Origin and diffusion of human Y chromosome haplogroup J1-M267

Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan

BACKGROUND

The Kazakhs are one of the biggest Turkic-speaking ethnic groups, controlling vast swaths of land from the Altai to the Caspian Sea. In terms of area, Kazakhstan is ranked ninth in the world. Northern, Eastern, and Western Kazakhstan have already been studied in relation to genetic polymorphism 27 Y-STR. However, current information on the genetic polymorphism of the Y-chromosome of Southern Kazakhstan is limited only by 17 Y-STR and no geographical study of other regions has been studied at this variation.

RESULTS

The Kazakhstan Y-chromosome Haplotype Reference Database was expanded with 468 Kazakh males from the Zhambyl and Turkestan regions of South Kazakhstan by having their 27 Y-STR loci and 23 Y-SNP markers analyzed. Discrimination capacity (DC = 91.23%), haplotype match probability (HPM = 0.0029) and haplotype diversity (HD = 0.9992) are defined. Most of this Y-chromosome variability is attributed to haplogroups C2a1a1b1-F1756 (2.1%), C2a1a2-M48 (7.3%), C2a1a3-F1918 (33.3%) and C2b1a1a1a-M407 (6%). Median-joining network analysis was applied to understand the relationship between the haplotypes of the three regions. In three genetic layer can be described the position of the populations of the Southern region of Kazakhstan-the geographic Kazakh populations of Kazakhstan, the Kazakh tribal groups, and the people of bordering Asia.

CONCLUSION

The Kazakhstan Y-chromosome Haplotype Reference Database was formed for 27 Y-STR loci with a total sample of 1796 samples of Kazakhs from 16 regions of Kazakhstan. The variability of the Y-chromosome of the Kazakhs in a geographical context can be divided into four main clusters-south, north, east, west. At the same time, in the genetic space of tribal groups, the population of southern Kazakhs clusters with tribes from the same region, and genetic proximity is determined with the populations of the Hazaras of Afghanistan and the Mongols of China.

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.

Assembly of 43 human Y chromosomes reveals extensive complexity and variation

The prevalence of highly repetitive sequences within the human Y chromosome has prevented its complete assembly to date1 and led to its systematic omission from genomic analyses. Here we present de novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution and report considerable diversity in size and structure. Half of the male-specific euchromatic region is subject to large inversions with a greater than twofold higher recurrence rate compared with all other chromosomes2. Ampliconic sequences associated with these inversions show differing mutation rates that are sequence context dependent, and some ampliconic genes exhibit evidence for concerted evolution with the acquisition and purging of lineage-specific pseudogenes. The largest heterochromatic region in the human genome, Yq12, is composed of alternating repeat arrays that show extensive variation in the number, size and distribution, but retain a 1:1 copy-number ratio. Finally, our data suggest that the boundary between the recombining pseudoautosomal region 1 and the non-recombining portions of the X and Y chromosomes lies 500 kb away from the currently established1 boundary. The availability of fully sequence-resolved Y chromosomes from multiple individuals provides a unique opportunity for identifying new associations of traits with specific Y-chromosomal variants and garnering insights into the evolution and function of complex regions of the human genome.

Challenges in the recovery of the genetic data from human remains found on the Western Balkan migration route

Traditional DNA-based identification of human remains relies on the system of matching STR profile of the deceased with the family references or antemortem samples. In forensic cases without any available samples for the comparison, the body remains unidentified. The aim of this study was to assess the applicability of massively parallel sequencing (MPS) approach in the forensic cases of five drowned individuals recovered on the Western Balkan migration route. Besides capillary electrophoresis (CE)-based genetic profiling (aSTR, Y STR, and mitochondrial control region sequencing) of postmortem samples, we applied ForenSeq DNA Signature Prep Kit/Primer Mix B on MiSeqFGx platform and concomitant ForenSeq Universal Analysis (UAS) software. The assay showed high reproducibility and complete concordance with CE-based data except in locus DYF387S1. Allele and locus drop was evident in 2.9% of total SNPs that slightly reduced the completeness of the data. We endeavored to predict the phenotype of the tested samples and accurate biogeographical ancestry of European individual. UAS was less informative for the remaining samples assigned to Admixed American cluster. Nevertheless, the application of FROG-kb and Snipper tools along with admixture analysis in STRUCTURE and lineage markers revealed likely Middle Eastern and North African ancestry. We conclude that the combination of the phenotype and biogeographical ancestry predictions, including paternal and maternal genetic ancestry, represent a promising tool for humanitarian identification of dead migrants. Nevertheless, the data interpretation remains a challenging task.

Population genetic study of 17 Y-STR Loci of the Sorani Kurds in the Province of Sulaymaniyah, Iraq

Background

The Kurds as an ethnic group are believed to be a combination of earlier Indo-European tribes who migrated and inhabited a mountainous area thousands of years ago. However, as it is difficult to describe the precise history of their origin, it is necessary to investigate their population relationship with other geographical and ethnic groups.

Results

Seventeen Short Tandem Repeat markers on the Y chromosome (Y-STR) included in the AmpFLSTR™ Yfiler™ PCR Amplification Kit (Thermo Fisher Scientific, USA) were used to type DNA samples from the Sorani (Central) Kurdish population in Sulaymaniyah province. One hundred fifty-seven haplotypes were obtained from 162 unrelated male individuals. The highest and lowest gene diversities were DYS385a/b (GD = 0.848) and DYS392 (GD = 0.392), respectively. The haplotypes were used to predict the most likely haplogroups in the Sulaymaniyah population.

Conclusion

Haplogroup prediction indicated predominance (28%) of subclade J2 (44/157) in the Sorani Kurds, northeast of Iraq. The pairwise genetic distance results showed that the Kurdish group clustered along with Asian populations, whereas the furthest countries were Europeans and Africans.

Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas

The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in the genetic history of Panamanians, as testified by the high proportions of Indigenous and sub-Saharan mitochondrial DNAs (mtDNAs) and by the prevalence of Western European/northern African Y chromosomes. Those studies were conducted on the general population without considering any self-reported ethnic affiliations. Here, we compared the mtDNA and Y-chromosome lineages of a new sample collection from 431 individuals (301 males and 130 females) belonging to either the general population, mixed groups, or one of five Indigenous groups currently living in Panama. We found different proportions of paternal and maternal lineages in the Indigenous groups testifying to pre-contact demographic events and genetic inputs (some dated to Pleistocene times) that created genetic structure. Then, while the local mitochondrial gene pool was marginally involved in post-contact admixtures, the Indigenous Y chromosomes were differentially replaced, mostly by lineages of western Eurasian origin. Finally, our new estimates of the sub-Saharan contribution, on a more accurately defined general population, reduce an apparent divergence between genetic and historical data.

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

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