Reconstructing the genetic formation of Han Chinese from ancient genomes

Abstract

Background The formation of the Han Chinese is deeply rooted in the Neolithic cultures of the Yellow River basin, particularly the pivotal Longshan cultural sphere which bridged prehistoric societies and early dynastic civilization. However, the genetic impact of Longshan-era populations on subsequent historical groups remains largely unexplored due to a critical lack of ancient genomic data from this key transitional period. This gap hinders a clear understanding of how early cultural integration in the heartland shaped the genetic structure of later Chinese populations. Results This study reports 28 newly sequenced ancient human genomes from the Han Dynasty Xujiacundong and Zhouhe archaeological sites in Shandong Province, which are integrated with previously published regional datasets to investigate the genetic legacy of Neolithic Longshan populations in the formation of Han Chinese ancestry. Our analyses reveal pronounced genetic differentiation between Longshan populations from the Central Plain and lower Yellow River basin during the Late Neolithic period. Most individuals from the Xujiacundong site exhibit mixed ancestry, predominantly derived from Central Plain Longshan-related ancestry (93.8%) with a minor contribution from southeastern coastal China-related ancestry (6.2%). In contrast, all individuals from the Zhouhe site exhibit genetic homogeneity with Central Plain Longshan-related ancestry. These results indicate substantial genetic heterogeneity within the lower Yellow River basin during the Han Dynasty. Moreover, we found a high degree of genetic homogeneity between ancient Han Dynasty populations and modern Han Chinese from Shandong. Admixture modeling and f-statistics further demonstrate that Longshan-related ancestries—particularly those associated with the Central Plain—played a dominant role in shaping the genetic structure of historical populations across a wide geographic range, including the Upper Yellow River, the West Liao River Basin, and Southwest China, etc. Conclusions These findings underscore the profound and pervasive genetic influence of the Central Plain Longshan populations on surrounding regions, driving the demographic expansion and genetic homogenization of the Han Chinese. This interplay of population movements and cultural diffusion highlights the central role of Longshan-era demic expansion in shaping the genetic landscape and cohesion of the Han people.