Ancient genomes illuminate the origins and dynamic history of East Asian cattle

The historical formation of domesticated cattle genetic diversity in East Asia for the last 5,000 years since the initial introduction remains largely unclear due to lack of genome-scale archaeogenetic studies. Here, we investigate the origins and evolution of cattle genetic diversity in China by analyzing whole genome sequences of 166 bovines ranging 10,000-200 years before present (yBP), encompassing now-extinct East Asian aurochs and domesticated cattle from key archaeological cultures across China. First, East Asian aurochs were distinct from European, Near Eastern, and North African aurochs and harbored a basal taurine ancestry. Second, the first domesticated cattle in the Yellow River region was formed by a mixture between incoming Western Eurasian taurine cattle and local aurochs, the latter of which contributed >10% of their ancestry, while distinct early cattle groups found in Xinjiang showed extra affinity with Western Eurasian taurine. Third, indicine admixture became widespread only in the Medieval period in northern China. This study provides a comprehensive overview of the complex genetic history of cattle diversity in East Asia.