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

The predictability of evolution across lineages remains unclear. We examine repeated adaptation in the globally distributed sibling species, Drosophila melanogaster and D. simulans. We assemble a high-quality reference genome for D. simulans, and integrate whole-genome data from approximately 2,000 strains sampled across major continents. Population genomic analyses indicate more recent global colonization of D. simulans than D. melanogaster. Using complementary selection scans, we quantify signatures of positive selection across evolutionary timescales and genomic contexts. Despite substantial divergence, 12%-17% of adaptively evolving genes are shared between species across methods, indicating repeated selection of the same genes and biological pathways. Convergence is particularly pronounced for insecticide resistance genes. Gene-level repeatability is further supported by oxidative stress experiments. Our study provides a quantitative, multiscale framework for dissecting hierarchical convergence and clarifies how genomic architecture, environmental change, and genetic background shape the repeatability of adaptation.