Genomic formation of lower Yellow River populations in the Han dynasty

Abstract

Background As a key region in the lower Yellow River Basin, Shandong Province plays a central role in understanding the genetic history of East Asia. However, detailed ancient DNA data across its historical periods remains limited. This study aims to characterise the genomic profiles of Shandong populations during the Western Han Dynasty and trace their genetic connections with neighbouring regions. Results Here, we newly generated 14 ancient genomes from the Wenshaobei site of the Western Han dynasty in Shandong Province. Genetic analyses, including principal component analysis (PCA), ADMIXTURE, and f-statistics, revealed that the Wenshaobei population was genetically distinct from Early Neolithic Shandong hunter-gatherers but closely aligned with Middle Neolithic to Iron Age populations from the middle and lower Yellow River Basin. This indicates strong genetic continuity with millet-farming societies from the middle Yellow River, supplemented by minor influences from southern rice-farming groups. Modern Han Chinese in Shandong share a core genetic foundation with ancient populations, such as Wenshaobei. Conclusions Our findings highlight the role of the lower Yellow River Basin as a nexus of genetic exchange between northern millet-farming and southern rice-farming cultures, with sustained genetic influences from the middle Yellow River shaping the demographic landscape from the Neolithic to the Han Dynasty. The study provides critical insights into the formation of East Asian populations, underscoring the interplay between agriculture, migration, and genetic diversity in this cradle of ancient Chinese civilization. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-025-02377-7.