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MBE Advance Access originally published online on November 3, 2004
Molecular Biology and Evolution 2005 22(3):542-546; doi:10.1093/molbev/msi038
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Molecular Biology and Evolution vol. 22 no. 3 © Society for Molecular Biology and Evolution 2004; all rights reserved.

Research Article

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

Robert Friedman and Austin L. Hughes

Department of Biological Sciences, University of South Carolina, Columbia

E-mail: austin{at}biol.sc.edu.

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 (3) 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.

Key Words: codon volatility • nucleotide content • positive selection • synonymous site • nonsynonymous site


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J. B. Plotkin, J. Dushoff, M. M. Desai, and H. B. Fraser
Estimating Selection Pressures from Limited Comparative Data
Mol. Biol. Evol., August 1, 2006; 23(8): 1457 - 1459.
[Abstract] [Full Text] [PDF]


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