Abstract
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans.
Highlights
Given the long history of Drosophila as a central model system in evolutionary genetics beginning with the origins of empirical population genetics in the 1930s, it is unsurprising that Drosophila data have inspired the development of methods to test population genetic theories using DNA variation within and between closely related species [1,2,3,4]
Another notable aspect of these population genetic approaches is that they facilitate inferences about recent selection—which may be manifest as reduced polymorphism or elevated linkage disequilibrium— or about selection that has occurred in the distant past— which may be manifest as unexpectedly high levels of divergence
Our analysis suggests that adaptive protein evolution is common and is often related to biological processes that may be associated with gene expression, chromosome biology, and reproduction
Summary
Given the long history of Drosophila as a central model system in evolutionary genetics beginning with the origins of empirical population genetics in the 1930s, it is unsurprising that Drosophila data have inspired the development of methods to test population genetic theories using DNA variation within and between closely related species [1,2,3,4]. A powerful aspect of inferring evolutionary mechanism in this population genetic context is that selection on sequence variants with miniscule fitness effects, which would be difficult or impossible to study in nature or in the laboratory but are evolutionarily important, may cause detectable deviations from neutral predictions Another notable aspect of these population genetic approaches is that they facilitate inferences about recent selection—which may be manifest as reduced polymorphism or elevated linkage disequilibrium— or about selection that has occurred in the distant past— which may be manifest as unexpectedly high levels of divergence.
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