Paternal genomic history and Y-chromosome phylogeny from the Chengdu Plain reveal multiple Indigenous East Asian farmer contributions to ancient Shu and their descendants.

The Chengdu Plain and surrounding regions (CPS) host a diverse mosaic of archaeological cultures and ethnolinguistic groups, yet the origins of these populations and the extent of Western Eurasian and East Asian influences remain unclear and underrepresented in genomic studies. As a molecular archaeological archive, Y-chromosome data provide vital insights into the paternal genetic history of ancient Shu populations and their descendants.Here, we combine our newly generated genomic data with publicly available large-scale whole-Y-chromosome sequences from East Asia to reconstruct the phylogeny and paternal history of both modern and ancient CPS populations. Our merged dataset includes 2737 whole-Y sequences and 312 ancient samples, revealing a complex regional paternal genetic history.We identify 970 Y-chromosome clades, covering both common East Asian indigenous haplogroups (O, C, D, N) and rare incoming haplogroups (Q, J, R, F, H), and observe distinct distribution patterns across ethnically diverse Han, Tibetan, Yi, Qiang, and Hui groups in CPS. Population modeling uncovers fine-scale substructures influenced by ethnolinguistic and geographic factors, emphasizing the dominant paternal contributions of indigenous East Asian millet- and rice-farming groups. Time-calibrated phylogenies indicate that the founding populations of the ancient Shu civilization primarily derived from East Asian millet- and rice-based agricultural communities, with limited gene flow from Western steppe pastoralists.Our findings enhance the understanding of the paternal genetic landscape of CPS populations and shed light on key demographic transitions during the Neolithic and Bronze Age.