BREAKTHROUGH OF THE YEAR: Evolution in Action

Science ^ | December 2005 | Elizabeth Culotta and Elizabeth Pennisi

[MRMEAN]

BREAKTHROUGH OF THE YEAR:
Evolution in Action

Elizabeth Culotta and Elizabeth Pennisi

Equipped with genome data and field observations of organisms from microbes to mammals, biologists made huge strides toward understanding the mechanisms by which living creatures evolve

The big breakthrough, of course, was the one Charles Darwin made a century and a half ago. By recognizing how natural selection shapes the diversity of life, he transformed how biologists view the world. But like all pivotal discoveries, Darwin's was a beginning. In the years since the 1859 publication of The Origin of Species, thousands of researchers have sketched life's transitions and explored aspects of evolution Darwin never knew.

See
Web links
on evolution

Today evolution is the foundation of all biology, so basic and all-pervasive that scientists sometimes take its importance for granted. At some level every discovery in biology and medicine rests on it, in much the same way that all terrestrial vertebrates can trace their ancestry back to the first bold fishes to explore land. Each year, researchers worldwide discover enough extraordinary findings tied to evolutionary thinking to fill a book many times as thick as all of Darwin's works put together. This year's volume might start with a proposed rearrangement of the microbes at the base of the tree of life and end with the discovery of 190-million-year-old dinosaur embryos.

Amid this outpouring of results, 2005 stands out as a banner year for uncovering the intricacies of how evolution actually proceeds. Concrete genome data allowed researchers to start pinning down the molecular modifications that drive evolutionary change in organisms from viruses to primates. Painstaking field observations shed new light on how populations diverge to form new species--the mystery of mysteries that baffled Darwin himself. Ironically, also this year some segments of American society fought to dilute the teaching of even the basic facts of evolution. With all this in mind, Science has decided to put Darwin in the spotlight by saluting several dramatic discoveries, each of which reveals the laws of evolution in action.

All in the family
One of the most dramatic results came in September, when an international team published the genome of our closest relative, the chimpanzee. With the human genome already in hand, researchers could begin to line up chimp and human DNA and examine, one by one, the 40 million evolutionary events that separate them from us.

The genome data confirm our close kinship with chimps: We differ by only about 1% in the nucleotide bases that can be aligned between our two species, and the average protein differs by less than two amino acids. But a surprisingly large chunk of noncoding material is either inserted or deleted in the chimp as compared to the human, bringing the total difference in DNA between our two species to about 4%.

Chimp champ. Clint, the chimpanzee whose genome sequence researchers published this year.

CREDIT: YERKES NATIONAL PRIMATE RESEARCH CENTER

Somewhere in this catalog of difference lies the genetic blueprint for the traits that make us human: sparse body hair, upright gait, the big and creative brain. We're a long way from pinpointing the genetic underpinnings of such traits, but researchers are already zeroing in on a few genes that may affect brain and behavior. This year, several groups published evidence that natural selection has recently favored a handful of uniquely human genes expressed in the brain, including those for endorphins and a sialic acid receptor, and genes involved in microcephaly.

The hunt for human genes favored by natural selection will be sped by newly published databases from both private and public teams, which catalog the genetic variability among living people. For example, this year an international team cataloged and arranged more than a million single-nucleotide polymorphisms from four populations into the human haplotype map, or HapMap. These genetic variations are the raw material of evolution and will help reveal recent human evolutionary history.

Probing how species split
2005 was also a standout year for researchers studying the emergence of new species, or speciation. A new species can form when populations of an existing species begin to adapt in different ways and eventually stop interbreeding. It's easy to see how that can happen when populations wind up on opposite sides of oceans or mountain ranges, for example. But sometimes a single, contiguous population splits into two. Evolutionary theory predicts that this splitting begins when some individuals in a population stop mating with others, but empirical evidence has been scanty. This year field biologists recorded compelling examples of that process, some of which featured surprisingly rapid evolution in organisms' shape and behavior.

For example, birds called European blackcaps sharing breeding grounds in southern Germany and Austria are going their own ways--literally and f iguratively. Sightings over the decades have shown that ever more of these warblers migrate to northerly grounds in the winter rather than heading south. Isotopic data revealed that northerly migrants reach the common breeding ground earlier and mate with one another before southerly migrants arrive. This difference in timing may one day drive the two populations to become two species.

CREDITS: C. GOLDSMITH/CDC (AVIAN FLU); W. A. CRESKO ET AL., PNAS 101, 6050 (2004) (STICKLEBACK); DAVID SCHARF/PETER ARNOLD (DROSOPHILA); ANDY BRIGHT (EUROPEAN BLACKCAP)

Two races of European corn borers sharing the same field may also be splitting up. The caterpillars have come to prefer different plants as they grow--one sticks to corn, and the other eats hops and mugwort--and they emit different pheromones, ensuring that they attract only their own kind.

Biologists have also predicted that these kinds of behavioral traits may keep incipient species separate even when geographically isolated populations somehow wind up back in the same place. Again, examples have been few. But this year, researchers found that simple differences in male wing color, plus rapid changes in the numbers of chromosomes, were enough to maintain separate identities in reunited species of butterflies, and that Hawaiian crickets needed only unique songs to stay separate. In each case, the number of species observed today suggests that these traits have also led to rapid speciation, at a rate previously seen only in African cichlids.

Other researchers have looked within animals' genomes to analyze adaptation at the genetic level. In various places in the Northern Hemisphere, for example, marine stickleback fish were scattered among landlocked lakes as the last Ice Age ended. Today, their descendants have evolved into dozens of different species, but each has independently lost the armor plates needed for protection from marine predators. Researchers expected that the gene responsible would vary from lake to lake. Instead, they found that each group of stranded sticklebacks had lost its armor by the same mechanism: a rare DNA defect affecting a signaling molecule involved in the development of dermal bones and teeth. That single preexisting variant--rare in the open ocean--allowed the fish to adapt rapidly to a new environment.

Biologists have often focused on coding genes and protein changes, but more evidence of the importance of DNA outside genes came in 2005. A study of two species of fruit flies found that 40% to 70% of noncoding DNA evolves more slowly than the genes themselves. That implies that these regions are so important for the organism that their DNA sequences are maintained by positive selection. These noncoding bases, which include regulatory regions, were static within a species but varied between the two species, suggesting that noncoding regions can be key to speciation.

That conclusion was bolstered by several other studies this year. One experimental paper examined a gene called yellow, which causes a dark, likely sexually attractive, spot in one fruit fly species. A separate species has the same yellow gene but no spot. Researchers swapped the noncoding, regulatory region of the spotted species' yellow gene into the other species and produced dark spots, perhaps retracing the evolutionary events that separated the two. Such a genetic experiment might have astonished and delighted Darwin, who lamented in The Origin that "The laws governing inheritance are quite unknown." Not any longer.

To your health
Such evolutionary breakthroughs are not just ivory-tower exercises; they hold huge promise for improving human well-being. Take the chimpanzee genome. Humans are highly susceptible to AIDS, coronary heart disease, chronic viral hepatitis, and malignant malarial infections; chimps aren't. Studying the differences between our species will help pin down the genetic aspects of many such diseases. As for the HapMap, its aims are explicitly biomedical: to speed the search for genes involved in complex diseases such as diabetes. Researchers have already used it to home in on a gene for agerelated macular degeneration.

And in 2005, researchers stepped up to help defend against one of the world's most urgent biomedical threats: avian influenza. In October, molecular biologists used tissue from a body that had been frozen in the Alaskan permafrost for almost a century to sequence the three unknown genes from the 1918 flu virus--the cause of the epidemic that killed 20 million to 50 million people. Most deadly flu strains emerge when an animal virus combines with an existing human virus. After studying the genetic data, however, virologists concluded that the 1918 virus started out as a pure avian strain. A handful of mutations had enabled it to easily infect human hosts. The possible evolution of such an infectious ability in the bird flu now winging its way around the world is why officials worry about a pandemic today.

A second group reconstructed the complete 1918 virus based on the genome sequence information and studied its behavior. They found that the 1918 strain had lost its dependence on trypsin, an enzyme that viruses typically borrow from their hosts as they infect cells. Instead, the 1918 strain depended on an in-house enzyme. As a result, the reconstructed bug was able to reach exceptionally high concentrations in the lung tissue of mice tested, helping explain its virulence in humans. The finding could point to new ways to prevent similar deadly infections in the future.

Darwin focused on the existence of evolution by natural selection; the mechanisms that drive the process were a complete mystery to him. But today his intellectual descendants include all the biologists--whether they study morphology, behavior, or genetics--whose research is helping reveal how evolution works.

Online Extras on Evolution

• Selected Papers and Articles
  
  • The Chimpanzee Genome
  • Human Evolution
  • Speciation
  • Avian Influenza
• Interesting Web Sites

Selected Papers and Articles

The Chimpanzee Genome

The Chimpanzee Sequencing and Analysis Consortium, "Initial Sequence of the Chimpanzee Genome and Comparison with the Human Genome," Nature 437, 69 (2005)

Z. Cheng et al., "A Genome-Wide Comparison of Recent Chimpanzee and Human Segmental Duplications," Nature 437, 88 (2005)

J. F. Hughes et al., "Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee," Nature 437, 100 (2005)

R.S. Hill and C.A. Walsh et al., "Molecular Insights into Human Brain Evolution," Nature 437, 64 (2005)

P. Khaitovich et al., "Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees," Science 309, 1850 (2005)

E. Culotta, "Chimp Genome Catalogs Differences With Humans," Science 309, 1468 (2005)

M.D. Hauser, "Beyond the Chimpanzee Genome: The Threat of Extinction," Science 309, 1498 (2005)

E. H. McConkey and A. Varki, "Thoughts on the Future of Great Ape Research," Science 309, 1499 (2005)

R. Nielsen et al., "A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees," PLoS Biol. 3, e170 (2005)

Human Evolution

M.V. Rockman et al., "Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans," PLoS Biol. 3, e387 (2005)

M. Balter, "Expression of Endorphin Gene Favored in Human Evolution," Science 310, 1257 (2005)

The International HapMap Consortium, "A Haplotype Map of the Human Genome," Nature 437, 1299 (2005)

J. Couzin, "New Haplotype Map May Overhaul Gene Hunting," Science 310, 601 (2005)

T. Hayakawa et al., "A Human-Specific Gene in Microglia," Science 309, 1693 (2005)

P.D. Evans et al., "Microcephalin, a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans," Science 309, 1717 (2005)

N. Mekel-Bobrov et al., "Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens," Science 309, 1720 (2005)

M. Balter, "Are Human Brains Still Evolving? Brain Genes Show Signs of Selection," Science 309, 1662 (2005)

Speciation

S. Bearhop et al., "Assortative Mating as a Mechanism for Rapid Evolution of a Migratory Divide," Science 310, 502 (2005)

P. Andolfatto, "Adaptive Evolution of Non-Coding DNA in Drosophila," Nature 437, 1149 (2005)

V. A. Lukhtanov, "Reinforcement of Pre-Zygotic Isolation and Karyotype Evolution in Agrodiaetus Butterflies," Nature 436, 385 (2005)

T. Malausa et al., "Assortative Mating in Sympatric Host Races of the European Corn Borer," Science 308, 258 (2005)

P.F. Colosimo et al., "Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles," Science 307, 1928 (2005)

G. Gibson, "The Synthesis and Evolution of a Supermodel," Science 307, 1890 (2005)

N. Gompel et al., "Chance Caught on the Wing: Cis-Regulatory Evolution and the Origin of Pigment Patterns in Drosophila," Nature 433, 481 (2005)

T.C. Mendelson and K.L. Shaw, "Sexual Behaviour: Rapid Speciation in an Arthropod," Nature 433, 375 (2005)

Influenza

T.M. Tumpey et al., "Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus," Science 310, 77 (2005)

J. Kaiser, "Resurrected Influenza Virus Yields Secrets of Deadly 1918 Pandemic," Science 310, 28 (2005)

J.K. Taubenberger et al., "Characterization of the 1918 Influenza Virus Polymerase Genes," Nature 437, 889 (2005)

M. Enserink, "Pandemic Influenza: Global Update," Science 309, 370 (2005)

G.F. Rimmelzwaan et al., "Full Restoration of Viral Fitness by Multiple Compensatory Co-Mutations in the Nucleoprotein of Influenza A Virus Cytotoxic T-Lymphocyte Escape Mutants ," J. Gen. Virol. 86, 1801 (2005)

D. Normile, "Genetic Analyses Suggest Bird Flu Virus Is Evolving," Science 308, 1234 (2005)

 

Interesting Web Sites

Understanding Evolution
An engaging educational Web site teaching the science and history of evolutionary biology; a collaborative project of the University of California Museum of Paleontology and the National Center for Science Education.

The Evolution Project
An online companion to a PBS television series on the science and history of evolution, this interactive Web site features conversations with experts, a multimedia library, teaching resources, and more.

Nature Web Focus: The Chimpanzee Genome
A collection of research papers, articles, and other online resources.

Ensemble Chimp Resource
Access to chimpanzee genome data and tools for analysis.

Becoming Human
An interactive journey through the story of human evolution, from the Institute of Human Origins at Arizona State University. (Requires Flash Player).

International HapMap Project
A multi-country effort to identify and catalog genetic similarities and differences in human beings.

Kimball's Biology Pages: Speciation
From Dr. John W. Kimball's online biology textbook.

Evolution 101: Speciation
An illustrated tutorial on the different ways to define a species and the various causes of speciation.

Avian Influenza
Information and resources from the U.S. Centers for Disease Control and Prevention.

WHO Avian Influenza Page
Resources from the World Health Organization's Global Influenza Programme.

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[CarolinaGuitarman]

"So then their was an intelligent creator? The one that created the first spark of life that may or may not have had successive minimal evolutions over time?"

I didn't say that either. But I know of nobody claiming life came from nothing.

[MEGoody]

Ah, so what they really mean is that there are 4 million differences between chimp and human DNA, not that there were 4 million evolutionary events.

[Antoninus]

Through the use of an inane analogy and a complete lack of any actual information regarding your position.

Yawn. You dogmatic Darwinians are a tiresome lot. I believe that the ToE is a compelling explanation of the development of life. However, I don't believe it can be elevated to the status of scientific law--nor have its adherents answered many of the tough questions that have been proposed of late.

When you have to depend on men in robes to enforce your scientific orthodoxy, something is deeply wrong.

[narby]

I find it reasonable to accept the idea that the current populations derived from original pairs. I do not find the idea that the current populations derived from eons of evolution wherein life began from non-life to be reasonable.

Actually, the folks studying species extinction say that about 8 pairs are required for any species to survive. For example they brought back the Condor with a dozen or so individuals.

I'm not sure why this is necessary, but I assume to prevent harmful mutations from becoming the norm. Like the old saw about not marrying your sister.

This is one of the problems with the story of Noah. Saving two of every species just wouldn't work.

[narby]

I believe that the ToE is a compelling explanation of the development of life. However, I don't believe it can be elevated to the status of scientific law

A scientific "theory" is as high as it gets in science. A scientific "law", like Ohm's law, is usually simple formulas, while theories are descriptions of processes that can be quite complex.

If we found exceptions to a scientific law, then it would be broken and discarded. But because theories are more complex, parts of them can be invalidated, or added to, without breaking the entire theory.

When you have to depend on men in robes to enforce your scientific orthodoxy, something is deeply wrong.

Evolution is mostly conducted in the realm of science. The Dover case and a couple of others are the rare exception required to protect the science.

On the other hand, ID is conducted solely in the public square, in politics and the courts. They have conducted zero actual original science on their own, and have yet to even propose tests for things like how ID would be falsified.

Since ID totally depends on "men in robes" and elected officials, something is deeply wrong with it.

[Condorman]

They look pretty good to me, all artists have a few unique abstract works.

Your original claim in post 31 was "ALL animals and humans are so symmetrical." Now that you have seen this is not the case (see also sponges, coral, most gastropods, and the digestive tracts and cardiovascular systems of ALL amphibians, reptiles, fish, birds and mammals), we have a new universal law about artists. How many other generalizations do you plan to toss out (and just as quickly abandon) in your haste to establish "design?"

[Tailback]

Great book. Pournelle and Niven write some excellent stuff.

[Antoninus]

Evolution is mostly conducted in the realm of science. The Dover case and a couple of others are the rare exception required to protect the science.

That sounds very similar to what various bishops told Gallileo. Science doesn't need "protection" from a guy in a black robe. Let the theory be questioned and let the proponents of the theory defend it without "devolving" into ad hominem invective. The fact that the pro-ToE crowd has been unable to refrain from attacking the motives and the persons of their questioners is the primary factor which makes me think that the ID people may be on to something.

[P-Marlowe]

At some level every discovery in biology and medicine rests on it, in much the same way that all terrestrial vertebrates can trace their ancestry back to the first bold fishes to explore land.

Fishes?

We can trace our ancestry back to fishes?

Does someone have a copy of the pedigree?

Does anyone have a picture of the family tree?

Or is this all pure speculation?

[Antoninus]

Here's one of my major problems with the ToE as it is currently formulated:



How is it that an organism like this can remain almost wholly unchanged for 140 million years? Is it not subject to genetic drift like everything else on the planet?

[Senator Bedfellow]

How is it that an organism like this can remain almost wholly unchanged for 140 million years? Is it not subject to genetic drift like everything else on the planet?

Sure it is, and of course the modern coelacanth is not the same species as the ancient fish - it has changed slightly since then.

Why not more change? If you're already well-adapted to your environment, and the environment doesn't change, then it becomes increasingly likely that any change will make you less well-adapted, and such changes will be selected against. So therefore, creatures that stick with the tried-and-true body plan will preferentially survive over radical newcomers who are less well-adapted, resulting in organisms that don't appear to change much over time.

It's not just coelacanths, either - sharks, cockroaches, dragonflies, ferns, and lots of other things haven't changed much in the last hundred million years either. If you have something that works, there's a strong incentive not to change.

[Antoninus]

Sure it is, and of course the modern coelacanth is not the same species as the ancient fish - it has changed slightly since then.

Proof of that? I thought that the main criterion for speciation was the ability of creatures to mate and produce viable offspring. As there is no way for a modern coelacanth to be paired with one that's 140 million years old, such an observation is speculative at best. By appearance alone, one is forced to conclude that the species has remained practically identical to its fossilized progenitors.

Why not more change? If you're already well-adapted to your environment, and the environment doesn't change, then it becomes increasingly likely that any change will make you less well-adapted, and such changes will be selected against. So therefore, creatures that stick with the tried-and-true body plan will preferentially survive over radical newcomers who are less well-adapted, resulting in organisms that don't appear to change much over time.

I've heard that argument before, but it doesn't answer the question of why this creature in particular, was not subject to the genetic drift that seems natural in almost every other species.

It's not just coelacanths, either - sharks, cockroaches, dragonflies, ferns, and lots of other things haven't changed much in the last hundred million years either. If you have something that works, there's a strong incentive not to change.

I appreciate that argument, and it may be true in the cases of all the creatures you mention above. However, the coelacanth is not exactly a model of evolutionary success that may be found spread over the whole world in vast numbers. In fact, they don't seem to be very successful at all, consigned as they are to a few tiny colonies.

In this case, you must argue either a.) the coelacanth has managed to exist into modern times because it is perfectly adapted to the few tiny environments in which it is currently found and has been able to maintain this for over 140 million years without any competitors or predators forcing it out (actually 400 million, but what's a few hundred million years between friends?). Or b.) there are actually large undiscovered populations of coelacanths scattered throughout the world, making it a fantastically successful species similar to sharks and cockroaches.

[CarolinaGuitarman]

Not only is the modern coelacanth not the same species as the ancient ones, it's a different genus entirely. It has changed; there just has been any great selective pressure to change drastically. Organisms like the coelacanth and the shark are exceptional anyway.

[narby]

Science doesn't need "protection" from a guy in a black robe

Science doesn't need protection from science. It needs protection from politicians such as those in Dover and Kansas that seek to impose non-science.

The fact that the pro-ToE crowd has been unable to refrain from attacking the motives and the persons of their questioners is the primary factor which makes me think that the ID people may be on to something.

The liars on the Dover school board are what they are. They are the ones who expressed their motives to promote Christianity in public schools, and then lied about it on the witness stand. And lied again about how the money for the Pandas book came to be raised.

If you don't like being on the side of proven liars, it's not my fault.

[PatrickHenry]

How many other generalizations do you plan to toss out (and just as quickly abandon) in your haste to establish "design?"

What's the problem here? We've got a guy who claims that: (a) symmetry is God's signature; and (b) the absence of symmetry is an example of God's flourishes. Neat. Bullet proof. He lives in a world that never fails to "prove" his beliefs. This seems to be rather primitive theology, but he's happy with it.

[narby]

Here's one of my major problems with the ToE as it is currently formulated:

The Coelacanth is a classic stawman. Merely because creatures can evolve doesn't mean that they must.

[Antoninus]

Not only is the modern coelacanth not the same species as the ancient ones, it's a different genus entirely. It has changed; there just has been any great selective pressure to change drastically. Organisms like the coelacanth and the shark are exceptional anyway.

Proof of that? Dropping fossilized ancient creatures in a particular taxonomic classification is a completely academic exercise. Of the articles I've read claiming that the modern coelacanth is different from ancient ones, none has posited such a great variance as you have offered. The more convincing ones suggested that the differences may be more subtle--like improvements in the immune system.

However, it should be pointed out that variances exist within human immune systems as well, which is why certain pathogens can decimate a population in one area of the world, and have no effect in another. No one would argue, however, that a European who gets sleeping sickness is not the same species as an African who doesn't. Alright, perhaps a late-19th century social-Darwinist might.

[Antoninus]

The Coelacanth is a classic stawman. Merely because creatures can evolve doesn't mean that they must.

No, it's not. I have yet to hear anyone come up with a truly convincing theory as to why it didn't.

[Senator Bedfellow]

By appearance alone, one is forced to conclude that the species has remained practically identical to its fossilized progenitors.

"Practically identical" is not a particularly useful designation. The modern coelacanth has scales of a different shape than the ancient coelacanth, the pelvic and dorsal fins are in a different place skeletally, and of course, the ancient coelacanths topped out at about fifteen inches - modern coelacanths are over four feet long.

I've heard that argument before, but it doesn't answer the question of why this creature in particular, was not subject to the genetic drift that seems natural in almost every other species.

Perhaps I was unclear in my previous answer, sorry. It was subject to genetic drift, just like every other organism. The only difference being that radical changes due to mutations produced by genetic drift resulted in animals that were less well-adapted, so they died out. The coelacanth has experienced genetic drift, resulting in the differences between the ancient fish and the modern one, but the basic plan is well-adapted, so it is selected for and preferentially retained.

However, the coelacanth is not exactly a model of evolutionary success that may be found spread over the whole world in vast numbers. In fact, they don't seem to be very successful at all, consigned as they are to a few tiny colonies.

Defining "success" in such a manner is essentially a value judgement. Wide geographic distribution is not required by the theory of evolution. Organisms that survive and reproduce are "successful" in evolutionary terms - by that standard, the coelacanth is no more or less successful than any other living organism. Coelacanths live in the Indian ocean, grizzly bears live in Alaska, penguins live in Antarctica - in all cases, they're more or less well-adapted to their environments, and they survive and reproduce, making them "successful" in evolutionary terms.

[Antoninus]

I wrote: The fact that the pro-ToE crowd has been unable to refrain from attacking the motives and the persons of their questioners is the primary factor which makes me think that the ID people may be on to something.

You responded: If you don't like being on the side of proven liars, it's not my fault.

Ah, guilt by association, eh? By merely entertaining questions on the ToE, I am "on the side of proven liars."

QED.