Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Sep;18(9):1393-402.
doi: 10.1101/gr.076992.108. Epub 2008 Jun 18.

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

Romain A Studer  1 , Simon Penel, Laurent Duret, Marc Robinson-Rechavi
Affiliations

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

Romain A Studer et al. Genome Res. 2008 Sep.

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 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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Tree topologies studied. Schematic representation of the tree topologies selected. (Black) speciation branches; (blue) duplication branches. Branches in bold were used as “foreground branches” in branch-site tests for positive selection. Bold italics indicate branch names used in the text and the tables. (A) “Singleton” tree type, with no duplication allowed. The dotted line represents gene loss after whole genome duplication. (B) “Fish-specific whole genome duplication” tree type. Duplication on other branches may be excluded or allowed. Because differences in dN/dS ratio have been reported between paralogs (Brunet et al. 2006; Scannell and Wolfe 2007), with higher dN/dS in the fast evolving paralog, we distinguish the longer and shorter branch after duplication, based on the PhyML protein phylogeny.
See this image and copyright information in PMC

References

    1. Al-Shahrour F., Minguez P., Tarraga J., Medina I., Alloza E., Montaner D., Dopazo J., Minguez P., Tarraga J., Medina I., Alloza E., Montaner D., Dopazo J., Tarraga J., Medina I., Alloza E., Montaner D., Dopazo J., Medina I., Alloza E., Montaner D., Dopazo J., Alloza E., Montaner D., Dopazo J., Montaner D., Dopazo J., Dopazo J. FatiGO +: A functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res. 2007;35:W91–W96. - PMC - PubMed
    1. Andolfatto P. Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res. 2007;17:1755–1762. - PMC - PubMed
    1. Anisimova M., Yang Z., Yang Z. Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol. Biol. Evol. 2007;24:1219–1228. - PubMed
    1. Anisimova M., Bielawski J.P., Yang Z., Bielawski J.P., Yang Z., Yang Z. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol. Biol. Evol. 2002;19:950–958. - PubMed
    1. Aparicio S., Chapman J., Stupka E., Putnam N., Chia J.-m., Dehal P., Christoffels A., Rash S., Hoon S., Smit A., Chapman J., Stupka E., Putnam N., Chia J.-m., Dehal P., Christoffels A., Rash S., Hoon S., Smit A., Stupka E., Putnam N., Chia J.-m., Dehal P., Christoffels A., Rash S., Hoon S., Smit A., Putnam N., Chia J.-m., Dehal P., Christoffels A., Rash S., Hoon S., Smit A., Chia J.-m., Dehal P., Christoffels A., Rash S., Hoon S., Smit A., Dehal P., Christoffels A., Rash S., Hoon S., Smit A., Christoffels A., Rash S., Hoon S., Smit A., Rash S., Hoon S., Smit A., Hoon S., Smit A., Smit A., et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002;297:1301–1310. - PubMed

Publication types

LinkOut - more resources