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Journal article Open Access

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

Romain A. Studer; Simon Penel; Laurent Duret; Marc Robinson-Rechavi

A stringent branch-site codon model was used to detect positive selection in vertebrate evolution. We show that the test is robust to the large evolutionary distances involved. Positive selection was detected in 77% of 884 genes studied. Most positive selection concerns a few sites on a single branch of the phylogenetic tree: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome duplication or the two rounds at the origin of vertebrates. Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.

Funding from Etat de Vaud and Swiss National Science Foundation grant 116798, and L.D. from the Agence Nationale de la Recherche (GIP ANR JC05_49162)
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