A 6,000-year genomic transect in the middle Yellow River

As a pivotal cradle of East Asian civilization, the middle Yellow River region has long been a focal point for studying human cultural and biological evolution. However, its peopling history and kinship practices remain unclear due to a lack of ancient genomic data. In this study, we present 112 newly sequenced ancient genomes from eight archaeological sites in the middle Yellow River region, dating from 6,200 to 100 years ago. Our analyses reveal that all later individuals ultimately traced their primary ancestry to local early populations represented by our newly generated 6,200-year-old genomes from western Henan—the earliest genomes from the core area of the Yangshao culture. We also identified two major subsequent demographic transformations. The first was a cultural transition-associated genetic shift around 4,500 years ago in western Henan during the Longshan period that may be linked to the spread of Shaanxi-Shanxi populations. This was followed by a two-millennia-long expansion of central Henan-related ancestry that homogenized the genetic landscape across the entire Yellow River basin, independent of significant genetic contributions from the Eurasian Steppe or other adjacent foreign regimes. Beyond demographic history, we provide insights into ancient social structures through two case studies. At the 2,500-year-old Shangshihe site, evidence suggests that the social status was stably inherited within families and among close biological kin. The society represented by the 2,000-year-old Dongxiaoli-Bailong site appears to have placed greater emphasis on the relationships forged through marriage alliances rather than on ancestral lineage inheritance. Collectively, our study illuminates the complex interplay between local continuity and long-distance population connectivity in one of the world’s earliest agricultural heartlands and provides new insights into social structure in Iron Age northern China.