and toxins has also occurred throughout many separate phyla; for example, sea anemones (Cnidaria), snakes (Vertebrates), scorpions (Arthropods) and cone snails (Molluscs) all produce neurotoxins which act similarly upon the neurotransmitter receptors of their prey. * The process by which organisms that are not closely related evolve similar adaptations as a result of independent episodes of natural selection. * Separate lineage "solve" the same problems the same way * On the other hand, structures showing analogy are called analogous structures. ... Analogy is one in which the anatomical structures (or behavioral traits) between two unrelated organisms perform the same functions but do not originate from an ancestral structure (or trait) that organisms ancestors had in common

DNA and relatedness / Phylogeny

DNA can hold potential to tell the similarities between species. Phylogeny: The evolutionary history of a species or group of related species

Descent with modification

Darwin's term for evolution, combining the ideas that all living things are related and that organisms have changed over time. * The theory of evolution—what Darwin called descent with modification—draws two main conclusions about life on Earth: that all living things are related, and that the different species we see today have emerged over time as a result of natural selection operating over millions of years. Many lines of evidence support this theory (remember that in science a "theory" is an idea supported by a tremendous amount of evidence and which has never been disproved; see Chapter 1). One of the most compelling lines of evidence for evolution comes from fossils, the preserved remains or impressions of once-living organisms. Fossils are like snapshots of past life, capturing what life was like at particular moments in time.

Extinction / mass extinction

Extinction: The elimination of all individuals in a species; extinction may occur over time or in a sudden mass die-off Mass: An extinction of between 50% and 90% of all species that occurs relatively rapidly. * Then, 250 million years ago, life was drastically cut down: roughly 95% of living species were extinguished in a mass die-off known as the Permian extinction. Scientists do not know what caused the Permian extinction, but some hypothesize that massive volcanic activity filled the atmosphere with heat-trapping gases that led to a rapidly changing climate. The Permian extinction wasn't bad for all organisms, though; some flourished as space and resources opened up for the survivors, who spread and diversified. This phenomenon is known as adaptive radiation. Among these surviving organisms were reptiles, who thrived in the hot, dry climate of the following Triassic Period. The most famous group of reptiles, the dinosaurs, dominated the land for nearly 200 million years, thanks to a combination of drought-resistant skin and fast-moving legs, until they died out in another mass extinction at the end of the Cretaceous Period, 65 million years ago.

Common ancestry / trait homology

In The Origin of Species, Darwin asked, "What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include similar bones, in the same relative positions?" To Darwin, this uncanny similarity was evidence that all these organisms were related—that they share a common ancestor in the ancient past. Homology: Anatomical, genetic, or developmental similarity among organisms due to common ancestry. * The fact that all tetrapods share the same forelimb bones, arranged in the same order, is an example of homology—a similarity due to common ancestry. Before Darwin, comparative anatomists had identified many such similarities in anatomy; what they lacked was a satisfactory explanation for why such similarity should exist. Darwin provided that explanation: homologous structures are ones that are similar because they are inherited from the same ancestor—in this case, an amphibious creature like Tiktaalik. Why is this significant? Think of it this way: every time you bend your wrist back and forth—to swipe a paint brush or hold a cell phone to your ear, for example—you are using structures that first evolved 375 million years ago in fish. As Shubin points out, "This is not just some archaic, weird branch of evolution; this is our branch of evolution" (INFOGRAPHIC 15.5).

Fossil dating (radiometric dating, half-life, isotopes, relative dating)

Radiometric: The use of radioactive isotopes as a measure for determining the age of a rock or fossil. Relative: Determining the age of a fossil from its position relative to layers of rock or fossils of known age. * The fossils they found looked like the elusive intermediate creature the team had been hunting for. But how could they be sure it was the right age? Logically, fossils are at least as old as the rocks that encase them, so if you know the age of the rocks, then you know the age of the fossils, too. Some types of rocks can be dated directly by radiometric dating, in which the proportion of certain radioactive isotopes in rock crystals serves as a geologic clock (isotopes and radiometric dating are described further in Chapter 16). Fossils found in or near these layers can be dated quite precisely. If fossils are found in rock layers that cannot be directly dated by radiometric dating, they can be dated indirectly by their position with respect to rocks or fossils of known age that are either deeper or shallower, a technique called relative dating. Generally speaking, the deeper the fossils, the older they are. Using a combination of both methods, scientists have determined that the rocks where Tiktaalik was found are 375 million years old, which means Tiktaalik is that old as well (INFOGRAPHIC 15.3). Radioactive Isotope: An unstable form of an element that decays into another element by radiation, that is, by emitting energetic particles. * How are such rocks, extraterrestrial or earthly, dated? The most important method is radiometric dating, in which the amount of radioactivity present in a rock is used as a geologic clock. When rocks form, the minerals in them contain a certain amount of radioactive isotopes—unstable atoms of elements such as uranium, potassium, and rubidium—that decay into other atoms. * Radioactive isotopes decay by releasing high-energy particles from the nucleus, a change that causes one element literally to transform into another. For example, an atom of the radioactive isotope uranium-238 (the number designates the mass number—protons plus neutrons—of this particular isotope of uranium) eventually decays into a stable atom of lead-206. The time it takes for half the isotope in a sample to break down is called its half-life. Half-Life: The time it takes for one-half of a sample of a radioactive isotope to decay. * Different radioactive isotopes decay at different rates. Uranium-238 has a half-life of 4.5 billion years, whereas potassium-40 has a half-life of 1.3 billion years. The half-life of carbon-14 (useful for dating once-living, organic remains) is relatively short: it decays to nitrogen-14 in just 5,730 years. Because the isotopes decay at a known and constant rate, they can be used to determine the age of the materials in which they're found (INFOGRAPHIC 16.1).

Vertebrate / invertebrate / tetrapod

Vertebrate: An animal with a bony or cartilaginous backbone. Invertebrate: An animal without a backbone. * Back then, what is now the Canadian Arctic had a warm, wet climate and a landscape veined by shallow, meandering streams. Early in the Devonian Period there was little plant growth, and the world would have looked fairly brown and empty. By the middle of the Devonian, says Daeschler, if you were standing on the bank of a stream you would have seen some of the first land plants, the first forests, as well as the first invertebrates—spiderlike creatures and millipedes, for example—crawling on land. Still, there would have been no land-dwelling vertebrates at this time: nothing with bony limbs, nothing with a backbone or skull. Tetrapod: A vertebrate animal with four true limbs, that is, jointed, bony appendages with digits. Mammals, amphibians, birds, and reptiles are tetrapods. * Of the many features that distinguish land animals from fish, biologists have singled out one as a key evolutionary milestone: limbs. Fish do not have limbs, in the sense of jointed, bony appendages with fingers and toes. Instead, they have webbed fins. In most fishes, the fin bones are thin and fan out away from each other. These so-called ray-finned fishes include the modern-day perch, trout, and bass. By contrast, amphibians, birds, most reptiles, and mammals all have two pairs of limbs, defining them as tetrapods (from the Greek for "four-footed"). * While having limbs is a key feature distinguishing tetrapods from fish, one small group of fish—the lobe-finned fish—seems to blur this distinction. First appearing in the fossil record about 400 million years ago, lobe-finned fish have fleshy fins supported by a stalk of bones that resemble primitive limb bones.

Tiktaalik

When not looking over their shoulders, the researchers drilled, chiseled, and hammered their way through rocks looking for fossils. Not just any rocks and fossils, but ones dating from 375 million years ago, when animals were taking their first tentative steps on land. For three summers, they scoured the site of what was once an active streambed but found little of interest. Then, in 2004, the team made a tantalizing discovery: the snout of a curious-looking creature protruding from a slab of pink rock. Further excavation revealed the well-preserved remains of several flat-headed animals between 4 and 9 feet long. In some ways, the animals resembled giant fish—they had fins and scales. But they also had traits that resembled those of land-dwelling amphibians—notably, a neck, wrists, and fingerlike bones. The researchers named the new species Tiktaalik roseae; tiktaalik (pronounced tic-TAH-lick) is a native word meaning "large freshwater fish." This ancient hybrid animal no longer exists, but it represents a critical phase in the evolution of four-legged, land-dwelling vertebrates—including humans. Tiktaalik "splits the difference between something we think of as a fish and something we think of as a limbed animal," says Daeschler, a curator of vertebrate zoology at the Academy of Natural Sciences in Philadelphia. "In that sense, it is a wonderful transitional fossil between two major groups of vertebrates." Shubin and Daeschler were lucky: the fossils they found were so well preserved that they were able to study Tiktaalik's skeletal anatomy in detail, even seeing how the bones interacted and where muscles attached. From these fossil bones, they determined that Tiktaalik was a predatory fish with sharp teeth, scales, and fins. In addition to these fishy attributes, it had a flat skull reminiscent of a crocodile head, as well as a flexible neck. To Shubin and Daeschler, the neck was one of the most surprising finds. Having a flexible neck meant that, unlike a fish, Tiktaalik could swivel its head independently of its body. This feature may have enabled it to catch a glimpse of predators sneaking up on it from behind, or to snap its jaws sideways like a crocodile. Tiktaalik also had the full-fledged ribs of a modern land animal, sturdy enough to support the animal's trunk out of water even against the force of gravity. But it is Tiktaalik's fins that have justly made it famous. While possessing many features of a lobe-finned fish, including a sturdy stalk of limblike bones, Tiktaalik appears also to have had a jointed elbow, wrist, and fingerlike bones. From the fossil pieces, Shubin and Daeschler were able to create a model of how the bones would have moved relative to one another, and they have visualized these movements on screen. The model shows that the bones and joints were strong enough to support the body and worked like those of the earliest known tetrapods—the early amphibians. "This animal was able to hold its fin below its body, bend the fin out toward what we think of as a wrist, and bend the elbow," explains Daeschler. In other words, it was a fish that could do a push-up. With this hybrid anatomy, Tiktaalik was not galloping on land, of course. It probably lived most of the time in water, but Shubin and Daeschler suspect that Tiktaalik may have used its supportive fins to pull itself out of the water for brief periods. "This is a fish that can live in the shallows and even make short excursions onto land," Shubin said. The ability to crawl onto land would certainly have been a useful trait in the Devonian, when open water was a brutal fish-eat-fish world, whereas land was a predator-free paradise, full of nourishing bugs. For all its amphibian-like adaptations, Tiktaalik is still considered a fish because its limbs lack the true jointed fingers and toes that characterize tetrapod limbs (in other words, they're still fins). But it's by far the most tetrapod-like of all the ancient fishes discovered to date. Scientists have jokingly referred to it as a "fishapod" (INFOGRAPHIC 15.4). * And that's what makes Tiktaalik such an important find: it occupies a midpoint between fish and tetrapods. "It very much fits in that gray area between things we typically call fish and things we typically call limbed animals," says Daeschler. Such intermediate, or transitional, fossils document important steps in the evolution of life on Earth. They help biologists understand how groups of organisms evolved, through natural selection, from one form into another. And they confirm that Darwin's theory of descent with modification—which predicts such intermediate forms—is correct.

DNA and molecular clocks

While all living organisms share DNA and the genetic code, no two species share the exact same sequence of DNA nucleotides. That's because (as described in Chapter 10) errors in DNA replication and other mutations are continually introducing variation into DNA sequences (and the proteins they encode). Over time, neutral and advantageous mutations will tend to be preserved, while harmful mutations will tend to be selected against and eliminated. In addition, much of our DNA consists of long stretches of noncoding sequences with no known function. Because mutations in these regions have no effect on an organism, they accumulate over time. As mutations are passed on to descendants, the number of sequence differences between the ancestor and its descendants grows—slowly in the case of sequences coding for critical proteins whose structures are well adapted to their functions, and more rapidly in the case of noncoding DNA, which is not involved in making proteins. Closely related species will therefore have more similar DNA sequences than species that are more distantly related. For example, when scientists looked at one specific region of DNA—the cystic fibrosis transmembrane regulator (or CFTR) region—they discovered that human DNA in this region is 99% identical to chimpanzee DNA. The fact that the DNA of these two species is nearly identical reflects the fact that humans and chimps share a common ancestor that lived relatively recently—just 5-7 million years ago. By contrast, human DNA is 85% identical to the DNA of a mouse at this same region, which makes sense given that humans and mice share a common ancestor that lived between 60 and 100 million years ago. Less sequence identity would be seen between a human and a toad, whose common ancestor—a lobed-finned fish—lived roughly 375 million years ago. The more distantly related two species are, the more sequence differences in DNA sequences, and the less homology, you will see. DNA serves as a kind of molecular clock: each additional sequence difference is like a tick of the clock, showing the amount of time that has elapsed since the two species shared a common ancestor (INFOGRAPHIC 15.7). * Assumes constant rates of mutation in each specific region of DNA

Comparative biology

comparing similarities and differences between organisms to determine evolutionary relationships