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

The evolutionary history of domesticated cattle in East Asia for the past 5000 years remains largely obscure. Here, we investigated the origins and evolution of cattle genetic diversity in China by analyzing shotgun genome sequences of 166 ancient bovines spanning a 10,000-year period and encompassing now-extinct East Asian aurochs and domesticated cattle from key archaeological cultures. East and North Asian aurochs were distinct from western aurochs, although East Asian aurochs harbored approximately 15% western ancestry. The first domesticated cattle in the Yellow River region derived approximately 10% of their ancestry from local aurochs with an uneven genome-wide distribution. Early cattle from Xinjiang were genetically distinct and partially contributed to the later northern Chinese cattle. Indicine admixture became widespread only in the Medieval period in northern China. Editor's summary: The aurochs (Bos primigenius) contributed to modern cattle populations, but this relationship has not been explored as deeply in East Asian bovines. Cai et al. performed shotgun sequencing on 166 ancient aurochs, taurine, and indicine cattle from across China and combined these data with those from 69 ancient and 595 modern previously published individuals. They found evidence of substantive gene flow between ancient populations of aurochs, particularly after the Last Glacial Maximum. Modern East Asian cattle appear to descend from West Eurasian domesticated cattle, with subsequent admixture with East Asian aurochs and later East Asian and European taurine lineages. These data illuminate the finer population dynamics that contributed to modern East Asian cattle. —Corinne Simonti INTRODUCTION: Cattle have long played a central role among agropastoral societies across East Asia. Genomic studies elsewhere reveal a complex evolutionary history involving multiple dispersal events and widespread admixture. Taurine cattle, initially domesticated from Near Eastern aurochs ~10,000 years before present (yBP), spread into Europe and Africa, where introgression with local wild aurochs left lasting genetic signatures. In South Asia, domesticated indicine cattle first appeared ~8000 yBP, and their later dispersals brought extensive taurine-indicine admixture in West, Central, and East Asia and Africa. RATIONALE: Although zooarchaeological and archaeogenetic studies have documented their presence since ~5000 yBP, the origins and dispersal processes of early East Asian cattle remain unclear because of limited ancient genomes. In addition, the presence of now-extinct aurochs and domesticated bovines such as indicine cattle, yaks, and gayals suggests a complex, yet underexplored, evolutionary history of East Asian cattle. To address this, we generated 166 ancient genomes spanning from 10,000 to 200 yBP across China. This rich dataset includes a well-curated temporal series of cattle genomes spanning the past 5000 years in the Central Plains and Xinjiang, along with East Asian aurochs genomes. RESULTS: Holocene East Asian aurochs primarily derive from the pre-LGM North Asian aurochs lineage, with ~15% admixture from western aurochs. Late Neolithic to Bronze Age cattle along the Yellow River basin (termed "YR_LNBA") form a homogeneous group that originated from incoming western Eurasian taurine cattle, with ~10% local aurochs introgression, followed by a severe population bottleneck. Aurochs-derived genomic segments are depleted on the X chromosome, suggesting selection and/or non-neutral breeding processes. Early Xinjiang cattle, unlike YR_LNBA, show Western taurine affinity and South Asian indicine admixture, suggesting multiple introductions into East Asia. During the Late Bronze and Iron Ages, Xinjiang-related ancestry spread into northern China, contributing to later cattle populations. Chinese indicine ancestry expanded into northern China during the Medieval period, forming the backbone of present-day cattle genetic diversity. Later, another layer of European taurine ancestry spread across northern China. CONCLUSION: Our findings reveal a deep, layered genomic history of East Asian cattle shaped by repeated transregional admixture. East Asian taurine cattle emerged through hybridization between introduced Western taurine and local aurochs, later reshaped by admixture from Xinjiang-related cattle and Chinese indicine. These results point to the Eurasian Steppe and Central Asia as key corridors in the early dispersal of cattle into East Asia, highlighting these regions as priorities for future archaeogenomic research. A dynamic history of East Asian cattle.: Shown is an admixture graph illustrating four ancestry waves in the formation of northern Chinese cattle. First, incoming taurine from the west admixed with local aurochs during the Late Neolithic, followed by a bottleneck. Second, genetically distinct Xinjiang cattle spread eastward and mixed during the Middle-Late Bronze and Iron Ages. Third, Chinese indicine cattle expanded northward in the Medieval period. Finally, European taurine ancestry entered the present-day breeds. [ABSTRACT FROM AUTHOR]