Polymorphisms and microvariant sequences in the Japanese population for 25 Y-STR markers and their relationships to Y-chromosome haplogroups

Watahiki, Haruhiko; Fujii, Koji; Fukagawa, Takashi; Mita, Yusuke; Kitayama, Tetsushi; Mizuno, Natsuko

doi:10.1016/j.fsigen.2019.03.004

Cited by 23 publications

(14 citation statements)

References 35 publications

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“…This study undertook molecular linkage analysis of major surnames among Japanese men with Y chromosomal polymorphisms. The Y-STR network of samples was consistent with recent observations of the Japanese population, in which Y-SNP haplogroups were biased on the divergent distribution of Y-STR haplotypes, as reported by Watahiki et al [27]. The combination of Y-STR haplotype with Y-SNP haplogroup provided a high-resolution network structure of the phylogeny of bearers [6].…”

Section: Discussionsupporting

confidence: 89%

Y chromosome analysis for common surnames in the Japanese male population

et al. 2021

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For many years of Japan's long history, Japanese surnames have been handed down patrilineally. This study investigated relations between major surnames and Y chromosomal polymorphism among the Japanese male population. To analyze genetic phylogeny in namesakes, the Y-single nucleotide polymorphism (SNP) plus Y-short tandem repeat (STR) approach was employed. A haplogroup based on SNPs and haplotypes at 17 STR loci were typed in 567 unrelated volunteers recruited in Kanagawa, Japan. Samples covered 27 common surnames such as Satoh and Suzuki, each name having 10-55 bearers. Significant difference was found for SNP haplogroup compositions and a multidimensional scaling plot using STR haplotypes in several surname groups. By contrast, these common surnames displayed wide diversity with phylogenetic networks, suggesting that no genetic drift event has occurred in their history. In all, 22 descent clusters were found, as judgcriteria ed by ad hoc of groups within five mutational steps in the 15 STR loci with the same haplogroup. The times of the most recent common ancestor ranged from 279 to over 2577 years. According to the approximate millennium span of Japanese surname history, descent criteria are expected to be reasonable for grouping within four step-neighbors. High heterogeneity of common surnames resembles that observed for England and Spain, but not for Ireland. Our results highlight that common Japanese surnames consist of descent clusters and many singletons, reflecting a mixture of long-term bearers and short-term bearers among the population. The genetic study of this population revealed characteristic features of Japanese surnames.

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Section: Discussionsupporting

confidence: 89%

Y chromosome analysis for common surnames in the Japanese male population

et al. 2021

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“…Duplications at DYF387S1 produced two instances of triallelic patterns similar to those reported in several populations (Ye et al 2015;Pickrahn et al 2016;Wang et al 2016;Iacovacci et al 2017;Spólnicka et al 2017;Watahiki et al 2019). In one predicted haplogroup J1a male the alleles 36, 37 and 38 were all detected with equal strength implying an equal copy number, as would be seen if just one DYF387S1 copy had been duplicated.…”

Section: Y-str Allele and Haplotype Diversitysupporting

confidence: 79%

Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs

et al. 2020

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We have determined the distribution of Y-chromosomal haplotypes and predicted haplogroups in the ethnically diverse Kingdom of Bahrain, a small archipelago in the Arabian Gulf. Paternal population structure within Bahrain was investigated using the 27 Y-STRs (short tandem repeats) in the Yfiler Plus kit to generate haplotypes from 562 unrelated Bahraini males, sub-divided into four geographical regions—Northern, Capital, Southern and Muharraq. Yfiler Plus provided a significant improvement over the 17-locus Yfiler kit in discrimination capacity (from 77% to 87.5% overall), but discrimination capacity differed widely between regions from 98.4% in Muharraq to 75.2% in the Northern region, an unusually low value possibly resulting from recent rapid population expansion. Clusters of closely related male lineages were seen, with only 79.4% of donors displaying unique haplotypes and 59% of instances of shared haplotypes occurring within, rather than between, regions. Haplogroup prediction indicated diverse origins of the population with a predominance of haplogroups J2 and J1, both typical of the Arabian Peninsula, but also haplogroups such as B2 and E1b1a likely originating in Africa, and H, L and R2 likely indicative of migration from South Asia. Haplogroup frequencies differed significantly between regions, with J2 significantly more common in the Northern region compared with the Southern, possibly due to differential settlement by Baharna and Arabs. Our study shows that paternal lineage population structure can exist even over small geographical scales, and that highly discriminating genetic tools are required where rapid expansions have occurred within tightly bounded populations.

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“…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 .…”

Section: Methodsmentioning

confidence: 99%

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

Song

Wang²,

Zhang

et al. 2021

Molec Gen & Gen Med

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Background Male‐specifically inherited Y‐STRs have been widely used in population genetics and forensic investigations. Methods We genotyped and analyzed Y chromosome haplotypes of 408 unrelated Tibeto‐Burman‐speaking Yi male individuals from Guizhou using Goldeneye® Y‐PLUS kit. Population comparisons between the Guizhou Yi and 67 reference groups were performed via the AMOVA, MDS, and phylogenetic relationship reconstruction. Results A total of 389 alleles and 396 haplotypes could be detected, and the allelic frequencies ranged from 0.0025 to 0.9875. The haplotype diversity, random match probability, and discrimination capacity values were 0.9999, 0.0026, and 0.9900, respectively. The gene diversity (GD) of 36 Y‐STR loci in the studied group ranged from 0.0248 (DYS645) to 0.9601 (DYS385a/b). Our newly genotyped Yi samples show a close affinity with other Tibeto‐Burman speaking groups in China and Southeast Asia. Conclusions The population stratification was almost consistent with the geographic distribution and language‐family, both among Chinese and worldwide ethnic groups. Our data may provide useful information for paternal lineage in the forensic application and population genetics, as well as evidence for archaeological and historical research.

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Polymorphisms and microvariant sequences in the Japanese population for 25 Y-STR markers and their relationships to Y-chromosome haplogroups

Cited by 23 publications

References 35 publications

Y chromosome analysis for common surnames in the Japanese male population

Y chromosome analysis for common surnames in the Japanese male population

Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs

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

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