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Bioinformatics Advance Access originally published online on April 28, 2008
Bioinformatics 2008 24(12):1421-1425; doi:10.1093/bioinformatics/btn205
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence

Jacob A. Tennessen

Department of Zoology, 3029 Cordley Hall, Oregon State University, Corvallis, OR 97331, USA


  Abstract

Motivation: Functional divergence among proteins is often assumed to be strongly influenced by natural selection, as inferred from the ratio of non-synonymous nucleotide divergence (dN) to synonymous nucleotide divergence (dS). That is, the more a mutation changes protein function, the more likely it is to be either selected against or selectively favored, and because the dN/dS ratio is a measure of natural selection, this ratio can be used to predict the degree of functional divergence (dF). However, these hypotheses have rarely been experimentally tested.

Results: I present a novel method to address this issue, and demonstrate that divergence in bacteria-killing activity among animal antimicrobial peptides is positively correlated with the log of the dN/dS ratio. The primary cause of this pattern appears to be that positively selected substitutions change protein function more than neutral substitutions do. Thus, the dN/dS ratio is an accurate estimator of adaptive functional divergence.

Contact: tennessj{at}science.oregonstate.edu

Supplementary information: Supplementary data, including GenBank Accession numbers, are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on March 6, 2008; revised on April 21, 2008; accepted on April 22, 2008

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