Ancient genomes reveal the genetic history of domestic goats on the Qinghai-Xizang Plateau approximately 3 600 years ago

The Qinghai-Xizang Plateau imposes severe environmental pressures that have driven extensive adaptive responses in both humans and animals. Among the domestic species that underpin high-altitude pastoral livelihoods, goats are of particular importance, yet their historical origins remain poorly resolved. In this study, ancient genomic data were generated from five goat remains recovered from the Lake Qinghai Basin and dated to approximately 3 600 years ago. After stringent authentication and filtering, three individuals with genomic coverages ranging from 0.152× to 1.45× were retained for subsequent population genetic analysis. These data revealed a close genetic affinity between ancient goats from the Lake Qinghai Basin and goat populations from West Eurasia. In contrast, most present-day Chinese goats predominantly carried ancestry related to Neolithic Iran. Notably, modern Dazu black goats (Capra hircus) were found to derive primarily from a lineage closely related to the ancient Lake Qinghai Basin goats, indicating marked genetic continuity across time. In addition, modern Alpas cashmere goats and Qinghai-Xizang goats carried approximately 4%–8% ancestry from the Lake Qinghai Basin-related lineage. Collectively, these findings refine current understanding of early herd management on the Qinghai-Xizang Plateau and provide new insight into the genetic history and population formation of Chinese goats.