The genomic rate of adaptive amino acid substitution in Drosophila.

Bierne, Nicolas and Eyre-Walker, Adam (2004) The genomic rate of adaptive amino acid substitution in Drosophila. Molecular Biology and Evolution, 21 (7). pp. 1350-1360. ISSN 0737-4038

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Abstract

The proportion of amino acid substitutions driven by adaptive evolution can potentially be estimated from polymorphism and divergence data by an extension of the McDonald-Kreitman test. We have developed a maximum-likelihood method to do this and have applied our method to several data sets from three Drosophila species: D. melanogaster, D. simulans, and D. yakuba. The estimated number of adaptive substitutions per codon is not uniformly distributed among genes, but follows a leptokurtic distribution. However, the proportion of amino acid substitutions fixed by adaptive evolution seems to be remarkably constant across the genome (i.e., the proportion of amino acid substitutions that are adaptive appears to be the same in fast-evolving and slow-evolving genes; fast-evolving genes have higher numbers of both adaptive and neutral substitutions). Our estimates do not seem to be significantly biased by selection on synonymous codon use or by the assumption of independence among sites. Nevertheless, an accurate estimate is hampered by the existence of slightly deleterious mutations and variations in effective population size. The analysis of several Drosophila data sets suggests that approximately 25% ± 20% of amino acid substitutions were driven by positive selection in the divergence between D. simulans and D. yakuba.

Item Type: Article
Schools and Departments: School of Life Sciences > Evolution, Behaviour and Environment
Depositing User: Adam Eyre-Walker
Date Deposited: 06 Feb 2012 19:32
Last Modified: 20 Mar 2012 16:20
URI: http://sro.sussex.ac.uk/id/eprint/21147
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