Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans

Abstract

In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence-in particular, conclusions about the rate and strength of beneficial substitutions-remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot), and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3%) that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis of adaptation.

Figure 1. The footprint of beneficial amino acid substitutions in neutral levels of diversity.

A. Average synonymous diversity level in D. simulans as a function of distance from amino acid (red) and synonymous (black) substitutions in the D. simulans lineage. B. Average synonymous divergence between D. melanogaster and D. yakuba (a proxy for the mutation rate) as a function of distance from amino acid (red) and synonymous (black) substitutions. C. Synonymous diversity levels divided by divergence as a function of distance from amino acid (red) and synonymous (black) substitutions (see Text S1). The curves in A–B were smoothed with LOESS on the left and right of substitutions separately, and C was calculated as a ratio of the value after smoothing (see Text S1). The gray sleeves represent the standard error of the mean of the synonymous control (black curve) estimated from 1000 bootstraps and smoothed by LOESS as above (see Text S1). D. A Manhattan plot of the one tailed p-value (on a logarithmic scale) testing the hypothesis that the average diversity divided by the average divergence around amino acid substitutions is the same as that around synonymous substitutions (shown in C). Results are shown as a function of distance from the substitution (based on 1000 bootstraps and calculated in bins of 0.5 kb; see Text S1 for details).

Figure 2. The reduction in diversity around amino acid substitutions, controlling for clustering.

A. The density of amino acid (red) and synonymous (black) substitutions as a function of distance from an amino acid substitution. The synonymous density was multiplied by 0.4 (the ratio of the average amino acid to the average synonymous densities) in order to make the comparison of densities more transparent. B. A comparison between the average diversity levels around amino acid (red) and synonymous substitutions (black) as a function of the density of amino acid substitutions in their vicinity. Diversity levels and density of amino acid substitutions were measured in a window size of 1kb centered at the substitution under consideration. C. The numbers of amino acid (red) and synonymous substitutions (black) used to estimate the average diversity levels at each density.

Figure 3. The fit of recurrent selective sweep models to diversity patterns around amino acid substitutions.

A. Observed and predicted curves for the average synonymous heterozygosity as a function of distance from amino acid substitutions. The curve based on the data (black) was smoothed using LOESS with a span of 0.5 and divided by divergence, as in Figure 1. The predicted curves correspond to maximum likelihood estimates based on different distributions of beneficial selection coefficients: “1 point” corresponds to a single selection coefficient (blue); “Gamma” to a Gamma distribution (green); “2 point” to two selection coefficients (red); “2 exponentials” to a mixture of two exponentials (orange). B. A close-up on distances up to 4 kb. To reveal more detail of the observed curve on this scale, we used LOESS smoothing with a smaller span of 0.002. See Text S1 for further details.