58 Ancient Genomes from Baligang Reveal a 5,000-Year-Old Patrilineal Community and Four Millennia of North–South Admixture in the Middle Yangtze

A Peking University team led by Huang Yanyi and Pang Yuhong, together with Zhang Chi, Wu Xiaohong, Yunnan University, Minzu University of China, and collaborators, has sequenced the whole genomes of 58 ancient individuals from the Baligang site in Nanyang, Henan, spanning the middle Neolithic to the late Bronze Age. The work appears in Nature Communications.

Baligang sits on the northern fringe of the middle Yangtze, at the transition between the Yellow and Yangtze river basins—making it a key node for observing prehistoric north-south interactions. The 58 genomes provide the most direct evidence yet for reconstructing some four thousand years of genetic exchange in this contact zone.

The data identify a clear turning point around 4,200 years ago, after which a substantial influx of southern East Asian ancestry arrived, followed by sustained bidirectional gene flow between northern and southern sources. Rather than a single event, admixture appears as a long, repeated process.

A second major finding is the region’s first evidence of a patrilineal clan structure already present around 5,000 years ago: multiple males within the same family shared a single Y-chromosome lineage—rare direct genetic evidence for the reconstruction of early social organization.

Methodologically, the team developed a new sex-estimation approach for extremely low-coverage ancient DNA, improving information recovery from poorly preserved samples. Together, the study reconstructs a four-thousand-year genetic map of the Yellow-Yangtze intersection and provides systematic genomic evidence for the ongoing north-south admixture underlying the formation of Chinese civilization.