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

Abstract

<jats:p>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.</jats:p>

RETRACTED: Genetic structure and forensic characterization of 36 Y‐chromosomal STR loci in Tibeto‐Burman‐speaking Yi population

“…A neighbor‐joining (NJ) phylogenetic tree was constructed on the basis of the Rst genetic matrixes using the Molecular Evolutionary Genetics Analysis Version 6.0 (MEGA 6.0) (Tamura et al, 2013). The 67 reference groups included 22 Chinese populations (Fan et al, 2019; Gayden et al, 2012; Hu et al, 2017; Ji et al, 2017; Kim et al, 2001; Liu et al, 2019; Luo et al, 2019; Song et al, 2020; Sun et al, 2019; Tang et al, 2020; Xie et al, 2019; Yang et al, 2014; Yin et al, 2020; Zhang et al, 2017; Zhou et al, 2016) and 45 worldwide populations (Aliferi et al, 2018; D'Atanasio et al, 2019; Füredi et al, 1999; García et al, 2016; Hallenberg et al, 2005; Henry et al, 2019; Jankauskiene et al, 2017; Jankova et al, 2019; Pickrahn et al, 2016; Purps et al, 2014; Rapone et al, 2016; Shonhai et al, 2020; Spólnicka et al, 2017; Watahiki et al, 2019; Zgonjanin et al, 2017; Zhabagin et al, 2019) and the information about these groups are listed in Table .…”

Insights Into Forensic Features and Genetic Structures of Guangdong Maoming Han Based on 27 Y-STRs

“…From the intercontinental perspective, a MDS was performed between Maoming Han and 21 worldwide populations (Kim et al, 2001;Miranda et al, 2001;Roewer et al, 2005;Mizuno et al, 2008;Alam et al, 2010;Laouina et al, 2011;Wolfgramm Ede et al, 2011;Ramos-Luis et al, 2014;Xu et al, 2015;Han et al, 2016;Rapone et al, 2016;Wang et al, 2017;Alonso Morales et al, 2018;Fan et al, 2018c;Singh et al, 2018;Henry et al, 2019;Lang et al, 2019;Li et al, 2019;Salvador et al, 2019;Reid and Heathfield, 2020). As shown in Supplementary Figure 1, (Yang et al, 2014;Shu et al, 2015;Han et al, 2016;Wang et al, 2016Wang et al, , 2017Xu et al, 2016;Yao et al, 2016;Jiang et al, 2017;Chen et al, 2018;Fan et al, 2018c;Lang et al, 2019;Yin et al, 2020) are listed in Supplementary 2B). We found that two main branches could be clearly identified in the N-J phylogenetic tree.…”

Special Issue “Forensic Genetics and Genomics”

“…A number of papers on population genetics have been published in this Special Issue [ 8 , 9 , 10 , 11 , 12 ]. These findings are crucial as they determine the theoretical foundations of the studies on ancestral information and migration.…”

“…These findings are crucial as they determine the theoretical foundations of the studies on ancestral information and migration. These articles have, in fact, investigated some aspects of population genetics using different markers, such as ancestry informative single nucleotide polymorphisms (AISNPs) and markers located on the Y chromosome and mtDNA [ 8 , 9 , 10 , 11 , 12 ].…”

“…The article Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs reports a comparative study through the use of Y-STRs and low-resolution Y-SNPs in two Chinese populations—Shandong Han and Yunnan Han—to characterize the patrilineal patterns within these populations [ 11 ]. As a result, the phylogenetic reconstruction at an individual level, using a Y chromosome database, confirmed that Y-STRs combined with Y-SNPs can increase the power of discrimination of male pedigrees [ 11 ].…”