Genetic origin and forensic analysis of han populations from four districts in Shanghai, China, based on Y-chromosome STR and SNP markers

Y-short tandem repeats (STRs) and Y-single nucleotide polymorphisms (SNPs) on the Y chromosome are genetic markers unique to men. They are widely used in identification, forensic medicine and paternal lineage tracing. Because of their strict paternal genetic characteristics, they have become a powerful means to trace the evolution of paternal lineages and populations. In this study, 38 Y-STR loci and 250 Y-SNP loci were genotyped, and a dataset was constructed for Qingpu Han (n = 396), Songjiang Han (n = 386), Jinshan Han (n = 384), and Fengxian Han (n = 372) populations in Shanghai. The Yfiler platinum genotyping system yielded the highest haplotype diversity (HD): Qingpu (0.99995), Songjiang (0.99996), Jinshan (0.99988) and Fengxian (0.99993); additionally, unique haplotypes accounted for 97.31%, 96.09%, 97.98%, and 98.45%, respectively. Y-STR variants, including null alleles, intermediate alleles and multi-allelic patterns, were also included. Moreover, Permutational Multivariate Analysis of Variance (PERMANOVA) and Principal Co-ordinates Analysis (PCoA)/classical multidimensional scale analysis (classical MDS) maps based on 17 Y-STRs revealed the unique genetic structure of each population. A joint analysis of Y-SNPs and Y-STRs clarified the evolutionary path of populations in the four districts. The results of haplotype network analysis showed that the Zhejiang Han population had more paternal genetic contributions to the formation of the Han populations in Shanghai's Qingpu, Songjiang, Jinshan, and Fengxian districts. In this study, through a joint analysis of Y-STRs and Y-SNPs, the paternal genetic structure of Han populations in four districts of Shanghai were explored in depth. The paternal origin of O1a in four districts of Shanghai may stem from population dispersal from the Zhejiang region. Applying Y-SNP haplogroups to forensic analyses can provide clues for familial investigations.