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The earliest whales, such as the 49-million-year-old Ambulocetus, still had legs. They were semi-aquatic, hunting for prey underwater but sleeping and breeding on land.
Roberts and Company Publishers, ISBN: 9781936221172, due August 15, 2012, For examination purposes only
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The Virus and the Whale
How Scientists Study Evolution
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Learning Objectives
Define biological evolution. Compare the roles of homologous and analogous traits in species relationships. Describe the relationship between modern and fossil whales. Identify the characteristics of viruses that allow them to escape attempts to control them. Compare and contrast natural selection and genetic drift as mechanisms of change. Define a scientific theory. Identify some misconceptions about the theory of evolution.
The blue whale, the biggest animal on Earth, can reach over
30 meters long and weigh up to 100,000 kilogramsequal to a village of over a thousand people. To grow to this staggering size, blue whales search for swarms of krill and other small animals. They drop open their lower jaws and enough water rushes in to fill two school buses. Swinging their mouths shut, the whales ram their tongues forward, forcing the water back out through rows of bristle-covered plates called baleen. The baleen traps the animals that the whale gulped, and it can then swallow them. In a single lunge, scientists calculate, a blue whale can gather half a million calories (Goldbogen et al. 2010). Youd need to eat a thousand hamburgers to get the same energyand eat them all at once. Blue whales are remarkable not just for their size or their massive gulps. Although they have fish-like bodies well suited for swimming, staying underwater for an hour is fatal for them. While fish draw oxygen from water through their gills, blue whales must rise to the oceans surface to breathe, opening a blowhole to draw air into their lungs. Another oddity about blue whales is that instead of laying eggs like many species of fishes, they give birth to live young, and their calves must travel with their mothers for years, drinking milk instead of searching for their own food. While blue whales are the largest animals on Earth, the smallest living things are viruses. They measure about a hundred nanometers across, about a thousand times smaller than the width of a human hair.
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Unlike animals, viruses are exquisitely simple. The virus that causes influenza, for example, has only 10 genes (we, by contrast have about 20,000). Yet just because viruses are small and simple doesnt mean that theyre not extremely important. Viruses replicate by invading cells and hijacking their molecules to assemble copies of themselves. As they spread through their hosts, they cause a wide range of diseasessome mild and some devastating. Each year, for example, human immunodeficiency virus kills 1.8 million people (UNAIDS 2010). Viruses infect every species of animal, plant, fungi, protozoan, and bacteria on Earth. No predator can challenge an adult blue whale, but viruses can kill it. Their success at infecting so many hosts has also made viruses the most abundant life-form on Earth. In a single drop of seawater, there may be millions of viruses. In the entire ocean, there are 1030 of them (Suttle 2007). Blue whales and viruses demonstrate the staggeringly different forms that life can take. Theyre so different, in fact, that it can be hard to imagine that a single explanation could account for them bothnot to mention all of the other living things that share the planet with them. And yet such an explanation does exist: viruses and whalesand all other living thingsare the products of evolution. In 1973, the Russian-born biologist Theodosius Dobzhansky wrote one of the most eloquent accounts for evolutions place in the study of life. He entitled his essay, Nothing in Biology Makes Sense Except in the Light of Evolution (Dobzhansky 1973). Seen in the light of evolution, biology is, perhaps, intellectually the most satisfying and inspiring science, he wrote. Without that light it becomes a pile of sundry facts some of them interesting or curious but making no meaningful picture as a whole. By understanding evolution, Dobzhansky explained, we can understand why the natural world is the way it is. We can understand the similarities among different species, as well as the differences. We can understand why some species are present in some parts of the world and not others. We can understand the adaptations of living things, as well as their weaknesses. This understanding is important simply for what it tells us about life. But its also important in practical ways. Evolution provides scientific tools we can use to address some of the challenges we face as a society. The viruses and bacteria that cause diseases are continually evolving, rendering many drugs ineffective. Insect populations that feed on crops can evolve resistance to pesticides, and weed populations evolve resistance to herbicides. We are altering the environment on a planetary scale, by introducing invasive species to new habitats, spreading pollution, and altering the climate. All these changes are driving animals and plants in new evolutionary trajectories. Globally we are witnessing a wave of extinctions the likes of which the Earth may not have seen for tens of millions of years. By studying evolution, we can learn how these extinctions compare with events of the past, begin to make predictions about which current populations will vanish, and devise strategies to slow their decline. Finally, evolution is a part of the answer to some of the biggest questions we all ask. How did we get here? How did we acquire our powers of reasoning and language? To fully address any of these questions we must first appreciate how and why populations change over time. We must understand the basic principles of evolutionary biology. This book is an introduction to evolution: both to the process by which life evolves and to the patterns evolution has produced over the past 4 billion years. It
Figure 1.1 Paleontologist Hans Thewissen discovered the first fossil of Ambulocetus in 1993.
Biological evolution is any change in the inherited traits of a population that occurs from one generation to the next (i.e., over a time period longer than the lifetime of an individual in the population).
chapter one the virus and the whale: how scientists study evolution Roberts and Company Publishers, ISBN: 9781936221172, due August 15, 2012, For examination purposes only
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is also about how scientists study evolution. When Charles Darwin studied evoluevolution in the mid-1800s, the most sophisticated tool he could use was a crude light microscope. Today, scientists study evolution by analyzing our DNA. They probe the atoms of ancient rocks to determine the age of fossils. They use powerful computers to apply new statistical equations to the diversity of life. They observe evolution unfolding in their laboratories. And they synthesize these different lines of evidence into a unified understanding of how life has evolved. To see what evolution can reveal about life, lets turn back to those giant and tiny life-forms, the whales and the viruses.
Key Concepts Evolution is a process by which populations of organisms change over time. By understanding evolution, we can understand why the natural world is the way it is.
1.1 Whales: Mammals Gone to Sea

Whales and dolphins, collectively known as cetaceans, form a group of 85 species. All living cetaceans share a number of traits: they have fish-like bodies, sculpted with the same sleek curves you can find on tunas and sharks, allowing them to use relatively little energy to shoot through the water. The tails of whales and dolphins narrow down to a small neck and then expand into horizontally flattened flukes, which they lift and lower to generate thrust, much like sharks and tuna generate thrust by moving their tails from side to side. Despite their superficial similarity with fishes, cetaceans possess many traits found only in mammals. Cetacean embryos develop in the uterus, forming a placenta to extract nutrients from their mothers. They are born alive and then drink milk produced by their mothers until theyre old enough to eat food. Whales and dolphins even have tiny bones embedded in their flesh just where the hips would be on land mammals. In his 1859 book The Origin of Species, Charles Darwin proposed a straightforward explanation for this puzzling pattern of similarities and differences. Cetaceans descended from mammals that lived on land, and their lineage evolved into marine
Lineage: A chain of ancestors and their descendants. A lineage may be the successive generations of organisms in a single population, the members of an entire species during an interval of a million years, or a group of related species descending from a common ancestor.
Figure 1.2 How did whales evolve? Clues come from everything from fossils to whale DNA.
1.1 whales: mammals gone to sea Roberts and Company Publishers, ISBN: 9781936221172, due August 15, 2012, For examination purposes only
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Incisors and canines aligned with cheek teeth Narrow postorbital/ temporal region Lateral view Bulla Ventral view Dorsal view
Bulla
Figure 1.3 A: Early clues to whale evolution came from the teeth of whale fossils. Dorudon, a 40-million-year-old whale, has different types of teeth, some of which have complicated surfaces. They bear a strong resemblance to the teeth of some extinct land mammals (adapted from Uhen 2010). When paleontologists found older cetacean skulls, they used traits such as the ones shown here to determine that they were related to Dorudon and living cetaceans. (The bulla houses the ear region, which is distinctive in whales.) B: Killer whales, by contrast, have simple peg-shaped teeth.
Natural selection is a mechanism that can lead to evolution, whereby differential survival or reproduction of individuals causes some genetic types to replace (out compete) others. Convergent evolution: The independent origin of similar traits in separate lineages.
mammals through natural selection. In a process of convergent evolution, the ancestors of modern whales lost their hind limbs and their front legs became shaped like flippers. Yet whales retain some traits from their mammalian ancestors, such as lungs and mammary glands. The mammary glands of whales and land mammals are examples of homology: structural characters that are similar due to a shared common ancestry. Darwin argued that evolution was a gradual process. If he was right, intermediate species of cetaceans must have existed in the past that had bodies more adapted for life on land. At the time, paleontologists were only starting to delve into the fossil record for extinct species. But as the decades passed, they found a growing number of fossils of ancient cetaceans. They knew that these fossils were cetaceans, because they shared a number of key skeletal traits with living whaleswhat scientists now call synapomorphies (Chapter 4). Figure 1.3 shows one of these fossils, the 40-millionyear-old Dorudon atrox. Its flippers and long vertebral column are very much like those of living whales. But some of the most important features for diagnosing it as a cetacean are subtle features of its skull. The mammalian middle ear is an air-filled cavity enclosed in a hollow shell known as the ectotympanic. In cetaceans, the inner wall
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of the ectotympanic, called the involucrum, forms a thick lip made of dense bone. The involucrum of Dorudon has the same dense, thick form (Thewissen et al. 2009). While Dorudon shares some unique features with living cetaceans, they also have some features not seen in any cetacean on Earth today. For example, some modern whales, such as dolphins and sperm whales, have peg-shaped teeth while others, such as blue whales, have baleen instead of teeth. Dorudon had teeth of different shapes pointed incisors in the front and shearing molars in the back. Each tooth had a complex structure with cusps and facets. Their teeth were thus more like those of land mammals. This difference suggested that the evolution of peg-like teeth and baleen occurred long after cetaceans had become aquatic. It was not until the late 1900s that whale evolution started to come into sharp focus, however. In 1979, a paleontologist from the University of Michigan named Philip Gingerich traveled to Pakistan to investigate a geological formation from the Eocene Period, rocks that formed from 56 million to 34 million years ago (mya). Gingerich wanted to document the mammals that existed in that region during that time. He and his colleagues brought back a number of fossils to Michigan and then slowly prepared them in his laboratory. One 50-million-year-old fossilthe teeth and back portion of a wolf-sized skullbore some striking synapomorphies with cetaceans such as Dorudon, especially in its teeth. Gingerich and his colleagues dubbed it Pakicetus, meaning whale of Pakistan in Latin (Gingerich et al. 1980). Gingerichs discovery was a dramatic one for two reasons. The first was the age of the fossil; Pakicetus was about 50 million years old, making it by far the oldest fossil of a cetacean found up till that point. The second reason was where Pakicetus lived. Whales and dolphins today live only in the watermost live in the ocean, and a few species of dolphins live in rivers. Studies on the rocks in which Pakicetus fossils have been discovered demonstrate that they did not form on an ocean floor. Instead, they were in a shallow stream that only flowed seasonally through a hot, dry landscape (Thewissen et al. 2009). Thus Pakicetus appeared to be a whale that lived on land. A
Homologous Homologous characteristics are simi similar in two or more species because they are inherited from a common ancestor. A synapomorphy is a derived form of a trait that is shared by a group of related species (i.e., one that evolved in the immediate common ancestor of the group and was inherited by all its descendants).
B
Figure 1.4 A: The 50-million-year-old Pakicetus was the first terrestrial whale ever discovered. This reconstruction is based on several different fossils. Fossil material is colored red. B: A painters reconstruction of what Pakicetus looked like in life. C: While Pakicetus may not look like a whale, synapomorphies reveal its relationship to more familiar cetaceans. Here, we show the right ectotympanic bone of Pakicetus and from a living dolphin species. This is a dorsal view of the bones, located within the grape-shaped bulla. The ectotympanic bone surrounds the middle ear cavity. The inner wall of the ectotympanic, known as the involucrum, is thick and dense in cetaceansand in fossils such as Pakicetus. But this trait is found in no other living or fossil mammals. Other synapomorphies include features of the teeth and skull indicated on the skull of Dorudon in Figure1.3 (adapted from Cooper et al. 2009; Gingerich et al. 1983; Luo and Gingerich 1999; Nummela et al. 2006; and Thewissen etal.2009).
Involucrum
Middle ear cavity Fossil Pakicetus Dolphin Lagenorhynchus
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Figure 1.5 The skeleton of Ambulocetus also has an involucrum, as well as other traits that are found today only in whales. It was the first fossil whale with legs that paleontologists discovered. A reconstruction of Ambulocetus is shown on page 2.
Ever since the discovery of Pakicetus, Gingerich and other paleontologists have been finding other important early whale fossils. One of the most important was discovered by one of Gingerichs students, Hans Thewissen, who now teaches at Northeast Ohio Medical University. In the early 1990s, Thewissen traveled to a different part of Pakistan to look for mammals that lived a few million years after Pakicetus. One day Thewissen and his Pakistani colleagues happened across a strange fossil of a large mammal. They slowly excavated its bones from the tail to the head. Its tail was massive, its legs were stubby, and its rear feet were shaped like paddles. Even as Thewissen was digging up the fossil, he could see that its head was long like an alligators, but it had teeth like those of fossil whales. Thewissen brought the fossil to the United States, where he continued preparing and analyzing it. He discovered more cetacean synapomorphies, like a thickened involucrum. He concluded that the fossil was, in fact, a whale that could walk. So he named it Ambulocetus: walking whale (Thewissen et al. 1997; Zimmer 1998). In the years that have followed, paleontologists have found many fossils of different species of whales with legs. Thewissen, for example, has found additional bones of the older cetacean ancestor Pakicetus. Fragments of its skull revealed it to have a cetacean-like involucrum and also showed that its eyes would have sat on top of its head. Fossil bones from other parts of its skeleton have led Thewissen to reconstruct Pakicetus as a wolf-sized mammal with slender legs and a pointed snout. Gingerich, meanwhile, found in Pakistan the fossils of a whale called Rodhocetus, whose short limbs gave it a resemblance to a seal. As the evidence that cetaceans evolved from land mammals grew, scientists wondered which group of land mammals in particular they had evolved from. One way to address this question is to compare the DNA in living species. As well see in Chapter 9, scientists can use genetic information to draw evolutionary trees showing the relationships between species. In the 1990s, several research groups began comparing small snippets of DNA from cetaceans and other mammals and concluded they were most closely related to a group of mammals called artiodactyls, which includes cows, goats, camels, and hippos. As they compared more DNA from these species,
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A B
Astragalus (ankle bone) 1 cm Astragalus Indohyus Pakicetus pig (Sus) deer (Odocoileus)
Figure 1.6 A: The leg of an ox, a typical artiodactyl. One synapomorphy of the artiodactyl clade is the distinctive double-pulley-like morphology of the astragalus, a bone in the ankle region. B: The astragali of two living artiodactyls are shown here next to the fossil astragali of two ancient members of the whale lineage. The fact that they share a double-pulley morphology is evidence that whales are within the artiodactyl clade (Thewissen et al. 2009).
ox (Bos)
the cetacean-artiodactyl link only strengthened. In fact, the scientists concluded that cetaceans were most closely related to hippos (Price et al. 2005). Paleontologists were surprised by this result; nothing in the first fossils of early whales suggested any such connection to artiodactyls, let alone hippos. But the scientists attitude changed when they began to find the limbs of whales. One of the synapomorphies of artiodactyls can be found on an ankle bone called the astragalus. The ends of the astragalus are pulley-shaped in artiodactyls. It turned out that Pakicetus and other early whales with limbs had double-pulleyed astraguli quite similar to those in pigs, deer, and other artiodactyls (see Figure 1.6). It may seem incredible that whales and cows are cousins, and yet we can see here how two lines of evidence independently lead us to that same conclusion. Darwin argued that life evolved like a branching tree with new lineages splitting off from old ones. To reconstruct this branching pattern, known as a phylogeny, scientists can analyze morphology (Chapter 4) and genes (Chapter 9). The phylogeny of cetaceans is illustrated in Figure 1.7. We will include a number of similar figures in this book and use them to explore the patterns of evolution. Figure 1.7, for example, allows us to synthesize a great deal of evidence in order to get an overall sense of the complex evolutionary history of cetaceans that transformed them from ordinarylooking mammals into such fish-like creatures. Indohyus and Pakicetus are considered whales, even though they had four long legs. They may have been able to swim, but only by kicking their legs like many land mammals do today. Other lineages were more adapted to life in water. Ambulocetus, which lived about 49 million years ago along the coastline of what is now Pakistan, had short legs and massive feet. It probably swam like an otter, kicking its large feet and bending its tail. Rodhocetus, with its seal-like limbs, probably could only drag itself around on land. As whales lived more and more in the ocean, legs were no longer adaptive. Instead, later whales used flat flippers to steer through the water. But evolution did not completely retool cetaceans from the ground up. Whales did not evolve gills, for example. Instead, the phylogeny of whales indicates that their nostrils gradually shifted up to the top of their skulls, allowing them to efficiently take in air each time they rose to the surface of the water.
Phylogeny: A visual representation of the evolutionary history of populations, genes, or species.
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55 50 45 40 35 30 25 Millions of years ago year s ago Hippopotamus Indohyus Pakicetus Involucrum Freshwater semiaquatic habitat Ambulocetus
Kutchicetus Large, powerful tail Shorter legs Fat pad in jaw for hearing Brackish water habitat
Rodhocetus
Saltwater habitat Dorudon Nasal opening shifted back Eyes on side of head
Tail ukes Very small hind legs Nasal opening shifted further back
Odontocetes
Complete loss of hind legs Nasal opening reaches position of blowhole in living whales Echolocation for hunting Baleen for ltering food Mysticetes
Figure 1.7 The relationship between

some extinct species of early whales and living species. The animals illustrated here are only a fraction of the fossil whales that paleontologists have discovered in recent decades. By studying fossils, paleontologists have been able to show how the traits found in living whales evolved gradually, not all at once.
Fossils show that the loss of hind legs took millions of years. By 40 million years ago, fully aquatic species such as Dorudon had evolved. But Dorudon, despite being six meters long, still had hind legscomplete with ankles and toesthat were smaller than those of a human childs. Scientists can get clues about the origins of whales and dolphins not just from the shapes of their fossils, but also from the individual atoms inside of them. For example, one way to tell if ancestors were terrestrial or aquatic is to look at whether they drank freshwater or salt water. Living whales and dolphins can drink seawater, while land mammals can drink only freshwater. The two kinds of water are different
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Living marine cetaceans (11) cetacean cetaceans (11) ceans Living freshwater dolphins (4) freshwater dolp ns freshwater dolphins (4) lphi Georgiacetus (1) Indian protocetids (3) Remingtonocetus (2) Attockicetus (1) Ambulocetids (12) Pakicetids (10) 10 14 16 18 20 22 24 Ratio of 18O to 16O as measured by 18Op, 0/00 (SMOW) Freshwater Seawater 12
Figure 1.8 This graph shows the ratio
in several ways, and not just because seawater is salty and freshwater is not. Both kinds of water contain oxygen atoms, but the oxygen atoms are slightly different. Like other elements, oxygen atoms are made up of a combination of negatively charged electrons, positively charged protons, and neutral neutrons. All oxygen atoms have 8 protons, and most have 8 neutrons. But a fraction of oxygen atoms on the Earth have extra neutrons, making them heavier. Scientists have observed that seawater has more oxygen atoms with 10 neutrons than does freshwater. And animals that live on land and at sea reflect this difference in the oxygen atoms incorporated in their bones. Living whales and dolphins have a larger percentage of heavy oxygen in their bones than do mammals that live on land. Thewissen wondered if the oxygen atoms in ancient whale fossils might indicate where they lived. So he and his colleagues ground up tiny samples of ancient whale teeth and measured the ratio of light and heavy oxygen. They discovered that Pakicetus still drank freshwater. Ambulocetus, which belongs to a younger branch of the whale tree, had an intermediate ratio, suggesting that it was drinking brackish water near the shore, or a mix of freshwater and seawater. More recent fossil whales had the ratios you would expect in animals that drank seawater alone. Together, these isotope ratios chart a transition from land to estuaries to the open oceanthe same transition documented in the changing shape of their skeletons (Figure 1.8, Thewissen and Bajpai 2001). Its almost certain that scientists will never be able to read the genes of 40-million-year-old whales, because DNA is too fragile to last for more than a few hundred thousand years. But it is possible to study the genes of living whales to learn about some of the genetic changes that occurred as they adapted to water. Some of the most important genetic changes that take place during major evolutionary transitions change the timing and pattern of gene activity in embryos (Chapter 10). When legs begin to develop on the embryos of humans or other land vertebrates, a distinctive set of genes become active. Thewissen and a team of embryologists discovered that these leg-building genes also become active in dolphin embryos. They help build tiny buds of tissue, but these buds stop growing after a few weeks and then die back. Thewissens discovery means that the evolutionary loss of hind legs in the ancestors of dolphins and whales occurred when animals stumbled on a mechanism
Weeks 49 of embryonic development
of oxygen isotopes in modern and fos fossil cetaceans. (The numbers after the cetacean names indicate the number of samples used in this study.) To the left of the graph, the ratio of 18O to 16O is low, and to the right it is high. Freshwater has a relatively low ratio of 18O to 16 O. Seawater has a higher ratio. As the top two rows indicate, living cetaceans that live in freshwater and seawater have a corresponding proportion of 18 O in their bones. The isotopic ratio of early fossil whales suggests that they drank freshwater. Ambulocetus and other forms that were more adapted to living in water had ratios spanning the two environments, suggesting they lived in brackish waters or traveled between the open ocean and rivers. Later whales acquired the isotopic signature of seawater, reflecting their permanent habitation in the ocean (Thewissen and Bajpai 2001).
Forelimb
Hindlimb
Figure 1.9 A developing dolphin grows forelimbs, which will eventually become flippers. It also sprouts hindlimb buds. But the genes that maintain their growth eventually become inactive, so the buds are eventually absorbed back into the embryo. Through such simple changes in the timing of gene expression, cetaceans have evolved a dramatically different body from their terrestrial ancestors (Thewissen et al. 2009).
1.1 whales: mammals gone to sea
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B
Indohyus Pakicetus Ambulocetus Tibia Basilosaurus Femur Bowhead whale Pelvis
Figure 1.10 A: Fossils of whales document the gradual reduction and simplification of the pelvis (Thewissen et al. 2009). B: In a living whale, the pelvis is still present, but only as a tiny vestige embedded in the body of the whale.
that stopped the growth of the limbs after they had already begun to form (Thewissen et al. 2006). The disappearing legs of dolphins illustrate how evolution depends on natural serendipity, not foresight. It might have been most efficient for whales to block the development of limb buds before they even began. But thats not what happened. Instead, mutations arose that only started to arrest the growth of the limb buds after they had formed. Its likely that a similar evolutionary process produced the vestiges of tiny hips in whales as well. The earliest lineages of whales are long extinct. The two lineages alive today evolved from a common ancestor that lived about 40 million years ago. One lineage, known as the toothed whales (Odontocetes), evolved muscles and special organs that they used to produce high-pitched sounds with their blowholes, allowing them to hear the echoes that bounced off animals and objects around them in the water. Today, dolphins and other toothed whales use these echoes to hunt for their prey. The other living lineage, the baleen whales (Mysticetes), lost their teeth and evolved huge, stiff pleats in their mouths that allowed them to filter prey from huge volumes of water. Scientists are now beginning to find important new clues to the origins of both groups. Fossils from about 25 million years ago, for example, show that the toothed ancestors of baleen whales probably grew small patches of baleen (Uhen 2010). Only later did their teeth disappear, much like hind legs of their ancestors. Baleen whales still carry genes for building teeth, but all of those genes have been disabled by mutations. Biologists have long been impressed with the size and complexity of whale brains. Aside from humans, dolphins have the biggest brains in proportion to their bodies of any animal (Marino 2007). Dolphins can also use their oversized brains to solve remarkably complicated puzzles that scientists make for them. A number of studies suggest that big brains evolved in dolphins as a way to solve a particular kind of natural puzzle: figuring out how to thrive in a large social group. Dozens of dolphins live together, forming alliances, competing for mates, and building relationships that persist for the duration of their long lives. They communicate with each other with high-frequency squeaks, and each dolphin can tell all the other dolphins
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A B
Human (Homo sapiens) 5 cm
Bottlenose dolphin (Tursiops truncatus) Figure 1.11 A: Dolphins live in large apart by their whistles. Natural selection appears to have favored dolphins with extra groups and can communicate with brainpower for processing social information (Connor 2007). In Chapter 16, we will each other. B: Their social life may have learn more about how evolution produces complex social behaviors, and in Chapter favored the evolution of big, power17, well learn about how human social behavior evolved. ful brains. Relative to their body size, The phylogeny of cetaceans indicates that they all descend from a common andolphins are second only to humans in cestor, rather than having evolved independently from separate ancestors on land. brain size. That ancestral cetacean gave rise to many new species over the past 50 million years.
By tallying the number of fossil species that have been discovered from different ages, paleontologists can chart the changing patterns of cetacean diversity. As Figure 1.12 shows, the number of known cetacean genera has risen and fallen dramatically (Uhen 2010). As well see in Chapter 14, there are many such patterns in the fossil record, and evolutionary biologists are testing hypotheses to explain them. Mark Uhen, a paleontologist at George Mason University, has argued that the early history of whales saw the explosion of semi-aquatic species such as Ambulocetus. By the end of the Eocene, however, fully aquatic forms like Basilosaurus had evolved, and the semi-aquatic forms had become extinct (Uhen 2010). The fully aquatic cetaceans became top predators in the ocean ecosystem. The two living lineages of cetaceans evolved very different strategies: the mysticetes trapped small animals with their baleen, while the odontocetes swam after fishes and larger prey. But in both cases, they depended on productivity of the ocean food web for their food. Uhen and Felix Marx of the University of Bristol have observed that cetacean diversity shot up after large, shelled algae called diatoms became diverse in the ocean starting about 20 million years ago (Marx and Uhen 2010). Uhen and Marx argue that the explosion of diatoms provided a food supply for animals that were preyed upon in turn by a diversity of cetaceans. Unfortunately for cetaceans, a new predator entered their lives in the past few centuries: humans. In the 1800s, sailors crisscrossed the world to hunt big whales for their oil and baleen. (The oil was used for lamps and the baleen for corset stays.) Many species of whales came perilously close to extinction before the whale-oil industry collapsed and laws were passed to protect the surviving animals. Whales reproduce slowly, and so their populations are still far from their prehunting levels. The small sizes of their populations put them at a greater risk of extinction. Diseases and other threats, such as pollution and heavy fishing, can destroy large fractions of small populations more readily than big ones. Small populations also have little genetic variability, making them more susceptible to genetic disorders (Chapter 6).
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A
80
Balaenoptera (middle Miocene to recent)
70
Modern diversity Llanocetus (Eocene/Oligocene boundary) Dorudon (late Eocene)
60
Number of cetacean genera
50
40
30
Georgiacetus (middle Eocene)
20
10
0 Ypresian Lutetian
Bartonian
Priabonian
Aquitanian
Burdigalian
Langhian
Serravallian
Tortonian
Messinian
Gelasian Piacenzian Zanclean
Rupelian
Chattian
E Eocene 55.8 mya
E L Oligocene 33.9 23.0
M Miocene NEOGENE
E L Pliocene 5.3
PALEOGENE
1.8
Holocene Pleistocene
B
Mysticete diversity
20 15 10 5 50
Odontocete diversity
40 30 20 10 350
Diatom diversity
250 150
Aquitanian
Burdigalian
Langhian
Serravallian
Tortonian
Messinian
Gelasian Piacenzian Zanclean
Chattian
Figure 1.12 A: Paleontologists have analyzed databases of

whale fossils to chart the changing diversity of cetaceans through time (Uhen 2010). B: The rise in diversity starting in the Oligocene may have been made possible by a rise in the diversity of diatoms, algae-like organisms that can support an ecological food web (Marx and Uhen 2010).
L Oligocene
M Miocene NEOGENE
E Pliocene 5.3
Holocene Pleistocene
23.0 mya
1.8
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Figure 1.13 Whale hunting in the 1.13 nineteenth century nearly drove many species of whales extinct.
In the 1950s, for example, there were 6000 Chinese river dolphins (Lipotes vexillifer, Figure 1.14) estimated to live in the Yangtze River. Rising pollution sickened the animals, which were also killed in fishing nets. The population began to crash; in 1997, an extensive search revealed only 13 individuals. And the last Chinese river dolphin was spotted in the river in 2007 (Turvey 2009). Even as we humans have come to understand the remarkable history of whales over the past 50 million years, we have taken control of their future evolution.
Key Concepts Whale and fish lineages, evolving independently, converged on body forms that are superficially similar. Ambulocetus was a fossil whale that had legs. This animal had traits that were intermediate between modern whales and their terrestrial ancestors. The chemistry of fossil whales documents a transition from land to estuaries to the open oceanthe same transition documented in the changing shape of their skeletons. Studying limb development in dolphins has revealed some of the mechanisms responsible for the evolutionary loss of hindlimbs. The fact that whales start the process of hind limb development is evidence for their evolution from terrestrial mammalian ancestors.
Figure 1.14 The Chinese river dolphin

(Lipotes vexillifer) is believed to have become extinct in recent years due to pollution and overfishing.
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1.2 Viruses: The Deadly Escape Artists
Figure 1.15 In spring 2009, a new
strain of influenza surfaced in Mexico, triggering a wave of illnesses and deaths. Evolutionary biologists helped solve the mystery of its appearance.
A mutation is any change to the genomic sequence of an organism.
In the spring of 2009, the world turned its worried attention to Mexico. Mexican hospitals were swelling with feverish patients, sick with a new kind of flu. Soon the same new strain was turning up in other countries. Within a matter of weeks, doctors had documented it around the world. Scientists faced a daunting mystery, one that could influence the health of millions of people: where did the new flu come from? The new flu viruses, like all flu viruses, were microscopic shells made of protein, each of which encases 10 genes. Flu viruses make us sick by traveling into our respiratory tracts. A protein that studs the surface of the virus, called hemagglutinin, latches onto proteins on the host cell. Once inside, the virus genome recruits our cells genetic machinery to mass-produce copies of itself. Each infected cell can make thousands of new copies of the viral genome, which are then packaged into new membrane envelopes that escape the cell to infect a new host. As well see in Chapter 5, all living things reproduce by making copies of their genes. But they make a few mistakes in each generation, known as mutations, so that ancestors and descendants do not have precisely identical genes. Some mutations will affect the ability of organisms to replicate. In the case of viruses, for example, a mutation may leave a virus unable to invade a host cell. But other mutations can enable the virus to replicate faster than it could beforeby allowing it to escape the attack of the hosts immune system, for example. Viruses with these beneficial mutations reproduce more than other viruses; as a result, their descendants come to dominate the virus population. This process, known as natural selection, helps create a diversity of new strains that change over time. Each year, several hundred thousand people die worldwide of the flu. To reduce this toll, doctors vaccinate children and old people, the individuals who are typically most vulnerable to the virus. The vaccine is made up of hemagglutinin proteins, which trigger the body to make antibodies to them. Once these antibodies begin to circulate, they enable the immune system to mount a swift defense against actual viruses with the same hemagglutinin proteins. For some diseases, a single vaccine will last a lifetime. For others, a shot every 10 years is enough. But the protection from a flu vaccine lasts only a year. Thats because flu viruses are evolving extraordinarily rapidly. Viruses that can evade immune sys-
Hemagglutinin
Neuraminidase
Proton channel
RNA
Figure 1.16 The influenza virus contains only 10 genes on eight segments of RNA. It is surrounded by a shell of proteins and a lipid bilayer. Proteins on its surface allow it to enter and exit host cells.
Matrix protein
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Mito chon dria
Virus enters cell New viruses bud off Protein synthesis Golgi
Endosome
En d ret opla icu sm lum ic
mRNA synthesis RNA replication
Figure 1.17 Flu viruses enter host cells, whereupon their genes enter the cell nucleus. The cell
makes new copies of the flu genes as well as the proteins in which they are encased. The parts of the virus are assembled at the cell membrane and then bud off to infect other cells.
tems will be more likely to survive and reproduce. Even if they begin as rare mutants, they can spread rapidly by means of natural selection. Scientists dont have to dig up fossils to document the evolution of viruses; they can watch it unfold in real time. In 2009, Jonathan Yewdell of the National Institute of Allergy and Infectious Diseases, and his colleagues ran an experiment in which they vaccinated mice against the flu and then exposed them to the virus (Hensley et. al 2009). They then allowed the animals to infect other mice, which then infected other mice in turn, for nine cycles in total. The scientists then compared the hemagglutinin proteins on the viruses. In all of the vaccinated mice, the hemagglutinin proteins were altered at their tip. Yewdell and his colleagues found that these changes allowed the viruses to bind more strongly to host cells and avoid being recognized by the immune systems of the mice. When the scientists infected non-vaccinated mice, on the other hand, the hemagglutinin proteins didnt undergo any significant change.
1.2 viruses: the deadly escape artists Roberts and Company Publishers, ISBN: 9781936221172, due August 15, 2012, For examination purposes only
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Figure 1.18 The replication of genes is not always precise. When a flu virus invades a host cell, some of its offspring may carry mutations.
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Identical to original virus Mutated virus Flu virus Host cell
Viral reassortment occurs when genetic material from different strains gets mixed into new combinations within a single individual.
Because flu viruses evolve so quickly, vaccine designers have to generate a hypothesis about which strains will come to dominate in the next flu season. Their job is quite difficult because sometimes new strains emerge that are dramatically different from previous ones. Such was the case in 2009. As well discuss in more detail in Chapter 18, all human influenza viruses descend from strains that infected other animals, most commonly birds. From time to time, bird flu crosses over, becoming adapted to replicating in humans. This transition is aided by the ability of viruses to swap genes, in a process known as reassortment. When two viruses infect a cell at once, their genes sometimes get shuffled together as they become packaged into protein shells. Reassortment can give rise to bird flu that produces proteins adapted to invading human cells, and these hybrid strains can spread easily from person to person. These reassortant strains can be particularly devastating because their surface proteins are distinctly different from those of viruses circulating in the human population. The immunity that people develop to these circulating strains cannot protect them against a new strain. When new strains emerge, they can trigger devastating waves of mortality. In 1918, for example, a new strain of flu evolved that killed an estimated 50 million people. Subsequent pandemics have evolved every few decades; the Asian flu of 195758 killed 1.5 million people, and the Hong Kong flu of 196869 killed 1 million people. These strains continue to circulate today, but they cause less mortality because human populations have developed immunity to them. When a new strain of flu evolved in 2009, experts rushed to learn everything they could about it. Since it was so new, they had little idea of how dangerous it would be. Unlike previous pandemics, however, this time evolutionary biologists joined in the effort. In 2009, they had tools that previous generations of biologists lacked to analyze the evolution of the new strain. A global network of experts on flu evolution launched an international collaboration. Rather than coming together in one lab, however, they worked over the Internet, each taking on part of the problem and then uploading the results to a central website. To carry out their analysis, the researchers downloaded genetic sequences of the new strain taken from patients all over the world and then scanned them for similarities and differences. They reconstructed the relationships of the viruses, much as
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Generations
paleontologists used morphological traits to reconstruct the relationships of whales. Paleontologists can estimate the minimum age of branches on an evolutionary tree based on the age of their fossils. The evolutionary biologists studying the flu used a different method, called the molecular clock (Chapter 9). Mutations arise at a roughly steady rate, and so the number of different mutations in two lineages provides a clue to how long ago they diverged from a common ancestor. First, the researchers traced all the samples of the new virus strain back to a common ancestor that they estimated lived around January 2009 (Figure 1.22). In other words, the new strain had already been circulating for several months from person to person before coming to the attention of medical authorities. And while the new strain first came to light in Mexico, it was not necessarily Mexican in origin. The deepest branches on the evolutionary tree belonged to samples that had been found in the United States. By the time the first cases emerged in Mexico, the virus was already present in many other countries (Smith et al. 2009). Next, the evolutionary biologists reached further back into the evolutionary history of the new strain. They compared it to other flu strains in humans and animals.
Figure 1.19 Some mutations are harmful to flu viruses, while others have no effect. A few will be beneficial in one way or another, such as helping a virus evade the immune system. They will reproduce more, making the mutation more common in the virus population. This is the essence of natural selection.
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HA PR8 (stock PR8 (stock 1) (stock
passaged 9x in vaccinated mice vaccinated vaccinated mice passaged 9x in naive mice
E158K E158K
PR8 (stock 1)
no change
PR8 (stock 2) PR8 (stock 2) PR8 (stock 3) PR8 (stock 3)
passaged 9x in vaccinated mice passaged 9x in naive mice passaged 9x in vaccinated mice passaged 9x in naive mice
E246G
no change
E156K
no change
HAI titer
E158K E246G E156K
C
pAb escape (HAI) 250 200 150 50 0 100
Hemagglutinin
PR8
E158K E246G E156K Experimental mutations to hemagglutinin
Figure 1.20 A: In a 2009 experiment, scientists infected vaccinated mice with flu viruses and then sequentially infected eight more hosts. In three separate trials, a new amino acid in the hemagglutinin protein evolved in the viruses. By contrast, viruses underwent no such change in non-vaccinated mice. B: The three colors show the location of each new amino acid in the purple hemagglutinin protein. Because each of the amino acid changes occurred on the surface of the viral protein, they changed the way in which antibodies attached to the viruses. (There are three spots of each color because the protein is made up of three of the same subunits.) C: In a test called hemagglutinin inhibition (HAI), the scientists compared how well the viruses could escape the antibodies used in the vaccine. The higher the HAI titer, the more viruses the antibiodies attach to. As this graph shows, the mutations in each trial significantly reduced the effectiveness of the vaccine. Evolution of the viral hemagglutinin protein let the viruses escape the immune system (adapted from Hensley et al. 2009).
Highly pathogenic avian strain
The new strain proved to have a complicated history that mingled viruses from three different species: humans, birds, and pigs (see Figure 1.23). Pigs probably first acquired the flu from humans after the 1918 pandemic. This so-called classic strain circulated among Human strain pigs for decades before a new kind of swine flu evolved in the 1970s. The new swine flu strain, which evolved in Europe, acquired some genes from a bird flu strain. Yet another pig-bird mix arose in the United States. In the late 1990s, American scientists discovered a triple reassortant that mixed genes from classic swine flu with genes from bird viruses and human viruses. All three virusesthe triple reassortant, and the American and European pig-bird blendscontributed genes to the latest strain. The 2009 H1N1 strain got its start in pigs, circulating among them for perhaps a decade before crossing into humans in 2009.
Figure 1.21 On rare occasion, two strains of influenza virus co-infecting

New highly pathogenic human strain the same cell shuffle their genes, producing a new genome. This process, known as reassortment, is responsible for the emergence of dangerous new strains of influenza.
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Mexico USA Europe South/Central America Canada Asia Australasia
Figure 1.22 Scientists analyzed 1.22 1.22 samples of the 2009 H1N1 flu strain collected from around the world during the first few months of the outbreak. The similarity of genes in the samples showed which were most closely related. By tallying mutations in each lineage, the scientists could estimate when their common ancestor lived. As this tree demonstrates, the virus had already spread around the world before it first came to light in Mexico. The strain probably was circulating for over two months before being discovered (adapted from Smith et al. 2009).
Common ancestor of all samples of 2009 H1N1 in uenza
January 0 30
February 60
March 90 Days
April 120
May 150
June 180
Fortunately, 2009 H1N1 turned out not to be like the 1918 pandemic. As flu viruses go, it was relatively mild. Still, that was little comfort to the families of the estimated 16,000 people in the United States who died of the strain in 2009. And 2009 H1N1 was a sobering warning for public health experts. The evolutionary analysis documented just how far flu strains can spread among human hosts before being detected. It also demonstrated how potential new human pathogens can circulateand evolvefor
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Figure 1.23 The 2009 H1N1 virus was 1.23
the product of several rounds of reasreassortment that took place over decades. The resulting virus was a mix of genes from viruses that originally infected pigs and birds (from Neumann et al. 2009).
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Classical swine North American avian Human (H3N2) Eurasian avian-like avian-like swine
PB2 PB1 PA H1 NP N1 M NS PB2 PB1 PA H1 NP N1 M NS PB2 PB1 PA H1 NP N1 M NS PB2 PB1 PA H1 NP N1 M NS PB2 PB1 PA H1 NP N1 M NS
PB2 PB1 PA H1 NP N1 M NS
In uenza A (H1N1)
Figure 1.24 Studying the evolution of

flu is essential to understanding why an outbreak in 1918 was able to kill 50 million peopleand to preventing it from happening again.
North American avian Human H3N2 North American avian Classical swine Classical swine Eurasian avian-like swine Eurasian avian-like swine Classical swine
years in pigs without ever being detected. The new research makes it clear that pig farms must be carefully monitored for new flu strains and that steps must be taken to keep the animals healthy. Their health and our health, we can now see, are intertwined.
Key Concepts Hemagglutinin is a protein on the surface of the influenza virus that latches it to a host cell; it is also the protein that is recognized by our immune system, and it is harvested to manufacture vaccines (the flu shot). This viral protein evolves extremely rapidly, rendering our vaccines obsolete months after they are made. Reassortment of the influenza virus is terrifying because it could blend dangerous elements of pig or bird flu with the infectious potential of human flu, instantaneously generating a deadly and infectious strain. Reassortment events can occur in any bird, pig, or human individual that is simultaneously infected with more than one strain. Mutations arise at a roughly steady rate, and so the number of different mutations in two lineages provides a clue to how long ago they diverged from a common ancestor.
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1.3 Evolution: A Tapestry of Concepts
As these two cases demonstrate, evolution is a complex phenomenon that plays out over both short and long timescales. In this book, well investigate the key concepts in evolutionary theory and observe how they combine to produce the diversity of life. Figure 1.25 shows the most important aspects of evolution that well explore, illustrating how the chapters are intimately interconnected. In Chapter 2, well examine how the history of biology led up to Darwins theory of evolution. Darwin observed the pattern of evolution in the fossil record and the morphology of living species. He interpreted this pattern as the result of descent with modification from common ancestors. To explain how that modification took place, Darwin noted that there were variations in every generation. Some individuals would have variations that allowed them to reproduce and pass down their traits more than others. Over time, natural selection and other processes would drive largescale changes, even giving rise to new species. In the decades since Darwin published his theory, the evidence for evolution has increased exponentially. In Chapter 3, we investigate the fossil record as it stands today, chronicling over 3.5 billion years of life on Earth. Scientists can analyze these fossils to reconstruct phylogenies. In Chapter 4, well explore how such phylogenies are built and what they can tell us about the history of life. Chapter 5 begins our investigation of the molecular mechanisms that allow this long-term evolutionary change to occur. We examine how DNA encodes RNA and proteins, and how mutations and other processes give rise to genetic variation. In Chapter 6, we look at the rise and fall of the frequency of gene variants in populations. Many mutations eventually disappear, while others spread widely. Sometimes these changes are the result of chance, a process called genetic drift; other times they are more predictable. Natural selection also changes the frequency of gene variants. Mutations spread if they cause their bearers to perform wellto thrive and be especially successful at reproducing. Mutations may decrease in frequency or be lost completely if their bearers perform poorly. The effect of a mutation can depend on more than just the mutation itself. It may be influenced by other genes that an organism carries. The environment in which an organism lives can also have a huge effect. As a result, the same mutation to the same gene may be devastating in one individual and harmless in another. Depending on the particular circumstances, natural selection may favor a mutation or drive it to oblivion. Charles Darwin believed that natural selection occurred so slowly that he couldnt hope to observe it directly. But in Chapter 8, we survey a number of cases in which scientists have documented selection taking place in our own lifetime. The discovery of DNA and mutations revolutionized the study of evolution. As well see in Chapter 9, your genes and the genes of all living things store a huge amount of historical information about evolution. As we saw with whales and flu
CHAPTER 1 2 3 4 5 6 7 8 9 10 11 12
Genetic drift is evolution arising from random changes in the genetic composition of a population from one generation to the next.
Figure 1.25 A flowchart showing how

the concepts in each chapter are linked to each other.
14 15 16 17 18 18 Evolutionary Medicine
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1 Introduction 2 History 5 Genetics 10 Mechanisms of Development 12 Family
8 Natural Selection 6 Population Genetics 7 Quantitative Genetics 9 Molecular Evolution
11 Sexual Selection
16 Behavior 17 Human Evolution
13 Speciation
15 Coevolution
3 Paleontology
4 Phylogeny
14 Radiation and Extinction
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Phenotypes are measurable aspects of organisms, such as morphology (structure), physiology, and behavior. Genes interact with other genes and with the environment during the development of the phenotype.
viruses in this chapter, genes provide a separate line of evidence about the phylogeny of species. They can also allow scientists to reconstruct ancient episodes of natural selection, pinpointing the molecular alterations that gave some individuals a reproductive advantage. Phylogenies based on fossils and DNA shed light on how complex new adaptations have evolved over the history of life. In Chapter 10, we examine the origins of adaptations. We focus in particular on how mutations affect the development of animals and other multicellular organisms. Relatively simple changes to developmental genes can have profound effects on an organisms phenotype. Some complex adaptations, like the eye, are essential for an organisms survival. Other adaptations, such as antlers or bright tail feathers, serve another vital function: attracting mates. In Chapter 11, we look at how sex has a profound influence on animals. In Chapter 12, we turn our attention to what happens after sexnamely, how evolution shapes the ways in which parents rear their young. Natural selection and sexual selection alike can play important roles in the origin of new species, the subject of Chapter 13. And over millions of years, the origin of new species leads to complex patterns of diversity through both time and space. In Chapter 14, we look at the evolution of biological diversity and examine the current drop in diversity through widespread extinctions. Chapter 15 is dedicated to coevolution, the process by which different lineages respond to each others adaptations and create ecological partnerships. The phenotype of an organism is more than just the anatomy we can see. Its also an organisms behavior. In Chapter 16, we look at how behavior evolves. We consider studies on the genetics of behavior and explore how the mating systems of species help shape their social behaviors. Behavior is an enormous part of the story of human evolution, the subject of Chapter 17. There, we look closely at the evidence of human evolution to be found in the fossil record, the human genome, and even in psychology experiments that probe the mind. Throughout this book, we pay special attention to the practical side of evolutionary biology. We discuss how resistance to the chemicals farmers use evolves in insects and weeds, for example. One of the most exciting areas of applied evolutionary biology is the subject of the final chapter: medicine. Doctors seek to treat our bodies, which are the product of some 3.5 billion years of evolution. They would do well to understand what that evolution has yielded.
1.4 Common Misconceptions about Evolution

Before we delve into evolutionary biology, its important to set aside misconceptions about it. Many people misunderstand evolution, in part because it is a counterintuitive process than can produce many different outcomeseverything from a virus to a whale. Here are some of the most common misconceptions about evolution (Le Page 2008; University of California Museum of Paleontology 2011). Misconception #1: Evolution is just a theory. Many people think a theory is simply a hunch: a vague guess based on little evidence. In fact, scientists use the word theory to describe an overarching set of mechanisms or principles that explain a major aspect of the natural world. A theory makes sense of what would otherwise seem like an arbitrary, mysterious collection of data. It is also supported by independent lines of evidence. Modern science is dominated by theories, from Newtons theory of gravitation to the theory of plate tectonics to the germ theory of disease to Darwins theory of evolution by natural selection. Others argue that evolution is a theory in crisis, and scientists are losing confidence and rejecting it. Scientists certainly debate aspects of this complex theory, like whether a massive increase in a diatom food source could lead to a diversity of cetaceans, but they do not argue that evolution of cetaceans did not occur.
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Box 1.1
What Is Science?
Evolutionary biologists want to understand things that are hidden from view. When they see a bee feeding on nectar from a flower, for example, and picking up pollen that will fertilize other flowers, they want to know how that partnership came to be over millions of years. But how can scientists possibly know anything about something that happened an unimaginably long time ago, something with which theyve had no direct experience? Thats a reasonable question, but it could be asked about anything that scientists study. Physicists cannot walk alongside electrons, making personal observations of how they behave. They must run experiments to gather indirect clues to how electrons act and then use that evidence to come up with an explanation. Geologists cannot lay their hands on an earthquake, but they can eavesdrop on the reverberations that earthquakes send out across the planet, and they can use those aftereffects to discover why the Earth shudders. Epidemiologists track epidemics without ever seeing the vast majority of the viruses or bacteria that are making people sick. All scientists, in other words, seek to understand the invisible. Their mission
is to find explanations that can account for indirect clues gathered through experiment and observation. If scientists must rely on indirect clues, how can they ever know that their explanations are correct? They must find a way to test their explanations against more evidence. The better the job that an explanation does in predicting the new evidence, the more confidence the scientists have in it. If the prediction fails, the scientists give their explanations a critical look and alter them to create a better one (National Academy of Sciences 2008; Okasha 2002). This cycle of evidence, explanation, and testing can work effectively only on phenomena that follow reliable rules. Today, for example, the bonds that join together atoms in a water molecule have the same energy as they did yesterday. You could imagine a world in which some supernatural force could alter the bonds from moment to moment based on some mysterious whim. It would not be possible to use science to learn about how such a world works, because you would have no idea whether new evidence would be produced by the same processes that you were observing before.
Misconception #2: Evolutionary biology has a complete explanation for everything that has happened in the history of life. Biologists still have only a limited knowledge of life. Taxonomists have described only a small fraction of species alive today. Paleontologists have discovered the fossils of a far smaller fraction of all the species that ever existed. Scientists are just starting to understand many important aspects of biology, such as the ways in which genes influence the development of phenotypes. But as biologists discover new things about life today and in the past, they continue to find that evolution is the best explanation. As a result, evolution is an increasingly well-supported theoryeven though evolutionary biologists have much left to learn about the history of life. Misconception #3: The theory of evolution is about the origin of life. Evolution is a process that occurs when populations of organisms change genetically over time. Before biological systems existed, there was no evolution. The origin of life is a vibrant field of research of its own (Deamer 2011). Scientists are investigating what the oceans and atmosphere of the early Earth were like, and they are testing hypotheses for how prebiotic chemicals could have entered cycles of reactions that led to the earliest cells. But evolutionary biologists generally study what happened to life after it originated, how and why it diversified in the ways that it did. Misconception #4: The study of evolution is the search for direct ancestors and missing links. The fossil record preserves only a tiny fraction of the history of life. Whats more, discovering fossils of new species is a slow, arduous process. Thus, scientists expect gaps in the fossil record, and they know its extremely unlikely to find the direct ancestor of any organism. Rather than search for missing links, paleontologists determine the relationship of species represented by fossils and by living individuals. The phylogeny itself can shed light on how new traits evolved. Misconception #5: Evolution violates the second law of thermodynamics. The second law of thermodynamics holds that disorder increases in closed systems. In our everyday life, this law explains why we can never drive a perfectly efficient car and why a broken glass will never spontaneously assemble itself back together. But
1.4 common misconceptions about evolution Roberts and Company Publishers, ISBN: 9781936221172, due August 15, 2012, For examination purposes only
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the evolution of complex phenotypes is not a violation of the second law of thermothermodynamics, because life does not evolve in a closed system. The Earth, after all, is not a sealed chamber. It receives energy from an external source the sun. This energy makes life possible, and allows evolution to occur. Misconception #6: Evolution is natural selection. Natural selection is a crucial element of evolution (Chapters 6 8), but it is not the entirety of evolution. We will encounter other processes, such as genetic drift (Chapter 6) and sexual selection (Chapter 9), that are also important. Misconception #7: Evolution is entirely random. Evolution includes elements of both randomness and order. Whether a particular mutation arises in a particular individual is a matter of chance. But how that mutation spreads in a population is often due to much more than chance, especially if that mutation affects the reproductive success of the individuals that have it. The non-randomness of evolution is apparent in the strikingly similar shape of whales and fish. Animals that occupy the same ecological niche in the same physical environment face the same selection pressures, resulting in convergent evolution. Misconception #8: Evolution provides species with the adaptations they need. The match between species and their environments can be striking. Giraffes, for example, can feed on leaves high on trees, thanks in part to their extraordinarily tall necks. But its neck did not evolve this way to fulfill the giraffes need. Instead, giraffes with longer necks left more offspring than those with shorter necks. Evolution cannot identify needs, because its based simply on processes such as random mutations and the change of gene frequencies from one generation to the next. Misconception #9: Evolution is a march of progress. The pattern of evolution is not a straight line. Darwin recognized that new species diverge like branches on a tree. More recently, scientists have also recognized weblike features in phylogenies, thanks to hybridization and horizontal gene transfer (Chapter 4). Misconception #10: Evolution always goes from simple to complex. This point is a variation on the march-of-progress misconception. Complex traits have indeed evolved from simpler precursors. In Chapter 10, for example, well look at the evidence for the evolution of our eyes from light-sensitive cells. But complex traits frequently evolve in the reverse direction. As well see in Chapter 15, bacteria gave rise to the energy-producing structures in eukaryote cells called mitochondria. Along the way, the bacteria lost most of the genes essential for surviving as free-living bacteria.
Figure 1.26 This illustration, synonymous with evolution for many, propagates the misconception that evolution proceeds like a linear march of progress (it also mistakenly implies that humans evolved from chimpanzees). In fact, the evolutionary process is better envisioned as a tree-like process of diversification.
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Box 1.2
Like other species, human beings are the product of evolution. The final chapters of this book are dedicated to the evolution of Homo sapiens, but humans appear from time to time in earlier chapters. Thats because biologists have studied humans so carefully that we provide excellent illustrations of the evolutionary processes that influence all life. Here is a list of the sections of this book in which we discuss humans: Humans in the fossil record: page TK The phylogeny of hominins: page TK Human height as a product of genotype and environment: page TK Human genes in HardyWeinberg equilibrium: page TK Balancing selection in humans (sickle-cell anemia): page TK Natural selection in humans (lactose digestion): page TK Molecular phylogeny of humans and other primates: page TK Molecular phylogeny and recent human evolution: page TK Detecting ancient natural selection in humans (the FOXP2 gene): page TK Using evolution to decipher function of human genes: page TK The origin of Homo sapiens: page TK Humans as agents of extinction: page TK Endogenous retroviruses and mobile elements in the human genome: page TK The evolution of human beings: Chapter 17 Evolutionary medicine: Chapter 18
Misconception #11: Evolution is the result of individuals adapting to their environment. Individual organisms undergo change during their own lifetime, and some of these changes are adaptive. But its generally not possible for these traits to be passed down to successive generations. If you dyed your hair purple, you wouldnt expect your children to have purple hair. As well see in Chapter 6, evolution occurs in populations and requires changes in the frequency of alleles. Misconception #12: Evolution has made living things perfectly adapted to their environment. As impressive as some adaptations may be, they are far from perfect. Natural selection can act only on what already exists, and it operates under tight constraints of physics and development. Humans have very large brains, for example, that have allowed us to become natures great thinkers (Chapter 16). But those big brains also make childbirth much more dangerous for human mothers than for other female primates. Misconception #13: Evolution happens for the good of the species. Just as evolution has no foresight, evolution cannot recognize what is best for a large group of organisms. Natural selection operates at the level of genes and the reproductive success of individuals.
1.4 common misconceptions about evolution Roberts and Company Publishers, ISBN: 9781936221172, due August 15, 2012, For examination purposes only
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Misconception #14: Evolution promotes selfishness and cruelty. Natural selection favors behaviors that boost the spread of genes from one generation to the next. But those behaviors will differ from one set of conditions to another. In many species, cooperation and altruism are winning strategies (Chapter 16). Whats more, different species can also cooperate (Chapter 15). Flowering plants, for example, provide food to insects that pollinate them. Misconception #15: Evolution seeks a peaceful harmony in nature. Predators are exquisitely adapted to finding and killing prey. Parasites can devour their hosts from the inside out, manipulating individual molecules within their hosts. Misconception #16: Some forms of life are higher on the ladder of life, and some are lower. Every living species can boast many adaptations to its environment. Humans have complex brains capable of abstract thought and language, but that does not make us better adapted than other species. After all, we lack many complex adaptations found in other species. A dolphin that can communicate underwater with its fellow dolphins could just as easily be considered a higher form of life than humans, because we lack echolocation. Misconception #17: Evolution has produced a stable diversity of life. More than 99 percent of all species that ever existed have become extinct, and, at some points in the Earths history, millions of species have disappeared over relatively short spans of time. We may be at the start of another period of mass extinctions, this time caused by our own actions (Chapter 12). Once we set aside these sorts of misconceptions, we can learn how evolution actually works, and, in so doing, gain a profound appreciation of the dense tapestry of lifes history. As Charles Darwin wrote at the end of On the Origin of Species, There is grandeur in this view of life, with its several powers, having been breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.
To sum up . . .
Evolution is descent with modification. Mutations are errors that arise when DNA is replicated. New mutations cause individuals to differ from each other genetically (i.e., they generate variation within populations). Natural selection and genetic drift are mechanisms of evolution because they can cause the genetic composition of a population to shift from generation to generation. Natural selection occurs when some genetic types of individuals survive and reproduce more successfully than others. Evolution does not respond to an individuals need. Evolution produces complex adaptations, but it does not move toward a particular goal. Evolutionary biologists test hypotheses about evolution using many different lines of evidence. Whales evolved from land mammals about 50 million years ago. Evolution has shaped many aspects of their biology, from their behavior to their aging. The rapid evolution of the influenza virus makes it difficult to fight. 28
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Multiple Choice Questions
1. Which is a definition of evolution? a. Descent with modification. b. Mutated genes becoming more or less common over the course of generations. c. Change within a lineage due to natural selection and other mechanisms. d. All of the above are possible definitions. e. None of the above are appropriate definitions. b. c. d. e. 2. Which of the following is a true statement? a. Mutations always cause the improvement of a trait. b. Having bigger brains gave both advantages and disadvantages to human ancestors. c. The ancestors to whales needed more food than could be found on land, so they evolved features that allowed them to survive in the water. d. Birds progressed toward having the best-adapted wings throughout their evolution. e. Answers b, c, and d are true. f. All of the above are true statements. g. None of the above are true statements. 3. Which of the following support(s) the concept of descent with modification? a. All living organisms share a common code of genetic instructions. b. Flowers and insects often share a helpful partnership. c. Many mammals have the same pattern of bones in their forelimbs. d. Both a and c. e. All of the above. f. None of the above. 4. Which of the following is NOT a place that scientists look for evidence of evolution? a. The fossil remains of extinct animals. 5. Which group of animals are whales most closely related to? a. Camels. b. Fish. c. Seals. d. They are equally related to all of the above.
Examination of similar traits in closely related species. Change within an individual organism. Change in populations in the wild. None of the above (scientists look to all of these sources).
6. Which is the best explanation of why baleen whales still have genes for building teeth? a. These genes are now used to make baleen. b. Their ancestors had teeth and they inherited these genes from them, even though they no longer function. c. Their descendents might need teeth, so evolution keeps the genes around. d. Evolution cant take away genes, only add new ones. e. All of the above are valid explanations. f. None of the above are accurate. 7. Hemagglutinin is important in the evolution of influenza viruses because: a. It allows a virus to attack the red blood cells of its host. b. It is the basic building block of virus cell walls. c. It allows the virus to bind to the cells of its host. d. All of the above are true. e. Hemagglutinin is not important to viruses.
Short Answer Questions

1. What kind of evidence do evolutionary biologists use to test hypotheses about how different species are related to each other? 2. Which aspects of the natural world help demonstrate that evolution does not produce a peaceful harmony? 3. How can knowledge about the evolution of big brains in human ancestors demonstrate that evolution is not based on need? 4. The text states, As impressive as some adaptations may be, they are far from perfect. Natural selection can act only on what already exists. How can you support this statement with evidence from whale evolution? 5. Explain how flu vaccines function to reduce infections in humans. Why does protection from a single vaccination rarely last longer than a year? 6. What evidence can scientists use to explain events that happened in the past? 7. Examine Connor (2007) from the Primary Literature section. Summarize the results. Do you agree with the author(s) conclusions? Why or why not?
short answer questions Roberts and Company Publishers, ISBN: 9781936221172, due August 15, 2012, For examination purposes only
29
Additional Reading
Barton, N. H., D. E. Briggs, J. A. Eisen, D. B. Goldstein, and N. H. Patel. 2007. Evolution. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
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Uhen, M. 2010. The Origin(s) of Whales. Annual Review of Earth and Planetary Sciences 38:189 219. Zimmer, C. 1998. At the Waters Edge: Macroevolution and the Transformation of Life. New York: Free Press. University of California Museum of Paleontology. 2011. Misconceptions about evolution and the mechanisms of evolution, Understanding Evolution. http://evolution. berkeley.edu/evolibrary/misconceptions_faq. php (accessed March 1, 2011).
Coyne, J. A. 2009. Why Evolution Is True. New York: Viking. Mayr, E. 2001. What Evolution Is. New York: Basic Books.
Primary Literature Cited in Chapter 1

Connor, R. C. 2007. Dolphin Social Intelligence: Complex Alliance Relationships in Bottlenose Dolphins and a Consideration of Selective Environments for Extreme Brain Size Evolution in Mammals. Philosophical Transactions of the Royal Society B: Biological Sciences 362 (1480):587 602. doi:10.1098/rstb.2006.1997. Deamer, D. 2011. First Life: Discovering the Connections between Stars, Cells, and How Life Began. Berkeley: University of California Press. Dobzhansky, T. 1973. Nothing in Biology Makes Sense except in the Light of Evolution. American Biology Teacher 35:125 29. Gingerich, P. D., K. D. Rose, and D. W. Krause. 1980. Early Cenozoic Mammalian Faunas of the Clarks Fork BasinPolecat Bench Area, Northwestern Wyoming. University of Michigan Papers on Paleontology 24:51 68. Gingerich, P. D., N. A. Wells, D. E. Russell, and S. M. I. Shah. 1983. Origin of Whales in Epicontinental Remnant Seas: New Evidence from the Early Eocene of Pakistan. Science 220:403 6. doi:10.1126/science.220.4595.403. Goldbogen, J. A., J. Potvin, and R. E. Shadwick. 2010. Skull and Buccal Cavity Allometry Increase Mass-Specific Engulfment Capacity in Fin Whales. Proceedings of the Royal Society B: Biological Sciences 277:861 68. doi:10.1098/rspb.2009.1680. Hensley, S. E., S. R. Das, A. L. Bailey, L. M. Schmidt, H. D. Hickman, et al. 2009. Hemagglutinin Receptor Binding Avidity Drives Influenza A Virus Antigenic Drift. Science 326:734 36. doi:10.1126/science.1178258. Le Page, M. 2008. Evolution: 24 Myths and Misconceptions. New Scientist. http://www. newscientist.com/article/dn13620-evolution24-myths-and-misconceptions.html (accessed February 18, 2012). Luo, Z., and P. D. Gingerich. 1999. Terrestrial Mesonychia to Aquatic Cetacea: Transformation of the Basicranium and Evolution of Hearing in Whales. University of Michigan Papers on Paleontology 31:1 98. Marino, L. 2007. Cetacean Brains: How Aquatic Are They? Anatomical Record 290 (6):694 700. doi:10.1002/ar.20530. Marx, F. G., and M. D. Uhen. 2010. Climate, Critters, and Cetaceans: Cenozoic Drivers of the Evolution of Modern Whales. Science 327:993 96. doi:10.1126/science.1185581. National Academy of Sciences and Institute of Medicine. 2008. Science, Evolution, and Creationism. Washington, DC: National Academies Press. Neumann, G., T. Noda, and Y. Kawaoka. 2009. Emergence and Pandemic Potential of SwineOrigin H1N1 Influenza Virus. Nature 459 (7249):93139. doi:10.1038/nature08157. Nummela, S., S. T. Hussain, and J. G. M. Thewissen. 2006. Cranial Anatomy of Pakicetidae (Cetacea, Mammalia). Journal of Vertebrate Paleontology 26 (3):746 59. Stable URL: http://www.jstor.org/stable/4524618. Okasha, S. 2002. Philosophy of Science: A Very Short Introduction. Oxford: Oxford University Press. Price, S. A., O. R. P. Bininda-Emonds, and J. L. Gittleman. 2005. A Complete Phylogeny of the Whales, Dolphins and Even-Toed Hoofed Mammals (Cetartiodactyla). Biological Reviews 80 (3):445 73. doi:10.1017/ s1464793105006743 Rambaut, A., D. Posada, K. A. Crandall, and E. C. Holmes. 2004. The Causes and Consequences of HIV Evolution. Nature Reviews Genetics 5 (1):52 61. doi:10.1038/nrg1246. Smith, G. J. D., D. Vijaykrishna, J. Bahl, S. J. Lycett, M. Worobey, et al. 2009. Origins and Evolutionary Genomics of the 2009 SwineOrigin H1N1 Influenza A Epidemic. Nature 459 (7250):1122 25. doi:10.1038/ nature08182. Suttle, C. A. 2007. Marine VirusesMajor Players in the Global Ecosystem. Nature Reviews Microbiology 5 (10):80112. doi:10.1038/nrmicro1750. Thewissen, J. G. M., and S. Bajpai. 2001. Whale Origins as a Poster Child for Macroevolution. Bioscience 15:1037 49. doi:10.1641/0006-3568(2001)051[1037: woaapc]2.0.co;2.
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Thewissen, J. G. M., M. J. Cohn, L. S. Stevens, S. Bajpai, J. Heyning, et al. 2006. Developmental Basis for Hind-Limb Loss in Dolphins and Origin of the Cetacean Bodyplan. Proceedings of the National Academy of Science 103:8414 18. doi:10.1073/ pnas.0602920103. Thewissen, J. G. M., S. I. Madar, E. Ganz, S. T. Hussain, M. Arif, et al. 1997. Fossil Yak (Bos Grunniens: Artiodactyla, Mammalia) from the Himalayas of Pakistan. Kirtlandia (Cleveland) 50:1116. Thewissen, J. G. M., E. M. Williams, L. J. Roe, and S. T. Hussain. 2001. Skeletons of Terrestrial Cetaceans and the Relationship of Whales to Artiodactyls. Nature 413 (6853):277 81. doi:10.1038/35095005. Turvey, S. T. 2009. Witness to Extinction: How We Failed to Save the Yangtze River Dolphin. Oxford: Oxford University Press. Uhen, M. 2010. The Origin(s) of Whales. Annual Review of Earth and Planetary Sciences 38:189 219. doi:10.1146/annurevearth-040809-152453. Thewissen, J. G. M., L. N. Cooper, M. T. Clementz, S. Bajpai, and B. N. Tiwari. 2007. Whales Originated from Aquatic Artiodactyls in the Eocene Epoch of India. Nature 450 (7173):1190 94. doi:10.1038/nature06343. Thewissen, J., L. Cooper, J. George, and S. Bajpai. 2009. From Land to Water: The Origin of Whales, Dolphins, and Porpoises. Evolution: Education and Outreach 2 (2):272 88. doi:10.1007/s12052-009-0135-2.
UNAIDS. 2010. Global Report: UNAIDS Report on the Global Aids Epidemic: Joint United Nations Programme on HIV/AIDS (UNAIDS). University of California Museum of Paleontology. 2011. Misconceptions about Evolution and the Mechanisms of Evolution, Understanding Evolution. http://evolution. berkeley.edu/evolibrary/misconceptions_faq. php(accessed March 1, 2011). Zimmer, C. 1998. At the Waters Edge: Macroevolution and the Transformation of Life. New York: Free Press.
primary literature cited in chapter 1 Roberts and Company Publishers, ISBN: 9781936221172, due August 15, 2012, For examination purposes only
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1.1 Whales: Mammals Gone to Sea

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Middle ear cavity Fossil Pakicetus Dolphin Lagenorhynchus

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Phylogeny: A visual representation of the evolutionary history of populations, genes, or species.

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Figure 1.7 The relationship between

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Figure 1.8 This graph shows the ratio

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Balaenoptera (middle Miocene to recent)

Modern diversity Llanocetus (Eocene/Oligocene boundary) Dorudon (late Eocene)

Number of cetacean genera

Georgiacetus (middle Eocene)

Gelasian Piacenzian Zanclean

E Eocene 55.8 mya

E L Oligocene 33.9 23.0

Gelasian Piacenzian Zanclean

Figure 1.12 A: Paleontologists have analyzed databases of

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Figure 1.14 The Chinese river dolphin

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A mutation is any change to the genomic sequence of an organism.

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En d ret opla icu sm lum ic

mRNA synthesis RNA replication

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PR8 (stock 2) PR8 (stock 2) PR8 (stock 3) PR8 (stock 3)

E158K E246G E156K

E158K E246G E156K Experimental mutations to hemagglutinin

Highly pathogenic avian strain

Figure 1.21 On rare occasion, two strains of influenza virus co-infecting

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Common ancestor of all samples of 2009 H1N1 in uenza

Figure 1.23 The 2009 H1N1 virus was 1.23

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Figure 1.24 Studying the evolution of

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Figure 1.25 A flowchart showing how

1 Introduction 2 History 5 Genetics 10 Mechanisms of Development 12 Family

8 Natural Selection 6 Population Genetics 7 Quantitative Genetics 9 Molecular Evolution

16 Behavior 17 Human Evolution

14 Radiation and Extinction

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1.4 Common Misconceptions about Evolution

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Short Answer Questions

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Primary Literature Cited in Chapter 1