"This is the first time that population genomics has been used to find genes important for adaptation without any idea of the environmental parameters, phenotype, candidate genes or even the population boundaries," said the study's principal investigator, John Taylor, UC Berkeley professor of plant and microbial biology.
Taylor pointed out that the normal route for adaptation studies is to first look at obvious differences such as hair or skin color between two closely related organisms. Scientists next observe the environment in which the organism lives to see if it might explain those differences, and then examine the genes to see if there is evidence of natural selection.
For example, the researchers referred to a 2003 study noting that rock pocket mice with tan-colored fur are often found among light-colored rocks, while those with black fur were found on dark lava flows. They identified the genetic basis of this adaptive trait by targeting genes for further study that were known to be involved in pigmentation and showed that different gene variants were associated with the different habitats.
"For our study, we turned this around, beginning with genes that showed evidence of selection, and then looking at the environmental factors that might influence those genes," said Taylor.
This "reverse-adaptation" approach is especially useful when studying microbes, the researchers argued.
"Microbes are inconspicuous by nature and, unlike mice which can have different colored coats, different strains and species look pretty much the same," said study lead author Christopher Ellison, a UC Berkeley graduate student in plant and microbial biology.
As if to demonstrate this point, the researchers discovered that what had been considered a single group of interrelated st
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University of California - Berkeley