Gene. 2009 Aug 15;443(1-2):64-9. Epub 2009 May 27.

Genetic robustness at the codon level as a measure of selection.

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Department of Zoology, University of Oxford, UK. archetti@fas.harvard.edu

Abstract

Selection at the DNA level is usually detected by analysing substitution rates from multiple-species comparisons. It has been suggested that measures of genetic robustness at the codon level, which can be measured by analysing a single coding sequence, can be used to estimate selection, but the validity of these measures has been questioned. Here I test the efficiency of different measures of genetic robustness at the codon level to estimate the level of selection acting on a gene. I find that volatility and other measures of robustness are correlated with dN/dS, and that this is not simply the effect of a preference for translationally optimal codons. I discuss the possible implications and the possible problems of these methods based on single-sequence codon usage analysis.

PMID:: 19477246; [PubMed - indexed for MEDLINE]

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Research Support, Non-U.S. Gov't

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Codon

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