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MBE Advance Access published online on November 3, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi037
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted October 26, 2004

Research Article

Codon Volatility as an Indicator of Positive Selection: Data from Eukaryotic Genome Comparisons

Robert Friedman 1 and Austin L. Hughes 1*

1 Department of Biological Sciences, University of South Carolina, Columbia SC 29208 USA

* To whom correspondence should be addressed.
Austin L. Hughes, E-mail: austin{at}biol.sc.edu


  Abstract

It has been suggested that codon volatility (the proportion of the point-mutation neighbors of a codon that encode different amino acids) can be used as an index of past positive selection. We compared codon volatility with patterns of synonymous and nonsynonymous nucleotide substitution in genome-wide comparisons of orthologous genes between three pairs of related genomes: (1) the protists Plasmodium falciparum and P. yoelii; (2) the fungi Saccharomyces cerevisiae and S. paradoxus; and the mammals mouse and rat. Codon volatility was not consistently associated with an elevated rate of nonsynonymous substitution, as would be expected under positive selection. Rather, the most consistent and powerful correlate of elevated codon volatility was nucleotide content at the second codon position, as expected given the nature of the genetic code.


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