Trans-Eurasian steppe herder and barley farmer migrations shaped paternal genomic dynamics in Northwest China and Hui evolution.

Human populations across Eurasia have long been connected through the steppe corridor and Silk Road, yet their paternal genetic history remains poorly understood. We integrated large-scale Y-chromosome data, including 1053 previously unreported sequenced genomes, to reconstruct Eurasian spatiotemporal paternal phylogeny. This resource identified 15,810 previously unidentified variants, improving the resolution of Y-chromosome phylogeny and enabling more accurate placement of ancient Eurasians. Paternal lineages in Northwest China changed gradually over time. Bronze Age Xinjiang populations were largely dominated by Xiaohe-related local lineages or western steppe herder lineages, while Iron Age and later populations showed increasing paternal contributions from East Asian farmers, eastern steppe pastoralists, and Southwest/Central Asian farmers. Modern Altaic-speaking populations showed strong paternal continuity with Iron Age ancestry, and northwestern Han displayed a west-to-east gradient of paternal lineages. Four Hui substructures showed differentiated paternal profiles shaped by both migration and cultural assimilation. Overall, the results revealed a complex pattern of population movements shaping paternal ancestry across northwestern East Asia.