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MBE Advance Access published online on June 15, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi192
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted June 9, 2005

Research Article

A Dissection of Volatility in Yeast

Nina Stoletzki 1*, John Welch 2, Joachim Hermisson 1, and Adam Eyre-Walker 2

1 Section of Evolutionary Biology, Department Biology II, Ludwig-Maximilians-University Munich, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany
2 Centre for the Study of Evolution, University of Sussex, Brighton, BN1 9QG

* To whom correspondence should be addressed.
Nina Stoletzki, E-mail: stoletzki{at}zi.biologie.uni-muenchen.de


  Abstract

It has been suggested that volatility, the proportion of mutations which change an amino acid, can be used to infer the level of natural selection acting upon a gene. This conjecture is supported by a correlation between volatility and the rate of non-synonymous substitution, or the ratio of non-synonymous and synonymous substitution rates, in a variety of organisms. These organisms include yeast, in which the correlations are quite strong. Here we show that these correlations are a by-product of a correlation between synonymous codon bias towards translationally optimal codons and the non-synonymous substitution rate. Although this analysis suggests that volatility is not a good measure of the selection, we suggest that it might be possible to infer something about the level of natural selection, from a single genome sequence, using translational codon bias.

Keywords: volatility; codon bias; selection; non-synonymous substitution rate.
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