Multidisciplinary analysis reveals genetic heterogeneity and millet farmer ancestry in late Xianbei individuals

The Xianbei were a prominent nomadic group in Chinese history, whose origins, cultural practices and subsistence strategies have long attracted scholarly attention. Despite previous studies, the genetic composition, migration history and integration of the Tuoba Xianbei into northern China remain poorly understood. To address these, we generated 39 ancient genomes, 66 stable carbon and nitrogen isotope measurements and 8 AMS radiocarbon dates from the Shanghuaju (SHJ) archaeological site in Datong, Shanxi, dating to the Pingcheng period of the Northern Wei dynasty. Our analyses reveal a complex genetic structure within the SHJ population, reflecting extensive admixture among local Han agriculturalists, ancient northeast Asian groups, Western Steppe herders and Near Eastern populations. While most individuals show ancestry related to Yellow River Basin populations, a subset retains genetic affinities with early Xianbei populations from the Greater Khingan Mountains, providing evidence for partial continuity with their ancestral lineage and supporting historical accounts of the Tuoba Xianbei's Donghu origin. Several individuals exhibit detectable Near Eastern ancestry, consistent with long-distance gene flow along the Eurasian Steppe during the Northern Wei dynasty. Stable isotope analyses indicate a predominantly C4-based diet supplemented with moderate animal protein, with males and females showing minor differences in intake, reflecting potential sex-biased dietary patterns. These findings highlight the high genetic diversity of the SHJ population and illustrate how migration, admixture and cultural integration shaped the demographic, dietary and cultural landscape of the Tuoba Xianbei in northern China.