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- Title
Estimating the Genomewide Rate of Adaptive Protein Evolution in Drosophila.
- Authors
Welch, John J.
- Abstract
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 α¯. But such tests are subject to many biases. Most serious is the possibility that high estimates of α¯ reflect demographic changes rather than adaptive substitution. Testing for between-locus variation in α is one possible way of distinguishing between demography and selection. However, such tests have yielded contradictory results, and their efficacy is unclear. Estimates of α¯ 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 α¯ 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.
- Subjects
GENETIC polymorphisms; DROSOPHILA; AMINO acids; DEMOGRAPHY; DROSOPHILA simulans; GENOMES; GENETICS
- Publication
Genetics, 2006, Vol 173, Issue 2, p821
- ISSN
0016-6731
- Publication type
Article
- DOI
10.1534/genetics.106.056911