Prevalence of positive selection among nearly neutral amino acid replacements inDrosophila

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Abstract
We have estimated the selective effects of amino acid replacements in natural populations by comparing levels of polymorphism in 91 genes in African populations ofDrosophila melanogasterwith their divergence fromDrosophila simulans. The genes include about equal numbers whose level of expression in adults is greater in males, greater in females, or approximately equal in the sexes. Markov chain Monte Carlo methods were used to sample key parameters in the stationary distribution of polymorphism and divergence in a model in which the selective effect of each nonsynonymous mutation is regarded as a random sample from some underlying normal distribution whose mean may differ from one gene to the next. Our analysis suggests that ≈95% of all nonsynonymous mutations that could contribute to polymorphism or divergence are deleterious, and that the average proportion of deleterious amino acid polymorphisms in samples is ≈70%. On the other hand, ≈95% of fixed differences between species are positively selected, although the scaled selection coefficient (Nes) is very small. We estimate that ≈46% of amino acid replacements haveNes< 2, ≈84% haveNes< 4, and ≈99% haveNes< 7. Although positive selection among amino acid differences between species seems pervasive, most of the selective effects could be regarded as nearly neutral. There are significant differences in selection between sex-biased and unbiased genes, which relate primarily to the mean of the distributions of mutational effects and the fraction of slightly deleterious and weakly beneficial mutations that are fixed.