Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

Abstract

Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau. Here, we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred. We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys (including 24 from the Tibetan Plateau). Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs. In Tibetan donkeys, however, another gene, i.e., EGLN1, was likely involved in their adaptation to high altitude. In addition, admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys. Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.

Keywords: Adaptation; Donkey; High altitude; Kiang; Selection.

Figure 1

Genome evolution in kiangs

Figure 2

Population genetics analysis of kiangs and domestic donkeys

Figure 3

Hard selective sweep in EPAS1 in kiangs

Figure 4

Rare hard selective sweep in kiangs at genome-wide scale

Figure 5

Evidence of high-altitude adaptation in Tibetan domestic donkeys

Figure 6

Selective sweep analysis by SweeD in kiang, Tibetan donkey, and plain donkey populations (A) and rare high CLR regions overlapped in the three populations(B)