Intra- and inter-population analysis of haplotype diversity in Yfiler ® Plus system using a wide set of representative data from Polish population

Spólnicka, Magdalena; Dąbrowska, Joanna; Szabłowska-Gnap, Emilia; Pałeczka, Anna; Jabłońska, Magdalena; Zbieć-Piekarska, Renata; Pięta, Anna; Boroń, Michał; Konarzewska, Magdalena; Kostrzewa, Grażyna; Płoski, Rafał; Rogalla, Urszula; Woźniak, Marcin; Grzybowski, Tomasz

doi:10.1016/j.fsigen.2017.01.014

Cited by 14 publications

(10 citation statements)

References 16 publications

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“…A high level of similarity between both datasets is visible; however, lack of prediction for 140 samples (>25% of the studied sample set) seems to be the main reason for the inconsistencies found. One of those is the overrepresentation of haplogroup R1a [56.93 vs. 68.6%-haplogroup prediction based on Spolnicka et al (2017)] and the remaining-the underrepresentation of hg I [15.71 vs. 6.8%-haplogroup prediction based on Spolnicka et al (2017)]. The frequencies of some of the remaining haplogroups predicted (R1b, N, G, Q) are consistent with our findings.…”

Section: Interpopulation Variability Of Y Chromosomesupporting

confidence: 89%

“…As an insight into the most recent Polish population, we performed a haplogroup prediction based on 496 27-Y-STR haplotypes published in 2017 by Spolnicka et al (2017). A high level of similarity between both datasets is visible; however, lack of prediction for 140 samples (>25% of the studied sample set) seems to be the main reason for the inconsistencies found.…”

Section: Interpopulation Variability Of Y Chromosomementioning

confidence: 99%

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Y-Chromosome Genetic Analysis of Modern Polish Population

et al. 2020

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The study presents a full analysis of the Y-chromosome variability of the modern male Polish population. It is the first study of the Polish population to be conducted with such a large set of data (2,705 individuals), which includes genetic information from inhabitants of all voivodeships, i.e., the first administrative level, in the country and the vast majority of its counties, i.e., the second level. In addition, the available data were divided into clusters corresponding to more natural geographic regions. Genetic analysis included the estimation of F ST distances, the visualization with the use of multidimensional scaling plots and analysis of molecular variance. Y-chromosome binary haplogroups were classified and visualized with the use of interpolation maps. Results showed that the level of differentiation within Polish population is quite low, but some differences were indicated. It was confirmed that the Polish population is characterized by a high degree of homogeneity, with only slight genetic differences being observed at the regional level. The use of regional clustering as an alternative to counties and voivodeships provided a more detailed view of the genetic structure of the population. Those regional differences identified in the present study highlighted the need for additional division of the population by cultural and ethnic criteria in such studies rather than just by geographical or administrative regionalization.

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Section: Interpopulation Variability Of Y Chromosomesupporting

confidence: 89%

Section: Interpopulation Variability Of Y Chromosomementioning

confidence: 99%

Y-Chromosome Genetic Analysis of Modern Polish Population

et al. 2020

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“…Duplications at DYF387S1 produced two instances of tri-allelic 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: Resultssupporting

confidence: 73%

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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Intra- and inter-population analysis of haplotype diversity in Yfiler ® Plus system using a wide set of representative data from Polish population

Cited by 14 publications

References 16 publications

Y-Chromosome Genetic Analysis of Modern Polish Population

Y-Chromosome Genetic Analysis of Modern Polish 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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