The Eurasian heartland: a continental perspective on Y-chromosome diversity

Testing the informativeness of Y-STR and mitochondrial DNA control region markers in an attempt to predict ancestry of World War II victims from Slovenian mass grave

Identification of human remains is a challenge in forensic genetics without relatives or personal items available. In Slovenia, a Konfin II mass grave from the Second World War (WWII) was found, containing skeletal remains of 65 victims. The archival documents detailing victims' information describe 45 persons of which 33 could be considered Germanic and 12 Slavic. This study aims to check for concordance between the victim list and actual victims found by using uniparental markers to differentiate between Slavic and non-Slavic origin by attempting to infer ancestry by analyzing the control region (CR) of mitochondrial DNA (mtDNA) and Y-chromosomal STRs. Diaphyses of femurs were used as a DNA source. Next Generation Sequencing (NGS) technology was used for mtDNA- namely HID Ion Chef™ Instrument, Precision ID mtDNA Control Region Panel, and Ion GeneStudio™ S5 System. For the Y-chromosome, PowerPlex® Y23 System (Promega) kit and SeqStudio™ for human identification (HID) were used. European DNA Profiling mtDNA Population Database (EMPOP) and Y-Chromosome STR Haplotype Reference Database (YHRD) were searched for haplotype matches. Closest haplogroups were predicted using EMPOP, Y-DNA Haplogroup Predictor- NevGen, and Whit Athey's Haplogroup Predictor. Despite mitotypes being more diverse than Y-haplotypes, the Y-haplotypes had more database matches and more unequivocal differentiation between populations. 16 victims could be considered Slavic, 15 non-Slavic, and the remaining 34 had a rather scarce informativeness- either unclear or not providing any match. To address ancestry inference more comprehensively, analysis of autosomal ancestry informative markers as well as expansion on haploid markers will be conducted in future research.

Ancestral Origins and Admixture History of Kazakhs

Kazakh people, like many other populations that settled in Central Asia, demonstrate an array of mixed anthropological features of East Eurasian (EEA) and West Eurasian (WEA) populations, indicating a possible scenario of biological admixture between already differentiated EEA and WEA populations. However, their complex biological origin, genomic makeup, and genetic interaction with surrounding populations are not well understood. To decipher their genetic structure and population history, we conducted, to our knowledge, the first whole-genome sequencing study of Kazakhs residing in Xinjiang (KZK). We demonstrated that KZK derived their ancestries from 4 ancestral source populations: East Asian (∼39.7%), West Asian (∼28.6%), Siberian (∼23.6%), and South Asian (∼8.1%). The recognizable interactions of EEA and WEA ancestries in Kazakhs were dated back to the 15th century BCE. Kazakhs were genetically distinctive from the Uyghurs in terms of their overall genomic makeup, although the 2 populations were closely related in genetics, and both showed a substantial admixture of western and eastern peoples. Notably, we identified a considerable sex-biased admixture, with an excess of western males and eastern females contributing to the KZK gene pool. We further identified a set of genes that showed remarkable differentiation in KZK from the surrounding populations, including those associated with skin color (SLC24A5, OCA2), essential hypertension (HLA-DQB1), hypertension (MTHFR, SLC35F3), and neuron development (CNTNAP2). These results advance our understanding of the complex history of contacts between Western and Eastern Eurasians, especially those living or along the old Silk Road.

Genetic Analysis of 27 Y-STR Haplotypes in 11 Iranian Ethnic Groups

BACKGROUND

The study of Y-chromosomal variations provides valuable insights into male susceptibility in certain diseases like cardiovascular disease (CVD). In this study, we analyzed paternal lineage in different Iranian ethnic groups, not only to identify developing medical etiology, but also to pave the way for gender-specific targeted strategies and personalized medicine in medical genetic research studies.

METHODS

The diversity of eleven Iranian ethnic groups was studied using 27 Y-chromosomal short tandem repeat (Y-STR) haplotypes from Y-filer® Plus kit. Analysis of molecular variance (AMOVA) based on pair-wise RST along with multidimensional scaling (MDS) calculation and Network phylogenic analysis was employed to quantify the differences between 503 unrelated individuals from each ethnicity.

RESULTS

Results from AMOVA calculation confirmed that Gilaks and Azeris showed the largest genetic distance (RST=0.35434); however, Sistanis and Lurs had the smallest considerable genetic distance (RST=0.00483) compared to other ethnicities. Although Azeris had a considerable distance from other ethnicities, they were still close to Turkmens. MDS analysis of ethnic groups gave the indication of lack of similarity between different ethnicities. Besides, network phylogenic analysis demonstrated insignificant clustering between samples.

CONCLUSION

The AMOVA analysis results explain that the close distance of Azeris and Turkmens may be the effect of male-dominant expansions across Central Asia that contributed to historical and demographics of populations in the region. Insignificant differences in network analysis could be the consequence of high mutation events that happened in the Y-STR regions over the years. Considering the ethnic group affiliations in medical research, our results provided an understanding and characterization of Iranian male population for future medical and population genetics studies.

Origins of East Caucasus Gene Pool: Contributions of Autochthonous Bronze Age Populations and Migrations from West Asia Estimated from Y-Chromosome Data

The gene pool of the East Caucasus, encompassing modern-day Azerbaijan and Dagestan populations, was studied alongside adjacent populations using 83 Y-chromosome SNP markers. The analysis of genetic distances among 18 populations (N = 2216) representing Nakh-Dagestani, Altaic, and Indo-European language families revealed the presence of three components (Steppe, Iranian, and Dagestani) that emerged in different historical periods. The Steppe component occurs only in Karanogais, indicating a recent medieval migration of Turkic-speaking nomads from the Eurasian steppe. The Iranian component is observed in Azerbaijanis, Dagestani Tabasarans, and all Iranian-speaking peoples of the Caucasus. The Dagestani component predominates in Dagestani-speaking populations, except for Tabasarans, and in Turkic-speaking Kumyks. Each component is associated with distinct Y-chromosome haplogroup complexes: the Steppe includes C-M217, N-LLY22g, R1b-M73, and R1a-M198; the Iranian includes J2-M172(×M67, M12) and R1b-M269; the Dagestani includes J1-Y3495 lineages. We propose J1-Y3495 haplogroup's most common lineage originated in an autochthonous ancestral population in central Dagestan and splits up ~6 kya into J1-ZS3114 (Dargins, Laks, Lezgi-speaking populations) and J1-CTS1460 (Avar-Andi-Tsez linguistic group). Based on the archeological finds and DNA data, the analysis of J1-Y3495 phylogeography suggests the growth of the population in the territory of modern-day Dagestan that started in the Bronze Age, its further dispersal, and the microevolution of the diverged population.

The HLA profile and genetic affinities of three primitive Tamil-speaking endogamous groups: Kallars of Thanjavur, Piramalai Kallar and Vanniyar

Background

The present study was aimed to study the frequencies of HLA-DRB1/-DQB1 alleles and haplotypes of three endogamous groups of Tamil Nadu state, South India. PCR-SSP typing of HLA-DRB1 and -DQB1 alleles were performed on 111 Kallars of Thanjavur, 80 Piramalai Kallar of Madurai and 119 Vanniyar. Genetic distances, neighbor-joining phylogenetic dendrograms and correspondence analysis have been performed.

Results

The HLA class II alleles, DRB1*07 (25.2%), DRB1*15 (15.7%), DRB1*14 (11.7%) and DRB1*12 (9.90%) among Kallars of Thanjavur; DRB1*15 (28.7%), DRB1*04 (15.6%), DRB1*10 (14.3%), DRB1*13 (11.2%) and DRB1*03 (9.37%) among Piamalai Kallar and DRB1*15 (24.7%), DRB1*04 (15.9%), DRB1*07 (11.7%), DRB1*12 (11.3%) and DRB1*10 (10.0%) among Vanniyar were more frequent. Similarly, alleles DQB1*06 (31.0%), DQB1*02 (26.5%) and DQB1*05 (24.7%) among Kallars of Thanjavur; DQB1*05 (32.5%), DQB1*06 (31.8%), DQB1*02 (16.2%) and DQB1*03:02 (12.5%) among Piramalai Kallar and DQB1*05 (52.9%), DQB1*06 (22.6%) and DQB1*02 (11.3%) among Vanniyar were more frequent. We genotyped the two most frequent two-locus haplotypes, such as DRB1*15-DQB1*06 and DRB1*07-DQB1*02 for HLA-A/-B/–C alleles to identify the 5-locus extended haplotypes to extrapolate global affinities. We identified a number of five locus extended haplotypes among south Indian population with stronger global affinities. Further, we identified the presence of a highly unique extended haplotypes such as A*11-B*35-C*12-DRB1*07-DQB1*02 (HF:0.1458) in Kallars of Thanjavur, A*03-B*35-C*04-DRB1*15-DQB1*06 (HF:0.1833) in Piramalai Kallar and A*03-B*07-C*07-DRB1*15-DQB1*06 (HF: 0.1800) in Kallars of Thanjavur and (HF: 0.1081) in Vanniyar population.

Conclusions

Allele distribution and haplotype analysis have demonstrated that the Kallars of Thanjavur, Piramalai Kallar and Vanniyar populations shared HLA alleles with other ethnic and other Indian populations, while showing population specific haplotypes. Analysis of population-specific distribution of HLA alleles is proved to be important in finding out the relatedness of the ethnic groups across continents. The extensive polymorphism of the HLA system also has useful application in the study of the origin, evolution and migration patterns of human populations.

Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia

As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.

Ancient Components and Recent Expansion in the Eurasian Heartland: Insights into the Revised Phylogeny of Y-Chromosomes from Central Asia

In the past two decades, studies of Y chromosomal single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) have shed light on the demographic history of Central Asia, the heartland of Eurasia. However, complex patterns of migration and admixture have complicated population genetic studies in Central Asia. Here, we sequenced and analyzed the Y-chromosomes of 187 male individuals from Kazakh, Kyrgyz, Uzbek, Karakalpak, Hazara, Karluk, Tajik, Uyghur, Dungan, and Turkmen populations. High diversity and admixture from peripheral areas of Eurasia were observed among the paternal gene pool of these populations. This general pattern can be largely attributed to the activities of ancient people in four periods, including the Neolithic farmers, Indo-Europeans, Turks, and Mongols. Most importantly, we detected the consistent expansion of many minor lineages over the past thousand years, which may correspond directly to the formation of modern populations in these regions. The newly discovered sub-lineages and variants provide a basis for further studies of the contributions of minor lineages to the formation of modern populations in Central Asia.

The genetic echo of the Tarim mummies in modern Central Asians

The diversity of Central Asians has been shaped by multiple migrations and cultural diffusion. Although ancient DNA studies have revealed the demographic changes of the Central Asian since the Bronze Age, the contribution of the ancient populations to the modern Central Asian remains opaque. Herein, we performed high-coverage sequencing of 131 whole genomes of Indo-European-speaking Tajik and Turkic-speaking Kyrgyz populations to explore their genomic diversity and admixture history. By integrating the ancient DNA data, we revealed more details of the origins and admixture history of Central Asians. We found that the major ancestry of present-day Tajik populations can be traced back to the admixture of the Bronze Age Bactria–Margiana Archaeological Complex and Andronovo-related populations. Highland Tajik populations further received additional gene flow from the Tarim mummies, an isolated ancient North Eurasian–related population. The West Eurasian ancestry of Kyrgyz is mainly derived from Historical Era populations in Xinjiang of China. Furthermore, the recent admixture signals detected in both Tajik and Kyrgyz are ascribed to the expansions of Eastern Steppe nomadic pastoralists during the Historical Era.

Distribution of Y-chromosome haplogroups in Serbian population groups originating from historically and geographically significant distinct parts of the Balkan Peninsula

Our study enrolled 1200 Serbian males originating from three geographical regions in the Balkan Peninsula inhabited by Serbs: present-day Serbia, regions of Old Herzegovina and Kosovo and Metohija. These samples were genotyped using the combination of 23 Y-chromosomal short tandem repeats (Y-STRs) loci and 17 Ychromosomal single nucleotide polymorphisms (Y-SNPs) loci for the haplotype and haplogroup analysis in order to characterize in detail Y chromosome flow in the recent history. Serbia's borders have changed through history, forcing Serbs constantly to migrate to different regions of Balkan Peninsula. The most significant migration waves in the recent history towards present-day Serbia occurred from the regions of Old- Herzegovina and Kosovo and Metohija that lie in the south-west/south. High haplotype diversity and discrimination capacity were observed in all three datasets, with the highest number of unique haplotypes (381) and discrimination capacity (0.97) detected in the samples originating from the present-day Serbia. Haplogroup composition didn't differ significantly among datasets, with three dominant haplogroups (I-M170, E-P170 and R-M198), and haplogroup I-M170 being the most frequent in all three datasets. Haplogroup E-P170 was the second most dominant in the dataset originating from geographical region of Kosovo and Metohija, whereas haplogroup R-M198 was the second most prevalent in the dataset from historical region of Old Herzegovina. Based on the phylogenetic three for haplogroup I constructed within this study, haplogroup I2a1-P37.2 was the most dominant within all three datasets, especially in the dataset from historical region of Old Herzegovina, where 182 out of 400 samples were derived for SNP P37.2. Genetic distances between three groups of samples, evaluated by the Fst and Rst statistical values, and further visualized through multidimensional scaling plot, showed great genetic similarity between datasets from Old Herzegovina and present-day Serbia. Genetic difference in the haplogroup distribution and frequency between datasets from historical region of Old Herzegovina and from geographical region of Kosovo and Metohija was confirmed with highest Fst and Rst vaules. In this study we have distinguished genetic structure, diversity and haplogroup frequencies within 1200 Serbian males from three datasets, relationships among them as well as with other Balkan and European populations, which is useful for studying recent demographic history.

Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers

Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.

Peculiarity of Pomors of Onega Peninsula and Winter Coast in the genetic context of Northern Europe

The peculiarity of the Russian North gene pool has long become scientific fact, but has yet to receive informative explanation. Genetic drift cannot be the only contributing factor in the striking genetic differences between not only northern Russian populations and the southern ones, but among individual northern populations as well. Studying Russian North gene pools previously underrepresented in scientific literature may help understand this phenomenon. The work aimed to perform a subtotal study of the gene pool of the Arkhangelsk Oblast Pomors (Onega Coast, Summer Coast, the western fragment of the Winter Coast; n = 130) using a panel of 60 Y-chromosome SNP markers through multidimensional scaling and mapping of genetic distances. The frequencies of 14 identified haplogroups differ drastically in Pomor populations: haplogroups I1, R1a, and N3 each comprise a quarter of the total Pomor gene pool, I2-P37.2, and R1b each comprise about 8%, and the rest of the haplogroups are rare. The Onega Coast Pomors showed genetic similarity to a wide range of North-Eastern Europe Finnic-speaking populations, as well as to Russian populations with a strong pre-Slavic substratum. The Summer Coast Pomors are close to the Scandinavian gene pools, and the Winter Coast Pomors are similar only to specific Finn and Swede populations. None of the Pomor populations demonstrate genetic similarity with the Novgorod Oblast Russian populations, with which the origin of the Pomors is traditionally associated. The genetic distances between Pomor populations are so great, they are comparable to the general range of variability between the Eastern Slavic, Baltic, and Finno-Ugric peoples of the region. The reasons for such pronounced originality of Pomor populations presumably include, along with genetic drift, the gene pool of each population being underlied by a different pre-Slavic substrate, with later gene flows as an additional factor.

Forensic features and phylogenetic analyses of the population of Nayagarh (Odisha), India using 23 Y-STRs

AIM

The present study was designed to explore the STR diversity and genomic history of the inhabitants of Nayagarh district of Odisha, India. We also tested the proficiency of the most recent, new generation PowerPlex^R Y23 multiplex system for forensic characterisation and to decipher the phylogenetic affinities.

SUBJECTS AND METHODS

The genetic diversity and polymorphism among 236 healthy unrelated male volunteers from Nayagarh district of Odisha, India was investigated. This investigation was carried out via 23 Y-chromosomal STRs using capillary electrophoresis.

RESULT

A total 223 unique haplotypes were reported. Discrimination capacity (DC), gene diversity (GD) and power of discrimination (PD) were observed as 0.945, 0.999999999998333, and 0.99999999999794, respectively. Polymorphic information content (PIC) and matching probability (PM) were reported as 0.999999999925535 and 2.06 × 10^-12, respectively. Simultaneously, the haplogroup analysis characterised with C2, E1b1a, E1b1b, G2a, H1, I2a, J2a, J2b, L, O, O1, O2, Q, R1a, R2, and T haplogroups, disclosing the possible geographical relatedness of the studied population to different areas of the world.

CONCLUSION

Phylogenetic analysis with previously reported Indian and Asian populations showed the genetic closeness of the studied population to different Indian populations and the Bangladeshi population of Dhaka, whereas the Bhotra population of Odisha and Han population of China showed much less genetic affinity.

Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia

Mongolia is located in a strategic position at the eastern edge of the Eurasian Steppe. Nomadic populations moved across this wide area for millennia before developing more sedentary communities, extended empires, and complex trading networks, which connected western Eurasia and eastern Asia until the late Medieval period. We provided a fine-grained portrait of the mitochondrial DNA (mtDNA) variation observed in present-day Mongolians and capable of revealing gene flows and other demographic processes that took place in Inner Asia, as well as in western Eurasia. The analyses of a novel dataset (N = 2,420) of mtDNAs highlighted a clear matrilineal differentiation within the country due to a mixture of haplotypes with eastern Asian (EAs) and western Eurasian (WEu) origins, which were differentially lost and preserved. In a wider genetic context, the prevalent EAs contribution, larger in eastern and central Mongolian regions, revealed continuous connections with neighboring Asian populations until recent times, as attested by the geographically restricted haplotype-sharing likely facilitated by the Genghis Khan’s so-called Pax Mongolica. The genetic history beyond the WEu haplogroups, notably detectable on both sides of Mongolia, was more difficult to explain. For this reason, we moved to the analysis of entire mitogenomes (N = 147). Although it was not completely possible to identify specific lineages that evolved in situ, two major changes in the effective (female) population size were reconstructed. The more recent one, which began during the late Pleistocene glacial period and became steeper in the early Holocene, was probably the outcome of demographic events connected to western Eurasia. The Neolithic growth could be easily explained by the diffusion of dairy pastoralism, as already proposed, while the late glacial increase indicates, for the first time, a genetic connection with western Eurasian refuges, as supported by the unusual high frequency and internal sub-structure in Mongolia of haplogroup H1, a well-known post-glacial marker in Europe. Bronze Age events, without a significant demographic impact, might explain the age of some mtDNA haplogroups. Finally, a diachronic comparison with available ancient mtDNAs made it possible to link six mitochondrial lineages of present-day Mongolians to the timeframe and geographic path of the Silk Route.

Contrasting maternal and paternal genetic histories among five ethnic groups from Khyber Pakhtunkhwa, Pakistan

Northwest Pakistan has served as a point of entry to South Asia for different populations since ancient times. However, relatively little is known about the population genetic history of the people residing within this region. To better understand human dispersal in the region within the broader history of the subcontinent, we analyzed mtDNA diversity in 659 and Y-chromosome diversity in 678 individuals, respectively, from five ethnic groups (Gujars, Jadoons, Syeds, Tanolis and Yousafzais), from Swabi and Buner Districts, Khyber Pakhtunkhwa Province, Pakistan. The mtDNAs of all individuals were subject to control region sequencing and SNP genotyping, while Y-chromosomes were analyzed using 54 SNPs and 19 STR loci. The majority of the mtDNAs belonged to West Eurasian haplogroups, with the rest belonging to either South or East Asian lineages. Four of the five Pakistani populations (Gujars, Jadoons, Syeds, Yousafzais) possessed strong maternal genetic affinities with other Pakistani and Central Asian populations, whereas one (Tanolis) did not. Four haplogroups (R1a, R1b, O3, L) among the 11 Y-chromosome lineages observed among these five ethnic groups contributed substantially to their paternal genetic makeup. Gujars, Syeds and Yousafzais showed strong paternal genetic affinities with other Pakistani and Central Asian populations, whereas Jadoons and Tanolis had close affinities with Turkmen populations from Central Asia and ethnic groups from northeast India. We evaluate these genetic data in the context of historical and archeological evidence to test different hypotheses concerning their origins and biological relationships.

Genetic continuity of Indo-Iranian speakers since the Iron Age in southern Central Asia

Since prehistoric times, southern Central Asia has been at the crossroads of the movement of people, culture, and goods. Today, the Central Asian populations are divided into two cultural and linguistic groups: the Indo-Iranian and the Turko-Mongolian groups. Previous genetic studies unveiled that migrations from East Asia contributed to the spread of Turko-Mongolian populations in Central Asia and the partial replacement of the Indo-Iranian populations. However, little is known about the origin of the latters. To shed light on this, we compare the genetic data on two current-day Indo-Iranian populations — Yaghnobis and Tajiks — with genome-wide data from published ancient individuals. The present Indo-Iranian populations from Central Asia display a strong genetic continuity with Iron Age samples from Turkmenistan and Tajikistan. We model Yaghnobis as a mixture of 93% Iron Age individual from Turkmenistan and 7% from Baikal. For the Tajiks, we observe a higher Baikal ancestry and an additional admixture event with a South Asian population. Our results, therefore, suggest that in addition to a complex history, Central Asia shows a remarkable genetic continuity since the Iron Age, with only limited gene flow.

Genetic Relationship Among the Kazakh People Based on Y-STR Markers Reveals Evidence of Genetic Variation Among Tribes and Zhuz

Ethnogenesis of Kazakhs took place in Central Asia, a region of high genetic and cultural diversity. Even though archaeological and historical studies have shed some light on the formation of modern Kazakhs, the process of establishment of hierarchical socioeconomic structure in the Steppe remains contentious. In this study, we analyzed haplotype variation at 15 Y-chromosomal short-tandem-repeats obtained from 1171 individuals from 24 tribes representing the three socio-territorial subdivisions (Senior, Middle and Junior zhuz) in Kazakhstan to comprehensively characterize the patrilineal genetic architecture of the Kazakh Steppe. In total, 577 distinct haplotypes were identified belonging to one of 20 haplogroups; 16 predominant haplogroups were confirmed by SNP-genotyping. The haplogroup distribution was skewed towards C2-M217, present in all tribes at a global frequency of 51.9%. Despite signatures of spatial differences in haplotype frequencies, a Mantel test failed to detect a statistically significant correlation between genetic and geographic distance between individuals. An analysis of molecular variance found that ∼8.9% of the genetic variance among individuals was attributable to differences among zhuzes and ∼20% to differences among tribes within zhuzes. The STRUCTURE analysis of the 1164 individuals indicated the presence of 20 ancestral groups and a complex three-subclade organization of the C2-M217 haplogroup in Kazakhs, a result supported by the multidimensional scaling analysis. Additionally, while the majority of the haplotypes and tribes overlapped, a distinct cluster of the O2 haplogroup, mostly of the Naiman tribe, was observed. Thus, firstly, our analysis indicated that the majority of Kazakh tribes share deep heterogeneous patrilineal ancestries, while a smaller fraction of them are descendants of a founder paternal ancestor. Secondly, we observed a high frequency of the C2-M217 haplogroups along the southern border of Kazakhstan, broadly corresponding to both the path of the Mongolian invasion and the ancient Silk Road. Interestingly, we detected three subclades of the C2-M217 haplogroup that broadly exhibits zhuz-specific clustering. Further study of Kazakh haplotypes variation within a Central Asian context is required to untwist this complex process of ethnogenesis.

Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A pilot study on male Chinese Yunnan Zhaoyang Han population

Improving the resolution of the current widely used Y-chromosomal short tandem repeat (Y-STR) dataset is of great importance for forensic investigators, and the current approach is limited, except for the addition of more Y-STR loci. In this research, a regional Y-DNA database was investigated to improve the Y-STR haplotype resolution utilizing a Y-SNP Pedigree Tagging System that includes 24 Y-chromosomal single nucleotide polymorphism (Y-SNP) loci. This pilot study was conducted in the Chinese Yunnan Zhaoyang Han population, and 3473 unrelated male individuals were enrolled. Based on data on the male haplogroups under different panels, the matched or near-matching (NM) Y-STR haplotype pairs from different haplogroups indicated the critical roles of haplogroups in improving the regional Y-STR haplotype resolution. A classic median-joining network analysis was performed using Y-STR or Y-STR/Y-SNP data to reconstruct population substructures, which revealed the ability of Y-SNPs to correct misclassifications from Y-STRs. Additionally, population substructures were reconstructed using multiple unsupervised or supervised dimensionality reduction methods, which indicated the potential of Y-STR haplotypes in predicting Y-SNP haplogroups. Haplogroup prediction models were built based on nine publicly accessible machine-learning (ML) approaches. The results showed that the best prediction accuracy score could reach 99.71% for major haplogroups and 98.54% for detailed haplogroups. Potential influences on prediction accuracy were assessed by adjusting the Y-STR locus numbers, selecting Y-STR loci with various mutabilities, and performing data processing. ML-based predictors generally presented a better prediction accuracy than two available predictors (Nevgen and EA-YPredictor). Three tree models were developed based on the Yfiler Plus panel with unprocessed input data, which showed their strong generalization ability in classifying various Chinese Han subgroups (validation dataset). In conclusion, this study revealed the significance and application prospects of Y-SNP haplogroups in improving regional Y-STR databases. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences.

Biologia futura: confessions in genes

Y-DNA and mtDNA have been a widely used tool not only in forensic genetic applications but in human evolutionary and population genetic studies. Its paternal or maternal inheritance and lack of recombination have offered the opportunity to explore genealogical relationships among individuals and to study the frequency differences of paternal and maternal clades among human populations at continental and regional levels. It is unbelievable, but true, that the disadvantages of paternal and maternal lineages in forensic genetic studies, i.e., everyone within a family have the same paternal or maternal haplotype and haplogroup, become advantages in human evolutionary studies, i.e., reveal the genetic history of successful mothers and successful fathers. Thanks to these amazing properties of haploid markers, they provide tools for mapping the migration routes of human populations during prehistoric and historical periods, separately as maternal and paternal lineages, and together as the genetic history of a population.

Efficacy and Safety of Ticagrelor and Clopidogrel in Patients with Stable Coronary Artery Disease Undergoing Percutaneous Coronary Intervention

AIM

The efficacy and safety of ticagrelor and clopidogrel in patients with stable coronary artery disease (SCAD) undergoing percutaneous coronary intervention (PCI) remain uncertain. Thus, this study aimed to compare the efficacy and safety of ticagrelor and clopidogrel in patients with SCAD treated with PCI.

METHODS

A total of 9,379 patients with SCAD undergoing PCI who received dual antiplatelet therapy (DAPT) were consecutively enrolled in two groups, namely, ticagrelor (n=1,081) and clopidogrel (n=8,298) groups. Major adverse cardiovascular and cerebrovascular events (MACCEs) and bleeding events according to ticagrelor or clopidogrel use were compared.

RESULTS

After propensity matching (n=1,081 in each group), ticagrelor was associated with fewer MACCEs compared with clopidogrel (3.6% vs. 5.7%, hazard ratio [HR]=0.62, 95% confidence interval [CI] 0.41-0.93, p=0.019), and the difference between ticagrelor and clopidogrel for bleeding events was nonsignificant (4.0% vs. 3.2%, HR=1.24, 95% CI 0.79-1.93, p=0.356). On the other hand, the difference between ticagrelor and clopidogrel for net adverse clinical events was significant (4.1% vs. 6.0%, HR=0.67, 95% CI 0.46-0.98, p=0.039). In a multivariate analysis, the use of ticagrelor, number of stents, previous history of diabetes, previous history of smoking, and ACC/AHA type B2 or C lesions were considered independent predictors of MACCEs, while radial artery access, previous history of stroke, and weight ＜60kg were independent predictors of bleeding events. Conclusions Ticagrelor was associated with a lower incidence of MACCEs without an increased risk of bleeding events in patients with SCAD receiving PCI.

Phylogeographic review of Y chromosome haplogroups in Europe

The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.

Paternal genetic structure of Kyrgyz ethnic group in China revealed by high-resolution Y-chromosome STRs and SNPs

Kyrgyz ethnic group is one of the nomads in China, with the majority in Xinjiang and a small part of them living in Heilongjiang province. Historically, they have went through five migrations westward due to the wars. The name "Kyrgyz" means 40 tribes, originating from the primary groups of Kyrgyz. However, it is a largely understudied population, especially from the Y chromosome. In this study, we used a previously validated high-resolution Y-chromosome single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) system to study Kyrgyz ethnic group. A total of 314 male samples of Kyrgyz ethnic group were genotyped by 173 Y-SNPs and 27 Y-STRs. After data analysis, the results unveiled that Kyrgyz ethnic group was a population with high percentage of both haplogroup C2a1a3a1d∼-F10091 (91/134) and R1a1a1b2a2-Z2124 (109/134), which has never been reported. This implied that Kyrgyz ethnic group might have gone through bottleneck effects twice, with these two main lineages left. Mismatch analysis indicated that the biggest mismatch number in haplogroup C2a1a3a1d∼-F10091 was 10, while that of haplogroup R1a1a1b2a2-Z2124 was 20. This huge difference reflected the different substructure in two lineages, suggesting that haplogroup C2a1a3a1d∼-F10091 might have the least admixture compared to the other two lineages. After admixture modelling with other datasets, the conclusion could be drawn that Kyrgyz ethnic group had great genetic affinity with Punjabi from Lahore, Pakistan, which supported that Kyrgyz ethnic group in China was close to central Asian.

Genetic analysis of 32 InDels in four ethnic minorities from Chinese Xinjiang

The present study used the previously constructed 32-plex InDels panel to investigated the genetic diversity of four ethnic minorities (Hui, Mongol, Uygur and Kazakh) from Xinjiang, and analyzed the genetic relationships between the four populations and 27 reference populations. No significant deviations were observed from the Hardy-Weinberg equilibrium (HWE) at the 32 InDels for each population. The average observed heterozygosity (H_exp), average polymorphic information content (PIC), combined power of discrimination (CPD) and cumulative probability of exclusion (CPE) for the 32 InDels were all higher than the Qiagen Investigator DIPplex kit in the four populations from Xinjiang. The CPD ranged from 0.999999999999903 (Kazakh) to 0.999999999999952 (Hui) and CPE ranged from 0.9971 (Uygur) to 0.9985 (Hui), which indicated that the 32 InDels were capable for individual identification and could be a supplementary tool in paternity test for these populations. Population genetic analysis by the method of analysis of molecular variance (AMOVA), F_ST, phylogenetic tree, TreeMix-based topology, multi-dimensional scale analysis (MDS), principal components analysis (PCA) and STRUCTURE analysis showed that Xinjiang Hui population has a close relationship with East Asians (EAS), especially Chinese Han, and the populations of Xinjiang Mongol, Uygur and Kazakh showed mixed ancestral components related to EAS and Europeans (EUR).

Population genomics of East Asian ethnic groups

East Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.

Mutations in Collagen Genes in the Context of an Isolated Population

Genetic studies of population isolates have great potential to provide a unique insight into genetic differentiation and phenotypic expressions. Galičnik village is a population isolate located in the northwest region of the Republic of North Macedonia, established around the 10th century. Alport syndrome-linked nephropathy with a complex inheritance pattern has been described historically among individuals in the village. In order to determine the genetic basis of the nephropathies and to characterize the genetic structure of the population, 23 samples were genotyped using a custom-made next generation sequencing panel and 111 samples using population genetic markers. We compared the newly obtained population data with fifteen European population data sets. NGS analysis revealed four different mutations in three different collagen genes in twelve individuals within the Galičnik population. The genetic isolation and small effective population size of Galičnik village have resulted in a high level of genomic homogeneity, with domination of R1a-M458 and R1b-U106* haplogroups. The study explains complex autosomal in cis digenic and X-linked inheritance patterns of nephropathy in the isolated population of Galičnik and describes the first case of Alport syndrome family with three different collagen gene mutations.

The Y Chromosome: A Complex Locus for Genetic Analyses of Complex Human Traits

The Human Y chromosome (ChrY) has been demonstrated to be a powerful tool for phylogenetics, population genetics, genetic genealogy and forensics. However, the importance of ChrY genetic variation in relation to human complex traits is less clear. In this review, we summarise existing evidence about the inherent complexities of ChrY variation and their use in association studies of human complex traits. We present and discuss the specific particularities of ChrY genetic variation, including Y chromosomal haplogroups, that need to be considered in the design and interpretation of genetic epidemiological studies involving ChrY.

Genetic polymorphisms and phylogenetic analyses of the Ü-Tsang Tibetan from Lhasa based on 30 slowly and moderately mutated Y-STR loci

As a result of the expansion of old Tibet on the Qinghai-Tibet Plateau, Tibetans diverged into three main branches, Ü-Tsang, Amdo, and Kham Tibetan. Ü-Tsang Tibetans are geographically distributed across the wide central and western portions of the Qinghai-Tibet Plateau while Lhasa is the central gathering place for Tibetan culture. The AGCU Y30, a 6-dye fluorescence kit including 30 slowly and moderately mutated Y-STR loci, has been validated for its stability and sensitivity in different biomaterials and diverse Chinese populations (Han and other minorities), and widely used in the practical work of forensic science. However, the 30 Y-STR profiling of Tibetan, especially for Ü-Tsang Tibetan, were insufficient. We utilized the AGCU Y30 to genotype 577 Ü-Tsang Tibetan unrelated males from Lhasa in the Tibet Autonomous Region of China to fill up the full and accurate Y-STR profiles. A total of 552 haplotypes were observed, 536 (97.10%) of which were unique. One hundred and ninety-four alleles were observed at 26 single copy loci and the allelic frequencies ranged from 0.0017 to 0.8180. For the two multi-copy loci DYS385a/b and DYS527a/b, 64 and 36 allelic combinations were observed, respectively. The gene diversity (GD) values ranged from 0.3079 at DYS391 to 0.9142 at DYS385a/b and the overall haplotype diversity (HD) was 0.9998, and its discrimination capacity (DC) was 0.9567. The population genetic analyses demonstrated that Lhasa Ü-Tsang Tibetan had close relationships with other Tibetan populations from Tibet and Qinghai, especially with Ü-Tsang Tibetan. From the perspective of Y haplogroups, the admixture of the southward Qiang people with dominant haplogroup O-M122 and the northward migrations of the initial settlers of East Asia with haplogroup D-M175 hinted the Sino-Tibetan homologous, thus, we could not ignore the gene flows with other Sino-Tibetan populations, especially for Han Chinese, to characterize the forensic genetic landscape of Tibetan.

Resurecting raciology? Genetic ethnology and pre-1945 anthropological race classification

This article places the current high-profile and controversial scientific project that I call 'genetic ethnology' within the same two-century tradition of biologically classifying modern peoples as pre-1945 race anthropology. Similarities in how these two biological projects have combined political and scientific agendas raise questions about the liberalism of genetics and stimulate concerns that genetic constructions of human difference might revive a politics of hate, division and hierarchy. The present article however goes beyond existing work that links modern genetics with race anthropology. It systematically compares their many similar practices and organisational features, showing that both projects were political-scientific syntheses. Studying how the origins, geography, filiations, 'travels and encounters of our ancestors' affect 'current genetic variation', both seem to have responded to a continuous public demand for biologists to explain the histories of politically significant peoples and give them a scientific basis. I challenge habitual contrasts between apolitical scientific genetics and racist pseudoscience and use race anthropology as a parable for how, in the era of Brexit and Trump, right-wing identity politics might infect genetic ethnology. I argue however that although biology-based identities carry risks of essentialism and determinism, the practices and organisation of classification pose greater political dangers.

Forensic characteristics and phylogenetic analyses of one branch of Tai-Kadai language-speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia™ Platinum System

BACKGROUND

Hainan Island, located in the South China Sea and separated from the Leizhou Peninsula by Qiongzhou Strait, is the second largest island after Taiwan in China. With the expansion of Han Chinese and the gradual formation of "South Hlai and North Han", nowadays, Hainan Hlai is the second largest population after Han Chinese in Hainan Island. Ha Hlai, distributed in southwest and southern Hainan Island, is the dominant branch of Hlai and speaks Ha localism.

METHODS

We utilized the Huaxia™ Platinum PCR Amplification System (including 23 autosomal STRs and 2 sex-linked markers) to obtain the first STR profiling batch of 657 Ha Hlai individuals (497 males and 160 females). In order to explore the genetic relationships between the studied Ha Hlai and other reference populations with different language families, population genetic analyses, including PCA, MDS, STRUCTURE, and phylogenetic analysis, were conducted based upon the raw data and allelic frequencies of the polymorphic autosomal STR markers.

RESULTS

In total, 271 distinct alleles were observed at the 23 STR loci. The number of diverse alleles ranged from 7 at TPOX locus to 23 at FGA locus, and the allelic frequencies varied from 0.0008 to 0.5533. In addition, the CPE and CPD were 1-7.39 × 10-10 and 1-3.13 × 10-28 , respectively. The phylogenetic analyses indicated that Ha Hlai is a Tai-Kadai language-speaking and relatively isolated population which has a close genetic and geographical relationship with Hainan Hlai, and M95 is the dominant haplogroup in Ha Hlai (56.18%).

CONCLUSION

The 23 autosomal STR genetic markers were highly polymorphic as well as potentially useful for forensic applications in Hainan Ha Hlai population. The phylogenetic analyses demonstrated that small geographic scale gene flows could not be ignored and the shaping of the unique gene pool for each population was the combination effects of geographic, language, and cultural isolations.

Sequencing of human identification markers in an Uyghur population using the MiSeq FGxTM Forensic Genomics System

Massively parallel sequencing (MPS) offers a useful alternative to capillary electrophoresis (CE) based analysis of human identification markers in forensic genetics. By sequencing short tandem repeats (STRs) instead of determining the fragment lengths by CE, the sequence variation within the repeat region and the flanking regions may be identified. In this study, we typed 264 Uyghur individuals using the MiSeq FGx™ Forensic Genomics System and Primer Mix A of the ForenSeq™ DNA Signature Prep Kit that amplifies 27 autosomal STRs, 25 Y-STRs, seven X-STRs, and 94 HID-SNPs. STRinNGS v.1.0 and GATK 3.6 were used to analyse the STR regions and HID-SNPs, respectively. Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were 3–4 times larger than those of alleles determined by repeat length alone. A relatively large number of flanking region variants (28 SNPs and three InDels) were observed in the Uyghur population. Seventeen of the flanking region SNPs were rare, and 12 of these SNPs had no accession number in dbSNP. The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85E−36 and 1.49E + 16, respectively. This was 10 000 times lower and 1 000 times higher, respectively, than the same parameters calculated from STR repeat lengths.

Key Points

Sequencing data on STRs and SNPs used for human identification are presented for the Uyghur population.

STRinNGS v.1.0 was used to analyse the flanking regions of STRs.

The concordance between PCR-CE and PCR-MPS results was 99.86%.

Detection of sequence variation in STRs and their flanking regions increased the allelic diversity.

Haplotypic diversity and population genetic study of a population in Kashi region by 27 Y-chromosomal short tandem repeat loci

BACKGROUND

Y-chromosomal short tandem repeats (Y-STRs) have been certified to be the serviceable markers for some paternity cases in the last few years.

METHODS

We presented the gene diversity, haplotypic diversity, and forensic statistical parameters of 340 unrelated Uighur males from Kashi region based on the 27 Y-STRs. Genomic DNA was extracted from bloodstain samples using the Chelex-100 method and amplified by Yfiler® Plus PCR Amplification kit.

RESULTS

Gene diversity values on the 27 Y-STRs ranged from 0.4749 (at DYS437 locus) to 0.9416 (at DYS385a,b loci). According to forensic parameters of the 27 Y-STR loci, 295 disparate haplotypes were acquired, 258 of which were unique. The haplotypic diversities and discrimination capacities at Yfiler plus 27 loci, Yfiler 17 loci, extended 11 loci, and minimal 9 loci were 0.9990 and 0.8676; 0.9961 and 0.6912; 0.9952 and 0.5941; and 0.9919 and 0.5676, respectively. Multidimensional scaling plot and neighbor-joining tree between the studied Uighur group and 17 reference populations were conducted, and the obtained results indicated the Kashi Uighur group had the closer genetic relationships with Uighur groups living in different regions.

CONCLUSION

To sum up, the present study may provide valuable population data and background information of Kashi Uighur group.

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler^™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.

Mitochondrial DNA diversity in the Khattak and Kheshgi of the Peshawar Valley, Pakistan

The strategic location of Pakistan and its presence at the crossroads of Asia has resulted in it playing a central role in both prehistoric and historic human migratory events, thereby linking and facilitating contacts between the inhabitants of the Middle East, Central Asia, China and South Asia. Despite the importance of this region and its inhabitants for our understanding of modern human origins and population dispersals, the nature of mitochondrial DNA (mtDNA) variation among members of the myriad populations of this area has largely been unexplored. Here, we report mtDNA control region sequences in 58 individuals from the Khattak and the Kheshgi, two major Pakhtun tribes residing within the Peshawar Valley of northwestern Pakistan. The results reveal that these ethnic groups are genetically heterogeneous, having 55.7% West Eurasian, 33.9% South Asian and 10.2% East Asian haplogroups. The genetic diversity observed for the Kheshgi was somewhat higher than that of the Khattak. A multidimensional scaling plot based on haplogroup frequencies for the Khattak, Kheshgi and neighboring populations indicates that the Khattak have close affinities with Baluch, Uzbek and Kazak populations but are only distantly related to the Kheshgi and other Pakistani populations. By contrast, the Kheshgi cluster closely with other Pakhtun or Pathan populations of Pakistan, suggesting a possible common maternal gene pool shared amongst them. These mtDNA data allow us to begin reconstructing the origins of the Khattak and Kheshgi and describe their complex interactions with populations from the surrounding regions.

New insights on intercontinental origins of paternal lineages in Northeast Brazil

Background

The current Brazilian population is the product of centuries of admixture between intercontinental founding groups. Although previous results have revealed a heterogeneous distribution of mitochondrial lineages in the Northeast region, the most targeted by foreign settlers during the sixteenth century, little is known about the paternal ancestry of this particular population. Considering historical records have documented a series of territorial invasions in the Northeast by various European populations, we aimed to characterize the male lineages found in Brazilian individuals in order to discover to what extent these migrations have influenced the present-day gene pool. Our approach consisted of employing four hierarchical multiplex assays for the investigation of 45 unique event polymorphisms in the non-recombining portion of the Y-chromosome of 280 unrelated men from several Northeast Brazilian states.

Results

Primary multiplex results allowed the identification of six major haplogroups, four of which were screened for downstream SNPs and enabled the observation of 19 additional lineages. Results reveal a majority of Western European haplogroups, among which R1b-S116* was the most common (63.9%), corroborating historical records of colonizations by Iberian populations. Nonetheless, F_ST genetic distances show similarities between Northeast Brazil and several other European populations, indicating multiple origins of settlers. Regarding Native American ancestry, our findings confirm a strong sexual bias against such haplogroups, which represented only 2.5% of individuals, highly contrasting previous results for maternal lineages. Furthermore, we document the presence of several Middle Eastern and African haplogroups, supporting a complex historical formation of this population and highlighting its uniqueness among other Brazilian regions.

Conclusions

We performed a comprehensive analysis of the major Y-chromosome lineages that form the most dynamic migratory region from the Brazilian colonial period. This evidence suggests that the ongoing entry of European, Middle Eastern, and African males in the Brazilian Northeast, since at least 500 years, was significantly responsible for the present-day genetic architecture of this population.

Analysis of Uyghur and Kazakh populations using the Precision ID Ancestry Panel

Autosomal ancestry informative markers (AIMs) are important markers for inferring ancestry of humans. In the present study, we typed 105 Uyghurs and 94 Kazakhs with the Precision ID Ancestry Panel that amplifies 165 autosomal AIMs. No statistically significant deviation from Hardy-Weinberg equilibrium and no linkage disequilibrium between loci was observed after Bonferroni correction. STRUCTURE and PCA analyses showed that Uyghurs and Kazakhs appeared as admixed individuals of primarily European and East Asian ancestry and were clearly differentiated from Europeans, Middle Easterners, South/Central Asians, and East Asians. However, it was not possible to differentiate the two populations from each other and they were also difficult to differentiate from Greenlanders, a population with European/Inuit admixture. GenoGeographer was used to evaluate the weight of the evidence. Initially, the results showed that the majority of AIM profiles from Uyghur and Kazakh individuals were not represented by any of the 36 reference populations of the GenoGeographer database. Consequently, it was not reasonable to infer the ancestry of these individuals. A randomly selected subset of the studied populations (75 Uyghur and 75 Kazakh individuals) was used to construct two new reference populations for GenoGeographer, and ancestry prediction was performed on the remaining test individuals. A total of 42 out of 49 test individuals were represented by at least one population after the introduction of Uyghur and Kazakh reference populations. Likelihood ratios ≥10⁶ were obtained when the alternative hypothesis was that the individual belonged to the South/Central Asian, East Asian, Middle Eastern, European, or the admixed Greenlandic population.

Phylogeography of Y-chromosome haplogroup Q1a1a-M120, a paternal lineage connecting populations in Siberia and East Asia

Background: Previous studies have suggested that the human Y-chromosome haplogroup Q1a1a-M120, a widespread paternal lineage in East Asian populations, originated in South Siberia. However, much uncertainty remains regarding the origin, diversification, and expansion of this paternal lineage.Aim: To explore the origin and diffusion of paternal Q-M120 lineages in East Asia.Subjects and methods: The authors generated 26 new Y chromosome sequences of Q-M120 males and co-analysed 45 Y chromosome sequences of this haplogroup. A highly-revised phylogenetic tree of haplogroup Q-M120 with age estimates was reconstructed. Additionally, a comprehensive phylogeographic analysis of this lineage was performed including 15,007 samples from 440 populations in eastern Eurasia.Results: An ancient connection of this lineage with populations in Siberia was revealed. However, this paternal lineage experienced an in-situ expansion between 5000 and 3000 years ago in northwestern China. Ancient populations with high frequencies of Q-M120 were involved in the formation of ancient Huaxia populations before 2000 years ago; this haplogroup eventually became one of the founding paternal lineages of modern Han populations.Conclusion: This study provides a clear pattern of the origin and diffusion process of haplogroup Q1a1a-M120, as well as the role of this paternal lineage during the formation of ancient Huaxia populations and modern Han populations.

Relating Clans Ao and Aisin Gioro from northeast China by whole Y-chromosome sequencing

The Y-chromosome haplogroup C2b1a3a2-F8951 is the paternal lineage of the Aisin Gioro clan, the most important brother branch of the famous Mongolic-speaking population characteristic haplogroup C2*-Star Cluster (C2b1a3a1-F3796). However, investigations on its internal phylogeny are still limited. In this study, we used whole Y-chromosome sequencing to update its phylogenetic tree. In the revised tree, C2b1a3a2-F8951 and C2*-Star Cluster differentiated 3852 years ago (95% CI = 3295-4497). Approximately 3558 years ago (95% CI = 3013-4144), C2b1a3a2-F8951 was divided into two main subclades, C2b1a3a2a-F14753 and C2b1a3a2b-F5483. Currently, samples of C2b1a3a2-F8951 were mainly from the House of Aisin Gioro clan, the Ao family from Daur and some individuals mainly from northeast China. Although other haplogroups are also found in the Ao family, including C2b1a2-M48, C2b1a3a1-F3796, C2a1b-F845, and N1c-M178, the haplogroup C2b1a3a2-F8951 is still the most distinct genetic component. For haplogroup C2b1a3a2-F8951, the time of the most recent common ancestor of the House of Aisin Gioro clan and the Ao family were both very late, just a few hundred years ago. Some family-specific Y-SNPs of the House of Aisin Gioro and the Ao family were also discovered. This revision evidently improved the resolving power of Y-chromosome phylogeny in northeast Asia, deepening our understanding of the origin of these two families, even the Mongolic-speaking population.

The genetic legacy of the Yaghnobis: A witness of an ancient Eurasian ancestry in the historically reshuffled central Asian gene pool

OBJECTIVES

The Yaghnobis are an ethno-linguistic minority historically settled along the Yaghnob River in the Upper-Zarafshan Valley in Tajikistan. They speak a language of Old Sogdian origin, which is the only present-day witness of the Lingua Franca used along the Silk Road in Late Antiquity. The aim of this study was to reconstruct the genetic history of this community in order to shed light on its isolation and genetic ancestry within the Euro-Asiatic context.

MATERIALS AND METHODS

A total of 100 DNA samples were collected in the Yaghnob and Matcha Valleys during several expeditions and their mitochondrial, Y-chromosome and autosomal genome-wide variation were compared with that from a large set of modern and ancient Euro-Asiatic samples.

RESULTS

Findings from uniparental markers highlighted the long-term isolation of the Yaghnobis. Mitochondrial DNA ancestry traced an ancient link with Middle Eastern populations, whereas Y-chromosome legacy showed more tight relationships with Central Asians. Admixture, outgroup-f3, and D-statistics computed on autosomal variation corroborated Y-chromosome evidence, pointing respectively to low Anatolian Neolithic and high Steppe ancestry proportions in Yaghnobis, and to their closer affinity with Tajiks than to Iranians.

DISCUSSION

Although the Yaghnobis do not show evident signs of recent admixture, they could be considered a modern proxy for the source of gene flow for many Central Asian and Middle Eastern groups. Accordingly, they seem to retain a peculiar genomic ancestry probably ascribable to an ancient gene pool originally wide spread across a vast area and subsequently reshuffled by distinct demographic events occurred in Middle East and Central Asia.

Deciphering DMET genetic data: comprehensive assessment of Northwestern Han, Tibetan, Uyghur populations and their comparison to eleven 1000 genome populations

We investigated the allele frequencies of drug absorption, distribution, metabolism and elimination (ADME)-related drug-metabolizing enzymes and transporters (DMET) genes in the Northwestern Han, Tibetan and Uyghur populations and compared the related genes in these three populations with those in eleven 1000 Genome populations. We examined 1936 single nucleotide polymorphisms of 225 DMET genes involved in ADME processes and found 732, 679 and 804 sites were polymorphic in Han, Tibetan and Uyghur. Tibetan differed from Han in only four sites (p < .05), whereas Uyghur differed from Han and Tibetan in 24 and 21 sites, respectively (p < .05). The distributions of 1058 genotyping data of 245 individuals from Han, Tibetan and Uyghur were compared with 1207 other individuals from the eleven 1000 Genomes populations. The top four populations in Han that exhibited the smallest pairwise Fst values were CHB, Tibetan, CHD and JPT; those in Tibetan were Han, CHB, Uyghur and CHD; and those in Uyghur were Han, Tibetan, GIH and CEU. MEGA results revealed that CHB, CHD, JPT, Han, Tibetan and Uyghur were grouped in cluster 1. GIH, MEX, CEU and TSI were grouped in cluster 2. MKK, ASW, LWK and YRI were grouped in cluster 3.

Dispersals of the Siberian Y-chromosome haplogroup Q in Eurasia

The human Y-chromosome has proven to be a powerful tool for tracing the paternal history of human populations and genealogical ancestors. The human Y-chromosome haplogroup Q is the most frequent haplogroup in the Americas. Previous studies have traced the origin of haplogroup Q to the region around Central Asia and Southern Siberia. Although the diversity of haplogroup Q in the Americas has been studied in detail, investigations on the diffusion of haplogroup Q in Eurasia and Africa are still limited. In this study, we collected 39 samples from China and Russia, investigated 432 samples from previous studies of haplogroup Q, and analyzed the single nucleotide polymorphism (SNP) subclades Q1a1a1-M120, Q1a2a1-L54, Q1a1b-M25, Q1a2-M346, Q1a2a1a2-L804, Q1a2b2-F1161, Q1b1a-M378, and Q1b1a1-L245. Through NETWORK and BATWING analyses, we found that the subclades of haplogroup Q continued to disperse from Central Asia and Southern Siberia during the past 10,000 years. Apart from its migration through the Beringia to the Americas, haplogroup Q also moved from Asia to the south and to the west during the Neolithic period, and subsequently to the whole of Eurasia and part of Africa.