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MBE Advance Access originally published online on September 15, 2004
Molecular Biology and Evolution 2005 22(1):174-177; doi:10.1093/molbev/msh265
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Molecular Biology and Evolution vol. 22 no. 1 © Society for Molecular Biology and Evolution 2005; all rights reserved.

Research Article

Adjusting for Selection on Synonymous Sites in Estimates of Evolutionary Distance

Aaron E. Hirsh*, Hunter B. Fraser{dagger} and Dennis P. Wall*,1

* Department of Biological Sciences, Stanford University, Stanford, California; {dagger} Department of Molecular and Cell Biology, University of California, Berkeley

E-mail: hunter{at}ocf.berkeley.edu.

Evolution at silent sites is often used to estimate the pace of selectively neutral processes or to infer differences in divergence times of genes. However, silent sites are subject to selection in favor of preferred codons, and the strength of such selection varies dramatically across genes. Here, we use the relationship between codon bias and synonymous divergence observed in four species of the genus Saccharomyces to provide a simple correction for selection on silent sites.

Key Words: synonymous sites • codon bias • evolutionary genomics • dS • dN/dS • selection


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