Estimating the genomewide rate of adaptive protein evolution in Drosophila
Welch JJ(2006) Genetics 173, 821-837.
When polymorphism and divergence data are available for multiple loci, extended forms of the McDonald-Kreitman test can be used to estimate the average proportion of the amino acid divergence due to adaptive evolution - a statistic denoted alpha_bar. But such tests are subject to many biases. Most serious is the possibility that high estimates of a reflect demographic changes rather than adaptive substitution. Testing for between-locus variation in alpha is one possible way of distinguishing between demography and selection. However, such tests have yielded contradictory results, and their efficacy is unclear. Estimates of alpha_bar from the same model organisms have also varied widely. This study clarifies the reasons for these discrepancies, identifying several method-specific biases in widely used estimators and assessing the power of the methods. As part of this process, a new maximum-likelihood estimator is introduced. This estimator is applied to a newly compiled data set of 115 genes from Drosophila simulans, each with each orthologs from D. melanogaster and D. yakuba. In this way, it is estimated that alpha_bar ~ 0.4 ± 0.1, a value that does not vary substantially between different loci or over different periods of divergence. The implications of these results are discussed.
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