Despite the pessimism of evolutionary biologists just 5 years ago, it will in fact be possible to sort out bacterial family trees, according to a new study. In the late 1990s, genome sequencers began finding that, through "lateral transfer," many genes had jumped, sometimes between distantly related species. This gene mixing caused prominent evolutionary biologists to conclude that the microbial tree of life was more like a bunch of intertwined vines and that ancestries would be difficult, if not impossible, to untangle (Science, 1 May 1998, p. 672).
Researchers have known for decades that bacteria can adopt new genes, possibly by absorbing DNA from their environments or engulfing or merging with other microbes. In the past few years, analyses of newly sequenced microbial genomes have revealed even more extensive gene jumping. Vincent Daubin, Nancy Moran, and Howard Ochman, evolutionary biologists at the University of Arizona in Tucson, decided to evaluate whether these foreign genes really made it impossible to build accurate family trees. They now report that they've identified plenty of genes that have stuck with their genomes, enough to make bacterial classification feasible.
The trio looked for genes shared by the genomes of a few closely related bacterial species. For these species, phylogenies are known based on studies of ribosomal RNA. Based on differences in the sequences of the shared genes, they built gene trees that established evolutionary relationships. Depending on the set of microbes being compared, as many as 1589 of the gene trees matched trees based on ribosomal RNA. Cases in which the trees put the wrong trees together--a sign of lateral transfer--were much rarer, they report in the 8 August Science.
The paper has its critics, however. W. Ford Doolittle, an evolutionary molecular biologist at Dalhousie University in Halifax, Nova Scotia, argues that the team "goes too far in minimizing the influence of [lateral] transfer." Others think the results may not apply to species that are distantly related. But some say the prospect of bacterial family trees is promising. "I think it will be more difficult with bacteria than with birds or frogs, but it's not going to be impossible," says Daniel Dykhuizen, a microbial population geneticist at the State University of New York, Stony Brook.