MBE Advance Access originally published online on December 22, 2004
Molecular Biology and Evolution 2005 22(4):807-809; doi:10.1093/molbev/msi073
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Gene "Volatility" Is Most Unlikely to Reveal Adaptation
Institute of Genetics, University of Nottingham, Nottingham, UK
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 use of 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 the result of internally repetitive structures, in which unusual codon usage was caused by the mechanisms that generated this repetition rather than by adaptive changes.
Key Words: volatility • adaptation • codon usage • Mycobacterium tuberculosis • Plasmodium falciparum
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