New work on fruit fly genomics suggests new ways to look at the much larger human genome, and gives insights into the role of adaptation in evolution.

In two recent papers, researchers led by David Begun and Charles Langley, professors of evolution and ecology at the UC Davis Center for Population Biology, compared the whole genomes of several individuals of the fly Drosophila simulans to close relatives D. melanogaster and D. yakuba.

The same approach could be extended to the much larger genomes of humans and our close relatives, Begun said, showing which changes in the genome are uniquely human.

Stretches of DNA that showed a lot of variability within D. simulans did not match up with areas that were most divergent between species. That could be because when beneficial mutations occur, natural selection increases their frequency and reduces variation at nearby sites. The data provide a comprehensive view of adaptive protein evolution, Begun said.

"You can let the genome tell you what processes have experienced adaptive evolution," Begun said. "The organism is telling you what's been important in its history."

The researchers also found the first evidence that the fly's X chromosome is evolving faster than other parts of the genome. The work is published in the journal Public Library of Science (PLoS) Biology.

A second recent paper by postdoctoral researcher Alisha Holloway and colleagues explores the relationship between genomic variation in D. simulans, D. melanogaster and D. yakuba and gene expression, or the pattern in which genes are turned on or off. That work is published in PLoS Genetics.

Holloway found that genes relatively highly expressed in D. simulans have experienced adaptive evolution in the three-prime regions immediately downstream. Those regions can regulate how DNA is translated into RNA. Genes that evolved higher expression levels in one species when compared with the others were also decelerating in their rates of evolution at the protein level, Holloway said. That agrees with previous work showing that highly expressed genes evolve slowly.

Begun, co-author Langley and two other UC Davis researchers are also among about 100 authors on a paper in the Nov. 8 issue of Nature describing the genomes of 12 species of Drosophila flies, including D. simulans, D. yakuba and D. melanogaster.

The other authors on the PLoS Biology paper were Holloway and Kristian Stevens at UC Davis; Yu-Ping Poh at UC Davis and National Tsing Hua University, Taiwan; Mathew Hahn and Phillip Nista at Indiana University, Bloomington; Corbin Jones at the University of North Carolina Chapel Hill; Andrew Kern, UC Santa Cruz; Colin Dewey, University of Wisconsin, Madison; Lior Pachter and Eugene Myers, UC Berkeley. Authors on the PLoS Genetics paper in addition to Holloway were: Begun, Jones, Mara Lawniczak, University College London, England, and Jason Mezey, Cornell University.

- UC Davis