Ancient hybridization with an unknown population facilitated high altitude adaptation of canids

Genetic introgression provides material for adaptive evolution, but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we use newly sequenced genomes of high-altitude Tibetan and Himalayan wolves to explore the evolutionary history and adaptation of this group. We find that Tibetan and Himalayan wolves are closely related to each other, and that approximately 39-49% of their nuclear genome are derived from an as-yet unrecognized wolf-like lineage that is deeply diverged from living Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high frequencies in Tibetan dog breeds and wolves and confers an adaptive advantage to animals living at high altitudes, was probably derived from this ancient lineage. Our study suggests the complexity of canid evolution and demonstrates how admixture and introgression shape the evolutionary trajectories and adaptation of species.