Genomic insights into population structure, adaptation, and archaic introgression at the Himalayan–East Asian crossroads

Tibetan-Yi Corridor (TYC) is a crucial agro-pastoral region in the eastern Himalayas, linking Qinghai‒Xizang Plateau with the lowlands of East Asia and facilitating human migration for millennia. However, genomic research on TYC populations remains limited, which limits the understanding of their origins and health. We provide genomic data from 1031 individuals belonging to Austroasiatic and Sino-Tibetan groups, including 147 whole-genome sequences from 13 underrepresented Tibeto-Burman and Austroasiatic communities. Our analysis reveals approximately 3.3 million new genetic variants and 4 distinct genetic backgrounds within TYC populations. Demographic reconstructions reveal strong genetic connections among Tibeto-Burman groups, Central Plain Sinitic populations, and Yangshao farmers, supporting a common origin for Sino-Tibetan speakers. We identify signatures of high-altitude adaptations typical of Tibetans and TYC-specific variants linked to pigmentation and hypoxia responses. Differentiation involves mechanisms such as HLA-DQB1, which are related to immune function. Several rare pathogenic variants, like CYP21A2 and PRX, are notably frequent. Variants influencing warfarin sensitivity show significant variation. Archaic human introgression further promotes genomic complexity, impacting cardiovascular and immune-related genes, which suggests adaptation through ancient human interactions. These findings refine the evolutionary history of TYC populations and underscore the need for broader genomic research to capture regional diversity and inform precision medicine.