Peopling of the North Circumpolar Region--insights from Y chromosome STR and SNP typing of Greenlanders

Application of Targeted Y-Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q

Y-chromosomal haplogroups and the Y-SNPs defining them are relevant for the exploration of male lineages, inference of paternal ancestry, and reconstruction of migration pathways, to name a few. Currently, over 300,000 Y-SNPs have been reported, defining 20 main haplogroups. However, ascertainment bias in the investigations has led to some haplogroups being overlooked, which hinders a representative depiction of certain populations and their migration events. For migration pattern analyses of the first settlers of the Americas, the Native American main founding lineage Q-M3 needs to be further investigated to allow clear genetic differentiation of individuals of different ethnogeographic origins. To increase the resolution within this haplogroup, a total of 7.45 Mb of the Y chromosome of 59 admixed South Americans of haplogroup Q was targeted for sequencing using hybridization capture enrichment. Data were combined with 218 publicly available sequences of Central and South Americans of haplogroup Q. After rigorous data processing, variants not meeting the quality criteria were excluded and 4128 reliable Y-SNPs were reported. A total of 2224 Y-SNPs had previously unknown positions in the phylogenetic tree, and 1291 of these are novel. The phylogenetic relationships between the Y-SNPs were established using the software SNPtotree in order to report a redesigned phylogenetic tree containing 300 branches, defined by 3400 Y-SNPs. The new tree introduces 117 previously undescribed branches and is the most comprehensive phylogenetic tree of the Native American haplogroup Q lineages to date. The 214 sequences were assigned to 135 different low- to high-resolution branches, while in the previous phylogenetic tree, only 195 sequences could be sorted into 14 low-resolution branches with the same quality criteria. The improved genetic differentiation of subhaplogroup Q-M3 has a great potential to resolve migration patterns of Native Americans.

Performance of a 74-Microhaplotype Assay in Kinship Analyses

Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes and Greenlanders. In addition to the 229 SNPs that originally made up the 74 MHs, 66 SNPs and 3 indels were identified in the two populations, and 45 of these variants were included in new definitions of the MHs, whereas 24 SNPs were considered rare and of little value for case work. The average effective number of alleles (Ae) was 3.2, 3.0, and 2.6 in Danes, West Greenlanders, and East Greenlanders, respectively. High levels of linkage disequilibrium were observed in East Greenlanders, which reflects the characteristics of this population that has a small size, and signs of admixture and substructure. Pairwise kinship simulations of full siblings, half-siblings, first cousins, and unrelated individuals were performed using allele frequencies from MHs, STRs and SNPs from Danish and Greenlandic populations. The MH panel outperformed the currently used STR and SNP marker sets and was able to differentiate siblings from unrelated individuals with a 0% false positive rate and a 1.1% false negative rate using an LR threshold of 10,000 in the Danish population. However, the panel was not able to differentiate half-siblings or first cousins from unrelated individuals. The results generated in this study will be used to implement MHs as investigative markers for relationship testing in our laboratory.

Genetic history of the Koryaks and Evens of the Magadan region based on Y chromosome polymorphism data

In order to clarify the history of gene pool formation of the indigenous populations of the Northern Priokhotye (the northern coast of the Sea of Okhotsk), Y-chromosome polymorphisms were studied in the Koryaks and Evens living in the Magadan region. The results of the study showed that the male gene pool of the Koryaks is represented by haplogroups C-B90-B91, N-B202, and Q-B143, which are also widespread in other peoples of Northeastern Siberia, mainly of Paleo-Asiatic origin. High frequency of haplogroup C-B80, typical of other Tungus-Manchurian peoples, is characteristic of the Evens of the Magadan region. The shared components of the gene pools of the Koryaks and Evens are haplogroups R-M17 and I-P37.2 inherited as a result of admixture with Eastern Europeans (mainly Russians). The high frequency of such Y chromosome haplogroups in the Koryaks (16.7 %) and Evens (37.8 %) is indicative of close interethnic contacts during the last centuries, and most probably especially during the Soviet period. The genetic contribution of the European males' Y chromosome significantly prevails over that of maternally inherited mitochondrial DNA. The study of the Y chromosome haplogroup diversity has shown that only relatively young phylogenetic branches have been preserved in the Koryak gene pool. The age of the oldest component of the Koryak gene pool (haplogroup C-B90-B91) is estimated to be about 3.8 thousand years, the age of the younger haplogroups Q-B143 and N-B202 is about 2.8 and 2.4 thousand years, respectively. Haplogroups C-B90-B91 and N-B202 are Siberian in origin, and haplogroup Q-B143 was apparently inherited by the ancestors of the Koryaks and other Paleo-Asiatic peoples from the Paleo-Eskimos as a result of their migrations to Northeast Asia from the Americas. The analysis of microsatellite loci for haplogroup Q-B143 in the Eskimos of Greenland, Canada and Alaska as well as in the indigenous peoples of Northeastern Siberia showed a decrease in genetic diversity from east to west, pointing to the direction of distribution of the Paleo-Eskimo genetic component in the circumpolar region of America and Asia. At the same time, the Evens appeared in the Northern Priokhotye much later (in the XVII century) as a result of the expansion of the Tungusic tribes, which is confirmed by the results of the analysis of haplogroup C-B80 polymorphisms.

Bidirectional dispersals during the peopling of the North American Arctic

It is thought that Paleo-Inuit were the first people that settled the American Arctic about 5000 BP (before the present) from a migration that crossed Beringia from Northeast Asia. It is theorized that this group initially migrated to the North Slopes of Alaska and subsequently expanded eastward, eventually reaching Greenland. A second circumpolar dispersal of Neo-Inuit from the North Slopes associated with the Thule-Inuk culture has been postulated to have extended eastward around 800 BP, totally replacing the original Paleo-Inuit without admixing. Although generally accepted, this migration scenario is incompatible with previously reported indications of east to west gene flow across the American Arctic. Here we report on the Y-chromosome haplogroup and Y-STR diversity of the four circumpolar populations of the Tuva Republic (N = 24), Northeast Siberia (N = 9), Bethel, Alaska (N = 40), and Barrow, Alaska (N = 31). Four haplogroup lineages (Q-NWT01, Q-M3, Q-M346, and Q-M120) were detected, Q-NWT01 and Q-M3 being the most abundant at 11.11 and 66.67% in Northeast Siberia, 32.50 and 65.00% in Bethel, and 67.74 and 32.26% in Barrow, respectively. The same samples genotyped for Y-chromosome SNPs were typed for 17 Y-STYR loci using the AmpFlSTR Yfiler system. Age estimates and diversity values for the Q-NWT01 and Q-M3 mutations suggest extensive movement of male individuals along the entire longitudinal stretch of the American circumpolar region. Throughout the entire region, Q-M3 exhibits a west to east decreasing gradient in age and diversity while Q-NWT01 indicates the opposite with older TMRCA and higher diversity values running from east to west with the most recent estimates in Canada and Alaska. The high age and diversity values in Greenland are congruent with an origin of the Q-NWT01 mutation in the east of the circumpolar range about 2000-3000 ya. This scenario is incompatible with a complete biological replacement starting about 700 BP of Paleo-Inuit like the Dorset by the Thule-Inuit (Neo-Inuit), as is currently thought, and more parsimonious with gene flow carrying the NWT01 mutation from a pre-Thule population to the ancestors of the present-day Inuit.

Forensic and genetic landscape explorations of Chinese Kyrgyz group based on autosomal SNPs, Y-chromosomal SNPs and STRs

To assess the effect of population genetic polymorphism on forensic research, we investigated the genetic polymorphisms of Chinese Kyrgyz group (n = 98) and evaluated forensic application values in Chinese Kyrgyz group and other 26 reference populations at 90 autosomal SNPs, and then combined with 34 SNPs and 37 STRs on Y chromosome to reveal the genetic background of Kyrgyz group in autosomal and Y-chromosomal inheritances, respectively. The 90 autosomal SNPs and 34 Y-chromosomal SNPs were sequenced base on next generation sequencing technology, and 37 Y-chromosomal STRs were analyzed by capillary electrophoresis platform. The results showed that cumulative power of discrimination and cumulative power of exclusion of 90 autosomal SNPs in the panel met the application need of forensic genetics in Kyrgyz group. The forensic effectivenesses of the panel were high in all 27 populations, although there were genetic differences among these populations. The forensic effectiveness of the panel was relatively higher in the European populations, but relatively lower in the African populations. The population genetic results indicated that the Kyrgyz group had the relatively closer genetic relationships with the reference East Asian populations at autosomal SNPs, and there were gene exchanges between the Kyrgyz group and East Asian, European populations based on the analytical results of autosomal SNPs, Y-chromosomal SNPs and STRs.

Y chromosome diversity in Aztlan descendants and its implications for the history of Central Mexico

Native Mexican populations are crucial for understanding the genetic ancestry of Aztec descendants and coexisting ethnolinguistic groups in the Valley of Mexico and elucidating the population dynamics of the prehistoric colonization of the Americas. Mesoamerican societies were multicultural in nature and also experienced significant admixture during Spanish colonization of the region. Despite these facts, Native Mexican Y chromosome diversity has been greatly understudied. To further elucidate their genetic history, we conducted a high-resolution Y chromosome analysis with Chichimecas, Nahuas, Otomies, Popolocas, Tepehuas, and Totonacas using 19 Y-short tandem repeat and 21 single nucleotide polymorphism loci. We detected enormous paternal genetic diversity in these groups, with haplogroups Q-MEH2, Q-M3, Q-Z768, Q-L663, Q-Z780, and Q-PV3 being identified. These data affirmed the southward colonization of the Americas via Beringia and connected Native Mexicans with indigenous populations from South-Central Siberia and Canada. They also suggested that multiple population dispersals gave rise to Y chromosome diversity in these populations.

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Enormous Y chromosome diversity observed in Native Mexican populations.

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Haplogroups Q-MEH2, Q-M3, Q-Z768, Q-L663, Q-Z780, and Q-PV3 were identified.

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Patterns of Y chromosome diversity not shaped by ethnicity, geography, or language.

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Multiple population dispersals contributed to Y chromosome diversity in Mexico.

Analysis of the human Y-chromosome haplogroup Q characterizes ancient population movements in Eurasia and the Americas

BACKGROUND

Recent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America by an ancestral Beringian population, from which two well-differentiated components originated and subsequently mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analysis of the Y-chromosome haplogroup Q, which is the only Pan-American haplogroup and accounts for virtually all Native American Y chromosomes in Mesoamerica and South America.

RESULTS

Our analyses of 1.5 Mb of 152 Y chromosomes, 34 re-sequenced in this work, support a "coastal and inland routes scenario" for the first entrance of modern humans in North America. We show a major phase of male population growth in the Americas after 15 thousand years ago (kya), followed by a period of constant population size from 8 to 3 kya, after which a secondary sign of growth was registered. The estimated dates of the first expansion in Mesoamerica and the Isthmo-Colombian Area, mainly revealed by haplogroup Q-Z780, suggest an entrance in South America prior to 15 kya. During the global constant population size phase, local South American hints of growth were registered by different Q-M848 sub-clades. These expansion events, which started during the Holocene with the improvement of climatic conditions, can be ascribed to multiple cultural changes rather than a steady population growth and a single cohesive culture diffusion as it occurred in Europe.

CONCLUSIONS

We established and dated a detailed haplogroup Q phylogeny that provides new insights into the geographic distribution of its Eurasian and American branches in modern and ancient samples.

Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences

The expansion of modern humans to the American continent after the Last Glacial Maximum led the way to the present-day distribution of American aborigines. Recent advances in autosomal DNA research and expanded testing of mtDNA lineages has provided a clearer picture of the number and timing of founding lineages. However, both autosomal DNA and mtDNA research have provided unresolved competing theories between the short-term and the long-term models of the Beringian standstill hypothesis. Further, the source of founding paternal lineages of American aborigines and their relationship with ancient Siberia populations remains ambiguous. In this study, we reanalyzed a 7.0 Mbp region of 132 paternal Y-chromosome sequences, including 39 newly reported ones, of male samples from American aborigines and Eurasian populations. Among Eurasian samples, we identified Y-chromosome branches that are most closely related to known American aborigine founding lineages, that is, Q1-L804 links to Q1-M3, Q1-L330 links to Q1-Z780, Q1-M120 links to Q1-B143, and C2-F1756 links to C2-P39. The revised phylogenetic tree and age estimates indicate a narrow timeframe (~15.3-14.3 kya) for the upper time limit of human entry to the American continent. Our analysis suggests that the in situ differentiation of Q-M242 in Central Eurasia and South Siberia region gave rise to numerous sub-lineages older than 15.3 kya, and the founding of Paleo-Indian paternal lineages is part of the great Q1-L53 diffusion throughout the Eurasia after the Last Glacial Maximum. The results of our study will assist in future studies of the history of modern populations in Eurasia and the Americas.

Tracing hepatitis B virus (HBV) genotype B5 (formerly B6) evolutionary history in the circumpolar Arctic through phylogeographic modelling

Background

Indigenous populations of the circumpolar Arctic are considered to be endemically infected (>2% prevalence) with hepatitis B virus (HBV), with subgenotype B5 (formerly B6) unique to these populations. The distinctive properties of HBV/B5, including high nucleotide diversity yet no significant liver disease, suggest virus adaptation through long-term host-pathogen association.

Methods

To investigate the origin and evolutionary spread of HBV/B5 into the circumpolar Arctic, fifty-seven partial and full genome sequences from Alaska, Canada and Greenland, having known location and sampling dates spanning 40 years, were phylogeographically investigated by Bayesian analysis (BEAST 2) using a reversible-jump-based substitution model and a clock rate estimated at 4.1 × 10⁻⁵ substitutions/site/year.

Results

Following an initial divergence from an Asian viral ancestor approximately 1954 years before present (YBP; 95% highest probability density interval [1188, 2901]), HBV/B5 coalescence occurred almost 1000 years later. Surprisingly, the HBV/B5 ancestor appears to locate first to Greenland in a rapid coastal route progression based on the landscape aware geographic model, with subsequent B5 evolution and spread westward. Bayesian skyline plot analysis demonstrated an HBV/B5 population expansion occurring approximately 400 YBP, coinciding with the disruption of the Neo-Eskimo Thule culture into more heterogeneous and regionally distinct Inuit populations throughout the North American Arctic.

Discussion

HBV/B5 origin and spread appears to occur coincident with the movement of Neo-Eskimo (Inuit) populations within the past 1000 years, further supporting the hypothesis of HBV/host co-expansion, and illustrating the concept of host-pathogen adaptation and balance.

High Y-chromosomal Differentiation Among Ethnic Groups of Dir and Swat Districts, Pakistan

The ethnic groups that inhabit the mountainous Dir and Swat districts of northern Pakistan are marked by high levels of cultural and phenotypic diversity. To obtain knowledge of the extent of genetic diversity in this region, we investigated Y-chromosomal diversity in five population samples representing the three main ethnic groups residing within these districts, including Gujars, Pashtuns and Kohistanis. A total of 27 Y-chromosomal short tandem repeats (Y-STRs) and 331 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) were investigated. In the Y-STRs, we observed very high and significant levels of genetic differentiation in nine of the 10 pairwise between-group comparisons (R_ST 0.179-0.746), and the differences were mirrored in the Y-SNP haplogroup frequency distribution. No genetic differences were found between the two Pashtun subethnic groups Tarklanis and Yusafzais (R_ST = 0.000). Utmankhels, also considered Pashtuns culturally, were not closely related to any of the other population samples (R_ST 0.451-0.746). Thus, our findings provide examples of both associations and dissociations between cultural and genetic legacies. When analyzed within a larger continental-scale context, these five ethnic groups fall mostly outside the previously characterized Y-chromosomal gene pools of the Indo-Pakistani subcontinent. Male founder effects, coupled with culturally and topographically based constraints upon marriage and movement, are likely responsible for the high degree of genetic structure in this region.

The study of human Y chromosome variation through ancient DNA

High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.

A study of the peopling of Greenland using next generation sequencing of complete mitochondrial genomes

OBJECTIVES

The Greenlandic population history is characterized by a number of migrations of people of various ethnicities. In this work, the analysis of the complete mtDNA genome aimed to contribute to the ongoing debate on the origin of current Greenlanders and, at the same time, to address the migration patterns in the Greenlandic population from a female inheritance demographic perspective.

METHODS

We investigated the maternal genetic variation in the Greenlandic population by sequencing the whole mtDNA genome in 127 Greenlandic individuals using the Illumina MiSeq^® platform.

RESULTS

All Greenlandic individuals belonged to the Inuit mtDNA lineages A2a, A2b1, and D4b1a2a1. No European haplogroup was found.

DISCUSSION

The mtDNA lineages seem to support the hypothesis that the Inuit in Greenland are descendants from the Thule migration. The results also reinforce the importance of isolation and genetic drift in shaping the genetic diversity in Greenlanders. Based on the mtDNA sequences, the Greenlandic Inuit are phylogenetically close to Siberian groups and Canadian Inuit.