Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes.

Arab populations are largely understudied, notably their genetic structure and history. Here we present an in-depth analysis of 6,218 whole genomes from Qatar, revealing extensive diversity as well as genetic ancestries representing the main founding Arab genealogical lineages of Qahtanite (Peninsular Arabs) and Adnanite (General Arabs and West Eurasian Arabs). We find that Peninsular Arabs are the closest relatives of ancient hunter-gatherers and Neolithic farmers from the Levant, and that founder Arab populations experienced multiple splitting events 12-20 kya, consistent with the aridification of Arabia and farming in the Levant, giving rise to settler and nomadic communities. In terms of recent genetic flow, we show that these ancestries contributed significantly to European, South Asian as well as South American populations, likely as a result of Islamic expansion over the past 1400 years. Notably, we characterize a large cohort of men with the ChrY J1a2b haplogroup (n = 1,491), identifying 29 unique sub-haplogroups. Finally, we leverage genotype novelty to build a reference panel of 12,432 haplotypes, demonstrating improved genotype imputation for both rare and common alleles in Arabs and the wider Middle East.

Landscape genetics and the genetic legacy of Upper Paleolithic and Mesolithic hunter-gatherers in the modern Caucasus.

This study clarifies the role of refugia and landscape permeability in the formation of the current genetic structure of peoples of the Caucasus. We report novel genome-wide data for modern individuals from the Caucasus, and analyze them together with available Paleolithic and Mesolithic individuals from Eurasia and Africa in order (1) to link the current and ancient genetic structures via landscape permeability, and (2) thus to identify movement paths between the ancient refugial populations and the Caucasus. The ancient genetic ancestry is best explained by landscape permeability implying that human movement is impeded by terrain ruggedness, swamps, glaciers and desert. Major refugial source populations for the modern Caucasus are those of the Caucasus, Anatolia, the Balkans and Siberia. In Rugged areas new genetic signatures take a long time to form, but once they do so, they remain for a long time. These areas act as time capsules harboring genetic signatures of ancient source populations and making it possible to help reconstruct human history based on patterns of variation today.

Origin of ethnic groups, linguistic families, and civilizations in China viewed from the Y chromosome.

East Asia, geographically extending to the Pamir Plateau in the west, to the Himalayan Mountains in the southwest, to Lake Baikal in the north and to the South China Sea in the south, harbors a variety of people, cultures, and languages. To reconstruct the natural history of East Asians is a mission of multiple disciplines, including genetics, archaeology, linguistics, and ethnology. Geneticists confirm the recent African origin of modern East Asians. Anatomically modern humans arose in Africa and immigrated into East Asia via a southern route approximately 50,000 years ago. Following the end of the Last Glacial Maximum approximately 12,000 years ago, rice and millet were domesticated in the south and north of East Asia, respectively, which allowed human populations to expand and linguistic families and ethnic groups to develop. These Neolithic populations produced a strong relation between the present genetic structures and linguistic families. The expansion of the Hongshan people from northeastern China relocated most of the ethnic populations on a large scale approximately 5300 years ago. Most of the ethnic groups migrated to remote regions, producing genetic structure differences between the edge and center of East Asia. In central China, pronounced population admixture occurred and accelerated over time, which subsequently formed the Han Chinese population and eventually the Chinese civilization. Population migration between the north and the south throughout history has left a smooth gradient in north-south changes in genetic structure. Observation of the process of shaping the genetic structure of East Asians may help in understanding the global natural history of modern humans.

The Y chromosome of autochthonous Basque populations and the Bronze Age replacement.

Here we report on the Y haplogroup and Y-STR diversity of the three autochthonous Basque populations of Alava (n = 54), Guipuzcoa (n = 30) and Vizcaya (n = 61). The same samples genotyped for Y-chromosome SNPs were typed for 17 Y-STR loci (DYS19, DYS385a/b, DYS398I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA H4) using the AmpFlSTR Yfiler system. Six major haplogroups (R, I, E, J, G, and DE) were detected, being R-S116 (P312) haplogroup the most abundant at 75.0% in Alava, 86.7% in Guipuzcoa and 87.3% in Vizcaya. Age estimates for the R-S116 mutation in the Basque Country are 3975 ± 303, 3680 ± 345 and 4553 ± 285 years for Alava, Guipuzcoa and Vizcaya, respectively. Pairwise Rst genetic distances demonstrated close Y-chromosome affinities among the three autochthonous Basque populations and between them and the male population of Ireland and Gascony. In a MDS plot, the population of Ireland segregates within the Basque cluster and closest to the population of Guipuzcoa, which plots closer to Ireland than to any of the other Basque populations. Overall, the results support the notion that during the Bronze Age a dispersal of individuals carrying the R-S116 mutation reached the Basque Country replacing the Paleolithic/Neolithic Y chromosome of the region.

Genetic history of Calabrian Greeks reveals ancient events and long term isolation in the Aspromonte area of Southern Italy.

Calabrian Greeks are an enigmatic population that have preserved and evolved a unique variety of language, Greco, survived in the isolated Aspromonte mountain area of Southern Italy. To understand their genetic ancestry and explore possible effects of geographic and cultural isolation, we genome-wide genotyped a large set of South Italian samples including both communities that still speak Greco nowadays and those that lost the use of this language earlier in time. Comparisons with modern and ancient populations highlighted ancient, long-lasting genetic links with Eastern Mediterranean and Caucasian/Near-Eastern groups as ancestral sources of Southern Italians. Our results suggest that the Aspromonte communities might be interpreted as genetically drifted remnants that departed from such ancient genetic background as a consequence of long-term isolation. Specific patterns of population structuring and higher levels of genetic drift were indeed observed in these populations, reflecting geographic isolation amplified by cultural differences in the groups that still conserve the Greco language. Isolation and drift also affected the current genetic differentiation at specific gene pathways, prompting for future genome-wide association studies aimed at exploring trait-related loci that have drifted up in frequency in these isolated groups.

Ancient DNA from Guam and the peopling of the Pacific.

Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.

Post-last glacial maximum expansion of Y-chromosome haplogroup C2a-L1373 in northern Asia and its implications for the origin of Native Americans.

OBJECTIVES: Subbranches of Y-chromosome haplogroup C2a-L1373 are founding paternal lineages in northern Asia and Native American populations. Our objective was to investigate C2a-L1373 differentiation in northern Asia and its implications for Native American origins. MATERIALS AND METHODS: Sequences of rare subbranches (n = 43) and ancient individuals (n = 37) of C2a-L1373 (including P39 and MPB373), were used to construct phylogenetic trees with age estimation by BEAST software. RESULTS: C2a-L1373 expanded rapidly approximately 17.7,000-14.3,000 years ago (kya) after the last glacial maximum (LGM), generating numerous sublineages which became founding paternal lineages of modern northern Asian and Native American populations (C2a-P39 and C2a-MPB373). The divergence pattern supports possible initiation of differentiation in low latitude regions of northern Asia and northward diffusion after the LGM. There is a substantial gap between the divergence times of C2a-MPB373 (approximately 22.4 or 17.7 kya) and C2a-P39 (approximately 14.3 kya), indicating two possible migration waves. DISCUSSION: We discussed the decreasing time interval of "Beringian standstill" (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the "Long-term Beringian standstill model," the "Short-term Beringian standstill model," and the "Multiple waves of migration model." Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of "Ancient Northern Siberians" and Paleolithic communities from the Amur region, which appeared during the post-LGM era, rather than ancient populations in greater Beringia, or an adjacent region, before the LGM.

Sex-biased patterns shaped the genetic history of Roma.

The Roma population is a European ethnic minority characterized by recent and multiple dispersals and founder effects. After their origin in South Asia around 1,500 years ago, they migrated West. In Europe, they diverged into ethnolinguistically distinct migrant groups that spread across the continent. Previous genetic studies based on genome-wide data and uniparental markers detected Roma founder events and West-Eurasian gene flow. However, to the best of our knowledge, it has not been assessed whether these demographic processes have equally affected both sexes in the population. The present study uses the largest and most comprehensive dataset of complete mitochondrial and Y chromosome Roma sequences to unravel the sex-biased patterns that have shaped their genetic history. The results show that the Roma maternal genetic pool carries a higher lineage diversity from South Asia, as opposed to a single paternal South Asian lineage. Nonetheless, the European gene flow events mainly occurred through the maternal lineages; however, a signal of this gene flow is also traceable in the paternal lineages. We also detect a higher female migration rate among European Roma groups. Altogether, these results suggest that sociocultural factors influenced the emergence of sex-biased genetic patterns at global and local scales in the Roma population through time.

Uniparental Genetic Analyses Reveal the Major Origin of Fujian Tanka from Ancient Indigenous Daic Populations.

The Fujian Tanka people are officially classified as a southern Han ethnic group, whereas they have customs similar to Daic and Austronesion people. Whether they originated in Han or Daic people, there is no consensus. Three hypotheses have been proposed to explain the origin of this group: (1) the Han Chinese origin, (2) the ancient Daic origin, (3) and the admixture between Daic and Han. This study addressed this issue by analyzing the paternal Y chromosome and maternal mtDNA variation of 62 Fujian Tanka and 25 neighboring Han in Fujian. The southern East Asian predominant haplogroups (e.g., Y-chromosome O1a1a-P203 and O1b1a1a-M95, and mtDNA F2a, M7c1, and F1a1) had relatively high frequencies in Tanka. The interpopulation comparison revealed that the Tanka have a closer affinity with Daic populations than with Han Chinese in paternal lineages but are closely clustered with southern Han populations such as Hakka and Chaoshanese in maternal lineages. Network and haplotype-sharing analyses also support the admixture hypothesis. The Fujian Tanka mainly originate from the ancient indigenous Daic people and have only limited gene flows from Han Chinese populations. Notably, the divergence time inferred by the Tanka-specific haplotypes indicates that the formation of Fujian Tanka was a least 1033.8-1050.6 years before present (the early Northern Song dynasty), indicating that they are an indigenous population, not late Daic migrants from southwestern China.

The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders.

OBJECTIVES: In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences. METHODS: We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools. RESULTS: The genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style. CONCLUSION: We conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia.

The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.

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.

Analysis of whole Y-chromosome sequences reveals the Japanese population history in the Jomon period.

The Jomon and the Yayoi are considered to be the two major ancestral populations of the modern mainland Japanese. The Jomon people, who inhabited mainland Japan, admixed with Yayoi immigrants from the Asian continent. To investigate the population history in the Jomon period (14,500-2,300 years before present [YBP]), we analyzed whole Y-chromosome sequences of 345 Japanese males living in mainland Japan. A phylogenetic analysis of East Asian Y chromosomes identified a major clade (35.4% of mainland Japanese) consisting of only Japanese Y chromosomes, which seem to have originated from indigenous Jomon people. A Monte Carlo simulation indicated that ~70% of Jomon males had Y chromosomes in this clade. The Bayesian skyline plots of 122 Japanese Y chromosomes in the clade detected a marked decrease followed by a subsequent increase in the male population size from around the end of the Jomon period to the beginning of the Yayoi period (2,300 YBP). The colder climate in the Late to Final Jomon period may have resulted in critical shortages of food for the Jomon people, who were hunter-gatherers, and the rice farming introduced by Yayoi immigrants may have helped the population size of the Jomon people to recover.

Analysis of biogeographic ancestry reveals complex genetic histories for indigenous communities of St. Vincent and Trinidad.

OBJECTIVES: From a genetic perspective, relatively little is known about how mass emigrations of African, European, and Asian peoples beginning in the 16th century affected Indigenous Caribbean populations. Therefore, we explored the impact of serial colonization on the genetic variation of the first Caribbean islanders. MATERIALS AND METHODS: Sixty-four members of St. Vincent's Garifuna Community and 36 members of Trinidad's Santa Rosa First People's Community (FPC) of Arima were characterized for mitochondrial DNA and Y-chromosome diversity via direct sequencing and targeted SNP and STR genotyping. A subset of 32 Garifuna and 18 FPC participants were genotyped using the GenoChip 2.0 microarray. The resulting data were used to examine genetic diversity, admixture, and sex biased gene flow in the study communities. RESULTS: The Garifuna were most genetically comparable to African descendant populations, whereas the FPC were more similar to admixed American groups. Both communities also exhibited moderate frequencies of Indigenous American matrilines and patrilines. Autosomal SNP analysis indicated modest Indigenous American ancestry in these populations, while both showed varying degrees of African, European, South Asian, and East Asian ancestry, with patterns of sex-biased gene flow differing between the island communities. DISCUSSION: These patterns of genetic variation are consistent with historical records of migration, forced, or voluntary, and suggest that different migration events shaped the genetic make-up of each island community. This genomic study is the highest resolution analysis yet conducted with these communities, and provides a fuller understanding of the complex bio-histories of Indigenous Caribbean peoples in the Lesser Antilles.

Megalithic tombs in western and northern Neolithic Europe were linked to a kindred society.

Paleogenomic and archaeological studies show that Neolithic lifeways spread from the Fertile Crescent into Europe around 9000 BCE, reaching northwestern Europe by 4000 BCE. Starting around 4500 BCE, a new phenomenon of constructing megalithic monuments, particularly for funerary practices, emerged along the Atlantic façade. While it has been suggested that the emergence of megaliths was associated with the territories of farming communities, the origin and social structure of the groups that erected them has remained largely unknown. We generated genome sequence data from human remains, corresponding to 24 individuals from five megalithic burial sites, encompassing the widespread tradition of megalithic construction in northern and western Europe, and analyzed our results in relation to the existing European paleogenomic data. The various individuals buried in megaliths show genetic affinities with local farming groups within their different chronological contexts. Individuals buried in megaliths display (past) admixture with local hunter-gatherers, similar to that seen in other Neolithic individuals in Europe. In relation to the tomb populations, we find significantly more males than females buried in the megaliths of the British Isles. The genetic data show close kin relationships among the individuals buried within the megaliths, and for the Irish megaliths, we found a kin relation between individuals buried in different megaliths. We also see paternal continuity through time, including the same Y-chromosome haplotypes reoccurring. These observations suggest that the investigated funerary monuments were associated with patrilineal kindred groups. Our genomic investigation provides insight into the people associated with this long-standing megalith funerary tradition, including their social dynamics.

The genomic history of the Iberian Peninsula over the past 8000 years.

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia's ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European-speaking regions but also into non-Indo-European-speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.

Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads.

For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.

A genomic Neolithic time transect of hunter-farmer admixture in central Poland.

Ancient DNA genome-wide analyses of Neolithic individuals from central and southern Europe indicate an overall population turnover pattern in which migrating farmers from Anatolia and the Near East largely replaced autochthonous Mesolithic hunter-gatherers. However, the genetic history of the Neolithic transition in areas lying north of the European Neolithic core region involved different levels of admixture with hunter-gatherers. Here we analyse genome-wide data of 17 individuals spanning from the Middle Neolithic to the Early Bronze Age (4300-1900 BCE) in order to assess the Neolithic transition in north-central Poland, and the local impacts of hunter-farmer contacts and Late Neolithic steppe migrations. We evaluate the influence of these on local populations and assess if and how they change through time, reporting evidence of recurrent hunter-farmer admixture over three millennia, and the co-existence of unadmixed hunter-gatherers as late as 4300 BCE. During the Late Neolithic we report the appearance of steppe ancestry, but on a lesser scale than previously described for other central European regions, with evidence of stronger affinities to hunter-gatherers than to steppe pastoralists. These results help understand the Neolithic palaeogenomics of another central European area, Kuyavia, and highlight the complexity of population interactions during those times.

The evaluation of Oryza sativa L (Black rice) extracts for detection of spermatozoa on the clothing and vaginal swab samples.

Investigation of sexual assault cases from the evidence involving vaginal swab, clothing and others is examined by a forensic scientist. The explanation of trace findings on spermatozoa on clothing is often problematic due to the use of different staining methods. Conventional staining method used either Papanicolaou (PAP) or Dip quick® stain as synthetic dyes which are expensive imported material and harmful to human health. Therefore, the present study aims to determine the ability of Oryza sativa L (black rice) extract as a natural dye to detect spermatozoa on the clothing and vaginal swab casework samples for routine forensic examination. Results revealed that black rice extract has a highly effective for detecting spermatozoa on cloth and vaginal swab casework samples. There was no significantly different in the detection of spermatozoa compared with rapid PAP stain and Dip quick® stain. Results also showed that the staining of vaginal swab casework with black rice extracted can be used for PCR amplification of centromeric alphoid repeat gene on chromosome Y for 60 days. Moreover, the DNA extracted from stained semen slide generates a full profile of 16 alleles of STR typing. The results indicate that a new natural staining dye which extracted from black rice can be used to detect spermatozoa and identify a person from the trace evidence. The application of natural dyes for routine staining of spermatozoa from forensic specimens will decrease the expense to be spent in purchasing the synthetic dye and reduce their side effects on human and environment.

Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe.

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals' genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.