Gene's 'selective signature' aids detection of natural selection in microbial evolution

“In a single species, a whole set of genes in the same module tend to change together,” said Shapiro. “Identifying these changes brings us a step closer to understanding the ecological basis of selection in a species and how changes at the genetic level affect the organisms interactions with its environment.”

For example, in Idiomarina loihiensis, a marine bacterium that has adapted to life near sulfurous hydrothermal vents in the ocean floor, the genes involved in metabolizing sugar and the amino acid phenylalanine underwent significant changes (over hundreds of millions of years) that may help the bacterium obtain carbon from amino acids rather than from sugars, a necessity for life in that ecological niche. In one of I. loihiensis’ sister species, Colwellia psychrerythraea, some of those same genes have been lost altogether, an indication that sugar metabolism is no longer important for Colwellia.

Shapiro and Alm focused on 744 protein families among 30 species of gamma-proteobacteria that shared a common ancestor roughly 1 to 2 billion years ago. These bacteria include the laboratory model organism E. coli, as well as intracellular parasites of aphids, pathogens like the bacteria that cause cholera, and soil and plant bacteria. They mapped the evolutionary distance of each species from the ancestor and incorporated information about the gene family (for instance, important proteins evolve more slowly than less vital ones) and the normal rate of evolution in a particular species’ genome in order to determine a gene’s selective signature.

“These are experiments we could never perform in a lab,” said Alm. “But Mother Nature has put genes into an environment and run an evolutionary experiment over billions of years. What we’re doing is mining that data to see if genes that perform a similar function, say motility, evolve at the same rate in different species. To the extent that they differ, it helps us to understand how change in core genes drives functional divergence between species across the tree of life.”

This work is part of the Virtual Institute for Microbial Stress and Survival. The research was also supported by additional grants from the U.S. Department of Energy Genomics: GTL Program, the National Institutes of Health, and a scholarship from the Natural Sciences and Engineering Research Council of Canada.