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Open AccessArticle

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

by 1,2,†, 1,2,†, 1,2, 3, 1,4, 3, 1,2,* and 5,6,*
1
Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
2
Human Phenome Institute, Fudan University, Shanghai 200438, China
3
Criminal Investigation Department of Yunnan Province, Kunming 650021, China
4
Public Security Bureau of Zibo City, Zibo 255000, China
5
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
6
Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2020, 11(7), 743; https://doi.org/10.3390/genes11070743
Received: 21 May 2020 / Revised: 30 June 2020 / Accepted: 2 July 2020 / Published: 3 July 2020
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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. View Full-Text
Keywords: population investigation; Y-STR; Y-SNP; population differentiation population investigation; Y-STR; Y-SNP; population differentiation
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MDPI and ACS Style

Yin, C.; Su, K.; He, Z.; Zhai, D.; Guo, K.; Chen, X.; Jin, L.; Li, S. Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs. Genes 2020, 11, 743. https://doi.org/10.3390/genes11070743

AMA Style

Yin C, Su K, He Z, Zhai D, Guo K, Chen X, Jin L, Li S. Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs. Genes. 2020; 11(7):743. https://doi.org/10.3390/genes11070743

Chicago/Turabian Style

Yin, Caiyong; Su, Kaiyuan; He, Ziwei; Zhai, Dian; Guo, Kejian; Chen, Xueyun; Jin, Li; Li, Shilin. 2020. "Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs" Genes 11, no. 7: 743. https://doi.org/10.3390/genes11070743

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