Multiple Genetic Shifts at the Crossroads of the Eastern Steppe and Loess Plateau Over 4,000 Years

Ningxia, located at a key crossroads between the Eurasian Steppe and East Asia, was an important corridor for cultural exchange and human migration, yet its genetic history has remained poorly understood. In this study, we sequenced 89 individuals from 23 archeological sites in Ningxia, dating from 4245 to 301 BP. Our findings show that late Neolithic inhabitants of Ningxia possessed ancestral components from the Yellow River, Ancient Northeast Asia, and the Tibetan Plateau. Over time, the region experienced major genetic shifts associated with historical migrations and political change. During the Western Zhou and Han periods (3.0-1.7kBP), expansions of Central Plains polities promoted the movement of Yellow River populations into Ningxia, influencing Ningxia’s genetic structure up to the Ming-Qing period (582-301BP). Individuals associated with the Eastern Zhou Northern Bronze Complex (2.7-2.0kBP) show mixture between Eurasian Steppe and Yellow River populations. In the Northern Dynasties and Sui-Tang periods (1.6-1.0kBP), Western Eurasian ancestry increased markedly, likely reflecting Silk Road mobility. Tangut groups of the Western Xia show close genetic ties to Di-Qiang-related populations from the upper Yellow River. Reconstructing the genetic history of Ningxia from the late Neolithic to Qing dynasty (4.2k-301BP), evidencing complex genetic dynamics shaped by historical processes.