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Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia
Abstract
The peopling history of North Asia remains largely unexplored due to the limited number of ancient genomes analyzed from this region. Here, we report genome-wide data of ten individuals dated to as early as 7,500 years before present from three regions in North Asia, namely Altai-Sayan, Russian Far East, and the Kamchatka Peninsula. Our analysis reveals a previously undescribed Middle Holocene Siberian gene pool in Neolithic Altai-Sayan hunter-gatherers as a genetic mixture between paleo-Siberian and ancient North Eurasian (ANE) ancestries. This distinctive gene pool represents an optimal source for the inferred ANE-related population that contributed to Bronze Age groups from North and Inner Asia, such as Lake Baikal hunter-gatherers, Okunevo-associated pastoralists, and possibly Tarim Basin populations. We find the presence of ancient Northeast Asian (ANA) ancestry-initially described in Neolithic groups from the Russian Far East-in another Neolithic Altai-Sayan individual associated with different cultural features, revealing the spread of ANA ancestry ∼1,500 km further to the west than previously observed. In the Russian Far East, we identify 7,000-year-old individuals that carry Jomon-associated ancestry indicating genetic links with hunter-gatherers in the Japanese archipelago. We also report multiple phases of Native American-related gene flow into northeastern Asia over the past 5,000 years, reaching the Kamchatka Peninsula and central Siberia. Our findings highlight largely interconnected population dynamics throughout North Asia from the Early Holocene onward.
... One individual of Q-M25-L712-YP832 was found in two samples (Kh7, RISE675) from the Uybat V site in Khakasia, South Siberia [4]. The earliest sample of this haplogroup, a 7500-year-old individual FRS002, was found in the Altai-Sayan region, South Siberia [28]. The haplogroup has also been found in large numbers among ancient Karasuk people [4], ancient Xiongnu [10], ancient Türk people, and ancient Avar people in Hungary [8]. ...
... Ancestral Uralic-speaking populations rapidly moved through the northern Eurasian taiga [29]. Between the Altai and Baikal, ANE populations differentiated rapidly, producing many genetic lineages and descendant groups [28]. These population movements and mixtures were very complex. ...
... These population movements and mixtures were very complex. Existing aDNA research has gradually revealed this demographic history [8,11,28,29]. This is reflected in the paternal genetic structure by the emergence of dozens of downstream lineages of C-L1373, Q-M242, and N-Tat and their extensive spread across northern Eurasia and the Eurasian steppe [18,21,22,30,31]. ...
... Although initial genetic surveys of European, African, and South Asian populations have detected no SCA10 expansions [1,3], subsequent studies identified the SCA10 repeat expansion in ataxic members of two Chinese Han families [8,9] and one Japanese family [10], all sharing the CGGC haplotype. The geographic distribution of the SCA10 mutation in the context of human migration has led to the hypothesis that the original SCA10 mutation arose in East Asia and spread to the Americas through the Bering landmass during the human migration to the New World 15 000 to 20 000 years ago [7,11] although the putative stagnation of human migration within the Beringia raises an alternative theory of the SCA10 origin in the Bering landmass followed by forward and backward spreads of the expansion to both continents [12]. However, the frequency of the CGGC haplotype, the putative ancestral SCA10 haplotype shared by SCA10 patients in the Americas and East Asia, is > 78% in the general population of South American countries [5] and is similarly frequent on both sides of the Pacific as estimated from allele frequencies of these four SNPs available in the 1000 Genomes database [13], hindering the exclusion of the possibility that the SCA10 expansion mutation occurred independently in East Asia and the Americas. ...
... The SCA10 expansion mutation persisted on this haplotype in East Asia and further migrated to the Americas through Beringia (Fig. 3). This tail end of the last glacial maximum coincides with the time of introgression of Denisovan and other hominins to our human ancestors [12]. We used the Introgression-Detection algorithm [15] and predicted that the origin of the haplotype segment was from the modern human genome rather than from a genome of these hominins introduced by introgression. ...
... Putting these data together, we postulate that the founder event for the SCA10 expansion arose in Asia on this extended haplotype prior to the human migration from East Asia to the American continent via the Bering landmass. While this period coincides with the time of introgression of Denisovan and other hominins to our human ancestors [12,24], our analysis showed that the SCA10 repeat expansion mutation originated in the human lineage rather than from an introgression from other hominin genomes. Whether other microsatellite repeat expansion disorders are unique to humans may be investigated in a similar strategy. ...
Spinocerebellar ataxia type 10 (SCA10) is a rare autosomal dominant ataxia caused by a large expansion of the (ATTCT)n repeat in ATXN10. SCA10 was described in Native American and Asian individuals which prompted a search for an expanded haplotype to confirm a common ancestral origin for the expansion event. All patients with SCA10 expansions in our cohort share a single haplotype defined at the 5'-end by the minor allele of rs41524547, located ~35 kb upstream of the SCA10 expansion. Intriguingly, rs41524547 is located within the miRNA gene, MIR4762, within its DROSHA cleavage site and just outside the seed sequence for mir4792-5p. The world-wide frequency of rs41524547-G is less than 5% and found almost exclusively in the Americas and East Asia-a geographic distribution that mirrors reported SCA10 cases. We identified rs41524547-G(+) DNA from the 1000 Genomes/International Genome Sample Resource and our own general population samples and identified SCA10 repeat expansions in up to 25% of these samples. The reduced penetrance of these SCA10 expansions may be explained by a young (pre-onset) age at sample collection, a small repeat size, purity of repeat units, or the disruption of miR4762-5p function. We conclude that rs41524547-G is the most robust at-risk SNP allele for SCA10, is useful for screening of SCA10 expansions in population genetics studies and provides the most compelling evidence to date for a single, prehistoric origin of SCA10 expansions sometime prior to or during the migration of individuals across the Bering Land Bridge into the Americas.
... Thus, the most ancient Late Paleolithic population of Siberia was replaced about 20-14 kya by East Asians, which resulted in the formation of a population in northeastern Siberia that gave rise to the ancestors of both ancient Paleo-Siberians and Amerindians [17][18][19][20][21]. In the early to mid-Holocene, this population was largely replaced by another group of East Asian origin, which gave rise to majority of present-day Siberian populations [17,19]. ...
... In the early to mid-Holocene, this population was largely replaced by another group of East Asian origin, which gave rise to majority of present-day Siberian populations [17,19]. Additional gene flows in both directions along the Bering Strait were also recorded over the past 5 kya [17,21,22]. These flows influenced the genetic structure of the Eskimo-Aleut and Chukotko-Kamchatkan peoples, as well as Na-Dene-speaking populations. ...
... Archaeological materials of the Tokarev culture also demonstrate the influence of the Paleo-Eskimo tradition. Results of recent paleogenomic study indicate that northeastern Siberians experienced a prolonged Native American-related gene flow over the last 5 kya that is evident in present-day populations from the Kamchatka and Chukotka peninsulas, such as Koryaks, Itelmens and Chukchi [21]. ...
Due to the geographical proximity of the northern coast of the Sea of Okhotsk and Kamchatka Peninsula to the Beringia, the indigenous populations of these territories are of great interest for elucidating the human settlement history of northern Asia and America. Meanwhile, there is a clear shortage of genetic studies of the indigenous populations of the northern coast of the Sea of Okhotsk. Here, in order to examine their fine-scale matrilineal genetic structure, ancestry and relationships with neighboring populations, we analyzed 203 complete mitogenomes (174 of which are new) from population samples of the Koryaks and Evens of the northern coast of the Sea of Okhotsk and the Chukchi of the extreme northeast Asia. The patterns observed underscore the reduced level of genetic diversity found in the Koryak, Even, and Chukchi populations, which, along with the high degree of interpopulation differentiation, may be the result of genetic drift. Our phylogeographic analysis reveals common Paleo-Asiatic ancestry for 51.1% of the Koryaks and 17.8% of the Evens. About third of the mitogenomes found in the Koryaks and Evens might be considered as ethno-specific, as these are virtually absent elsewhere in North, Central and East Asia. Coalescence ages of most of these lineages coincide well with the emergence and development of the Tokarev and Old Koryak archaeological cultures associated with the formation of the Koryaks, as well as with the period of separation and split of the North Tungusic groups migrated northwards from the Lake Baikal or the Amur River area.
... В то же время, у последних существенно выше удельный вес ымыяхтахского компонента. Благодаря этому они занимают промежуточное положение между Диринг-Юряхом и БОО в пространстве КВ I. Западносибирский компонент, судя по морфологическим данным, в их составе присутствует как минимум в том же объеме, как у неолитических носителей серовской и глазковской культуры, где он фиксируется не только по морфологическим, но и по генетическим данным [Wang et al., 2023]. ...
This study was triggered by the results of previous anthropological and genetic studies. Earlier we demonstrated the existence of close biological affi nities of the people from Bolshoi Olenyi Ostrov (BOO) with both the ancient Western Siberian populations and people of the Ymyyakhtakh culture. At the same time, the results of the analysis of genetic markers reveal presence of the strong Nganasan-like component in genetic structure of the BOO sample. In this study, we tried to synchronize these two sets of data and reveal interplay between biological affi nities of BOO, Ymyakhtakh and Nganasans basing on analysis of cranial metric data. We analyzed data on 14 cranial metric characteristics of BOO, 24 ancient series from Western Siberia, 11 series from Eastern Siberia and Russian Far East and Nganasans using canonical variate analysis and k-means clustering algorithm. The results of statistical analysis confi rm the dual structure of the BOO population, which includes both Western Siberian and East Siberian (Ymyyakhtakh) components. We also demonstrate that Nganasans have similar biological affi nities but with less infl uence of the Western Siberian component comparing with BOO. This result confi rms the widespread opinion about the rather ancient origin of the population core of the Nganasans. We assume that its appearance on the territory of Eastern Siberia is associated with the migration of the Ymyyakhtakh people and, therefore, cannot be dated much earlier than the beginning of the 2 nd mil. BC. We also assume that a certain Western Siberian component in the structure of Nganasans could appear during the interaction of descendants of Ymyyakhtakh people with later Western Siberian migrants in Taimyr.
... Using USR1's high-quality genome (14× coverage), the following scenario was proposed in Moreno-Mayar et al. (2018a;summarized in Fig. 4), which is still consistent with current genetic research (Kilinc et al. 2021;Sikora et al. 2019;Wang et al. 2023). A single founding population of ancestral Native Americans began to diverge from East Asians about 36,000 years ago, with strong gene flow until ~25,000 years ago. ...
In the late summer about 11,500 years ago, probably in the space of a few weeks, three young Paleoindian children died and were buried in a residential camp alongside Xasaa Na’ (Upward Sun River). An infant and neonate were buried together with associated funerary objects below a central cooking hearth, and later a ~three-year-old child was cremated and buried above the same feature. This article explores the lifeways of the Ancient Beringians that summer, reconstructed through zooarchaeology, stable isotope, spatial, and artifact analyses and implications of the mortuary treatment of these individuals with respect to the regional group, theDenali Complex, and early Paleoindian ideologies.
... Range expansions would have been part of a continuum of varying extent (Groucutt et al., 2021), with local and regional extinctions, subsequent range expansions and even back into areas settled in previous expansions (e.g. Timmermann and Friedrich, 2016;Ruan et al., 2023) and also back into source areas Wang et al., 2023). In areas of contact between expanding and established populations, the outcome would have been determined by a range of variables including time and degree to which the meeting populations had been previously isolated, and hence the degree of genetic, phenetic and behavioural isolation, the densities of the two populations relative to environmental carrying capacity and the degree of ecological isolation (Finlayson, 2004;Sanchez-Quinto and Lalueza-Fox, 2015;Lalueza-Fox, 2021;Vahdati et al., 2022;Ruan et al., 2023). ...
Recent advances in the study of ancient DNA recovered from fossils and cave sediments have profoundly changed our views on the biological and cultural interactions between populations and lineages of fossil Homo in the Later Pleistocene of Eurasia. A spatiotemporally complex picture emerges, with multiple population admixture and replacement events. Focusing on the evidence from Western Eurasia, we consider here how the mapping out of between-species interactions based on fossil and material cultural evidence is being replaced by a broader approach. Traditional narratives about human migrations and the biological and/or cultural advantages of our own species over the Neanderthals are now giving way to the study of the biological and cultural dynamics of past human populations and the nature of their interactions in time and space.
... Так, американские (палеоиндейские) по происхождению гаплогруппы мтДНК (A2a и A2b) и Yхромосомы (Q-B34) обнаружены не только у эскимосов, но и у чукчей, коряков, ительменов и даже у эвенов, проживающих по соседству с коряками [Malyarchuk et al., 2011;Dryomov et al., 2015;Grugni et al., 2019]. Недавнее палеогеномное исследование также показало, что от 5 до 20% в генофондах коряков, чукчей и ительменов приходится на палеоиндейский генетический компонент, накопившийся у палеоазиатских народов на протяжении последних 1500 лет [Wang et al., 2023]. Наиболее вероятными в данном случае представляются процессы, связанные с ассимиляцией отдельных групп неоэскимосов коренными народами Чукотки, Камчатки и Приохотья. ...
Introduction. A dinucleotide deletion of AG at the rs781470490 locus of the SI gene (SI delAG variant) causes dysfunction of the sucrase-isomaltase enzyme and the inability to digest sugar. The deletion frequency in the world is 0.0021%, while among the Inuit (Eskimo) it reaches 17–20%. Research hypothesis: the SI delAG variant is common in all the populations of indigenous northerners. The study aimed to ascertain the prevalence of the SI delAG variant in the Cis-Ural, Siberian, and Far East populations of the Russian Federation and compare it to that of the Inuit people. Materials and methods. DNA genotyping and the SI delAG variant frequency analysis were carried out in the samples from study groups of Russians, Komi, Mansi, Khanty, Nenets, Shors, Evenks, Evens, Koryaks, Chukchi (n =613). Corresponding data for the Canadian and Greenlandic Inuit (n =391) were used for comparison. Results and discussion. The deletion in samples from the Chukchi, Koryak, and Even study groups occurred in 14, 7, and 4%, respectively; there was no the deletion found in the samples of the other Siberian and Cis-Ural groups. The carriage of the SI delAG variant decreases with the distance from the area of the Greenlandic Inuit. The Inuit, Chukchi, and Koryak groups form a distinct cluster. The Paleo-Eskimo do not carry the deletion. Minimal amounts of sugar-containing products appeared in the diet of the Greenlandic and Canadian Inuit at the end of the 19th century, 200 years later than in the diet of aboriginal northerners of Eurasia. Conclusions. There was no SI delAG variant found in the samples of the indigenous people of West Eurasia high latitude regions. The deletion emerged in Neo-Eskimo population 1.2–2 thousand years ago and has been retained in the small numbered isolate due to their way of existence and diet. In the populations of the northwest coast of the Sea of Okhotsk and the Chukchi Peninsula, the SI delAG variant was brought by the gene flow from the Inuit people. @ 2023. This work is licensed under a CC BY 4.0 license.
Several scholars have in the past hypothesized a northward movement by Hunnic contingents which ultimately reached Scandinavia on the basis of archaeological and philological evidence, an event which should be detectable in both ancient and modern DNA if true. In the book, The Huns and their allies in Scandinavia, the author Karl O. Högström utilizes an interdisciplinary approach centered around genomics to trace a westward migration by the Huns from Inner Asia via southeastern Europe to Scandinavia. The significance and implications of this become clear when looking at the philological evidence which suggests that the Huns had a formative and lasting impact on the development of the peoples, cultures and beliefs in Scandinavia during the Late Iron Age.
Throughout the Upper Palaeolithic and Neolithic of Northeast Asia, several large-scale obsidian exchange networks existed. In the southern part of the region (Russian Far East, Japan, Korea, and Northeast China), the main sources of high quality lithic raw material.
This conclusion to the book is based on 30 + years of my own research in eastern Russia, and on summarising the existing knowledge related to obsidian provenance in Northeast Asia and its implications.
Hunter-gatherer mobility patterns are extremely variable across the world and through time, in ways that have been shown to profoundly affect, among other things, cultural dynamics throughout our species' evolutionary history. Unlike studies of contemporary hunter-gatherers, where culture and social interactions can be sampled separately, the archaeological record is the product of a social system in the past which we cannot directly observe. Yet, methods derived from the analyses of social networks have been increasingly used to make inferences about patterns of past social interactions using archaeological material as a proxy. It remains a question whether networks built from material cultural remains are indeed representative of the social processes that created them. Here, we use the ArchMatNet agent-based model to investigate how variability in hunter-gatherer mobility patterns and social organization affect our ability to reconstruct prehistoric social networks from artefact stylistic similarities. We find that variability in daily mobility, seasonal aggregations and patterns of migration have profound effects on our ability to recover social networks from archaeological assemblages. Moreover, that several metrics commonly used in SNA should not be interpreted in the same manner when applied to networks built from archaeological datasets. Our results highlight the fact that the archaeological record is the product of social interactions rather than analogous to them. Moreover, it points at a need to better understand the role of mobility in shaping human evolutionary patterns.
Southern Africa has one of the longest records of fossil hominins and harbours the largest human genetic diversity in the world. Yet, despite its relevance for human origins and spread around the globe, the formation and processes of its gene pool in the past are still largely unknown. Here, we present a time transect of genome-wide sequences from nine individuals recovered from a single site in South Africa, Oakhurst Rockshelter. Spanning the whole Holocene, the ancient DNA of these individuals allows us to reconstruct the demographic trajectories of the indigenous San population and their ancestors during the last 10,000 years. We show that, in contrast to most regions around the world, the population history of southernmost Africa was not characterized by several waves of migration, replacement and admixture but by long-lasting genetic continuity from the early Holocene to the end of the Later Stone Age. Although the advent of pastoralism and farming substantially transformed the gene pool in most parts of southern Africa after 1,300 bp, we demonstrate using allele-frequency and identity-by-descent segment-based methods that the ‡Khomani San and Karretjiemense from South Africa still show direct signs of relatedness to the Oakhurst hunter-gatherers, a pattern obscured by recent, extensive non-Southern African admixture. Yet, some southern San in South Africa still preserve this ancient, Pleistocene-derived genetic signature, extending the period of genetic continuity until today.
Human populations across a vast area in northern Eurasia, from Fennoscandia to Chukotka, share a distinct genetic component often referred to as the Siberian ancestry. Most enriched in present-day Samoyedic-speaking populations such as Nganasans, its origins and history still remain elusive despite the growing list of ancient and present-day genomes from Siberia. Here, we reanalyze published ancient and present-day Siberian genomes focusing on the Baikal and Yakutia, resolving key questions regarding their genetic history. First, we show a long-term presence of a unique genetic profile in southern Siberia, up to 6,000 yr ago, which distinctly shares a deep ancestral connection with Native Americans. Second, we provide plausible historical models tracing genetic changes in West Baikal and Yakutia in fine resolution. Third, the Middle Neolithic individual from Yakutia, belonging to the Belkachi culture, serves as the best source so far available for the spread of the Siberian ancestry into Fennoscandia and Greenland. These findings shed light on the genetic legacy of the Siberian ancestry and provide insights into the complex interplay between different populations in northern Eurasia throughout history.
The purpose of the study is estimation of direction and dynamics of population processes from Neolithic to historical times on the vast territories of Northern Eurasia including Siberia, Russian Far East and Japanese archipelago. To achieve this cranial metric data on 62 ancient and 40 historical samples were analyzed by means of canonical variate analysis using mean intra-group correlation matrix. The obtained results reveal that in Neolithic three basal group of population can be detected in Siberia and Far East mainland. Basically the interaction of these groups explains morphological population landscape in post-Neolithic times. The first group, represented by the Baraba Neolithic series, is obviously the descendants of the Upper Paleolithic tribes of Western and Central Siberia. The second group is related to Boisman-2 sample from Primorye. The cranial characteristics of this series can be detected in Neolithic from Primorye to Baikal region. The third group is represented by a cranial series from the Diring-Yuryakh burial ground of the Ymyakhtakh culture located in Yakutia (Sаkha). Although this sample is not closely related to other ancient series used in the analyses it contributed to historical ethnic groups adjacent to Tuva and Mongolia. In Western Siberia massive gene flow related to Afanasievo in Eneolithic and especially Andronovo people in Bronze Age is detected. At the end of the Early Iron Age, the western migration vector changed to the eastern one. The results of canonical variate analysis reveal high level of morphological similarity between Baraba Neolithic sample, Jomon, and Epi-jomon. This result needs to be verified by other independent sources including morphologic and genetic studies.
The territory of modern China was a zone of active population transformations from the time of its occupation by human species. There was the formation zone of the progenitors of all Mongoloid populations associated with the eastern trunk of non-Africans. The most ancient group is associated with the population of Tianyuan cave (田園洞). The basal steam split, after Tianyuan branch separation into two clusters of southern and northern populations. The north groups formed a gene pool base for the modern population of the northern half of China, Japan, Korea, as well as Mongolia, Siberia, and America. The southern groups formed a gene pool core for the population of Indochina, Indonesia, eastern Oceania. From the beginning of the Neolithic era, two-way interaction begins between both groups. During the agricultural spread, people from the region of the upper Yellow River actively settled in Tibet, the southwestern provinces of China, the lower reaches of the Yellow River, forming the basis of the gene pool of modern Tibetans, other Tibetan-Burmans and progenitors of the Han. Also, the migrants from the valley of Yellow River influence the population of the western Liao River, associated with another subgroup of the northern Mongoloid cluster. And the basin of this river, this population inhabits the Korean Peninsula, and from there to the Japanese archipelago. In historical time, especially in the Jin, Tang and Song eras, the penetration of northerners south of the Yellow River intensified. It absorbs local groups and affects the gene pools of local Sino-Tibetan and Hmong-Mien groups that have escaped assimilation. At the same time, the southern groups of Han Chinese also receive a noticeable admixture from the southern Mongoloid groups of the southern cluster. The arrival of the Han Chinese probably causes the outflow of part of the Tibeto-Burman groups to northeast India. The invasions of the steppe nomads did not change the gene pool of China. On the contrary, the resettlement of Han farmers in the steppe left a noticeable admixture in the population of Mongolia from the Xiongnu era to the present. Thus, the population of China since ancient times has not only a turbulent internal population history but had been influencing since the earliest epochs to rest of the population of the Inhabited parts of the World like Siberia, both Americas, India, South-East Asia and Oceania.
How we teach human genetics matters for social equity. The biology curriculum appears to be a crucial locus of intervention for either reinforcing or undermining students’ racial essentialist views. The Mendelian genetic models dominating textbooks, particularly in combination with racially inflected language sometimes used when teaching about monogenic disorders, can increase middle and high school students’ racial essentialism and opposition to policies to increase equity. These findings are of particular concern given the increasing spread of racist misinformation online and the misappropriation of human genomics research by white supremacists, who take advantage of low levels of genetics literacy in the general public. Encouragingly, however, teaching updated information about the geographical distribution of human genetic variation and the complex, multifactorial basis of most human traits, reduces students’ endorsement of racial essentialism. The genetics curriculum is therefore a key tool in combating misinformation and scientific racism. Here, we describe a framework and example teaching materials for teaching students key concepts in genetics, human evolutionary history, and human phenotypic variation at the undergraduate level. This framework can be flexibly applied in biology and anthropology classes and adjusted based on time availability. Our goal is to provide undergraduate-level instructors with varying levels of expertise with a set of evidence-informed tools for teaching human genetics to combat scientific racism, including an evolving set of instructional resources, as well as learning goals and pedagogical approaches. Resources can be found at https://noto.li/YIlhZ5. Additionally, we hope to generate conversation about integrating modern genetics into the undergraduate curriculum, in light of recent findings about the risks and opportunities associated with teaching genetics.
This study will review previously published Proto-Athabaskan (P-A) linguistic reconstructions related to weapons and ceramics technologies present on both sides of the Bering Strait. Na-Dene (N-D) is a large family of indigenous languages of North America, consisting mostly of the Athabaskan languages of the western interior, plus the Eyak and Tlingit languages of the southern Alaska coast. Athabaskan-Eyak (A-E) constitutes a distinct branch of Na-Dene. Dene-Yeniseian (D-Y) is a proposed transpacific family comprised of Na-Dene in addition to the Yeniseian languages of Siberia. Reconstructions pertaining to several specific technologies will be discussed in relation to likely cognates within broader A-E, N-D and D-Y historical contexts. Although D-Y is sometimes assumed to have originated near the conclusion of the Pleistocene Epoch (prior to ~11,500 years BP), this study will refocus fundamental questions on the current Holocene Epoch (after ~11,500 BP), and particularly the Late Holocene (after ~3000 BP).
The Xinjiang region in northwest China is a historically important geographical passage between East and West Eurasia. By sequencing 201 ancient genomes from 39 archaeological sites, we clarify the complex demographic history of this region. Bronze Age Xinjiang populations are characterized by four major ancestries related to Early Bronze Age cultures from the central and eastern Steppe, Central Asian, and Tarim Basin regions. Admixtures between Middle and Late Bronze Age Steppe cultures continued during the Late Bronze and Iron Ages, along with an inflow of East and Central Asian ancestry. Historical era populations show similar admixed and diverse ancestries as those of present-day Xinjiang populations. These results document the influence that East and West Eurasian populations have had over time in the different regions of Xinjiang.
An especially noteworthy part of the Firsovo archaeological area is a group of early burials at the fl at-grave cemeteries Novoaltaisk-Razvilka, Firsovo XI, and Firsovo XIV. Nine radiocarbon dates have been generated for those cemeteries at various laboratories: two by the liquid-scintillation (LSC) method and seven using the accelerator mass spectrometry (AMS) method. The dates were calibrated using OxCal version 3.10 software. Dates for the Chalcolithic Bolshoy Mys culture burials at Novoaltaisk-Razvilka and Tuzovskiye Bugry-1 burial 7 match the previously suggested ones (around 3000 BC). Certain Neolithic burials in the Altai differ from others in the position of the bodies (fl exed on the side). They were dated to the late 5th to the early 4th millennia BC by the AMS method. Burials belonging to the “cultural core” of Firsovo XI, then, fall within the Early Neolithic (68 % interval, 5710–5460 BC; 95 % interval, 5740–5360 BC). The date 9106 ± 80 BP (GV-02889), obtained for Firsovo XI burial 18, may be somewhat accurate, pointing to the Final Mesolithic or Early Neolithic. Both the date and the cultural characteristics of this burial (sitting position, abundant ocher) are accompanied by the craniometric distinctness of the male cranium (huge total size).
The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious1. Here we present genomic data from 5 individuals dating to around 3000–2800 bc from the Dzungarian Basin and 13 individuals dating to around 2100–1700 bc from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early–Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo1,2 or to have originated among the Bactria–Margiana Archaeological Complex3 or Inner Asian Mountain Corridor cultures4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert. A genomic analysis of human remains from the Bronze Age provides insights into the origin of the Tarim Basin mummies from the Xinjiang region.
Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.
Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide. Little is known about how human parental relatedness varied across ancient populations. Runs of homozygosity (ROH) in the offspring’s genome can give clues. Here, the authors present a method to identify ROH in ancient genomes and infer low rates of close kin unions across most ancient populations.
The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people1,2. We report genome-wide data from 166 East Asians dating to 6000 BCE – 1000 CE and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan plateau are linked by a deeply-splitting lineage likely reflecting a Late Pleistocene coastal migration. We follow Holocene expansions from four regions. First, hunter-gatherers of Mongolia and the Amur River Basin have ancestry shared by Mongolic and Tungusic language speakers but do not carry West Liao River farmer ancestry contradicting theories that their expansion spread these proto-languages. Second, Yellow River Basin farmers at ~3000 BCE likely spread Sino-Tibetan languages as their ancestry dispersed both to Tibet where it forms up ~84% to some groups and to the Central Plain where it contributed ~59-84% to Han Chinese. Third, people from Taiwan ~1300 BCE to 800 CE derived ~75% ancestry from a lineage also common in modern Austronesian, Tai-Kadai and Austroasiatic speakers likely deriving from Yangtze River Valley farmers; ancient Taiwan people also derived ~25% ancestry from a northern lineage related to but different from Yellow River farmers implying an additional north-to-south expansion. Fourth, Yamnaya Steppe pastoralist ancestry arrived in western Mongolia after ~3000 BCE but was displaced by previously established lineages even while it persisted in western China as expected if it spread the ancestor of Tocharian Indo-European languages. Two later gene flows affected western Mongolia: after ~2000 BCE migrants with Yamnaya and European farmer ancestry, and episodic impacts of later groups with ancestry from Turan.
We present genome-wide data from 40 individuals dating to c.16,900 to 550 years ago in northeast Asia. We describe hitherto unknown gene flow and admixture events in the region, revealing a complex population history. While populations east of Lake Baikal remained relatively stable from the Mesolithic to the Bronze Age, those from Yakutia and west of Lake Baikal witnessed major population transformations, from the Late Upper Paleolithic to the Neolithic, and during the Bronze Age, respectively. We further locate the Asian ancestors of Paleo-Inuits, using direct genetic evidence. Last, we report the most northeastern ancient occurrence of the plague-related bacterium, Yersinia pestis . Our findings indicate the highly connected and dynamic nature of northeast Asia populations throughout the Holocene.
The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region’s population history. Here, we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.
Radiocarbon (C) ages cannot provide absolutely dated chronologies for archaeological or paleoenvironmental studies directly but must be converted to calendar age equivalents using a calibration curve compensating for fluctuations in atmospheric C concentration. Although calibration curves are constructed from independently dated archives, they invariably require revision as new data become available and our understanding of the Earth system improves. In this volume the international C calibration curves for both the Northern and Southern Hemispheres, as well as for the ocean surface layer, have been updated to include a wealth of new data and extended to 55,000 cal BP. Based on tree rings, IntCal20 now extends as a fully atmospheric record to ca. 13,900 cal BP. For the older part of the timescale, IntCal20 comprises statistically integrated evidence from floating tree-ring chronologies, lacustrine and marine sediments, speleothems, and corals. We utilized improved evaluation of the timescales and location variable C offsets from the atmosphere (reservoir age, dead carbon fraction) for each dataset. New statistical methods have refined the structure of the calibration curves while maintaining a robust treatment of uncertainties in the C ages, the calendar ages and other corrections. The inclusion of modeled marine reservoir ages derived from a three-dimensional ocean circulation model has allowed us to apply more appropriate reservoir corrections to the marine C data rather than the previous use of constant regional offsets from the atmosphere. Here we provide an overview of the new and revised datasets and the associated methods used for the construction of the IntCal20 curve and explore potential regional offsets for tree-ring data. We discuss the main differences with respect to the previous calibration curve, IntCal13, and some of the implications for archaeology and geosciences ranging from the recent past to the time of the extinction of the Neanderthals.
Ancient human movements through Asia
Ancient DNA has allowed us to begin tracing the history of human movements across the globe. Narasimhan et al. identify a complex pattern of human migrations and admixture events in South and Central Asia by performing genetic analysis of more than 500 people who lived over the past 8000 years (see the Perspective by Schaefer and Shapiro). They establish key phases in the population prehistory of Eurasia, including the spread of farming peoples from the Near East, with movements both westward and eastward. The people known as the Yamnaya in the Bronze Age also moved both westward and eastward from a focal area located north of the Black Sea. The overall patterns of genetic clines reflect similar and parallel patterns in South Asia and Europe.
Science , this issue p. eaat7487 ; see also p. 981
Much of the American Arctic was first settled 5,000 years ago, by groups of people known as Palaeo-Eskimos. They were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yup’ik1–3. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup’ik and Aleut populations remains uncertain4–6. Here we present genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyse these data with data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Using methods based on rare-allele and haplotype sharing, as well as established techniques4,7–9, we show that Palaeo-Eskimo-related ancestry is ubiquitous among people who speak Na-Dene and Eskimo–Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that Na-Dene-speaking peoples, people of the Aleutian Islands, and Yup’ik and Inuit across the Arctic region all share ancestry from a single Palaeo-Eskimo-related Siberian source.
Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
The indigenous populations of inner Eurasia—a huge geographic region covering the central Eurasian steppe and the northern Eurasian taiga and tundra—harbour tremendous diversity in their genes, cultures and languages. In this study, we report novel genome-wide data for 763 individuals from Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine and Uzbekistan. We furthermore report additional damage-reduced genome-wide data of two previously published individuals from the Eneolithic Botai culture in Kazakhstan (~5,400 bp). We find that present-day inner Eurasian populations are structured into three distinct admixture clines stretching between various western and eastern Eurasian ancestries, mirroring geography. The Botai and more recent ancient genomes from Siberia show a decrease in contributions from so-called ‘ancient North Eurasian’ ancestry over time, which is detectable only in the northern-most ‘forest-tundra’ cline. The intermediate ‘steppe-forest’ cline descends from the Late Bronze Age steppe ancestries, while the ‘southern steppe’ cline further to the south shows a strong West/South Asian influence. Ancient genomes suggest a northward spread of the southern steppe cline in Central Asia during the first millennium bc. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe.
Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300–2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380–975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups.
DNA preserved in ancient bones, teeth and sediments is typically highly fragmented and present only in minute amounts. Here, we provide a highly versatile silica-based DNA extraction protocol that enables the retrieval of short (≥35 bp) or even ultrashort (≥25 bp) DNA fragments from such material with minimal carryover of substances that inhibit library preparation for high-throughput sequencing. DNA extraction can be performed with either silica spin columns, which offer the most convenient choice for manual DNA extraction, or silica-coated magnetic particles. The latter allow a substantial cost reduction as well as automation on liquid-handling systems. This protocol update replaces a now-outdated version that was published 11 years ago, before high-throughput sequencing technologies became widely available. It has been thoroughly optimized to provide the highest DNA yields from highly degraded samples, as well as fast and easy handling, requiring not more than ~15 min of hands-on time per sample. © 2018, The Author(s), under exclusive licence to Springer Nature Limited.
Ancient migrations in Southeast Asia
The past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipson et al. generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred individuals from five sites yielded ancient DNA from 18 individuals. Comparisons with present-day populations suggest two waves of mixing between resident populations. The first mix was between local hunter-gatherers and incoming farmers associated with the Neolithic spreading from South China. A second event resulted in an additional pulse of genetic material from China to Southeast Asia associated with a Bronze Age migration. McColl et al. sequenced 26 ancient genomes from Southeast Asia and Japan spanning from the late Neolithic to the Iron Age. They found that present-day populations are the result of mixing among four ancient populations, including multiple waves of genetic material from more northern East Asian populations.
Science , this issue p. 92 , p. 88 ; see also p. 31
Ancient steppes for human equestrians
The Eurasian steppes reach from the Ukraine in Europe to Mongolia and China. Over the past 5000 years, these flat grasslands were thought to be the route for the ebb and flow of migrant humans, their horses, and their languages. de Barros Damgaard et al. probed whole-genome sequences from the remains of 74 individuals found across this region. Although there is evidence for migration into Europe from the steppes, the details of human movements are complex and involve independent acquisitions of horse cultures. Furthermore, it appears that the Indo-European Hittite language derived from Anatolia, not the steppes. The steppe people seem not to have penetrated South Asia. Genetic evidence indicates an independent history involving western Eurasian admixture into ancient South Asian peoples.
Science , this issue p. eaar7711
Despite broad agreement that the Americas were initially populated via Beringia, the land bridge that connected far northeast Asia with northwestern North America during the Pleistocene epoch, when and how the peopling of the Americas occurred remains unresolved1–5. Analyses of human remains from Late Pleistocene Alaska are important to resolving the timing and dispersal of these populations. The remains of two infants were recovered at Upward Sun River (USR), and have been dated to around 11.5 thousand years ago (ka)6. Here, by sequencing the USR1 genome to an average coverage of approximately 17 times, we show that USR1 is most
closely related to Native Americans, but falls basal to all previously sequenced contemporary and ancient Native Americans1,7,8. As such, USR1 represents a distinct Ancient Beringian population. Using demographic modelling, we infer that the Ancient Beringian population and ancestors of other Native Americans descended
from a single founding population that initially split from East Asians around 36 ± 1.5 ka, with gene flow persisting until around 25 ± 1.1 ka. Gene flow from ancient north Eurasians into all Native Americans took place 25–20 ka, with Ancient Beringians branching off around 22–18.1 ka. Our findings support a long-term genetic structure in ancestral Native Americans, consistent with the Beringian ‘standstill model’9. We show that the basal northern and southern Native American branches, to which all other Native Americans belong, diverged around 17.5–14.6 ka, and that this probably occurred south of the North American ice sheets. We
also show that after 11.5 ka, some of the northern Native American populations received gene flow from a Siberian population most closely related to Koryaks, but not Palaeo-Eskimos1, Inuits or Kets10, and that Native American gene flow into Inuits was through northern and not southern Native American groups1. Our findings
further suggest that the far-northern North American presence of northern Native Americans is from a back migration that replaced or absorbed the initial founding population of Ancient Beringians.
Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 BCE, from Natufian hunter–gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter–gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter–gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Afri
Dietary changes in the populations inhabiting southwest Siberia and northern Kazakhstan indicate concurrent changes in the economy, at the same time marking the beginnings of East–West interaction across northern Eurasia. The introduction of domestic animal species of Near Eastern origin, such as sheep and goat, dramatically changed the lives of the local population. Past palaeodietary research using stable isotope analysis has mainly focussed on pastoral populations of the Bronze Age period. It is crucial, however, to assess the diets of humans and animals from earlier periods (Neolithic/Chalcolithic) in order to understand the timing and nature of dietary change during the Bronze Age of southwest Siberia and northern Kazakhstan, in particular the possible contribution of environmental change influencing dietary shifts. In this paper, we report the results of stable isotope analysis on 55 human and 45 faunal samples from southwest Siberia (Upper Ob River) and northern Kazakhstan (Tobol River basin), ranging from the Neolithic to the Bronze Age. These data, combined with published human and faunal collagen results from the region as well as new accelerator mass spectrometer (AMS) radiocarbon dating results, indicate little change in animal diet over time, but a notable change in human diet at ca. 2500 cal. BC. The data allow us to determine the time when pastoralism came to the fore, with concomitant economic differences to the local population.
Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3-6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.
Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics. With the extensive growth of the underlying phylogenetic tree summarizing the published mtDNA sequences, the manual process of haplogroup classification would be too time-consuming. The previously published classification tool HaploGrep provided an automatic way to address this issue. Here, we present the completely updated version HaploGrep 2 offering several advanced features, including a generic rule-based system for immediate quality control (QC). This allows detecting artificial recombinants and missing variants as well as annotating rare and phantom mutations. Furthermore, the handling of high-throughput data in form of VCF files is now directly supported. For data output, several graphical reports are generated in real time, such as a multiple sequence alignment format, a VCF format and extended haplogroup QC reports, all viewable directly within the application. In addition, HaploGrep 2 generates a publication-ready phylogenetic tree of all input samples encoded relative to the revised Cambridge Reference Sequence. Finally, new distance measures and optimizations of the algorithm increase accuracy and speed-up the application. HaploGrep 2 can be accessed freely and without any registration athttp://haplogrep.uibk.ac.at.
The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted
process.Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale
genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants.EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools
tailored for ancient DNA data within a single integrated solution in an easily accessible format.
As high-throughput sequencing platforms produce longer and longer reads, sequences generated from short inserts, such as those obtained from fossil and degraded material, are increasingly expected to contain adapter sequences. Efficient adapter trimming algorithms are also needed to process the growing amount of data generated per sequencing run.
We introduce AdapterRemoval v2, a major revision of AdapterRemoval v1, which introduces (i) striking improvements in throughput, through the use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support, (ii) the ability to handle datasets containing reads or read-pairs with different adapters or adapter pairs, (iii) simultaneous demultiplexing and adapter trimming, (iv) the ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets, and (v) native gzip and bzip2 support.
We show that AdapterRemoval v2 compares favorably with existing tools, while offering superior throughput to most alternatives examined here, both for single and multi-threaded operations.
Dental anthropologists focus on the variation around a commonly shared pattern, a variation expressed by differences in tooth size and morphology. This book centers on the morphological characteristics of tooth crowns and roots that are either present or absent in any given individual and that vary in frequency among populations. These nonmetric dental traits are controlled largely by genetic factors and provide a direct link between extinct and extant populations. The book illustrates more than thirty tooth crown and root traits and reviews their biological and genetic underpinnings. From a database of more than 30,000 individuals, the geographic variation of twenty-two crown and root traits is graphically portrayed. A global analysis of tooth morphology shows both points of agreement and disagreement with comparable analyses of genetic and craniometric data. These findings are relevant to the hotly contested issue of timing and geographic context of modern human origins.
Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.
Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates. Availability: https://bioinf.eva.mpg.de/schmutzi/
license:GPLv3.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-015-0776-0) contains supplementary material, which is available to authorized users.
How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the
ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration
wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia.
After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka,
one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted
in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians.
Putative “Paleoamerican” relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians,
are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
Neanderthals are thought to have disappeared in Europe approximately 39,000-41,000 years ago but they have contributed 1-3% of the DNA of present-day people in Eurasia. Here we analyse DNA from a 37,000-42,000-year-old modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6-9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.
Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon-dated to 8,340-9,200 calibrated years before present (bp). His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans. In order to resolve Kennewick Man's ancestry and affiliations, we have sequenced his genome to ∼1× coverage and compared it to worldwide genomic data including the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genomic-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.
The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.
We generated genome-wide data from 69 Europeans who lived between 8,000-3,000
years ago by enriching ancient DNA libraries for a target set of almost four
hundred thousand polymorphisms. Enrichment of these positions decreases the
sequencing required for genome-wide ancient DNA analysis by a median of around
250-fold, allowing us to study an order of magnitude more individuals than
previous studies and to obtain new insights about the past. We show that the
populations of western and far eastern Europe followed opposite trajectories
between 8,000-5,000 years ago. At the beginning of the Neolithic period in
Europe, ~8,000-7,000 years ago, closely related groups of early farmers
appeared in Germany, Hungary, and Spain, different from indigenous
hunter-gatherers, whereas Russia was inhabited by a distinctive population of
hunter-gatherers with high affinity to a ~24,000 year old Siberian6 . By
~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred
throughout much of Europe, but in Russia, the Yamnaya steppe herders of this
time were descended not only from the preceding eastern European
hunter-gatherers, but from a population of Near Eastern ancestry. Western and
Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded
Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya,
documenting a massive migration into the heartland of Europe from its eastern
periphery. This steppe ancestry persisted in all sampled central Europeans
until at least ~3,000 years ago, and is ubiquitous in present-day Europeans.
These results provide support for the theory of a steppe origin of at least
some of the Indo-European languages of Europe.
The challenge of sequencing ancient DNA has led to the development of specialized laboratory protocols that have focused on reducing contamination and maximizing the number of molecules that are extracted from ancient remains. Despite the fact that success in ancient DNA studies is typically obtained by screening many samples to identify a promising subset, ancient DNA protocols have not, in general, focused on reducing the time required to screen samples. We present an adaptation of a popular ancient library preparation method that makes screening more efficient. First, the DNA extract is treated using a protocol that causes characteristic ancient DNA damage to be restricted to the terminal nucleotides, while nearly eliminating it in the interior of the DNA molecules, allowing a single library to be used both to test for ancient DNA authenticity and to carry out population genetic analysis. Second, the DNA molecules are ligated to a unique pair of barcodes, which eliminates undetected cross-contamination from this step onwards. Third, the barcoded library molecules include incomplete adapters of short length that can increase the specificity of hybridization-based genomic target enrichment. The adapters are completed just before sequencing, so the same DNA library can be used in multiple experiments, and the sequences distinguished. We demonstrate this protocol on 60 ancient human samples.
© 2014 The Author(s) Published by the Royal Society. All rights reserved.
Background
High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously.ResultsWe present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods.Conclusions
The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd. The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.
We have developed an algorithm to rapidly and accurately identify the Y-chromosome haplogroup of each male in a sample of one to millions. The algorithm, implemented in the yHaplo * software package (yHaplo), does not rely on any particular genotyping modality or platform. Full sequences yield the most granular haplogroup classifications, but genotyping arrays can yield reliable calls, provided a reasonable number of phylogenetically informative variants has been assayed. The algorithm is robust to missing data, genotype errors, mutation recurrence, and other complications. We have tested the software on full sequences from phase 3 of the 1000 Genomes Project and on subsets thereof constructed by downsampling to SNPs present on each of four genotyping arrays. We have also run the software on array data from more than 600,000 males.
It has been shown that highly fragmented DNA is most efficiently converted into DNA libraries for sequencing if both strands of the DNA fragments are processed independently. We present an updated protocol for library preparation from single-stranded DNA, which is based on the splinted ligation of an adapter oligonucleotide to the 3′ ends of single DNA strands, the synthesis of a complementary strand using a DNA polymerase and the addition of a 5′ adapter via blunt-end ligation. The efficiency of library preparation is determined individually for each sample using a spike-in oligonucleotide. The whole workflow, including library preparation, quantification and amplification, requires two work days for up to 16 libraries. Alternatively, we provide documentation and electronic protocols enabling automated library preparation of 96 samples in parallel on a Bravo NGS Workstation (Agilent Technologies). After library preparation, molecules with uninformative short inserts (shorter than ~30−35 base pairs) can be removed by polyacrylamide gel electrophoresis if desired. Here the authors describe an updated protocol for single-stranded sequencing library preparation suitable for highly degraded DNA from ancient remains or other sources. The procedure can be performed manually or in an automated fashion.
Modern humans have inhabited the Lake Baikal region since the Upper Paleolithic, though the precise history of its peoples over this long time span is still largely unknown. Here, we report genome-wide data from 19 Upper Paleolithic to Early Bronze Age individuals from this Siberian region. An Upper Paleolithic genome shows a direct link with the First Americans by sharing the admixed ancestry that gave rise to all non-Arctic Native Americans. We also demonstrate the formation of Early Neolithic and Bronze Age Baikal populations as the result of prolonged admixture throughout the eighth to sixth millennium BP. Moreover, we detect genetic interactions with western Eurasian steppe populations and reconstruct Yersinia pestis genomes from two Early Bronze Age individuals without western Eurasian ancestry. Overall, our study demonstrates the most deeply divergent connection between Upper Paleolithic Siberians and the First Americans and reveals human and pathogen mobility across Eurasia during the Bronze Age.
By at least 45,000 years before present, anatomically modern humans had spread across Eurasia [1-3], but it is not well known how diverse these early populations were and whether they contributed substantially to later people or represent early modern human expansions into Eurasia that left no surviving descendants today. Analyses of genome-wide data from several ancient individuals from Western Eurasia and Siberia have shown that some of these individuals have relationships to present-day Europeans [4, 5] while others did not contribute to present-day Eurasian populations [3, 6]. As contributions from Upper Paleolithic populations in Eastern Eurasia to present-day humans and their relationship to other early Eurasians is not clear, we generated genome-wide data from a 40,000-year-old individual from Tianyuan Cave, China, [1, 7] to study his relationship to ancient and present-day humans. We find that he is more related to present-day and ancient Asians than he is to Europeans, but he shares more alleles with a 35,000-year-old European individual than he shares with other ancient Europeans, indicating that the separation between early Europeans and early Asians was not a single population split. We also find that the Tianyuan individual shares more alleles with some Native American groups in South America than with Native Americans elsewhere, providing further support for population substructure in Asia [8] and suggesting that this persisted from 40,000 years ago until the colonization of the Americas. Our study of the Tianyuan individual highlights the complex migration and subdivision of early human populations in Eurasia.
Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon dated to 8,340-9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans. In order to resolve Kennewick Man's ancestry and affiliations, we have sequenced his genome to ∼1× coverage and compared it to worldwide genomic data including for the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genome-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.
Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil’s Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
The results are presented of a new program of radiocarbon dating undertaken on 88 human skeletons. The individuals derived from Eneolithic to Early Iron Age sites-Afanasievo, Okunevo, Andronovo (Fedorovo), Karasuk, and Tagar cultures-in the Minusinsk Basin of Southern Siberia. All the new dates have been acquired from human bone, which is in contrast to some of the previous dates for this region obtained from wood and thus possibly unreliable due to old-wood effects or re-use of the timber. The new data are compared with the existing 14C chronology for the region, thereby enabling a clearer understanding to be gained concerning the chronology of these cultures and their place within the prehistory of the Eurasian steppes. © 2009 by the Arizona Board of Regents on behalf of the University of Arizona.
