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MBE Advance Access published online on September 15, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh265
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted September 9, 2004

Research Article

Adjusting for Selection on Synonymous Sites in Estimates of Evolutionary Distance

Aaron E. Hirsh 1, Hunter B. Fraser 2*, and Dennis P. Wall 1

1 Department of Biological Sciences, Stanford University, Stanford, CA 94305
2 Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720

* To whom correspondence should be addressed. E-mail: hunter{at}ocf.berkeley.edu.


  Abstract

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.

Keywords: synonymous sites; codon bias; evolutionary genomics; dS; dN/dS; selection.
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