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Ten Great Advances in Evolution
 By Carl Zimmer
 Posted 10.26.09
 NOVA
To celebrate the 150th anniversary of the Origin of Species, here's a list—by no means exhaustive—of
some of the biggest advances in evolutionary biology over the past decade. These advances include not just
a better understanding of how this or that group of species first evolved, but insights into the evolutionary
process itself. In some cases those insights would have given Darwin himself a pleasant jolt of surprise.
Ten significant leaps forward in evolution research in the past decade, as chosen and described by noted
science writer Carl Zimmer Enlarge Photo credit: (Earth) © NASA; (text) © WGBH Educational
Foundation
EVOLUTION IN ACTION
Darwin envisioned natural selection acting so slowly that its effects would be imperceptible in a human
lifetime. But in the late 1900s, evolutionary biologists began to detect small but significant changes taking
place in a handful of species. In the past decade, many more cases of natural selection have come to light,
and scientists now realize that species can adapt quickly to changes in their environment. In fact, they are
finding that we humans are unwittingly driving some of the fastest bursts of evolution right now. As
greenhouse gases drive up the planet's average temperature, for instance, some species are adapting to the
changing climate. In California, University of Toronto biologist Arthur Weis and his colleagues found that
a seven-year drought had spurred the evolution of field mustard plants. In 2007, they reported that the
plants were now genetically programmed to flower eight days earlier in the spring.
If he were alive today, Darwin would be astonished at the pace and nature of discoveries being made in
evolutionary biology, including the witnessing of evolution in action. Enlarge Photo credit: © Louie
Psihoyos/Science Faction/Corbis
Thanks to powerful, cheap DNA sequencing technology, scientists can now pinpoint the molecular changes
underlying this rapid evolution. Bernard Palsson and his colleagues at the University of California in San
Diego have observed bacteria evolve in their lab. Over the course of a few weeks, the bacteria adapted to a
new kind of food (a chemical called glycerol). The scientists sequenced the complete genome of the
ancestral germ and its evolved descendants and looked for differences in their DNA. They identified a
handful of new mutations that has arisen in the bacteria and spread throughout the population. When the
scientists added those mutations to the ancestral germ, it became able to feed on the new food just as its
descendants did.
TRANSITIONAL FOSSILS
Darwin argued that even though different groups of species today might seem very different from each
other, they were linked by common ancestry. His theory predicted the existence of species that would
document that link. Just a year after the Origin of Species was published, Darwin was gratified to learn of
the discovery of a bird called Archaeopteryx that did just that. While it had feathers and wings, it also had
reptilian traits not seen in living birds, such as a long tail and claws on its "hands." It's too bad that Darwin
was not around to read the news about transitional fossils discovered just in the past decade. Many have
been just as spectacular as Archaeopteryx, if not more so.
Tiktaalik, here as depicted by artist Carl Buell, represents a key transitional creature between marine- and
land-dwelling animals. Enlarge Photo credit: Courtesy Carl Buell
In 2004, for example, scientists digging in the Arctic unearthed the fossil bones of a fishy relative of all
land vertebrates, including us, called Tiktaalik. This 375 million-year-old animal had limbs complete with
elbows, wrists, and a flexible neck. But it still lived underwater, where it used its gills to breathe. [For more
on Tiktaalik, see "The Zoo of You" (in Editors' Picks at left).]
Whales in particular intrigued Darwin, because they were clearly mammals on the inside yet were so fishlike on the outside. In 1994, paleontologists reported the first fossil of a whale with legs, as Darwin had
predicted. And over the past decade, they've uncovered a number of new fossils that fill in many of the
details in the transition that whales made from land to sea between 50 and 40 million years ago.
For example, in 2001, Philip Gingerich of the University of Michigan and his colleagues reported the first
ankle bone of a whale. This bone is particularly important to tracing the origin of whales, because it had a
distinctive shape seen only in one group of mammals: even-toed hoofed mammals known as artiodactyls.
Studies on whale DNA also completed over the past decade have consistently pointed to artiodactyls—and
hippos in particular—as the closest living relatives of whales on land.
ORIGIN OF COMPLEX TRAITS
Studying DNA doesn't just help scientists figure out which species are most closely related to one another.
They can also discover how genes build structures like eyes in different species. That comparison has, in
just the past decade, revealed some key insights into how those structures arose.
Complex eyes have evolved in several different lineages of animals. But each kind of eye contains
crystallins for directing incoming light and opsins for capturing it. Enlarge Photo credit: (diagram) Echo
Medical Media; (jellyfish) © ANT Photo Library/Photo Researchers Inc.; (octopus) © Kerry L.
Werry/Shutterstock; (fly) © Stana/Shutterstock; (human eye) © Bplucinski/Shutterstock
Complex eyes evolved in a number of different lineages of animals, such as vertebrates like us, octopi and
other cephalopods, and insects. For decades, the evidence suggested that these complex eyes had evolved
independently in each lineage. Today, however, scientists see a much more intertwined history.
In 2007, for example, Todd Oakley of the University of California at Santa Barbara and his colleagues
demonstrated that the different kinds of light receptors evolved from simple signal-detecting proteins in our
distant ancestors some 600 million years ago. By the time early animals had evolved, these signal detectors
had evolved into two different kinds of light receptors. Those early animals probably had eyes that were
nothing more than simple light-sensitive spots. Only later did complex eyes evolve, and different lineages
recruited different kinds of light receptors to capture images. Studies like Oakley's indicate that complex
eyes did indeed evolve independently, but they also co-opted many of the same ancient genetic tools to do
so.
It's a pattern that's strikingly similar to the one other scientists have discovered in other traits in the past
decade, from bird feathers to beetle horns: Evolution is the great recycler.
THE GENOMIC WILDERNESS
Natural selection, as Darwin recognized, is an important force in evolution. And in the past decade,
scientists studying genes have found many examples of its power. When mutations change the way a
protein-coding gene works—altering the structure of the protein, for example, or the signals that turn the
gene on and off—those mutations can help or harm an organism's reproductive success. Beneficial
mutations can then spread, and over time they can transform a species dramatically.
DNA can experience a number of different kinds of mutations, several of which are shown here. Enlarge
Photo credit: © Lineworks
But natural selection is far from the full story of evolution. Many mutations can spread throughout an entire
species thanks not to natural selection but through lucky rolls of the genetic dice. This so-called neutral
evolution has been particularly important in shaping the parts of the genome that do not contain proteincoding genes. Most of the news you read about DNA concerns protein-coding genes, so you might well
think that there's not much of the genome that doesn't contain them. But just the opposite is true. Some 98.8
percent of the human genome is this so-called noncoding DNA.
Only in the past few years have scientists started to explore this genomic wilderness in great detail, and
they've used evolution as their guide. In the human genome, for example, there are an estimated 11,000 socalled pseudogenes—stretches of DNA that once encoded proteins but no longer do so thanks to disabling
mutations. These vestiges of genes once had important functions, such as synthesizing vitamins or allowing
us to smell certain molecules. Scientists know that these pseudogenes were once full-blown protein-coding
genes, because they can find related versions of them in our primate relatives, in good working order.
Evolution lets scientists find needles in the genomic haystack.
While some of your noncoding DNA started out as your own genes, much more of it started out in invading
viruses. Certain kinds of viruses can insert their DNA into host cells in such a way that it gets carried down
from one generation of host to the next. Eventually these in-house viruses mutate so much they can no
longer infect a new host. But they can still make copies of themselves, which get inserted into their old
host's genome. About 40 percent of the human genome is made up of this viral DNA. Scientists can trace
the ancestry of this virus DNA by comparing its remnants in our own genomes to the ones left in other
primates.
Much of this viral DNA has now mutated to such a degree that it has become little more than padding in the
genome. But even these inert relicts hold clues to their past. All human beings carry versions of an ancient
virus called HERV-K. The differences in those versions evolved after the original virus infected a single
human and was then passed down to his or her descendants. French scientists compared these versions of
HERV-K, tallying up the mutations in one. Based on those new mutations, the scientists estimated that the
virus first infected a human ancestor a few million years ago.
To prove that it had indeed once been a full-fledged virus, the scientists then used the different versions of
its DNA to infer what its original genetic sequence had been. They synthesized that piece of DNA and
injected it into human cells. The synthesized DNA hijacked the cells and caused them to spew out viruses
with the same genetic sequence. The scientists, in other words, had brought a dead virus back to life.
Parts of genes within, say, a red blood cell serve as switches, telling other genes when to turn on or off, and
for how long (see “Gene Switches” in Editors’ Picks). Enlarge Photo credit: © Micro Discovery/Corbis
Sprinkled among the dead virus DNA and disabled pseudogenes are some useful elements of noncoding
DNA. Some of these elements are switches, where proteins can attach to turn neighboring genes on and off.
Our genome also contains stretches of DNA that can produce RNA molecules, but no proteins. These RNA
molecules have their own essential roles to play in our lives, for example as signal detectors and gene
regulators.
Scientists rely on evolution to find these elements as well. If a piece of noncoding DNA has no important
function, mutations to it will have little effect on the survival of the organism that carries it. But if it does
have an essential function, mutations will be far more likely to cause devastating harm. As a result,
organisms with those harmful mutations will have fewer offspring, and so the piece of DNA will not
change as easily. Scientists can find these functional elements by comparing many different species and
looking for stretches of noncoding DNA that are unusually similar from species to species. In many cases,
they've been able to demonstrate that these elements do indeed play crucial roles in the survival of
organisms. Evolution thus lets scientists find needles in the genomic haystack.
THE POWER OF SEX
Darwin himself recognized that sex created an evolutionary force as powerful as natural selection. If
animals have traits that members of the opposite sex find attractive—be they horns, feathers, or bright blue
posteriors—those traits will become more common over the generations.
Darwin came up with his theory of sexual selection to explain the peacock's over-the-top tail feathers,
among other extravagant physical traits in animals. Enlarge Photo credit: © Lee Pettet/istockphoto
The past decade of research has confirmed that sex is indeed a potent force. But it's powerful in ways that
Darwin could not have appreciated. Studies in the past few years have demonstrated that the sexual
preference that females have for one kind of male over another is potent enough to carve an old species
apart into several new ones. In the lakes of East Africa, for instance, sexual selection has driven the origin
of hundreds of new species from fish that live and breed side by side.
Sexual selection does more than favor the sexy, however. Any adaptation that enables an individual to have
more offspring than other members of its own sex may be favored by sexual selection. For example, male
flies that inject chemicals along with their sperm into females can make them less receptive to mating with
other males. Unfortunately for the females, these chemicals are toxic. So the female flies respond by
evolving defenses against the chemicals, which the males then evolve strategies to overcome. Scientists
have documented this so-called sexual conflict in great detail in the past decade, and they can even see its
fingerprints on millions of years of evolution by measuring how quickly different genes have evolved.
Some of the fastest-evolving genes build semen proteins in many species (including humans).
COEVOLUTION OF LOCKS AND KEYS
Darwin made one of his gutsiest predictions when he heard about a bizarre orchid in Madagascar called
Angraecum sesquipedale. It grew a tube-shaped spur on its flower measuring over a foot long, at the
bottom of which it produced nectar. Darwin was convinced that the extravagant shapes and colors of
flowers evolved not to please the eye of man, but to use pollinating animals in many clever ways to
promote the plants' own reproduction. One common strategy Darwin recognized was the way a flower
would dust insects with pollen as they drank up its nectar. So Darwin proposed that somewhere in the
forests of Madagascar lived an insect with a tongue long enough to drink up A. sesquipedale's well-hidden
nectar. As the mystery insect drank, the orchid's pollen would cover its body pressed against the flower.
Angraecum sesquipedale has cut a symbiotic deal with a species of long-tongued moth in its native
Madagascar. Other such matches are not so mutually beneficial. Enlarge Photo credit: © 2004 Prem
Subrahmanyam, used with permission/www.orchidstockphotos.com
Twenty-one years after Darwin's death, his prediction came true. A moth with a foot-long tongue turned up
in Madagascar.
We depend on ecosystems for many services, and in many cases those services are only possible thanks to
coevolution.
Since then, scientists have discovered many other extreme matches in nature. Not all of them are so
friendly as the one between the orchid and its long-tongued pollinator. Rough-skinned newts in western
North America produce poison in their skin powerful enough to kill a crowd of people. The toxins do their
damage by latching onto a particular receptor on the surface of neurons, disabling them. The reason for the
newt's overkill is its predator, the garter snake. Garter snakes make special versions of the receptor in
question, with a shape that thwarts the toxin's attachment. This precise defense allows the snake to dine on
newts with impunity.
In the past decade, this back-and-forth kind of evolution, known as coevolution, has come much more
sharply into focus. For example, scientists have long puzzled over exactly how intimate partnerships like
the one between Darwin's moth and orchid came about. In 2005, John Thompson of the University of
California at Santa Cruz offered a theory, which he called the geographic mosaic model of coevolution.
Thompson argued that, in some places, two species will drive each other's evolution towards more extreme
adaptations, while in other places, they may have little or no effect on each other. At the same time,
individuals are steadily moving from one population to another, carrying their coevolved genes. Rather
than just evolving in lockstep, coevolutionary partners actually evolve in a complex fashion, which
Thompson called a geographic mosaic.
The rough-skinned newt has long been in an evolutionary arms race with the garter snake, to the point
where its skin has become extremely toxic. Enlarge Photo credit: © Visuals Unlimited/Corbis
Remarkably, it only took a few years for scientists to test Thompson's model—and find support for it.
Some looked at pine trees and birds that spread their seeds, others at bacteria and the viruses that infect
them, still others at the rough-skinned newts and their garter snake predators. In each case, they discovered
an intricate landscape of coevolutionary hotspots and coldspots, just as Thompson predicted.
Insights like these are some of the most important in evolution, particularly for our own well-being. We
depend on ecosystems for many services, and in many cases those services are only possible thanks to
coevolution. Many of the plants we depend on for food and building materials, for example, have
coevolved with fungi that help them get nutrients out of the soil. They also depend on pollinating animals
in many cases to reproduce. We, too, have coevolved with friendly microbes and harmful ones (see
"Evolutionary medicine" entry).
EXTINCTION'S FOOTPRINT
Unfortunately, over the past decade, it has become increasingly clear that the world's biodiversity is
imperiled on a scale unmatched for millions of years. As forests are cleared, oceans acidified, diseases
spread, and the atmosphere warmed, many species face serious threats to their survival. While this wave of
extinctions is new, the history of life has seen many pulses in which vast numbers of species have been
wiped out. Studies on extinction are revealing that it has a profound influence on the evolutionary process
itself, reorganizing entire ecosystems and offering new opportunities for surviving species to exploit the
niches left empty by vanished ones.
Our planet has suffered five mass extinctions in the roughly three billion years since life first evolved.
Many scientists believe it is now facing its sixth, this one caused by us. Enlarge Photo credit: © NASA
Volcanoes in particular appear to have wreaked a lot of havoc, warming the planet with heat-trapping gases
and helping to trigger drastic changes in the ocean's chemistry. Under some circumstances, these kinds of
assaults can trigger ecological collapse.
It can take millions of years for the planet to recover from mass extinctions, and in some important ways it
is never quite the same. Some of the groups of species that once dominated the planet were snuffed out in
mass extinctions. In the past decade, scientists have seen major shifts in the planet's ecology—particularly
in the oceans—that hint that it is in the midst of yet another reorganization. As coral reefs die off and fish
are hauled out of the sea, for example, less familiar forms of life such as jellyfish or even sulfide-belching
bacteria may come to dominate the seas.
THE TREE AND THE WEB
Now that we live in the genome age, scientists are getting an unprecedented look at how species evolved
from common ancestors. That's because their common ancestry is recorded in their DNA, which is passed
down from generation to generation. Using supercomputers and sophisticated new statistical methods to
analyze DNA, scientists can test old hypotheses about how species are related to one another. They are
starting to resolve some puzzles that previous generations of scientists simply couldn't crack.
Paleontologists have long argued, for example, that our closest living aquatic relatives are lungfishes and
coelacanths, a conclusion that geneticists now confirm. Among our primate relatives, chimpanzees and
bonobos are now widely recognized as our closest living kin.
A tree of life drawn from DNA studies, with length denoting number of mutations in each branch. Note
how animals comprise a very small part of the genetic diversity of life on Earth. Enlarge Photo credit: ©
Lineworks
DNA is not a magic wand that instantly gives us answers to all our questions, however. At some stages in
the evolution of life, many new lineages have evolved over a relatively short period of time. Many of the
major groups of animals alive today may have evolved over roughly 50 million years, some 550 million
years ago. It can be difficult to make out the details of these periods of life's history, much as it's hard to use
a telescope to make out individual people on a distant island.
Scientists have found that fungi and animals share a closer ancestry than either does to plants.
At the same time, DNA is revealing new patterns in the history of life. Darwin first envisioned evolution as
a tree, with new branches budding off like young branches. Today, that metaphor still has great power to
explain. Chimpanzees and bonobos are two branches joined at the base by a common ancestor about two
million years ago; our own branch split off from their lineage about seven million years ago. On a far
grander scale, scientists have found that fungi and animals share a closer ancestry than either does to plants.
But genes don't always respect the boundaries of species. That's especially true among bacteria and other
microbes, in which genes can be shuttled from one species to another. To understand the evolution of
single-celled organisms, scientists are increasingly focusing on individual genes, tracing their journeys
through time and among species. The path of their journeys looks more like a web. And since life was
almost entirely single-celled for the first two billion years of its history, we must see the opening chapters
of our biological history as a tapestry rather than a tree.
THE HUMAN RECIPE
Over the past decade, scientists have sequenced not just the human genome, but the genomes of
chimpanzees, monkeys, and many other animals. Now that they can comb through these genetic archives,
they are starting to work out how the genomes of our ancestors changed after they branched off from other
primates. The work begins with a catalog. Scientists have tallied up genes that were accidentally duplicated
in our lineage, for example, so that we now have more copies of them than do other primates. They've also
identified genes that became pseudogenes. And some genes in humans got their start as noncoding DNA in
other primates. Recently Aoife McLysaght of the Smurfit Institute of Genetics at Trinity College Dublin
discovered three proteins produced by humans that aren't found in our closest non-human relatives.
McLysaght then discovered that the genes for these three human proteins correspond almost precisely to
stretches of noncoding DNA in the other species. It appears that mutations transformed these pieces of
genetic material into genes capable of making proteins.
Geneticists have begun to ferret out the genetic differences that have accumulated in our lineage since it
diverged from the lineage of chimpanzees, our closest living relatives. Enlarge Photo credit: © Gary
Wales/istockphoto
Our genomes are unique in other ways that are subtle yet no less important. While we share just about all
our protein-coding genes in common with chimpanzees, the actual sequence of some of them differs
slightly. In many cases, those differences are biologically meaningless; both versions of the protein in
question work perfectly well. But in some cases, natural selection was at work. Scientists are amassing a
growing list of genes in which they find compelling evidence that mutations in our ancestors boosted their
reproductive success. Natural selection has also left its mark on noncoding DNA since our ancestors
branched off from other primates, too.
We are, of course, more than just a unique catalog of genetic elements. Scientists are only now starting to
find the meaning in the bits of DNA unique to our species. In some cases, these differences evolved as a
result of the unique kinds of viruses and other pathogens we face. In other cases, these differences emerged
as we evolved the secret to human success: our unmatched mental versatility. Scientists are beginning to
identify genes involved in language and other uniquely human kinds of behavior that underwent dramatic
changes in the past few million years. Today, 150 years after the Origin of Species, we're just getting to
know our evolutionary selves.
EVOLUTIONARY MEDICINE
In 1996, Randolph Nesse, a psychiatrist, and George Williams, an evolutionary biologist, published a book
entitled Why We Get Sick. They argued that in order to understand health and disease, scientists had to
consider our evolutionary heritage. The book helped inspire a number of scientists—both medical
researchers and evolutionary biologists—to establish a new field of inquiry called evolutionary medicine.
The flu virus forces us through its continual evolution to develop new vaccines each year to combat its
novel strains. Here, the new H1N1 swine flu that appeared in the spring of 2009. Enlarge Photo credit:
Courtesy CDC
In a sense, evolutionary biologists have been investigating medicine for a long time now. In the late 1950s,
for example, Williams first began to ponder why we—and other animals—get old. Williams argued that
natural selection favors adaptations for reproducing early in life, even if those adaptations have harmful
side effects later on. In recent years, evolutionary biologists have joined forces with medical researchers to
analyze these ideas together. Many recent studies on the molecular biology of aging support Williams's
basic concepts. Knowing that, in effect, aging is a side effect of a vibrant youth is helping researchers
investigate new ways to slow the aging process itself.
Evolution also makes viruses and other pathogens such powerful threats to our survival, even in an age
when we can sequence their DNA. That's because their DNA is a moving target, mutating and hitting upon
new solutions to the age-old challenge of turning us into breeding grounds for disease. But tracing the
evolution of our microscopic enemies can also reveal their vulnerabilities—the ways in which they can't
evolve effectively. These weak spots are becoming new targets for preventions and treatments. We may not
be able to stop evolution, but we can at least learn how to use it to our advantage. [See an interview with
swine flu expert Peter Palese (in Editors' Picks at left).]
Carl Zimmer writes about evolution in the New York Times, a number of
magazines, and his award-winning blog, The Loom. His latest book, The Tangled
Bank: An Introduction to Evolution, was published by Roberts and Company in
October 2009.
Sources
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EVOLUTION IN ACTION
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ORIGIN OF COMPLEX TRAITS
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evolution. Journal of Experimental Zoology. Part B. Molecular and Developmental Evolution 298, no. 1
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THE GENOMIC WILDERNESS
Birney, Ewan, John A. Stamatoyannopoulos, Anindya Dutta, et al. 2007. Identification and analysis of
functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, no. 7146 (June
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Dewannieux, Marie, Francis Harper, Aurélien Richaud, et al. 2006. Identification of an infectious
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Gerstein, Mark B., Can Bruce, Joel S. Rozowsky, et al. 2007. What is a gene, post-ENCODE? History and
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Nei, Masatoshi. 2005. Selectionism and neutralism in molecular evolution. Molecular Biology and
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THE POWER OF SEX
Arnqvist, Göran. 2005. Sexual Conflict. Monographs in behavior and ecology. Princeton, N.J: Princeton
University Press.
Seehausen, Ole, Yohey Terai, Isabel S. Magalhaes, Karen L. Carleton, Hillary D. J. Mrosso, Ryutaro
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COEVOLUTION OF LOCKS AND KEYS
Hanifin, Charles T., Edmund D. Brodie, Jr., and Edmund D. Brodie III. 2008. Phenotypic mismatches
reveal escape from arms-race coevolution. PLoS Biology 6, no. 3 (March 11): e60. doi:PMC2265764.
Siepielski, Adam M., and Craig W. Benkman. 2008. A seed predator drives the evolution of a seed
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Thompson, John N. 2005. The Geographic Mosaic of Coevolution. Chicago: University of Chicago Press.
EXTINCTION'S FOOTPRINT
Bambach, Richard K. 2006. Phanerozoic biodiversity mass extinctions. Annual Review of Earth and
Planetary Sciences 34 (May 1): 127-155.
Ehrlich, Paul R., and Robert M. Pringle. 2008. Colloquium paper: where does biodiversity go from here? A
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Jackson, Jeremy B. C. 2008. Colloquium paper: ecological extinction and evolution in the brave new
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Mayhew, Peter J., Gareth B. Jenkins, and Timothy G. Benton. 2008. A long-term association between
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Payne, Jonathan L., and Seth Finnegan. 2007. The effect of geographic range on extinction risk during
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THE TREE AND THE WEB
Cotton, James A., and Mark Wilkinson. 2009. Supertrees join the mainstream of phylogenetics. Trends in
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Doolittle, W. Ford. 2009. The practice of classification and the theory of evolution, and what the demise of
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THE HUMAN RECIPE
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EVOLUTIONARY MEDICINE
Nesse, Randolph M. 1994. Why We Get Sick: The New Science of Darwinian Medicine. 1st ed. New York:
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Stearns, S. C., and Jacob C. Koella, eds. 2008. Evolution in Health and Disease. Ed. S. C. Stearns and
Jacob C. Koella. 2nd ed. Oxford biology. Oxford: Oxford University Press.
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