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Mol Biol Evol. 2005 Jan;22(1):174-7. Epub 2004 Sep 15.

Adjusting for selection on synonymous sites in estimates of evolutionary distance.

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  • 1Department of Biological Sciences, Stanford University, Stanford, California, USA.


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.

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