High rate of strong adaptation in Drosophila

In a study just published in Genetics and authored by Macpherson, J.M., Sella, G., Davis, J.C., and D. A. Petrov, we study the correspondence between divergence at protein-coding sites and neutral polymorphism using genomewide data from Drosophila simulans. We find that neutral polymorphism is both lower and less homogeneous where nonsynonymous divergence is higher and that the spatial structure of this correlation is best explained by the action of strong positive selection. We introduce a method to infer the rate and selective strength of adaptation. Our results independently confirm a high rate of adaptive substitution (~1/3000 generations) and newly suggest that many adaptations are of surprisingly great selective effect (~1%), reducing the effective population size by ~15% even in highly recombining regions of the genome.

Shigella loses genes at a very high rate

Shigella strains are ecotypes of E.coli and were only given a separate name because all Shigella strains cause a distinct disease (dysentery). Ruth Hershberg led a study (just published in Genome Biology) that demonstrated that Shigella strains lose genes at much higher rates than other E. coli strains and that this is largely due to a genome-wide reduction in the strength of purifying selection. This reduction in the strength of selection might be a result of the different lifestyle of Shigella strains compared to other E. coli strains.

Tempo and mode of genome size evolution

Eukaryotic genome size varies over five orders of magnitude. The genome size distribution is strongly skewed to small values. Genome size is highly correlated to a number of phenotypic traits, suggesting that the relative lack of large genomes in eukaryotes is due to selective removal. In a study by Oliver, M.J., Petrov, D.A., Ackerly, D., Falkowski, P.G., and O.M. Schofield that just came out in Genome Research we demonstrated that the rate of genome size evolution is proportional to genome size, with the fastest rates occurring in the largest genomes. Such a simple proportional model of genome size evolution appears to be virtually universal across eukaryotes. This model explains the skewed distribution of eukaryotic genome sizes without invoking strong selection against large genomes.