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MBE Advance Access published online on December 22, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi073
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Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved.
Accepted December 20, 2004

Letter

Gene "volatility" is Most Unlikely to Reveal Adaptation

Paul M. Sharp 1*

1 Institute of Genetics, University of Nottingham, Nottingham, UK

* To whom correspondence should be addressed.
Paul M. Sharp, E-mail: paul{at}evol.nott.ac.uk


  Abstract

It has recently been claimed that adaptive molecular evolution can be detected within single genome sequences, by using gene "volatility" scores. However, the approach used was entirely based on the assumption that synonymous codon usage is normally shaped by selection for low volatility; this is most unlikely to be true. Furthermore, even if that assumption could be justified, the method would clearly lack power, detecting only genes where a very large number of nonsynonymous substitutions had occurred. Volatility scores are susceptible to other influences. The unusually high volatilities of the Mycobacterium tuberculosis and Plasmodium falciparum genes that were identified as putatively having undergone adaptive changes were largely due to internally repetitive structures, where unusual codon usage was caused by the mechanisms that generated this repetition rather than by adaptive changes.

Keywords: volatility; adaptation; codon usage; Mycobacterium tuberculosis; Plasmodium falciparum.
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