MBE Advance Access published online on March 24, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh134
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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1 Centre for the Study of Evolution & School of Biological Sciences, University of Sussex, Brighton, BN1 9QG, UK
* To whom correspondence should be addressed. E-mail: a.c.eyre-walker{at}sussex.ac.uk.
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 datasets 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 which are adaptive appears to be the same in fast 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 datasets suggests that Key Words:
Adaptive evolution, McDonald-Kreitman test, amino acid substitutions, Drosophila
© 2004 Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved.
Original Articles
The Genomic Rate of Adaptive Amino-Acid Substitution in Drosophila
Abstract 
25±20% of amino acid substitutions were driven by positive selection in the divergence between D. simulans and D. yakuba.
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