Abstract
Understanding the evolution of local adaptations is a central aim of evolutionary biologyand key for the identification of unique populations and lineages of conservationrelevance. By combining RAD sequencing and whole-genomesequencing, we identifygenetic signatures of local adaptation in mountain hares (Lepus timidus) from isolatedand distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia.Demographic modelling suggested that the split of these mountain hares occurredaround 20 thousand years ago, providing the opportunity to study adaptive evolutionover a short timescale. Using genome-widescans, we identified signatures of extremedifferentiation among hares from distinct geographic areas that overlap with area-specificselective sweeps, suggesting targets for local adaptation. Several identifiedcandidate genes are associated with traits related to the uniqueness of the differentenvironments inhabited by the three groups of mountain hares, including coat colour,ability to live at high altitudes and variation in body size. In Irish mountain hares, avariant of ASIP, a gene previously implicated in introgression-drivenwinter coat colourvariation in mountain and snowshoe hares (L. americanus), may underlie brownwinter coats, reinforcing the repeated nature of evolution at ASIP moulding adaptiveseasonal colouration. Comparative genomic analyses across several hare species suggestedthat mountain hares’ adaptive variants appear predominantly species-specific.However, using coalescent simulations, we also show instances where the candidateadaptive variants have been introduced via introgressive hybridization. Our studyshows that standing adaptive variation, including that introgressed from other species,was a crucial component of the post-glacialdynamics of species.