Ancient genomes reveal basal Asian ancestries and dynamic population interactions over time on the southern Tibetan Plateau

The southern Tibetan Plateau is a key region for the settlement and flourishing of Tibetan populations, but the long-term population dynamics in this area remain poorly understood. By analyzing 16 newly sequenced genomes from the Mabu Co site (4400 masl), we reconstructed the population history on the southern Tibetan Plateau spanning 4,400-3,500 BP. While the local southern plateau ancestry was maintained over a millennium, genetic diversity within these populations was observed over time. We revealed multiple admixtures, including Basal Asian Xingyi-related ancestry linked to hunter-gatherer populations from southwestern China, and provided the first evidence of this ancestry influencing the ancient southern Tibetan Plateau populations again after 4,000 BP. Moreover, mtDNA and Y haplogroups reveal that individuals exhibit greater maternal genetic diversity alongside restricted paternal lineage conservation. This study provides a higher-resolution population history in the ultra-highlands, contributing to understanding human adaptation to extreme environments.