Abstract
Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.
Highlights
Y chromosomal short tandem repeats (Y-STRs) refer to simple repeats of a 2–6 bp spreading across the Y chromosome and are a set of polymorphic genetic markers in linkage
Determined by the genetic make-up of various Han populations, Han populations were divided into northern Han, central Han, and southern Han [9], which is nearly consistent with their geographic locations in latitude
In order to dissect the genetic structure of male populations, co-analysis of Y-STR and Y-single-nucleotide polymorphisms (SNPs) was conducted for diverse populations [10,11,12,13,14,15,16,17] but not for the majority of Chinese Han populations
Summary
Y chromosomal short tandem repeats (Y-STRs) refer to simple repeats of a 2–6 bp spreading across the Y chromosome and are a set of polymorphic genetic markers in linkage. They are used in practical work for forensic purposes, such as paternity tests [1], criminal detections [2], and body identifications in natural disasters [3]. In order to dissect the genetic structure of male populations, co-analysis of Y-STR and Y-SNP was conducted for diverse populations [10,11,12,13,14,15,16,17] but not for the majority of Chinese Han populations. Preliminary comparative studies were conducted by genotyping commonly used Y-STRs and low-resolution Y-SNPs in two Chinese populations—Shandong
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