Ancient Pig Genomes Reveal Interactions between Southern China and Southeast Asia

ZHAO Zhihan* and YU He

Domestic pigs are key livestock in agricultural societies, and their evolution history often parallels human migration and management practices. In Southern China—an important crossroads linking East and Southeast Asia—the ancestry, dispersal history, and interactions of domestic pigs with Southeast Asian populations remain poorly understood. To address this question, we generated 15 nuclear genomes from ancient domestic pigs and wild boar remains from Southwestern China, Southern Coastal China, and Northern Vietnam, dating from ~4,300 to 880 BP. By integrating these data with published suid genomes from across Eurasia, we identified a distinctive genetic composition in early domestic pigs from Southwestern China that shows strong genetic affinity with Neolithic pigs from Northern Vietnam, suggesting close genetic connections between the two regions. Through time, pigs in Southwestern China experienced increasing genetic influence from Northern Chinese domestic pigs, eventually forming the mixed north–south ancestry observed in modern Southwestern Chinese breeds. In Southern Coastal China, evidence of genetic interaction between northern and southern lineages can be traced back to the Neolithic period, with pigs carrying ancestry related to both Northern China and Southeast Asia. Our findings illuminate the dynamic ancestry of domestic pigs in Southern China and provide genomic evidence for prehistoric interactions between Southern China and Southeast Asia.