Evolutionary genetic relationships coming into focus

Scientists are closer to unraveling the genetic pedigree of all backboned creatures, but the fish branches of the vertebrate family tree lack detail compared with those of flesh and fowl, a new analysis suggests.

The complete bird and mammal branches of the tree of life are within reach, scientists report online March 8 in BMC Biology. But the genetic genealogies of other backboned creatures, especially marine species, are woefully understudied.

Understanding phylogenetics — the branching patterns of evolution — can inform numerous aspects of science, from controlling invasive species to developing new vaccines, says study coauthor Robert Thomson of the University of California, Davis. “It really is limitless the places where phylogenetics is important in science today,” he says.

Using DNA sequences logged since 1993 in the database GenBank, which is maintained by the National Institutes of Health, Thomson and UC Davis colleague H. Bradley Shaffer constructed an evolutionary tree of vertebrates. The researchers analyzed 210,000 chunks of DNA from nearly 12,000 vertebrate species.

About 40 percent of the branching pattern in the mammal and bird section of the tree is resolved, the researchers report. But a mere 15 percent of relationships are understood among the ray-finned fishes, which make up more than half of all living vertebrate species and include sturgeon, flounder, herring and perch.

The relationships among amphibians and scaled reptiles such as lizards and snakes are also coming into focus, with 30 percent resolution. And the cetaceans — whales, dolphins and porpoises — are quite well resolved, with 61 percent of their tree worked out.

Three technological innovations have led to the surge in progress, comments David Hillis, director of the computational biology and bioinformatics center at the University of Texas at Austin: a huge push in collecting genetic data, the development of algorithms to analyze that information and better computers for processing it.

Understanding evolutionary relationships creates predictive power in biology, Hillis notes. For example, the close relatives of a plant already known to have cancer-fighting compounds would be good starting points in a search for more such compounds. 

Unlike fields such as chemistry, in which every hydrogen atom behaves the same way as every other hydrogen atom, in biology “none of the units are independent or replaceable,” Hillis says. “Whether we’re looking at genes, cells or species, they are different from each other and related by evolutionary history.”