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J Evol Biol. 2009 Mar;22(3):515-26. doi: 10.1111/j.1420-9101.2008.01672.x. Epub 2008 Dec 18.

Selection efficiency and effective population size in Drosophila species.

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Group of Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.


A corollary of the nearly neutral theory of molecular evolution is that the efficiency of natural selection depends on effective population size. In this study, we evaluated the differences in levels of synonymous polymorphism among Drosophila species and showed that these differences can be explained by differences in effective population size. The differences can have implications for the molecular evolution of the Drosophila species, as is suggested by our results showing that the levels of codon bias and the proportion of adaptive substitutions are both higher in species with higher levels of synonymous polymorphism. Moreover, species with lower synonymous polymorphism have higher levels of nonsynonymous polymorphism and larger content of repetitive sequences in their genomes, suggesting a diminished efficiency of selection in species with smaller effective population size.

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