Ancient genomes reveal the genetic legacy of domestic goats on the Tibetan Plateau ~3,600 years ago

The extreme environment of the Tibetan Plateau necessitates exceptional adaptations for both humans and animals. Domestic goats are vital to the livelihoods of high-altitude herders, yet their historical origins remain elusive. In this study, we generated ancient genomic data from five goat individuals dating back approximately 3,600 years before present (BP) in the Lake Qinghai Basin. After rigorous processing, three samples (with sequencing coverages ranging from 0.152× to 1.45×) were retained for subsequent population genetic analyses. Our findings revealed a strong genetic connection between these ancient Lake Qinghai Basin goats and goats from West Eurasia. In contrast, modern Chinese goats predominantly carry ancestry related to Neolithic Iran. Notably, modern Dazu black goats (Capra hircus) are mainly descended from a lineage associated with the ancient Lake Qinghai Basin goats, exhibiting clear genetic continuity. Additionally, modern Alpas cashmere goats and Tibetan goats derive approximately 4%-8% of their ancestry from the Lake Qinghai Basin-related lineage. These results shed light on the faunal management strategies of early herders and the genetic evolutionary history of Chinese goats.