Ancient DNA reveals pig domestication history in Northeastern China

Pigs (Sus scrofa) were independently domesticated in the Near East and East Asia about 10,000 years ago. As one of the earliest livestock, their domestication process is closely intertwined with human activities. Previous studies have identified the Qinghai-Tibet Plateau, the Yellow River basin, and the middle-lower reaches of the Yangtze River as major domestication centers for indigenous Chinese pig breeds. However, whether Northeast China served as another independent center remains debated. To address this issue, we obtained ten near-complete mitochondrial genomes from pig teeth collected from Northeast China. Using phylogenetic analysis, we examined the maternal genetic relationships between these ancient individuals and other pig populations across different historical periods in China. Our results reveal the presence of an ancient, now-extinct lineage of domestic pigs in Northeast China, with no genetic links between ancient and modern pig populations in this region. These findings suggest that the available molecular data do not support Northeast China as an independent pig domestication center. Moreover, we demonstrate that the continuous and diverse human cultures in China significantly influenced the effective population size dynamics of domestic pigs over time.