Antonis Rokas is a member of a small cadre of scientists who are 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” refers to 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.
Rokas, an assistant professor of biological sciences, has received a CAREER award from the National Science Foundation. The Faculty Early Career Development award is considered NSF’s most prestigious honor for junior faculty members. Rokas will receive $688,000 in Recovery Act funding for five years to develop new statistical methods that make it easier to accurately determine the relationships between various species.
“In many cases we are trying to resolve events that transpired billions of years ago,” says Rokas. “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: It is less than one-tenth the size of that of fruit flies and nematodes 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.
Although trees depicting evolutionary relationships are the cornerstones of evolutionary theory, Rokas is concerned that they are frequently misinterpreted by students and professionals alike. So he will be using part of his grant to train high school students and teachers on the concepts of phylogenetics and will develop an undergraduate course that will integrate research results into the curriculum.
The award will support a post-doctoral fellow and a graduate student full time and an undergraduate for summer research. In addition, $15,000 will go toward the purchase of computer nodes for Vanderbilt’s Advanced Computing Center for Research & Education.
[Note: A multimedia version of this story is available on Exploration, Vanderbilt’s online research magazine, at www.exploration.vanderbilt.edu]
Contact: David F. Salisbury, (615) 322-NEWS