Confirmation of Y haplogroup tree topologies with newly suggested Y-SNPs for the C2, O2b and O3a subhaplogroups

Kwon, So Yeun; Lee, Hwan Young; Lee, Eun Young; Yang, Woo Ick; Shin, Kyoung Jin

doi:10.1016/j.fsigen.2015.06.003

Cited by 6 publications

(5 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To discern the detailed relationship between the Ha Hlai and other language‐speaking populations with different language families, we performed a PCA which included 193 populations (Cadenas, Zhivotovsky, Cavalli‐Sforza, Underhill, & Herrera, 2008; Cai et al, 2011; Chennakrishnaiah et al, 2013; Deng et al, 2013; Fan et al, 2020; Fan, Wang, Chen, Long, et al, 2018; Fan, Zhang, et al, 2018; Gan et al, 2008; Gayden et al, 2007; Khurana et al, 2014; Kwon, Lee, Lee, Yang, & Shin, 2015; Li, Wen, et al, 2008; Regueiro, Cadenas, Gayden, Underhill, & Herrera, 2006; Rowold et al, 2016, 2019; Wells et al, 2001; Wen et al, 2004) from all over the world with eight language families, 11,197 individuals in total (dataset 1). The PC1, PC2, and PC3 of the total variances accounted for 13.97%, 10.83%, and 8.91%, respectively.…”

Section: Resultsmentioning

confidence: 99%

RETRACTED: Forensic characteristics and phylogenetic analyses of one branch of Tai‐Kadai language‐speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia^™ Platinum System

Wang

et al. 2020

Molec Gen & Gen Med

View full text Add to dashboard Cite

show abstract

Section: Resultsmentioning

confidence: 99%

RETRACTED: Forensic characteristics and phylogenetic analyses of one branch of Tai‐Kadai language‐speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia^™ Platinum System

Wang

et al. 2020

Molec Gen & Gen Med

View full text Add to dashboard Cite

show abstract

“…Additional population data of newly discovered Y-SNPs still remains necessary to obtain as Y-SNP expansion gives rise to some complications. First, universal names for Y-SNPs are non-existing, meaning that equality and comparisons between studies and different phylogenetic trees remain extremely difficult to achieve [ 55 ]. For example, the Y-SNP R-L11 has also been described as R-S127 and R-PF6539 .…”

Section: Discussionmentioning

confidence: 99%

“…Second, many Y-SNPs are already mapped in a phylogenetic tree despite the lack of large-scale population data. Consequently, their position on the phylogenetic tree is deceitful and cannot be used as additional biogeographical background information [ 2 , 55 , 56 ]. For 183 Y-SNPs, a combination between ancestral and derivative alleles was observed within our samples indicating that these markers exhibit larger diversity within the population of the Low Countries (Belgium and the Netherlands).…”

Section: Discussionmentioning

confidence: 99%

CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics

et al. 2021

View full text Add to dashboard Cite

Male-specific Y-chromosome (chrY) polymorphisms are interesting components of the DNA for population genetics. While single nucleotide polymorphisms (Y-SNPs) indicate distant evolutionary ancestry, short tandem repeats (Y-STRs) are able to identify close familial kinships. Detailed chrY analysis provides thus both biogeographical background information as paternal lineage identification. The rapid advancement of high-throughput massive parallel sequencing (MPS) technology in the past decade has revolutionized genetic research. Using MPS, single-base information of both Y-SNPs as Y-STRs can be analyzed in a single assay typing multiple samples at once. In this study, we present the first extensive chrY-specific targeted resequencing panel, the ‘CSYseq’, which simultaneously identifies slow mutating Y-SNPs as evolution markers and rapid mutating Y-STRs as patrilineage markers. The panel was validated by paired-end sequencing of 130 males, distributed over 65 deep-rooted pedigrees covering 1,279 generations. The CSYseq successfully targets 15,611 Y-SNPs including 9,014 phylogenetic informative Y-SNPs to identify 1,443 human evolutionary Y-subhaplogroup lineages worldwide. In addition, the CSYseq properly targets 202 Y-STRs, including 81 slow, 68 moderate, 27 fast and 26 rapid mutating Y-STRs to individualize close paternal relatives. The targeted chrY markers cover a high average number of reads (Y-SNP = 717, Y-STR = 150), easy interpretation, powerful discrimination capacity and chrY specificity. The CSYseq is interesting for research on different time scales: to identify evolutionary ancestry, to find distant family and to discriminate closely related males. Therefore, this panel serves as a unique tool valuable for a wide range of genetic-genealogical applications in interdisciplinary research within evolutionary, population, molecular, medical and forensic genetics.

show abstract

“…To clear up the detailed relationship between the Lhasa € U-Tsang Tibetan population and other populations with diverse language families, the PCA was performed among 194 populations (in total 10 721 individuals) which included Austro-Asiatic, Austronesian, Altaic, Semito-Hamitic, Caucasian, Uralic, Dravidian, Indo-European, Tai-Kadai, Hmong-Mien, Tibeto-Burman, and Chinese (Southern and Northern Han) populations all over the world [37][38][39][40][41][42][43][44][45][46][47][48][49][50]. We used our in-house dataset, including 37 754 pieces of Y SNP/STR data and 109 142 Y-STR in total which mainly from Asia, to make predictions for Lhasa € U-Tsang Tibetan in this study [51].…”

Section: Y-haplogroup Estimationmentioning

confidence: 99%

Genetic polymorphisms and phylogenetic analyses of the Ü-Tsang Tibetan from Lhasa based on 30 slowly and moderately mutated Y-STR loci

Ding

Fan

Zhou

et al. 2020

Forensic Sciences Research

View full text Add to dashboard Cite

As a result of the expansion of old Tibet on the Qinghai-Tibet Plateau, Tibetans diverged into three main branches, € U-Tsang, Amdo, and Kham Tibetan. € U-Tsang Tibetans are geographically distributed across the wide central and western portions of the Qinghai-Tibet Plateau while Lhasa is the central gathering place for Tibetan culture. The AGCU Y30, a 6dye fluorescence kit including 30 slowly and moderately mutated Y-STR loci, has been validated for its stability and sensitivity in different biomaterials and diverse Chinese populations (Han and other minorities), and widely used in the practical work of forensic science. However, the 30 Y-STR profiling of Tibetan, especially for € U-Tsang Tibetan, were insufficient. We utilized the AGCU Y30 to genotype 577 € U-Tsang Tibetan unrelated males from Lhasa in the Tibet Autonomous Region of China to fill up the full and accurate Y-STR profiles. A total of 552 haplotypes were observed, 536 (97.10%) of which were unique. One hundred and ninety-four alleles were observed at 26 single copy loci and the allelic frequencies ranged from 0.0017 to 0.8180. For the two multi-copy loci DYS385a/b and DYS527a/b, 64 and 36 allelic combinations were observed, respectively. The gene diversity (GD) values ranged from 0.3079 at DYS391 to 0.9142 at DYS385a/b and the overall haplotype diversity (HD) was 0.9998, and its discrimination capacity (DC) was 0.9567. The population genetic analyses demonstrated that Lhasa € U-Tsang Tibetan had close relationships with other Tibetan populations from Tibet and Qinghai, especially with € U-Tsang Tibetan. From the perspective of Y haplogroups, the admixture of the southward Qiang people with dominant haplogroup O-M122 and the northward migrations of the initial settlers of East Asia with haplogroup D-M175 hinted the Sino-Tibetan homologous, thus, we could not ignore the gene flows with other Sino-Tibetan populations, especially for Han Chinese, to characterize the forensic genetic landscape of Tibetan.

show abstract

Confirmation of Y haplogroup tree topologies with newly suggested Y-SNPs for the C2, O2b and O3a subhaplogroups

Cited by 6 publications

References 20 publications

RETRACTED: Forensic characteristics and phylogenetic analyses of one branch of Tai‐Kadai language‐speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia^™ Platinum System

RETRACTED: Forensic characteristics and phylogenetic analyses of one branch of Tai‐Kadai language‐speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia^™ Platinum System

CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics

Genetic polymorphisms and phylogenetic analyses of the Ü-Tsang Tibetan from Lhasa based on 30 slowly and moderately mutated Y-STR loci

Contact Info

Product

Resources

About

Confirmation of Y haplogroup tree topologies with newly suggested Y-SNPs for the C2, O2b and O3a subhaplogroups

Cited by 6 publications

References 20 publications

RETRACTED: Forensic characteristics and phylogenetic analyses of one branch of Tai‐Kadai language‐speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia™ Platinum System

RETRACTED: Forensic characteristics and phylogenetic analyses of one branch of Tai‐Kadai language‐speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia™ Platinum System

CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics

Genetic polymorphisms and phylogenetic analyses of the Ü-Tsang Tibetan from Lhasa based on 30 slowly and moderately mutated Y-STR loci

Contact Info

Product

Resources

About

RETRACTED: Forensic characteristics and phylogenetic analyses of one branch of Tai‐Kadai language‐speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia^™ Platinum System

RETRACTED: Forensic characteristics and phylogenetic analyses of one branch of Tai‐Kadai language‐speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia^™ Platinum System