Patrilineages of ethnolinguistically diverse populations reveal multifactorial influences on Chinese paternal population stratification

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Abstract: Background

Large-scale Y-chromosome genetic resources provide critical insights into human evolutionary history. However, the limited high-density Y-chromosomal data from ethnolinguistically diverse Chinese populations hinder the reconstruction of fine-scale population stratification and the exploration of its complex influencing factors.
Objectives

We report microarray-based high-density Y-SNP data from 5311 unrelated males in the pilot phase of the 10K Chinese People Genomic Diversity Project (10K_CPGDP) and merge it with spatiotemporally high-coverage reference data from both ancient and modern individuals from public sources and the Huaxi Biobank dataset.
Results

We identified clear north–south and west–east genetic substructures among Chinese populations, reflecting distinct regional genetic origins and migration patterns. We illuminated how multiple cultural and demographic factors, including subsistence strategies, language barriers, and geographic isolation, have shaped the Chinese paternal population dynamics via genetic diversity analysis coupled with phylogenetic and phylogeographic analyses. Paternal genetic diversity followed complex patterns, with a haplogroup frequency spectrum and a variation-based phylogenetic tree indicating that more than 95% of paternal lineages belong to haplogroups O, C, N, D, and Q. The phylogeographic analysis revealed distinct regional distributions of haplogroups linked to subsistence strategies and ancestral population dispersal. The predominance of Neolithic farmer-related lineages suggested that the spread of ancestral agricultural populations promotes population differentiation between ancient northern and southern East Asians. We observed significant lineage sharing between Han Chinese and ethnic minority groups, with the northwestern paternal gene pool contributing lineages associated with farming and herding. Spatial autocorrelation and principal component analyses revealed genetic connections between the Han Chinese and ethnic minorities, highlighting paternal population substructures shaped by complex admixture and migration patterns that align with geographical and linguistic divisions.
Conclusions

These findings support the influence of the farming-language dispersal hypothesis on Chinese paternal lineage formation and underscore the role of geographic and linguistic isolation in shaping the genetic landscape. This study demonstrates the unique value of large-scale Y-chromosome data in uncovering human evolutionary complexity.