Y-chromosome Analysis Research Articles

Y-chromosome analysis recapitulates key events of Mediterranean populations

The remarkable geographical situation of the Mediterranean region, located between Europe, Africa, and Asia, with numerous migratory routes, has made this area a crucible of cultures. Studying the Y-chromosome variability is a very performant tool to explore the genetic ancestry and evaluate scenarios that may explain the current Mediterranean gene pool. Here, six Mediterranean populations, including three Balearic Islands (Ibiza, Majorca, and Minorca) and three Southern Italian regions (Catanzaro, Cosenza, and Reggio di Calabria) were typed using 23 Y-STR loci and up to 39 Y-SNPs and compared to geographically targeted key reference populations to explore their genetic relationship and provide an overview of Y-chromosome variation across the Mediterranean basin. Pairwise RST genetic distances calculated with STRs markers and Y-haplogroups mirror the West to East geographic distribution of European and Asian Mediterranean populations, highlighting the North-South division of Italy, with a higher Eastern Mediterranean component in Southern Italian populations. In contrast, the African populations from the Southern coast of the Mediterranean clustered separately. Overall, these results support the notion that migrations from Magna Graecia or the Byzantine Empire, which followed similar Neolithic and post-Neolithic routes into Southern Italy, may have contributed to maintaining and/or reinforcing the Eastern Mediterranean genetic component in Southern Italian populations.

Genetic origins and migration patterns of Xinjiang Mongolian group revealed through Y-chromosome analysis

Genetic origins and migration patterns of Xinjiang Mongolian group revealed through Y-chromosome analysis

Unraveling the paternal genetic structure and forensic traits of the Hui population in Liaoning Province, China using Y-chromosome analysis

The Hui people are the second-largest ethnic minority in China, and they are distributed throughout the country. A previous study explored the paternal genetic structure of the Hui population in nine different regions of China, but it overlooked the Liaoning province. In this study, we examined the paternal genetic makeup and forensic traits of the Hui population in Liaoning province by analyzing 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 26 short tandem repeats (Y-STRs). We successfully genotyped 282 unrelated male individuals from the Hui population of Liaoning province using the SNaPshot® single base extension assay and Goldeneye™ Y26 system kit (PEOPLESPOT R&D, Beijing, China). The results revealed high haplotypic diversity (0.9998) and identified 46 terminal haplogroups for the Hui population. Additional analyses, such as heat maps, principal component analysis (PCA), genetic distance (FST), Multidimensional scaling (MDS) analysis, and median-joining network (MJ) analysis, showed that the Hui population could be classified into three groups: Northwest Hui populations (NWH), including Liaoning, Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, and Henan; Hui populations from Sichuan and Shandong (SSH); and Yunnan Hui populations (YNH). Pairwise genetic distance (Rst) comparisons with other Chinese populations revealed that the Hui population displayed genetic affinity with the Han population. The comprehensive understanding of the Hui population in Liaoning province, explored by Y-SNPs and Y-STRs, can be utilized to interpret their genetic structure and enhance the accuracy of forensic databases.

Inka Child Mummy Found in Cerro Aconcagua (Argentina) Traced Back to Populations of the Northern Peruvian Coast through Y-Chromosome Analysis

The mummy of a seven-year-old child that was discovered in 1985 in Cerro Aconcagua (Mendoza, Argentina) was likely part of an Inka sacrificial religious practice known as capacocha. Previous uniparental DNA marker studies conducted by some scholars have suggested that the mummified child may be related to the southern Andean population of Peru. However, autosome genome-wide analysis performed by others has indicated that the child was more closely related to the population along the northern Peruvian coast than to that of the southern Andes. In this study, we aimed to determine possible genealogical connections in the male lineage of the mummified child. To achieve this, we compared the genetic profile of the mummy with an extensive database of contemporary individuals from the northern Peruvian coastal and southern Andean regions. We used single nucleotide polymorphisms and short tandem repeats from the nonrecombining region of the Y-chromosome for our analysis. Our results confirmed that the Inka child mummy was closely related to individuals from the north coast of Peru. This suggests that the child was likely descended from the Muchik–Chimor-speaking people.

The role of DNA in forensic science: A comprehensive review

Forensic genetics, leveraging molecular tools and scientific applications, has witnessed significant advancements in DNA analysis over the last three decades. These progressions have enhanced the discrimination power, speed, and sensitivity of DNA profiling methods, enabling the analysis of challenging samples. This article explores the significance of forensic genetics in criminal investigations, traces the historical evolution of DNA analysis techniques, and presents recent developments in the field. The article aims to provide a comprehensive understanding of the crucial role of forensic genetics in criminal investigations and sheds light on the latest trends and breakthroughs in this area. The evolution of DNA typing from ABO blood typing to the current standard of short tandem repeat (STR) analysis is discussed, along with alternative DNA analysis methods, such as Y-chromosome analysis and single nucleotide polymorphism (SNP) typing. Massively parallel sequencing (MPS) represents a groundbreaking advancement, enabling whole genome sequencing and addressing complex cases. The article also covers recent innovations, including DNA methylation analysis, body fluid identification, forensic DNA phenotyping, and genetic genealogy, highlighting their potential benefits in forensic investigations. Despite these advancements, standard STR profiling remains the gold standard due to its established protocols and databases. Ethical considerations regarding data privacy and cost implications are crucial as these technologies continue to progress in their pursuit of justice.

(255) Operating Characteristics of Sperm Concentration and FSH for Predicting Chromosomal Abnormalities

Abstract Introduction Microdeletions of the Y-chromosome (Yq) and karyotype abnormalities are frequent causes of male factor infertility. Current AUA/EUA guidelines recommend obtaining Yq microdeletion analysis, karyotype, and genetic counseling in men with non-obstructive azoospermia or severe oligospermia (<5 mil/mL). A recent retrospective cohort study suggests that Yq microdeletions are primarily found at a sperm concentration < 0.5 mil/mL and that by lowering the concentration threshold for genetic testing, specificity could be increased and relative financial cost decreased without adversely affecting the sensitivity. Studies have shown that FSH is the best predictor of NOA in combination with testicular volume as well as a significant predictor of microdeletion presence. Identification of Yq microdeletions and karyotype abnormalities have implications when counseling patients (and their partners) about the likelihood of retrieving sperm and need for further genetic counseling. Objective We hypothesized that the combination of sperm concentration and FSH would better predict the presence of chromosome abnormalities in infertile men. Methods A retrospective cohort study was conducted with subjects who were referred to a military tertiary Urology clinic between 2010 to 2020 and who underwent an infertility evaluation to include genetic testing (karyotype, Y-chromosome analysis), hormone profile (FSH), and at least one semen analysis. Sperm density and FSH were analyzed as independent predictors of chromosomal abnormalities using logistic regression. Receiver operating characteristics were generated for each independent variable that achieved significance in regression. Results A total of 356 patients met inclusion criteria. Over the ten-year period, the prevalence of Y-chromosome microdeletions and karyotype abnormalities was 3.3% (n=12) and 8.4% (n=30), respectively. The ability to predict chromosomal abnormality based on logistic regression was statistically significant for each independent variable. The area under the curve for sperm concentration and FSH was found to be statistically better in combination than concentration alone (0.71 vs 0.66, p=0.033). The best balance of sensitivity and specificity (i.e. for a diagnostic test) for concentration and FSH were found at cut-points of 8.345 mIU/mL, respectively. To optimize performance as a screening test and maintain sensitivity >90%, the cut points for concentration and FSH were 2.74 mIU/mL, respectively. There was no difference in sensitivity for concentration between 2-7 mil/mL and no abnormalities were found if concentration exceeded 7 mil/mL; thus a cutoff of 7 mil/mL would capture 100% of all chromosome abnormalities. Conclusions Based on receiver operating characteristics, lowering the threshold for chromosomal analysis to a sperm concentration of <1 mil/mL maintains acceptable performance as a screening test for genetic abnormality, with resulting cost savings expected. Incorporating FSH into this decision appears to improve both sensitivity and specificity in prediction of chromosomal abnormalities. Our military single-institution ten-year cohort, exemplifies the potential improvement in patient selection and results that can be achieved if the sperm concentration is lowered from the current cutoff Disclosure No

DNA profiling in forensic investigation – A review

DNA Profiling is a revolutionary method for individual and relationship analysis, crime investigation, hereditary disorders, etc. It is a universal method used to establish accurate results during the process of forensic investigation. DNA profiling techniques, which are based on repetitive sequences within DNA, have proven to be of paramount importance, albeit the complete utilization of knowledge still remaining unexplored. Even a hair strand, blood drop or even skin flakes can be used to identify DNA sequences. It has a wide range of applications both in forensics and law. Because of the advancement in the field of forensics in the past four decades, DNA evidence now stands as one of the most reliable forms of proof in a court of law. In the following article, the authors explore the main concepts of DNA Profiling, and the techniques which are widely used in forensic laboratories such as RFLP, VNTR, STR, AFLP, mtDNA analysis, Y-chromosome analysis and gender typing.

Междисциплинарный подход к изучению этногенеза: геногеография и филогеография тувинских родовых групп

Introduction. The territory of South Siberia has historically been a crossroads of ancient migration routes. So, the complex process of ethnogenesis across the region requires multidisciplinary insights of historians, ethnographers, anthropologists, linguists, and geneticists. Goals. The work aims to substantiate the possibility of a comprehensive study of Tuvan tribal groups on the basis of the latter’s gene pools and structures. Materials and methods. The most efficient tool thereto is the Y chromosome since it is inherited — like the clan/tribal name proper — paternally, has a high variety, makes it possible to reconstruct migration waves, and may yield genetic dates. These properties of the Y chromosome make it an additional historical source within comprehensive ethnographic, historical, linguistic, anthropological, and genetic studies of ancestral groups among peoples to have retained the memory of clan/tribal structures. Results. The early 21st century has witnessed an intensive research of the Tuvan Y-chromosomal gene pool — with no sufficient data on corresponding tribal groups mentioned. The analysis of Tuvan tribal structures is complicated by a number of factors, such as the administrative/territorial system of the Qing Empire in Tuva (1757–1912), introduction of a passport system in Tuva (1945–1947) when not clan/tribal names but rather personal ones were registered as surnames, and an increase in unmarried cohabitation that violates the patrilineal system. Y-chromosomal analyses of the largest Tuvan tribal groups Mongush and Oorzhak show that the bulk of their gene pool are North Eurasian haplogroups (N*, N1a2, N3a, Q) associated with the autochthonous population of the area nowadays inhabited by Tuvans. At the same time, Central Asian haplogroups (C2, O2) make up less than a fifth (17 %) of the gene pool. A targeted analysis of the most frequent branch (C2a1a2a2a2-SK1066) of the Central Asian haplogroup C2 shows it had originated about 900 years ago in the territory of Northeast Mongolia, and thus could not have reached Tuva before the 11th–12th centuries AD. Anthropological data also attest to the late admixture of the Central Asian cluster into the Tuvans and their tribal groups. The North Eurasian haplogroups completely dominate within the gene pool of tribal groups Kol, Oyun, and Khertek, which results in that the share of Central Asian lineages drops to 3%. Conclusions. In general, the paper shows the Mongolian expansion had no essential genetic impacts on the Y-chromosomal gene pool of Tuvan tribal groups, but — in contrast — did overwhelmingly influence ethnocultural, economic, and linguistic spheres.

Large-scale pedigree analysis highlights rapidly mutating Y-chromosomal short tandem repeats for differentiating patrilineal relatives and predicting their degrees of consanguinity

Rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) were suggested for differentiating patrilineally related men as relevant in forensic genetics, anthropological genetics, and genetic genealogy. Empirical data are available for closely related males, while differentiation rates for more distant relatives are scarce. Available RM Y-STR mutation rate estimates are typically based on father–son pair data, while pedigree-based studies for efficient analysis requiring less samples are rare. Here, we present a large-scale pedigree analysis in 9379 pairs of men separated by 1–34 meioses on 30 Y-STRs with increased mutation rates including all known RM Y-STRs (RMplex). For comparison, part of the samples were genotyped at 25 standard Y-STRs mostly with moderate mutation rates (Yfiler Plus). For 43 of the 49 Y-STRs analyzed, pedigree-based mutation rates were similar to previous father–son based estimates, while for six markers significant differences were observed. Male relative differentiation rates from the 30 RMplex Y-STRs were 43%, 84%, 96%, 99%, and 100% for relatives separated by one, four, six, nine, and twelve meioses, respectively, which largely exceeded rates obtained by 25 standard Y-STRs. Machine learning based models for predicting the degree of patrilineal consanguinity yielded accurate and reasonably precise predictions when using RM Y-STRs. Fully matching haplotypes resulted in a 95% confidence interval of 1–6 meioses with RMplex compared to 1–25 with Yfiler Plus. Our comprehensive pedigree study demonstrates the value of RM Y-STRs for differentiating male relatives of various types, in many cases achieving individual identification, thereby overcoming the largest limitation of forensic Y-chromosome analysis.

Evolution of the Indian population through the ages

The Indian subcontinent is synonymous with increased genetic diversity essentially attributed to migratory forces. Many theories that provide different perspectives regarding the current nature of the Indian subpopulation have been proposed. Each of these theories is equally insightful albeit contradictory in nature. Thus, there is ambiguity in terms of tracing the course taken by individuals forming the Indian subpopulation. A comparative analysis of the pre-existing hierarchal caste system and primitive Europeans, matrilineal factors, and increased incidence of population bottlenecks gives an insight into plausible theories that could have led to infringement across the borders of the Indian subcontinent. The Aryan exodus forms the crux of various migratory theories along with analysis of ancient DNA and Y-chromosome which are indicative of external infusion into the Indian gene pool. Thus, this review is a retrospective analysis based on concrete evidence generated from studies undertaken to map the evolution of population in the Indian context.

DNA in forensic odontology: An overview

Human remains are tremendously damaged and degraded in forensic cases and the identification becomes very difficult, in those cases teeth and bones are often the only reliable sources of DNA for identification. Advances in DNA extraction techniques and short-amplicon DNA typing have greatly increased our potential to identify human remains which were previously considered to be too compromised for genetic analysis. As the teeth are largely protected within the jawbones and remains protected from the environmental conditions and prevent these tissues from postmortem decomposition and DNA decay. DNA profile tests which are performed nowadays are totally reliable and give details about an individual’s physical characteristics, ethnicity, place of origin and sex. These tests are also accepted as legal proofs in courts. These tests are: Restriction Fragment Length Polymorphism Typing, STRs Typing, Mitochondrial DNA Analysis, Y-Chromosome Analysis, X-Chromosome STR, Single Nucleotide Polymorphism. The aim of this review is to provide a better understanding and knowledge about the latest techniques in DNA for human identification in the field of forensic odontology.

Genetic Genealogy Using Y-STR Markers in Conjunction with Reverse Parentage Testing Aid Efforts in Human Identification and Familial Search Investigation (Case Study)

The personal identification of victim of mass disasters is one of the powers of forensic DNA typing. Genetic genealogy using Y-chromosome STR markers and reverse parentage testing (RPT) aid efforts in familial search investigation. A Dornier aircraft with commandants on board was declared overdue and a month later, skeletal remains found under sea, were subjected to DNA analysis. The case was quite challenging as the skeletal remains exhibited different rates of degradation. The skeletal remains along with reference samples from blood relatives of victims were subjected to different protocols to generate reproducible and typeable, amelogenin, autosomal and Y-STR profiles. Y-chromosome analysis in conjunction with RPT led to establishment of victim identity and rendered fruitful results in familial search investigation.

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.

Paternal ancestry of Peruvian creole cattle inferred from Y-chromosome analysis

The aim of this study was the identification of the genetic diversity and paternal origin of Peruvian creole cattle. A panel of 7 Y-chromosome specific markers (INRA189, UMN0103, BM861, UMN307, BYM-1, DDX3Y_1STR and ZFY10) were analyzed in 229 cattle from 6 regions of the Peruvian highlands. The creole cattle exhibited low genetic diversity (H= 0.50) mostly explained by within-population variation (98%) and absence of population structure (FST = 0.019) in the analyzed regions. These results are in concordance to other studies in Spanish cattle populations. The overall frequency and distribution of the major B. taurus haplogroups: Y1 (19%) and Y2 (81%), suggests that Peruvian creole cattle derived from the Iberian Peninsula cattle. Furthermore, our results some degree of male-mediated African cattle influence in the Peruvian creoles, supporting the findings of other studies in South American creole cattle populations. Altogether, our results revealed unique genetic characteristics of Peruvian creole cattle that may have important implications for future conservation programs.

Indication for Y Chromosome Microdeletion Analysis in Infertile Men: Is a New Sperm Concentration Threshold Needed?

To describe the prevalence of Y-chromosome deletions in patients with a sperm concentration of less than 5 million/mL. To also determine a new sperm threshold for Y-chromosome analysis in men with infertility. A total of 3023 patients who had a semen concentration of less than 5 million/mL included in this retrospective study. All of these patients had a genetic evaluation, hormonal evaluation, and 2 abnormal semen analyses. Y-chromosome deletions were present in 116 (3.8 %) patients with sperm concentration <5 million/mL. The frequency of a Y-chromosome deletions was 6.8%, 1.0%, 0.15% in azoospermic men, in men with sperm concentrations of 0-1 million /mL, in men with sperm concentrations of 1-5 million/mL. Patients were divided into 2 groups regarding the determined new sperm threshold. The sensitivity and specificity of the Y-chromosome deletions test were 92.2.7% and 49.3 %, 99.1%, and 22.1% in patients with azoospermia and sperm concentrations <1 million/mL, respectively. If the sperm concentration thresholds of azoospermia or <1 million/mL, are applied, the number of tests decreased to 50.5% (1442 tests) and 23.1% (643 tests), respectively. Approximately $108,150 and $48,225 would be saved if the sperm thresholds were azoospermia and <1 million/mL, respectively CONCLUSION: The current threshold of sperm concentration for Y-chromosome deletions is controversial. The new proposed sperm threshold for genetic testing of 1 million/mL would increase sensitivity and more cost-effective compared to the current threshold.

Determination of the phylogenetic origins of the \xc1rp\xe1d Dynasty based on Y chromosome sequencing of B\xe9la the Third

We set out to identify the origins of the Árpád Dynasty based on genome sequencing of DNA derived from the skeletal remains of Hungarian King Béla III (1172–1196) and eight additional individuals (six males, two females) originally interred at the Royal Basilica of Székesfehérvár. Y-chromosome analysis established that two individuals, Béla III and HU52 assign to haplogroups R-Z2125 whose distribution centres near South Central Asia with subsidiary expansions in the regions of modern Iran, the Volga Ural region and the Caucasus. Out of a cohort of 4340 individuals from these geographic areas, we acquired whole-genome data from 208 individuals derived for the R-Z2123 haplogroup. From these data we have established that the closest living kin of the Árpád Dynasty are R-SUR51 derived modern day Bashkirs predominantly from the Burzyansky and Abzelilovsky districts of Bashkortostan in the Russian Federation. Our analysis also reveals the existence of SNPs defining a novel Árpád Dynasty specific haplogroup R-ARP. Framed within the context of a high resolution R-Z2123 phylogeny, the ancestry of the first Hungarian royal dynasty traces to the region centering near Northern Afghanistan about 4500 years ago and identifies the Bashkirs as their closest kin, with a separation date between the two populations at the beginning of the first millennium CE.

How history and geography may explain the distribution in the Comorian archipelago of a novel mutation in DNA repair-deficient xeroderma pigmentosum patients.

Xeroderma pigmentosum (XP) is a rare, genetic, autosomal nucleotide excision repair-deficient disease characterized by sun-sensitivity and early appearance of skin and ocular tumors. Thirty-two black-skinned XP from Comoros, located in the Indian Ocean, were counted, rendering this area the highest world prevalence of XP. These patients exhibited a new homozygous XPC mutation at the 3’-end of the intron12 (IVS 12-1G>C) leading to the absence of XPC protein. This mutation, characteristic of the consanguineous Comorian families, is associated with a founder effect with an estimated age of about 800 years. Analysis of mt-DNA and Y-chromosome identified the haplogroups of patients, who are derived from the Bantu people. Although the four Comorian islands were populated by the same individuals during the 7-10th centuries, XP was found now only in the Comorian island of Anjouan. To avoid the slavery process caused by the arrival of the Arabs around the 11-13th centuries, inhabitants of Anjouan, including XP-heterozygotes, hid inland of the island protected by volcanoes. This population lived with an endogamic style, without connection with the other islands. XP patients still live in the same isolated villages as their ancestries. Local history and geography may, thus, explain the high incidence of XP located exclusively in one island.

X-InDels efficacy evaluation in a critical samples paternity case: A Spanish Civil War case from the memorial of the camposines (Tarragona, Spain)

The Memorial of the Camposines (la Fatarella, Tarragona, Spain) consists in a place that honours all combatants of the Spanish Civil War (1936–1939), without distinction of sides. The site was included in the research carried out by the multidisciplinary team coordinated by the program of the General Directorate of Democratic Memory, Generalitat of Catalonia, Spain, for the identification of the victims of the Spanish Civil War. The case investigated on the present study consisted on a presumable paternity. To accomplish the study of the presumptive father critical samples, one of the combatants found on the Memorial, two bone samples were selected - a petrous portion of left temporal bone, and a condyle of foramen magnum, both fractured and at a very bad stage of conservation. After a specific DNA extraction for critical bone sample, the next step was an autosomal and Y-chromosome analysis, trying to find a possible coincidence with any possible familiar, from the familial database. A potential match was found, indicating a possible living daughter. However, between both autosomal profiles one Mendelian incompatibility was detected, and also several allelic dropout phenomena in the presumptive father’s profile. Therefore, samples were analysed for a 32 X-chromosome Insertion-Deletion (InDel) polymorphisms battery, assessing their ability to solve, or at least complementing autosomal information, in a complex paternity case.It was possible to confirm the efficacy of these 32 X-InDels polymorphisms, by solving undoubtedly the case. Due to the five incompatibilities detected between both X-InDels profiles, it was now possible to discard immediately a possible paternity case.

Genetic Architecture of Southeast-coastal Indian tribal populations: A Y-chromosomal phylogenetic analysis

BackgroundY chromosome single nucleotide polymorphisms (Y-SNPs) are useful markers for reconstructing male lineages, haplogroup determinations, and paternity identifications. Since Y chromosome lacks recombination, the haplogroups of this series show a greater extent of diverse genome-specific geographical distributions and these haplogroups have been found to play a major role in forensic investigations and population genetics.Materials and methodsThe present study is aimed at determining the Y chromosomal phylogeny of two southeast coastal Indian tribal populations (Porja and Savara; N = 217), using a set of 15 bi-allelic markers on the non-recombining region of Y chromosome, representing two Austro-Asiatic (AA) language speaking populations.Results and conclusionsThe phylogenetic analysis revealed four paternal haplogroups, viz., H1*-M52, H1a*-M82, O2a*-M95, and R2-M124, with high frequency (84.79%) represented by the Austro-Asiatic-specific haplogroup O2a* (M95), confirming to the fact of O2a* haplogroup being the paternal signature of AA language family of Southeast Asians.

Y-chromosomal analysis of clan structure of Kalmyks, the only European Mongol people, and their relationship to Oirat-Mongols of Inner Asia

Kalmyks, the only Mongolic-speaking population in Europe, live in the southeast of the European Plain, in Russia. They adhere to Buddhism and speak a dialect of the Mongolian language. Historical and linguistic evidence, as well a shared clan names, suggests a common origin with Oirats of western Mongolia; yet, only a limited number of genetic studies have focused on this topic. Here we compare the paternal genetic relationship of Kalmyk clans with ethnographically related groups from Mongolia, Kyrgyzstan and China, within the context of their neighbouring populations. A phylogeny of 37 high-coverage Y-chromosome sequences, together with further genotyping of larger sample sets, reveals that all the Oirat-speaking populations studied here, including Kalmyks, share, as a dominant paternal lineage, Y-chromosomal haplogroup C3c1-M77, which is also present in several geographically distant native Siberian populations. We identify a subset of this clade, C3c1b-F6379, specifically enriched in Kalmyks as well as in Oirat-speaking clans in Inner Asia. This sub-clade coalesces at around 1500 years before present, before the Genghis Khan era, and significantly earlier than the split between Kalmyks and other Oirat speakers about 400 years ago. We also show that split between the dominant hg C variant among Buryats—C3-M407—and that of C3-F6379, took place in the Early Upper Palaeolithic, suggesting an extremely long duration for the dissipation of hg C3-M217 carriers across northern Eurasia, which cuts through today’s major linguistic phyla.