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.