Abstract
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.