Cattle at the Crossroad: Ancient Cattle Genomes reveal Human Interactions across
South, East, and Southeast Asia and Early Gaur Management

LIU Xinmeng Liu* and YU He

At the crossroads of South, East, and Southeast Asia, Southwest China is a critical hub for prehistoric human movements and harbors rich cattle diversity. To understand the formation of cattle diversity and associated human activities, we generated 44 nuclear genomes and 113 mitogenomes from Bos samples spanning ~4000–800 BP in Southwest China. We identified three waves of cattle introduction associated with different groups of people: taurine cattle arrived ~3300–3000 BP from northern East Asia, East Asian indicine arrived ~2300–2000 BP from Southeast Asia or southern China, and South Asian indicine arrived ~1700–1500 BP directly from South Asia. These incoming cattle replaced the locally utilized gaur, with a strong sex bias in the transient gaur–cattle gene flow suggesting human management of female gaurs. Interestingly, we identified two almost contemporaneous but genetically distinct cattle populations around 2300–1800 BP, associated with two human settlements only ~1 km apart but belonging to culturally different groups—the local Dian people and newly arrived Han people—reflecting potential cultural interactions. Together, these results provide important insights into human interactions across southern and eastern Asia and their livestock management practices.