Early Neolithic genomes suggest a local origin for millet farmers in East Asia

Millet cultivation in northern China served as a critical catalyst for Neolithic sedentism and East Asian civilization, yet the demographic origins of the inaugural millet farmers remain contentious. We analyze genome-wide data from seven individuals from the Donghulin (DHL), Dengcaogouliang, and Sitai sites, spanning 11,000 to 7300 years ago, and identify the DHL lineage as the predominant genetic structure in inland northern East Asia following the Last Glacial Maximum. Our results demonstrate profound genetic continuity from the Early Holocene through the intensification of millet agriculture, lending robust support to a model of local development rather than demic diffusion from external territories. Furthermore, we identify the earliest occurrence of the hypoxia-adaptive EGLN1 variant in a 9200-year-old DHL individual, suggesting that the physiological adaptations currently prevalent in Tibeto-Burman populations have deep Neolithic roots. Collectively, these findings necessitate a reevaluation of the early demographic and adaptive landscape of East Asia.