New !   Selectome: a Database of Positive Selection

Pervasive positive selection on duplicated and non duplicated vertebrate protein coding genes
Romain Studer 1,2, Simon Penel 3, Laurent Duret 3, Marc Robinson-Rechavi 1,2,4

1: Department of Ecology and Evolution, Biophore, Lausanne University, CH-1015 Lausanne, Switzerland
2: Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
3: Université; de Lyon; Université Lyon 1 ; CNRS ; UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, Villeurbanne F-69622, France
4: to whom correspondence should be addressed: marc.robinson-rechavi AT

Keywords: positive selection, whole genome duplication, vertebrate evolution.
Non standard abbreviations: FSGD, fish specific genome duplication.
Running head: Positive selection on vertebrate genes

Abstract: 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 branches. No functional category was over-represented 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, nor to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.

Access to the paper:
Genome Research. 2008; 18(9):1393-1402.


Singleton gene family (Strict orthologs) (767 families)

Fish-Specific-Gene-Duplication with no other duplication (46 families)

Fish-Specific-Gene-Duplication with other duplication allowed
(71 families)