Incorrect species delimitation will lead to inappropriate conservation decisions, especially for threatened species. The takin (Budorcas taxicolor) is a large artiodactyl endemic to the Himalayan-Hengduan-Qinling Mountains and is well-known as its threatened status and the peculiar appearance. However, the speciation, intraspecies taxonomy, evolutionary history and adaptive evolution of this species still remain unclear, which greatly hampers its scientific conservation. Here, we de novo

more »

... ed a high-quality chromosome-level genome of takin and resequenced genomes of 75 wild takins. Phylogenomics revealed that takin was positioned at the root of Caprinae. Population genomics based on autosome, X chromosome, and Y chromosome SNPs and mitochondrial genomes consistently revealed the existence of two phylogenetic species and recent speciation in takins: the Himalayan takin (B. taxicolor) and the Chinese takin (B. tibetana), with the support of morphological evidence. Two genetically-divergent subspecies were identified in both takin species, rejecting three previously-proposed taxonomical viewpoints. Furthermore, their distribution boundaries were determined, suggesting that large rivers play important roles in shaping the genetic partition. Compared with the other subspecies, the Qinling subspecies presented the lowest genomic diversity, higher linkage disequilibrium, inbreeding and genetic load, thus in urgent need of genetic management and protection. Moreover, the coat color gene (PMEL) variation may be responsible for the adaptive coat color difference between the two species following the Gloger's rule. Our findings provide novel insights into the recent speciation, local adaptation, scientific conservation of takins, and biogeography of Himalaya-Hengduan biodiversity hotspot.