Ancient genomes uncover dynamic cultural and genetic interplay in the eastern Tianshan

The eastern Tianshan range in Xinjiang, serving as a crucial link between the East and the West, acts as an important channel for the eastward spread of East Asian millet and painted pottery, as well as the westward diffusion of West Asian wheat and barley, bronze wares, and livestock. However, due to the scarcity of ancient genomic data, the history of population interaction and admixture in this region remains unclear. We sequenced 23 ancient individuals from 12 archaeological sites from the Bronze Age to historical periods in Xinjiang. We identified intraregional population interactions, demonstrating that an indigenous local ancestry, represented by Tarim_EMBA1, spread to the Tianshan and persisted into the historical period. The incoming East Asian millet farmers, along with Western Steppe herders characterized by Afanasievo, contributed to the formation of the eastern Tianshan populations during the Iron Age, which is consistent with archaeological findings of painted pottery and pastoral subsistence in this area. The genetic affinity to East Asian millet farmers in the eastern Tianshan increased over time, likely reflecting geographic proximity and geopolitical changes. In contrast, in line with archaeological observations, the Iron Age individuals in the western Tianshan derived their Steppe-related ancestry from populations associated with the Andronovo culture. Our results illustrated the interplay between genetics and culture in the eastern Tianshan.