Human Y Chromosome Research Articles

Results of determination of the Y-DNA haplogroup for an individual from the Nikultsinsky burial ground of the Gavrilov-Yamsky district of the Yaroslavl region

The purpose of the study of this article is to establish, through DNA analysis, the Y-chromosome haplogroup of an ancient burial found within the location of the famous Nikultsinsky burial ground (Fatyanovo culture) in the Gavrilov-Yamsky district of the Yaroslavl region on the right-bank plateau of the Vondel river. The article describes the archaeological context and the history of the site discovery. The predicted belonging of the individual to the Y-haplogroup R1a and the observed borderline position of the haplotype between the variants R1a-Z280 and R1a-Z93 does not allow rejecting the hypothesis that the described remains belong to the Fatyanovo culture of the Bronze Age III-II thousand BC. At the moment, Y-haplotypes of carriers of the Fatyanovo culture have not yet been cited in scientific articles. Only one work is known in which SNPs of a "high level" were given, which is not enough to identify the genesis and connections of the Fatyanovo culture. In addition, the task of dating and archaeological attribution of the described burial found within the Nikultsinsky burial ground in the zone of its destruction is important. This is due to the fact that the Fatyanovo burials are rare and of high scientific value. The resulting data on the Y-STR haplotype does not contradict the results obtained earlier, and does not allow us rejecting the hypothesis about the Fatyanovo character of this burial.

Microhaplotype and Y-SNP/STR (MY): A novel MPS-based system for genotype pattern recognition in two-person DNA mixtures

BackgroundsY-chromosomal haplotypes based on Y-short tandem repeats (STRs) and Y-single nucleotide polymorphisms/insertion and deletion polymorphisms (SNPs/InDels) are used to characterize paternal lineages of unknown male trace donors. However, Y-chromosomal genetic markers are not currently sufficient for precise individual identification. Microhaplotype (MH), generally < 200 bp on autosomes and consisting of two or more SNPs, was recently introduced in forensic genetics with the development of massive parallel sequencing technology and may facilitate identification and DNA mixture deconvolution. Therefore, combining the two kinds of genetic markers may be beneficial in many forensic scenarios, especially crime scenes with male suspects, such as sexual assault cases. MethodsIn the present study, we developed a novel MPS-based panel, Microhaplotype and Y-SNP/STR (MY), by multiplex PCR and 150-bp paired-end sequencing, including 114 Y-SNPs (twelve dominant Y-DNA haplogroups), 45 Y-STRs (N-1 stutter < 0.09; estimated mutation rate < 5 × 10−3), and 22 MHs (allele coverage ratio > 0.91; pairwise distance > 10 Mb). Additionally, MY system-based genotype pattern recognition (GPR), a regression-based method to identify the genotype pattern for each MH locus, is proposed for two-person DNA mixture deconvolution. We integrated 26 two-person genotype combinations into nine genotype patterns and validated the application range of GPR based on DNA profiles of ten sets of simulated male-male DNA mixtures (1:10–1:2). ResultsThe effective number of alleles (Ae) ranged from 3.62 to 14.72, with an average of 7.17, in 100 Chinese Guangdong Han individuals. The cumulative discrimination power was 1–5.00 × 10−31, and the cumulative power of exclusion was 1–5.00 × 10−8 and 1–4.85 × 10−12 for duo and trio paternity testing, respectively. Furthermore, the actual mixing ratio-depth of coverage (DoC) ratio (RDoC) regression relationships were established for different genetic markers and genotype patterns. In five overlapping areas, genotype differentiation of the major and minor contributors required likelihood ratio methods. In nonoverlapping areas, the genotype pattern could be recognized by comparing the observed RDoC and RDoC ranges. ConclusionThe GPR can be used to deconvolute two-person DNA mixtures (application range: 1:10–1:2) for individual identification.

Sheep Post-Domestication Expansion in the Context of Mitochondrial and Y Chromosome Haplogroups and Haplotypes.

Mitochondrial DNA and nonrecombinant parts of Y-chromosome DNA are a great tool for looking at a species’ past. They are inherited for generations almost unaffected because they do not participate in recombination; thus, the time of occurrence of each mutation can be estimated based on the average mutation rate. Thanks to this, male and female haplogroups guide confirming events in the distant past (potential centers of domestication, settlement of areas, trade connections) as well as in modern breeding (crossbreeding, confirmation of paternity). This research focuses mainly on the development of domestic sheep and its post-domestication expansion, which has occurred through human trade from one continent to another. So far, five mitochondrial and five Y-chromosome haplogroups and dozens of their haplotypes have been detected in domestic sheep through studies worldwide. Mitochondrial DNA variability is more or less correlated with distance from the domestication center, but variability on the recombinant region of the Y chromosome is not. According to available data, central China shows the highest variability of male haplogroups and haplotypes.

THE NEED FOR OPTIMUM NUTRITIONAL STRATEGIES FOR CARDIOVASCULAR HEALTH IN PAKISTANI POPULATION

THE NEED FOR OPTIMUM NUTRITIONAL STRATEGIES FOR CARDIOVASCULAR HEALTH IN PAKISTANI POPULATION

Identification and assessment of a subset of Y-SNPs with recurrent mutation for forensic purpose

Y chromosome has an important role in the forensic practice due to its unique paternal inheritance pattern. Y-chromosomal single nucleotide polymorphisms (Y-SNPs) could provide supplementary information while the application of Y-chromosomal STR (Y-STR) haplotypes encounter their limitations. Y-SNPs with recurrent mutation can be seen in different Y-chromosomal haplogroups, which might help discriminate different paternal pedigrees. In this study, a host of candidate Y-SNPs with recurrent mutation were obtained based on population data from 1000 Genome Project. Further, 8 Y-SNPs from a small part of candidates were confirmed to be polymorphic in 2 or more Y-chromosomal haplogroups (sub-haplogroups) in the Chinese Han population. With a haplotype diversity value of 0.9367, the investigated subset of Y-SNPs with recurrent mutation shows a high discrimination power. Therefore, Y-SNPs with recurrent mutation should function as useful markers to provide information in the forensic applications.

Archaeological DNA Data from the XII-XIV Centuries from Ancient Klyazma Settlements

PaleoDNA testing is becoming one of the most complex areas of modern biotechnology. Modern technologies make it possible to qualitatively extract DNA and test it by various methods, including the determination of the Y-chromosome haplogroup and mitochondrial DNA. The paper describes the results of determining the Y-DNA haplogroups of two ancient burial sites of the XII-XIV centuries from the middle course of the Klyazma. The data obtained make it possible to determine the Y-haplogroup by the markers identified in the study. The article describes the technology using bioinformatics methods and the result obtained, which with high probability determines the Y-haplogroups R1a-M458-L1029 and I1-Z58. This work summarizes the initial stage of research undertaken in 2019-2020. The first evidence of the presence of R1a-M458 and I1-Z58 among the Klyazma population of Northeastern Russia in the XII-XIV centuries not only supports the point of view of the presence of Y-haplogroup R1a for all medieval Russian lands (inhabited by descendants of Eastern Slavs), but also hints that a certain genetic unity with the western parts of the area of the Slavs may exist (since the most serious concentrations of R1a-M458 and I1-Z58 are observed in the western part of the Slavic area).

Molecular Diagnosis of Y-Chromosome Microdeletions in Some Kurdish Infertile Males: EAA/EMQN PCR Protocol Optimization.

Molecular Diagnosis of Y-Chromosome Microdeletions in Some Kurdish Infertile Males: EAA/EMQN PCR Protocol Optimization.

Human Y-chromosome data for the paper "Placing ancient DNA sequences into reference phylogenies"

Human Y-chromosome data for the paper "Placing ancient DNA sequences into reference phylogenies"

Development a multiplex panel of AISNPs, multi-allelic InDels, microhaplotypes, and Y-SNP/InDel loci for multiple forensic purposes via the NGS.

Recently, next generation sequencing has shown the promising application value in forensic research. In this study, we constructed a multiplex amplification system of different molecular genetic markers based on the previous selected ancestry informative single nucleotide polymorphisms (SNPs), multi-allelic insertion/deletion (InDel) polymorphisms, microhaplotypes, and Y-chromosomal SNP/InDel loci, and evaluated forensic efficiencies of the system in Chinese Shaanxi Han, Chinese Hui, and Chinese Mongolian groups via the next generation sequencing platform. Ancestry information analyses of Shaanxi Han, Hui, and Mongolian groups revealed that most Mongolian individuals could be differentiated from Shaanxi Hans and Huis based on the selected ancestry informative SNPs. Multi-allelic InDels and microhaplotypes showed the multiple allele variations and possessed relatively high genetic polymorphisms in these three groups, indicating these loci could provide higher forensic efficiencies for individual identification and paternity testing. Based on Y-chromosomal SNPs, different haplogroup distributions were observed among Shaanxi Han, Hui, and Mongolian groups. In conclusion, the self-developed system could be used to simultaneously carry out the individual identification, paternity analysis, mixture deconvolution, forensic ancestry information analysis, and Y-chromosomal haplogroup inference, which could provide more valuable investigative clues in forensic practices.

A mutation modulating DDX3Y gene expression cosegregates with the major Y-chromosomal haplogroups and with testis size in Hu sheep.

Variations in the Y-chromosome are usually correlated with male-specific traits. However, this condition has been described only sporadically, even in human genetics. The present study was conducted to clone the full-length gene sequence of ovine DEAD-box helicase 3, Y-linked (DDX3Y), and investigate the effect of the expression and variation of DDX3Y on the reproductive traits of Hu sheep. Consequently, we identified the full coding sequence and genomic sequence of ovine DDX3Y. Quantitative PCR (qPCR) analysis showed that ovine DDX3Y was highly expressed in testis, and the expression level increased during testicular development. Furthermore, individuals with larger testis at 6months expressed significantly more DDX3Y mRNA in the testis than individuals with smaller testis. Notably, a novel SNP (g. 12657 C>A) in the 3' untranslated region was identified in Hu sheep and Tan sheep according to the investigation of the full DDX3Y genomic sequence of 1069 individuals from nine sheep breeds. Association analysis revealed that the SNP was significantly related to testis size in Hu sheep. Meanwhile, Hu rams with the derived C allele showed significantly higher expression levels of DDX3Y in testis than those with the ancestral A allele. In addition, data mining in a previous study showed that the C allele cosegregated with the globally major Y-chromosomal haplogroups y-HA and y-HC, and the A allele is found in all rams with haplogroups y-HB1, y-HB2 and y-HD. This study suggests that the association of the Y-chromosomal haplogroups with testis size in Hu sheep can be extrapolated to the sheep population worldwide.

A Genetic Variation in the Y Chromosome Among Modern Japanese Males Related to Several Physiological and Psychological Characteristics.

Previous studies in population genetics have proposed that the Y-chromosomal (Y-DNA) haplogroup D ancestor likely originated from Africa. The haplogroup D branch next started Out-of-Africa migration, rapidly expanded across Eurasia, and later diversified in East Asia. Y-DNA haplogroup D-M55, one of the branches of haplogroup D, is only found in modern Japanese males, suggesting that individuals with Y-DNA haplogroup D migrated from the Eurasian continent. Based on previous observations, Y-DNA haplogroup D is expected to be associated with some male characteristics including personality. Therefore, this study investigated whether the Y-DNA haplogroup D-M55 is associated with several physiological and psychological characteristics, including exploratory motivation and human relationship-related perception. We recruited Japanese young adult males and females and investigated the association between Y-DNA haplogroup D-M55, physiological [body mass index (BMI)], and several psychological parameters [perceived number of close friends, behavioral inhibition system/behavioral activation system (BIS/BAS), perceived happiness, and perceived loneliness]. The results indicated that males with haplogroup D-M55 had a higher BMI and more close friends, compared with non-carrier males. Additional multiple regression analyses, which tested the hypothesis that haplogroup D-M55 predicts BMI and perceived number of close friends, confirmed our hypothesis, even after controlling for the potentially confounding variables of age and sex. We also analyzed the gene–gene interaction between haplogroup D-M55 and an autosomal gene polymorphism associated with BMI and human relationships, such as the dopamine D2 receptor gene (DRD2: rs1800497). Results showed gene–gene interactions between haplogroups D-M55 and DRD2 in BMI. Based on these findings, it is demonstrated that Y-DNA haplogroup D is associated with human personality.

Средневековый генофонд Водской земли Великого Новгорода

The DNA of 17 individuals of the 12th—15th centuries from the burial grounds of Teglitsa I and II, Ratchino I, Velikino was studied. There were identified Y-chromosomal haplogroups of 12 males, mitochondrial haplogroups of 12 males and females. In the genetic structure of the population of the Izhora plateau, the presence of three Y-chromosomal haplogroups, confined to certain sites, was identified. Individuals from Teglitsa I belong to haplogroup E1b1b1a1b (V13), from the Teglitsa II to R1a1a1b1a (Z282), individuals with haplogroup N1a1 (M46) have been identified in Velikino. In Ratchino I, three haplogroups were identified: N1a1 (M46), N1a1a1a1a (CTS2929), E1b1b1a1b (V13). Phylogenetic networks built on the basis of STR haplotypes of the Y chromosome for haplogroup N1a (M46) showed the genetic proximity of the medieval collectives from Ratchino I and Velikino to the modern populations of the Baltic-Finnish peoples. A surprise was the good representation in Teglitsa and Ratchino of the haplogroup E1b1b1a1b (V13), which has a predominantly Carpathian-Balkan distribution. The study of mitochondrial DNA showed a high diversity of female lines and the absence of their confinement to certain sites. Among the mt-DNA haplogroups of archaeological individuals of the Izhora plateau, there are Western Eurasian and Eastern Eurasian haplogroups, however, most haplogroups belong to Western Eurasian — H2a2a1, U5a, U5b, J1c, J1b1a, T2b, K1, and only two Eastern Eurasian — W6 and D4g2.

Paternal Origins of Mongolic-Speaking Populations: A Review of Studies from Recent Decades (1999–2019) and Their Implications for Multidisciplinary Research in the Future

abstract: The activities of Mongolic-speaking populations, a large group of people in eastern Eurasia, have important impacts on the history of East Asia and other parts of Eurasia. Most previous genetic research of East Asian populations, including ancient DNA studies, has involved samples from Mongolic-speaking populations or their ancient relatives. This review summarizes frequency data of paternal Y-chromosome haplogroups from all available literature about Mongolic-speaking populations from 1999 to 2019. Fourteen paternal components were identified, and six of them are proposed as major and common components in ancestor groups of Mongolic-speaking populations. The article thoroughly discusses the possible origin, migration patterns, and the roles of these six components in the evolutionary history of Mongolic-speaking populations, as well as implications of present achievements in human genetics for future multidisciplinary research in ethnology, history, archaeology, and linguistics.

Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

Haplogroup Prediction Using Y-Chromosomal Short Tandem Repeats in the General Population of Bosnia and Herzegovina.

Human Y-chromosomal haplogroups are an important tool used in population genetics and forensic genetics. A conventional method used for Y haplogroup assignment is based on a set of Y-single nucleotide polymorphism (SNP) markers deployed, which exploits the low mutation rate nature of these markers. Y chromosome haplogroups can be successfully predicted from Y-short tandem repeat (STR) markers using different software packages, and this method gained much attention recently due to its labor-, time-, and cost-effectiveness. The present study was based on the analysis of a total of 480 adult male buccal swab samples collected from different regions of Bosnia and Herzegovina. Y haplogroup prediction was performed using Whit Athey’s Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex® Y23 kit. The results revealed the existence of 14 different haplogroups, with I2a, R1a, and E1b1b being the most prevalent with frequencies of 43.13, 14.79, and 14.58%, respectively. Compared to the previously published studies on Bosnian-Herzegovinian population based on Y-SNP and Y-STR data, this study represents an upgrade of molecular genetic data with a significantly larger number of samples, thus offering more accurate results and higher probability of detecting rare haplogroups.

К вопросу о самодийском субстрате в генофонде коренного населения Южной Сибири: филогеография Y-хромосомной гаплогруппы N-L666

We studied the diversity of Y-chromosomal haplogroup N-L666 in Southern Siberia, where this lineage itself is an approximate equivalent to N2-P43. The whole sample included 590 representatives of western, central, southern, southeastern and northeastern (Tojin) Tuvans, who identified themselves as one of 21 tribal groups, as well as Tofalars. The N-L666 subsample consisted of 138 individuals and was studied using 15 STR markers in two scales: local (considering the areal groups and tribal clans of Tuvans) and regional (in comparison with the populations of Southern and Western Siberia). Results. Two clusters of N-L666 STR haplotypes were identified: cluster A, specific for Tuvans and Tofalars (covering 19% and 16% of their gene pools respectively) and cluster B, widely scattered throughout Siberia from the West to the Transbaikalia (reaching ~30% in Tofalars). The ubiquity and a greater age of the cluster B favor the idea of its origin in the ancestral population – the ultimate source of the haplogroup N-L666 in Siberia – commonly alleged to be Samoyedic by language. On the contrary, the narrow geographic range and a relatively recent age of the cluster A indicate its formation in the area inhabited by Tuvans and Tofalars during the last thousand years. The emergence of subclusters A1, A2, B1 may be the result of demographic growth in the populations of Tuvans, southern Altaians and Khakas about 300-450 years ago. The spread of the same haplotypes, clusters and subclusters among different regional groups and clans of Tuvans indicates a common source of haplogroup N-L666 for them, which existed in the gene pool long before the separation of the studied populations. Conclusions. A specific cluster of haplogroup N-L666 in Tuvans was presumably founded by a representative of one of the Samoyedic tribes, whose numerous descendants participated in the formation of the Tuvans, Tofalars and southern Altaians over the last thousand years.

Sequencing and comparative genome analysis of three Indians.

Remarkable advancement in DNA sequencing (NGS) technology has made personal genome analysis feasible and affordable. Here we present the whole genome sequencing and analysis of three individuals, two males and one female, from different parts of India. Comparison with the Reference Human Genome and the variant database showed a total of 4.0-4.85 million variants, primarily single nucleotide variants (SNVs), 350-600K small insertions and deletions (INDELs), and previously unreported novel variants. The analysis of Y-chromosome and mitochondrial haplogroups revealed that the ancestors of the individual arrived on the subcontinent at very different times using distinctly different migration routes. Approximately, 500,000 novel SNPs and about 89,000 novel INDELs have been submitted to the NCBI as novel variants. PCA and Admix analysis revealed that the IHGP03, a Mizoram male from the Northeast region, is strikingly different from the other two Indian genomes. Collectively, the data suggest the complexity of the Indian population admix developed from several distinct waves of human migration over tens of thousands of years.

Improved Models of Coalescence Ages of Y-DNA Haplogroups.

Databases of commercial DNA-testing companies now contain more customers with sequenced DNA than any completed academic study, leading to growing interest from academic and forensic entities. An important result for both these entities and the test takers themselves is how closely two individuals are related in time, as calculated through one or more molecular clocks. For Y-DNA, existing interpretations of these clocks are insufficiently accurate to usefully measure relatedness in historic times. In this article, I update the methods used to calculate coalescence ages (times to most-recent common ancestor, or TMRCAs) using a new, probabilistic statistical model that includes Y-SNP, Y-STR and ancilliary historical data, and provide examples of its use.

Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes.

The most frequent Y-chromosomal (chrY) haplogroups in northern and eastern Europe (NEE) are well-known and thoroughly characterised. Yet a considerable number of men in every population carry rare paternal lineages with estimated frequencies around 5%. So far, limited sample-sizes and insufficient resolution of genotyping have obstructed a truly comprehensive look into the variety of rare paternal lineages segregating within populations and potential signals of population history that such lineages might convey. Here we harness the power of massive re-sequencing of human Y chromosomes to identify previously unknown population-specific clusters among rare paternal lineages in NEE. We construct dated phylogenies for haplogroups E2-M215, J2-M172, G-M201 and Q-M242 on the basis of 421 (of them 282 novel) high-coverage chrY sequences collected from large-scale databases focusing on populations of NEE. Within these otherwise rare haplogroups we disclose lineages that began to radiate ~1-3 thousand years ago in Estonia and Sweden and reveal male phylogenetic patterns testifying of comparatively recent local demographic expansions. Conversely, haplogroup Q lineages bear evidence of ancient Siberian influence lingering in the modern paternal gene pool of northern Europe. We assess the possible direction of influx of ancestral carriers for some of these male lineages. In addition, we demonstrate the congruency of paternal haplogroup composition of our dataset with two independent population-based cohorts from Estonia and Sweden.

Y-Chromosome Haplogroup Diversity in Khazar Burials from Southern Russia

Genetic studies of archaeological burials open up new possibilities for investigating the cultural-historical development of ancient populations, providing objective data that can be used to investigate the most controversial problems of archeology. In this work, we analyzed the Y-chromosomes of nine skeletons recovered from elite burial mounds attributed to the 7th–9th centuries of the Khazar Khaganate in the modern Rostov region. Genotyping of polymorphic microsatellite loci of the Y chromosome made it possible to establish that among the nine skeletons studied, three individuals had R1a Y-haplogroup, two had C2b, and one each had G2a, N1a, Q, and R1b Y-haplogroups. Such results were noteworthy for the mixture of West Eurasian and East Asian paternal lineages in these samples. The Y-chromosome data are consistent with the results of the craniological study and genome-wide analysis of the same individuals in showing mixed genetic origins for the early medieval Khazar nobility. These findings are not surprising in light of the history of the Khazar Khaganate, which arose through its separation from the Western Turkic Khaganate and establishment in the North Caucasus and East European steppes.