Comparative population genomics reveals adaptive convergence in two Drosophila species across global environments

Abstract

The extent to which evolution is predictable across lineages remains unclear. To address this question, we investigated convergent adaptation in a pair of globally distributed sibling species, Drosophila melanogaster and D. simulans. We integrated whole-genome data from approximately 2,000 strains sampled across major continents, and revealed a more recent global colonization of D. simulans relative to D. melanogaster. Using a suite of complementary selection scans, we quantified signatures of positive selection across evolutionary timescales and genomic contexts. Despite substantial divergence, approximately 9-13% of adaptively evolving genes were shared between species across methods, revealing widespread convergence at the gene and pathway levels. Convergence was particularly pronounced for insecticide resistance genes, and was also evident in oxidative stress experiment. This study provides a quantitative, multiscale framework for dissecting molecular convergence, offering insights into the predictability of evolution, the constraints imposed by genomic architecture, and the dynamics of adaptation under global environmental change.