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Tree of life continues to evolve
The Boston Globe April 28, 2008

Casey Dunn has gathered his share of weird animals. He dredged up sea spiders that live around the docks in Waikiki. He dived to the sea floor to scoop up mud, in search of bizarre, spiny creatures called kinorhynchs that are smaller than a grain of sand.

Dunn, a biologist at Brown University, hunts for weird animals to get his hands on their DNA. Hidden in their genes is a record of the history of the entire animal kingdom, some 700 million years of evolutionary change.

By analyzing the DNA of dozens of different kinds of animals, he and his colleagues have made some astounding discoveries about animal evolution. For one thing, the common ancestor of all living animals may have been more complicated than once thought.

While scientists have been analyzing DNA for a few decades now, this work is different. Instead of comparing a fragment of a single gene, as a scientist might have done 10 years ago, Dunn and his contemporaries can search through all of the DNA in an animal - its entire genome.

Comparative genomics, as this young science is known, is having a huge impact on biology, helping scientists answer many of science's deepest questions. It promises, for example, to shed light on how our genes make us prone to diseases, and how the genes of pathogens make them deadly.

"It has created a revolution in our ability to understand biology," said Steven Brenner, a computational biologist at the University of California at Berkeley.

Before comparative genomics, some researchers worried that they might never understand early animal evolution well. It's like watching a card game a mile away through a telescope. The details can be blurry.

"You have to look over this long distance to something that was relatively quick," Dunn said. "A lot of people wondered if we could ever find out how the major groups of animals are related to each other."

Dunn and his colleagues have now shown that they can.

The scientists have analyzed the biggest collection of data on animals ever assembled. They combined data on DNA from 77 different species, as varied as sponges, oysters, and humans. Some of the data came from earlier research by other scientists. Dunn and his colleagues also searched for obscure animals to get a wider selection. "It took us a couple years to get everything together," Dunn said.

With that information, they were able to reconfigure the tree of life.

They identified pivotal genes in all 77 species that they thought would provide insight into evolution. They then narrowed down this list of 3,000 or so genes to 150 that would provide the most insight into evolution.

"We needed to run over 100 computers for months on end to even make sense of this data," Dunn said.

"One of the most important results is that we get a result," he said. Instead of being lost in an ancient blur, many of the branches of the animal kingdom came into focus in their study. "It was a bit of a relief."

Some of the results confirmed relationships based on anatomy. The closest relatives to vertebrates, for example, include echinoderms (a group that includes starfish). But other results were surprising.

Two of the most species-rich groups of animals are the insects and nematodes, such as roundworms. For years, many scientists argued that insects were more closely related to us than nematodes. For evidence, they pointed to traits that insects and vertebrates share, such as an inner body cavity, which nematodes lack. But the new study supports a different view of animal evolution: Insects and nematodes are more closely related to each other than either is to us.

This result is not just important for understanding how animals evolved. (In this case, it appears that nematodes lost their body cavity after they branched off from the ancestors of insects.) The better scientists understand how insects and nematodes are related to us, the better they can translate the results of experiments on these animals to human biology.

"The human genome sequence would be nearly worthless without the value added by evolutionary comparisons to other organisms," said Mark Pallen, an evolutionary biologist at the University of Birmingham in England.

The biggest surprise of the new study lies at the very base of the animal tree. Traditionally, scientists have considered sponges to belong to the oldest lineage of living animals. The next oldest lineages produced a group of species that included jellyfish and comb jellies, known as ctenophores. According to this view, the common ancestor of living animals was relatively simple. Only after the ancestors of sponges branched off did a nervous system begin to evolve.

Dunn and his colleagues discovered to their surprise that the comb jelly lineage is the oldest. To test this result, Steven Haddock of the Monterey Bay Aquarium used a remote submersible to catch another species of comb jelly to analyze. It turned out that their original comb jelly had not been a genetic fluke.

Their discovery does not mean that our ancestors looked like comb jellies, Dunn stresses. "That's like saying that your cousin is your grandpa," he said. Much of the comb jelly's anatomy probably evolved after its ancestors split off from the ancestors of other living animals.

But the fact that comb jellies and most other animals share a nervous system suggests that their common ancestor did as well. Rather than being simple, as once thought, the common ancestor of living animals had already evolved to be relatively complex. And once the ancestors of sponges branched off, they must have lost their nervous system and evolved into filter feeders anchored to the sea floor. (They'd hardly be the only animals to have lost traits - consider the missing body cavity in nematodes, or our own vestigial tail bones.)

"It looks like there are both gains of complexity and reductions across the animal tree," Dunn said.

Other experts have praised the new study. "While clearly not the last word, this study represents the state of the art in animal phylogenies," Maximilian Telford of University College London wrote in the journal Developmental Cell.

Dunn predicts that comparative genomics will help tease out the relationships of other major groups of species, such as plants and bacteria. As prices continue to fall and methods continue to improve, the entire tree of life will come increasingly into focus. Scientists will be able to use the tree to trace the history of individual genes. Some of those genes make humans vulnerable to diseases such as diabetes and obesity. Other genes, shared among bacteria, boost their danger to our health.

Computers and DNA sequencers can't substitute for the hard work of searching for life's diversity. "If we're going to get serious about understanding how all things are related to each other, the real challenge is going to be the one that naturalists faced 200 years ago," he said. The one bottleneck Dunn foresees is the need to find more species.

Copyright 2008 The New York Times Company. Reprinted with permission 
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