Deep phylogenetic analysis of haplogroup G1 provides estimates of SNP and STR mutation rates on the human Y-chromosome and reveals migrations of Iranic speakers

Population dataset for 23 Y-STR in the Merkit clan form Kazakh population

This study presents a comprehensive analysis of 23 Y-STR data for the Merkit clan, a subgroup within the Kerey tribe of the Kazakh people. A total of 64 complete haplotypes were generated using the PowerPlex Y23 System. The data obtained using 23 Y-STR markers has been submitted to the Y Chromosome Haplotype Reference Database (YHRD) at yhrd.org, which will significantly enhance the forensic database for the Kazakh population in Kazakhstan. The research focuses on the distribution of haplotypes within the clan and their genealogical lines, which were visualized using a Median-joining network and Multidimensional scaling plot. The study identifies four distinct haplogroup clusters, revealing important insights into the genetic makeup and historical lineage of the Merkits. This dataset not only enriches our understanding of Kazakh genetic structure but also holds significant value for anthropological and population genetic research, as well as for forensic genetics. This work bridges a notable gap in genetic research on the Merkit clan, contributing to a deeper understanding of Central Asian nomadic tribes.

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.

Investigation on the genetic-inconsistent paternity cases using the MiSeq FGx system

Mutations might challenge the paternity index calculation in forensic identification. While many studies have focussed on the autosomal short tandem repeats (A-STR), the mutation status of sex chromosomes and single nucleotide polymorphism (SNP) remain blank. Next generation sequencing (NGS), known as high throughput and large sequence polymorphism, is a promising tool for forensic genetics. To describe the mutation landscapes in the paternity cases with genetic inconsistencies, a total of 63 parentage confirmed paternity cases contained at least one mismatched locus have been collected. The mutations were subsequently evaluated using Verogen's MPS ForenSeq^TM DNA Signature Kit and a microsatellite instability (MSI) detection kit. The result showed 98.41% (62/63) of the cases had no additional autosomal mutations even when the number of A-STRs increased to 27. As for the sex chromosomes, about 11.11% (7/63) of the cases exhibited either X-STR or Y-STR mutations. D2S1338, FGA and Penta E were the most frequent altered STRs, which suggested they might be the mutation hotspots. In addition, a male with sex chromosome abnormality was observed accidently, whose genotype might be 47, XXY, rather than MSI. Nearly 56.90% of the STR loci possessed isoalleles, which might result in higher STR polymorphisms. No Mendelian incompatibility was detected among the SNP markers, which indicated that SNP was a more reliable genetic marker in the genetic-inconsistent paternity cases. Supplemental data for this article is available online at https://doi.org/10.1080/20961790.2021.2009631 .

Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Eastern Kazakhstan

BACKGROUND

The establishment of a national haplotype database is important for forensic and genetic applications and requires studying genetic polymorphisms at Y-STR sites. However, the genetic structure of the Eastern Kazakhstan population is poorly characterised.

AIM

To investigate the genetic polymorphisms of 27 Y-STR loci in the Kazakh population from Eastern Kazakhstan and analyse the population genetic relationships of the Eastern Kazakhs with other populations.

SUBJECTS AND METHODS

The Yfiler Plus kit was utilised to genotype 246 healthy, unrelated males from Eastern Kazakhstan. Based on the raw data, haplotype and allele frequencies along with forensic parameters were calculated, and an MDS plot was constructed.

RESULTS

A total of 207 haplotypes were detected, of which 186 were unique. The haplotype diversity and discrimination capacity were 0.997 and 0.841, respectively. Population comparisons showed that Eastern Kazakhs have close genetic relationships with Kazakhs from Xinjiang, China. At the same time, a difference was found between the studied population and the previous one in the same part of Kazakhstan.

CONCLUSIONS

The obtained haplotypes will help to expand the Kazakhstan Y-chromosome reference database and will be useful for future genetic research and forensic applications.

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.

Whole-Genome Sequencing and Genomic Variant Analysis of Kazakh Individuals

Kazakhstan, the ninth-largest country in the world, is located along the Great Silk Road and connects Europe with Asia. Historically, its territory has been inhabited by nomadic tribes, and modern-day Kazakhstan is a multiethnic country with a dominant Kazakh population. We sequenced and analyzed the genomes of five ethnic Kazakhs at high coverage using the Illumina HiSeq2000 next-generation sequencing platform. The five Kazakhs yielded a total number of base pairs ranging from 87,308,581,400 to 107,526,741,301. On average, 99.06% were properly mapped. Based on the Het/Hom and Ti/Tv ratios, the quality of the genomic data ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Genetic variants were identified and annotated. Functional analysis of the genetic variants identified several variants that were associated with higher risks of metabolic and neurogenerative diseases. The present study showed high levels of genetic admixture of Kazakhs that were comparable to those of other Central Asians. These whole-genome sequence data of healthy Kazakhs could contribute significantly to biomedical studies of common diseases as their findings could allow better insight into the genotype–phenotype relations at the population level.

Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Northern Kazakhstan

BACKGROUND

Previous studies of the genetic polymorphism of the Y-chromosome of Kazakhs were focused on the Eastern, Central, Southern, and Western regions of Kazakhstan. In addition, many of these studies were limited to 17 Y-STR loci from the Yfiler.

AIM

To enrich the existing Kazakhstan Y-chromosome Haplotype Reference Database from the Northern Kazakh population data by a wide set of 27 Y-STR and investigate the population genetic relationships with previously published data.

SUBJECTS AND METHODS

27 Y-STR loci from the Yfiler Plus PCR Amplification Kit were analysed in 382 healthy unrelated Kazakh males from Northern Kazakhstan. Genetic polymorphism was analysed using Arlequin software.

RESULTS

A total of 326 distinct haplotypes of the 27 Y-STR loci were observed in 382 individuals. The discrimination capacity (0.9982) and haplotype diversity (0.8534) were computed. A total of 168 alleles at single-copy loci were observed, and their frequencies ranged from 0.003 to 0.843. The pairwise genetic distance (R_ST) showed that the Northern Kazakh population is genetically distinct from the Chinese Kazakh population.

CONCLUSIONS

Genetic polymorphism shows that the potential value of 27 Y-STR loci for forensic casework in the Northern Kazakh population, and the current findings, might be beneficial for paternal lineages in the study of population genetics.

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.

Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome

The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.

Medieval Super-Grandfather founder of Western Kazakh Clans from Haplogroup C2a1a2-M48

Western Kazakhstan is populated by three clans totaling 2 million people. Since the clans are patrilineal, the Y-chromosome is the most informative genetic system for tracing their origin. We genotyped 40 Y-SNP and 17 Y-STR markers in 330 Western Kazakhs. High phylogenetic resolution within haplogroup C2a1a2-M48 was achieved by using additional SNPs. Three lines of evidence indicate that the Alimuly and Baiuly clans (but not the Zhetiru clan) have a common founder placed 700 ± 200 years back by the STR data and 500 ± 200 years back by the sequencing data. This supports traditional genealogy claims about the descent of these clans from Emir Alau, who lived 650 years ago and whose lineage might be carried by two-thirds of Western Kazakhs. There is accumulation of specific haplogroups in the subclans representing other lineages, confirming that the clan structure corresponds with the paternal genetic structure of the steppe population.

Cartographic atlas of frequency variation for 45 pharmacogenetic markers in populations of Russia and its neighbor states

The lack of information about the frequency of pharmacogenetic markers in Russia impedes the adoption of personalized treatment algorithms originally developed for West European populations. The aim of this paper was to study the distribution of some clinically significant pharmacogenetic markers across Russia. A total of 45 pharmacogenetic markers were selected from a few population genetic datasets, including ADME, drug target and hemostasis-controlling genes. The total number of donors genotyped for these markers was 2,197. The frequencies of these markers were determined for 50 different populations, comprised of 137 ethnic and subethnic groups. A comprehensive pharmacogenetic atlas was created, i.e. a systematic collection of gene geographic maps of frequency variation for 45 pharmacogenetic DNA markers in Russia and its neighbor states. The maps revealed 3 patterns of geographic variation. Clinal variation (a gradient change in frequency along the East-West axis) is observed in the pharmacogenetic markers that follow the main pattern of variation for North Eurasia (13% of the maps). Uniform distribution singles out a group of markers that occur at average frequency in most Russian regions (27% of the maps). Focal variation is observed in the markers that are specific to a certain group of populations and are absent in other regions (60% of the maps). The atlas reveals that the average frequency of the marker and its frequency in individual populations do not indicate the type of its distribution in Russia: a gene geographic map is needed to uncover the pattern of its variation.

Paternal genetic history of the Yong population in northern Thailand revealed by Y-chromosomal haplotypes and haplogroups

We have determined the distribution of Y-chromosomal haplotypes and haplogroups in the Yong population, one of the largest and well-known ethnic groups that began migrating southward from China to Thailand centuries ago. Their unique mass migration pattern provided great opportunities for researchers to study the genetic links of the transboundary migration movements among the peoples of China, Myanmar and Thailand. We analysed relevant male-specific markers, such as Y-STRs and Y-SNPs, and the distribution of 23 Y-STRs of 111 Yong individuals and 116 nearby ethnic groups including the Shan, Northern Thai, Lawa, Lua, Skaw, Pwo and Padong groups. We found that the general haplogroup distribution values were similar among different populations; however, the haplogroups O1b-M268 and O2-M112 constituted the vast majority of these values. In contrast with previous maternal lineage studies, the paternal lineage of the Yong did not relate to the Xishuangbanna Dai people, who represent their historically documented ancestors. However, they did display a close genetic affinity to other prehistoric Tai-Kadai speaking groups in China such as the Zhuang and Bouyei. Low degrees of genetic admixture within the populations who belonged to the Austroasiatic and Sino-Tibetan linguistic families were observed in the gene pool of the Yong populations. Resettlement in northern Thailand in the early part of the nineteenth century AD, by way of mass migration trend, was able to preserve the Yong's ancestral genetic background in terms of the way they had previously lived in China and Myanmar. Our study has revealed similar genetic structures among ethnic populations in northern Thailand and southern China, and has identified and emphasized an ancient Tai-Kadai patrilineal ancestry line in the Yong ethnic group.

Forensic Y-SNP analysis beyond SNaPshot: High-resolution Y-chromosomal haplogrouping from low quality and quantity DNA using Ion AmpliSeq and targeted massively parallel sequencing

Y-chromosomal haplogroups assigned from male-specific Y-chromosomal single nucleotide polymorphisms (Y-SNPs) allow paternal lineage identification and paternal bio-geographic ancestry inference, both being relevant in forensic genetics. However, most previously developed forensic Y-SNP tools did not provide Y haplogroup resolution on the high level needed in forensic applications, because the limited multiplex capacity of the DNA technologies used only allowed the inclusion of a relatively small number of Y-SNPs. In a proof-of-principle study, we recently demonstrated that high-resolution Y haplogrouping is feasible via two AmpliSeq PCR analyses and simultaneous massively parallel sequencing (MPS) of 530 Y-SNPs allowing the inference of 432 Y-haplogroups. With the current study, we present a largely improved Y-SNP MPS lab tool that we specifically designed for the analysis of low quality and quantity DNA often confronted with in forensic DNA analysis. Improvements include i) Y-SNP marker selection based on the "minimal reference phylogeny for the human Y chromosome" (PhyloTree Y), ii) strong increase of the number of targeted Y-SNPs allowing many more Y haplogroups to be inferred, iii) focus on short amplicon length enabling successful analysis of degraded DNA, and iv) combination of all amplicons in a single AmpliSeq PCR and simultaneous sequencing allowing single DNA aliquot use. This new MPS tool simultaneously analyses 859 Y-SNPs and allows inferring 640 Y haplogroups. Preliminary forensic developmental validation testing revealed that this tool performs highly accurate, is sensitive and robust. We also provide a revised software tool for analysing the sequencing data produced by the new MPS lab tool including final Y haplogroup assignment. We envision the tools introduced here for high-resolution Y-chromosomal haplogrouping to determine a man's paternal lineage and/or paternal bio-geographic ancestry to become widely used in forensic Y-chromosome DNA analysis and other applications were Y haplogroup information from low quality / quantity DNA samples is required.

Reconstructing the genetic structure of the Kazakh from clan distribution data

Applying quasigenetic markers - non-biological traits which are nevertheless inherited in generations - is one of the research fields within human population genetics. For the West European, East European, and Caucasus populations, surnames are typical quasigenetic markers. For Central Asian populations, particularly Kazakh, the clan affiliation serves as a good marker: a set of papers demonstrated that many clans include mainly persons which biologically descent from a recent common ancestor. In this study, we analyzed a large (~4.2 million persons) dataset on quasigenetic markers - the geographic distribution of 50 Kazakh clans at the beginning of the 20th century, and compared the dataset with the direct data of the Y-chro-mosomal diversity in modern Kazakh populations. The analysis included three steps: the isonymy method, which is standard for quasigenetic markers, comparing frequencies of quasigenetic markers, and comparing the quasigenetic and genetic datasets. We constructed 50 maps of frequency of the distribution of each clan and revealed that these maps correlate with the maps of genetic distances. The Mantel test also demonstrated a significant correlation between geographic and quasigenetic distances (г = 0.60; p < 0.05). The analysis of inter-population variability revealed the largest diversity between geographic territories corresponding to the social-territorial groups of the Kazakh Khanate (zhuzes) rather than to other historical groups that existed on the territory of Kazakhstan in preceding and modern epochs. The same is evidenced by the principal components and multidimensional scaling plots, which grouped geographic populations into three clusters corresponding to three zhuzes. This indicates that the final structuring of the Kazakh gene pool might have occurred during the Kazakh Khanate period.

Non-invasive prenatal paternity testing using cell-free fetal DNA from maternal plasma: DNA isolation and genetic marker studies

Invasive prenatal paternity tests can result in miscarriage and congenital malformations; therefore, a non-invasive method of testing is preferable. However, little progress could be made in this field until the introduction of cell-free fetal DNA (cffDNA) in 2009. In this review, two aspects regarding the history and development of non-invasive prenatal paternity testing (NIPAT) are summarized: (1) extraction and enrichment of cffDNA and (2) genetic marker-based studies. Although column-based kits are used widely for NIPAT, some researchers have suggested that an automated method, such as magnetic extraction, generally has a higher cffDNA yield than that of manual column-based extraction; therefore, its popularity might increase in the near future. In addition, size- and methylation-based enrichment methods are expected to perform better than formaldehyde-based methods. On the other hand, single nucleotide polymorphism-based techniques have contributed to NIPAT, whereas the application of short tandem repeat testing has so far been restricted to pregnant women bearing male fetuses only. Additional methods and techniques are expected to be innovated to facilitate the forensic practice of NIPAT.

The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana

We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged.

Human Y-chromosome variation in the genome-sequencing era

The properties of the human Y chromosome - namely, male specificity, haploidy and escape from crossing over - make it an unusual component of the genome, and have led to its genetic variation becoming a key part of studies of human evolution, population history, genealogy, forensics and male medical genetics. Next-generation sequencing (NGS) technologies have driven recent progress in these areas. In particular, NGS has yielded direct estimates of mutation rates, and an unbiased and calibrated molecular phylogeny that has unprecedented detail. Moreover, the availability of direct-to-consumer NGS services is fuelling a rise of 'citizen scientists', whose interest in resequencing their own Y chromosomes is generating a wealth of new data.

Toward a consensus on SNP and STR mutation rates on the human Y-chromosome

The mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies. Large-scale sequencing efforts have produced several independent estimates of Y-SNP mutation rates. Genealogical, or pedigree, rates tend to be slightly faster than evolutionary rates obtained from ancient DNA or calibrations using dated (pre)historical events. It is, therefore, suggested to report TMRCAs using an envelope defined by the average aDNA-based rate and the average pedigree-based rate. The current estimate of the "envelope rate" is 0.75-0.89 substitutions per billion base pairs per year. The available Y-SNP mutation rates can be applied to high-coverage data from the entire X-degenerate region, but other datasets may demand recalibrated rates. While a consensus on Y-SNP rates is approaching, the debate on Y-STR rates has continued for two decades, because multiple genealogical rates were consistent with each other but three times faster than the single evolutionary estimate. Applying Y-SNP and Y-STR rates to the same haplogroups recently helped to clarify the issue. Genealogical and evolutionary STR rates typically provide lower and upper bounds of the "true" (SNP-based) age. The genealogical rate often-but not always-works well for haplogroups less than 7000 years old. The evolutionary rate, although calibrated using recent events, inflates ages of young haplogroups and deflates the age of the entire Y-chromosomal tree, but often provides reasonable estimates for intermediate ages (old haplogroups). Future rate estimates and accumulating case studies should further clarify the Y-SNP rates.

Phylogeography of human Y-chromosome haplogroup Q3-L275 from an academic/citizen science collaboration

Background

The Y-chromosome haplogroup Q has three major branches: Q1, Q2, and Q3. Q1 is found in both Asia and the Americas where it accounts for about 90% of indigenous Native American Y-chromosomes; Q2 is found in North and Central Asia; but little is known about the third branch, Q3, also named Q1b-L275. Here, we combined the efforts of population geneticists and genetic genealogists to use the potential of full Y-chromosome sequencing for reconstructing haplogroup Q3 phylogeography and suggest possible linkages to events in population history.

Results

We analyzed 47 fully sequenced Y-chromosomes and reconstructed the haplogroup Q3 phylogenetic tree in detail. Haplogroup Q3-L275, derived from the oldest known split within Eurasian/American haplogroup Q, most likely occurred in West or Central Asia in the Upper Paleolithic period. During the Mesolithic and Neolithic epochs, Q3 remained a minor component of the West Asian Y-chromosome pool and gave rise to five branches (Q3a to Q3e), which spread across West, Central and parts of South Asia. Around 3–4 millennia ago (Bronze Age), the Q3a branch underwent a rapid expansion, splitting into seven branches, some of which entered Europe. One of these branches, Q3a1, was acquired by a population ancestral to Ashkenazi Jews and grew within this population during the 1st millennium AD, reaching up to 5% in present day Ashkenazi.

Conclusions

This study dataset was generated by a massive Y-chromosome genotyping effort in the genetic genealogy community, and phylogeographic patterns were revealed by a collaboration of population geneticists and genetic genealogists. This positive experience of collaboration between academic and citizen science provides a model for further joint projects. Merging data and skills of academic and citizen science promises to combine, respectively, quality and quantity, generalization and specialization, and achieve a well-balanced and careful interpretation of the paternal-side history of human populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0870-2) contains supplementary material, which is available to authorized users.

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.

Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements

Background

The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization.

Results

Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA). However, analyses of molecular variance (AMOVA) of haplogroups using 92 binary markers genotyped in 629 Cypriots revealed that the proportion of variance among the districts was irregularly distributed. Principal component analysis (PCA) revealed potential genetic associations of Greek-Cypriots with neighbor populations. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography.

Conclusions

Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively. The persistent pre-Greek component is represented by elements of G2-U5(xL30) haplogroups: U5*, PF3147, and L293. J2b-M205 may contribute also to the pre-Greek strata. The majority of R1b-Z2105 lineages occur in both the westernmost and easternmost districts. Distinctively, sub-haplogroup R1b- M589 occurs only in the east. The absence of R1b- M589 lineages in Crete and the Balkans and the presence in Asia Minor are compatible with Late Bronze Age influences from Anatolia rather than from Mycenaean Greeks.

Electronic supplementary material

The online version of this article (doi:10.1186/s13323-016-0032-8) contains supplementary material, which is available to authorized users.