Twig by twig, climbing Earth’s ‘Tree of Life’

VANDERBILT (US)—Antonis Rokas is a member of a small cadre of scientists applying the growing power of genomics to untangle and correctly arrange the branches of the Tree of Life.

In the world of science, the Tree of Life depicts the evolutionary relationship among all the species on Earth. The information it contains is the central organizing principle of biology. It originated from the only illustration in Darwin’s On the Origin of Species—a branched diagram that looks remarkably like a tree.

“In many cases we are trying to resolve events that transpired billions of years ago,” says Rokas, an assistant professor of biological sciences at Vanderbilt University. “During the intervening period, the DNA of the species involved wasn’t just sitting there inertly: It was shaped by powerful forces like natural selection and genetic drift. It’s amazing how much information you can get by comparing species, but it is not a magic bullet.”

Fifteen years ago, scientists did not know the entire genome of a single species. So they had to use short snippets of DNA from different species in their attempts to establish evolutionary relationships. Today, however, scientists have sequenced the genomes of nearly 4,000 species.

Most of these are bacteria and other microorganisms called prokaryotes. However, 400 to 600 are eukaryotes, organisms whose cells contain complex structures enclosed within membranes, including animals, plants, and fungi. This has provided scientists with a lot of genetic information to analyze, and the next generation of DNA sequencers is much faster and cheaper, so the amount of this kind of information is likely to grow exponentially.

Rokas will be analyzing the genomic data of more than two dozen species of yeast to identify the most reliable methods for determining their evolutionary relationships. He is using yeasts because their gene functions are the most completely studied of any eukaryote. Also, the yeast genome is relatively compact—less than one-tenth the size of that of fruit flies and one-hundredth the size of that of humans—which reduces the computational demands significantly.

“Our goal is to use all this information to identify genes that are good predictors of phylogeny and those that are poor predictors, and see if we can identify any underlying principles that we can apply to other clades, including our own twig of the tree of life, mammals,” he says.

His work is supported through a CAREER award from the National Science Foundation.

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