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.

We de novo assembled mitochondrial genomes for HAW using NOVOPlasty2.7.2 (Dierckxsens, et al. 2017) using with dog mitochondrial genome (GenBank accession: NC_002008.4 ) as a seed sequence. K-mer of 31 was used to perform the assembly independently. These mitogenomes and those downloaded from NCBI-Genbank are aligned together using MUSCLE.

Genotypes for dog and wolf in this study were got using BWA-GATK pipeline.

In this dataset, genotype with more than 10% missing rate among these samples was removed.

Mitochondrial genomes are partially assembled and control regions contain missing bases.