Genetic structure and paternal admixture of the modern Chinese Zhuang population based on 37 Y-STRs and 233 Y-SNPs

The Zhuang are the largest minority group in China and the aboriginal people of the Guangxi Zhuang Autonomous Region. Over thousands of years, the gene pool of the Zhuang has been shaped by the genetic admixture with the Han Chinese. However, little is known about the paternal genetic structure of the modern Zhuang people. Here, we used a high-resolution panel comprising 233 Y-chromosomal single-nucleotide polymorphisms (Y-SNPs) and 37 Y-chromosomal short tandem repeats (Y-STRs) to illuminate the paternal genetic structure and affinities of the Zhuang population. Their Y-SNP haplogroup diversity reached 0.9580 with 44 different subhaplogroups and their Y-STR haplotype diversity reached 1.0. Several bioinformatics analyses were conducted comparing the Zhuang to various reference populations worldwide. Mismatch analysis suggested extensive intermarriages between the Zhuang and O2-dominant groups such as the Han. Genetic clustering analysis of Y-STRs revealed broad genetic affinities between the Zhuang and several geographically, linguistically, and the ethnically related groups such as the southern Han, Bouyei, Li, Miao, and Yao from China. Principal Component Analysis of Y-SNPs demonstrated long-term close genetic relationships among the Zhuang people, Hainan Han, Guangdong Han, and Southeast Asians. Combined Y-STR/Y-SNP analysis showed the Zhuang people and the Hainan Han share common ancestry, illuminating the patrilineal descent of the Zhuang and lending genetic support to commonly accepted ideas regarding the origin of the Hainan Han. Our analysis of Y-SNPs and Y-STRs not only revealed the fine-scale genetic structure of the Zhuang population, but also illuminated their paternal derivation, which is defined by the common ancestry with the Hainan Han, the introgression of southern Chinese groups such as the Han, Bouyei, Li, Miao, and Yao, the long-term phylogenetic relationships with Southeast Asians.