Convergence of Y Chromosome STR Haplotypes from Different SNP Haplogroups Compromises Accuracy of Haplogroup Prediction

Wang, Chuan‐Chao; Wang, Ling-Xiang; Shrestha, Rukesh; Wen, Shaoqing; Zhang, Manfei; Tong, Xin-Zhu; Jin, Li; Li, Hui

doi:10.1016/j.jgg.2015.03.008

Cited by 24 publications

(16 citation statements)

References 23 publications

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“…We used Haplogroup Predictor [ 45 ]to assign all Y-STR haplotypes to paternal haplogroups. Due to the possible convergence of Y-STR allele sizes in different NRY haplotypes [ 46 , 47 ], we confirmed the haplogroup predictions by genotyping the relevant diagnostic SNPs using custom TaqMan assays (see above). The Y-chromosome haplogroup frequencies were calculated by hand, while summary statistics were estimated using Arlequin v.3.11 software [ 48 ].…”

Section: Methodsmentioning

confidence: 56%

Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin

et al. 2015

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Historical discourses about the Caribbean often chronicle West African and European influence to the general neglect of indigenous people’s contributions to the contemporary region. Consequently, demographic histories of Caribbean people prior to and after European contact are not well understood. Although archeological evidence suggests that the Lesser Antilles were populated in a series of northward and eastern migratory waves, many questions remain regarding the relationship of the Caribbean migrants to other indigenous people of South and Central America and changes to the demography of indigenous communities post-European contact. To explore these issues, we analyzed mitochondrial DNA and Y-chromosome diversity in 12 unrelated individuals from the First Peoples Community in Arima, Trinidad, and 43 unrelated Garifuna individuals residing in St. Vincent. In this community-sanctioned research, we detected maternal indigenous ancestry in 42% of the participants, with the remainder having haplotypes indicative of African and South Asian maternal ancestry. Analysis of Y-chromosome variation revealed paternal indigenous American ancestry indicated by the presence of haplogroup Q-M3 in 28% of the male participants from both communities, with the remainder possessing either African or European haplogroups. This finding is the first report of indigenous American paternal ancestry among indigenous populations in this region of the Caribbean. Overall, this study illustrates the role of the region’s first peoples in shaping the genetic diversity seen in contemporary Caribbean populations.

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Section: Methodsmentioning

confidence: 56%

Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin

et al. 2015

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“…18 out of the 21 possible haplogroup assignments that could be made were observed in the combined dataset, hence pointing out to the high heterogeneity of the Northern Iraqi populations. However, it must be noted that without proper haplogroup assignments by Y-SNP typing, such in silico haplogroup assignments should be treated solely as preliminary findings since being based on Y-STR data alone, they may not always be accurate [ 34 ]. In other words, caution should always be exercised when making relevant conclusions based on such in silico produced data alone.…”

Section: Resultsmentioning

confidence: 99%

A glimpse at the intricate mosaic of ethnicities from Mesopotamia: Paternal lineages of the Northern Iraqi Arabs, Kurds, Syriacs, Turkmens and Yazidis

Doğan

Gürkan²,

Doğan

et al. 2017

PLoS ONE

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Widely considered as one of the cradles of human civilization, Mesopotamia is largely situated in the Republic of Iraq, which is also the birthplace of the Sumerian, Akkadian, Assyrian and Babylonian civilizations. These lands were subsequently ruled by the Persians, Greeks, Romans, Arabs, Mongolians, Ottomans and finally British prior to the independence. As a direct consequence of this rich history, the contemporary Iraqi population comprises a true mosaic of different ethnicities, which includes Arabs, Kurds, Turkmens, Assyrians, and Yazidis among others. As such, the genetics of the contemporary Iraqi populations are of anthropological and forensic interest. In an effort to contribute to a better understanding of the genetic basis of this ethnic diversity, a total of 500 samples were collected from Northern Iraqi volunteers belonging to five major ethnic groups, namely: Arabs (n = 102), Kurds (n = 104), Turkmens (n = 102), Yazidis (n = 106) and Syriacs (n = 86). 17-loci Y-STR analyses were carried out using the AmpFlSTR Yfiler system, and subsequently in silico haplogroup assignments were made to gain insights from a molecular anthropology perspective. Systematic comparisons of the paternal lineages of these five Northern Iraqi ethnic groups, not only among themselves but also in the context of the larger genetic landscape of the Near East and beyond, were then made through the use of two different genetic distance metric measures and the associated data visualization methods. Taken together, results from the current study suggested the presence of intricate Y-chromosomal lineage patterns among the five ethic groups analyzed, wherein both interconnectivity and independent microvariation were observed in parallel, albeit in a differential manner. Notably, the novel Y-STR data on Turkmens, Syriacs and Yazidis from Northern Iraq constitute the first of its kind in the literature. Data presented herein is expected to contribute to further population and forensic investigations in Northern Iraq in particular and the Near East in general.

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“…Males share the same Y‐chromosome haplotype that belongs to Q haplogroup (100% frequency with Haplogroup Predictor) and specifically to Q1a3a (Q‐M3) haplogroup (10% with Haplogroup & Haplo‐I Subclade Predictor). Despite the low percentage obtained with Cullen's predictor, this haplotype can be classified as Q‐M3 since it has been proposed that haplotypes belonging to Q‐M242 haplogroup can be predicted through STRs with high accuracy (Wang et al., ). Interestingly, no match was found among 2116 Native American haplotypes from YHRD or among 46 from the other pre‐Hispanic populations analyzed (Table S1), probably due to the rare allele 26 at DYS390.…”

Section: Resultsmentioning

confidence: 99%

Pre‐Hispanic Mortuary Practices in Quebrada de Humahuaca (North‐Western Argentina): Genetic Relatedness among Individuals Buried in the Same Grave

Russo

Mendisco

Avena

et al. 2016

Annals of Human Genetics

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Almost all pre-Hispanic societies from Quebrada de Humahuaca (north-western Argentina) buried their defuncts in domestic areas, demonstrating the importance of death and its daily presence among the living. Presumably, the collective graves contained related individuals, a hypothesis that can be tested through the study of ancient DNA. This study analyzes autosomal and uniparental genetic markers in individuals from two archaeological sites in Quebrada de Humahuaca occupied during the Late Formative (1450-1050 BP) and Regional Developments I (1050-700 BP) periods. Mitochondrial and Y-chromosome haplotypes were compared in order to establish possible maternal and paternal relatedness. Genotypes for 15 autosomal STRs were used to calculate pairwise relatedness coefficients and pedigree probabilities. High kinship levels among individuals buried in the same graves were found in both sites. Although only two particular cases were analyzed, these results represent an important contribution to the study of mortuary practices in the region by means of ancient DNA.

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Convergence of Y Chromosome STR Haplotypes from Different SNP Haplogroups Compromises Accuracy of Haplogroup Prediction

Cited by 24 publications

References 23 publications

Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin

Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin

A glimpse at the intricate mosaic of ethnicities from Mesopotamia: Paternal lineages of the Northern Iraqi Arabs, Kurds, Syriacs, Turkmens and Yazidis

Pre‐Hispanic Mortuary Practices in Quebrada de Humahuaca (North‐Western Argentina): Genetic Relatedness among Individuals Buried in the Same Grave

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