Ancient DNA unveils population dynamics and integration in Pingcheng, the first Northern Wei capital established by the Tuoba Xianbei

Pingcheng, the first capital of the Northern Wei dynasty, was also the first city in Chinese history established by a nomadic regime following Han Chinese cultural norms. To investigate the genetic history of its inhabitants, this study analyzed complete mitochondrial genomes from 145 ancient individuals excavated from three major cemeteries in Pingcheng. The results reveal a complex and diverse maternal genetic structure, dominated by high-frequency haplogroups characteristic of northern steppe populations, admixed with lineages from the Yellow River Basin, southern China, Xinjiang, and western Eurasia. The maternal gene pool underwent a recent and rapid expansion, accompanied by continuous gene flow from exogenous sources. Individuals from Pingcheng exhibit substantial genetic similarity and homogeneity with the Tuoba Xianbei, underscoring their foundational role in shaping the city's maternal genetic landscape. Additional maternal inputs from Yellow River populations—and more limited but direct connections with southern China, Xinjiang, and beyond—reflect a typical pattern of multi-ethnic integration. Notably, within-group analyses reveal a paradoxical pattern: distinct haplogroup-level structuring coexists with minimal sequence-level divergence. This suggests a temporal lag between admixture events and the emergence of statistically significant genetic differentiation, pointing to an ongoing process of multi-source integration and dynamic genetic reorganization. Moreover, the integration process varied across cemetery groups in direction, tempo, and intensity, shaped by interwoven factors including Tuoba traditions of incorporation, social hierarchy, cultural identity, and political governance. These findings highlight a dynamic model of population formation characterized by unity within diversity and harmony amidst differences. Together, these findings provide novel genetic insights into population dynamics in Pingcheng and offer a representative snapshot of the broader processes of ethnic amalgamation during early medieval China.