|
Post by Admin on Dec 20, 2021 4:17:21 GMT
Holocene transformations across Siberia and Beringia Our genomic data provide further insights into the timing and the ori-gins of peoples involved in more-recent gene flow during the Holocene, across what was by then the Bering Sea. The Saqqaq individual from Greenland (dated to 4ka23)—representing Palaeo-Eskimos—clusters with the Kolyma1 individual, but shows a greater affinity to East Asians than Kolyma1 (Fig.1, Extended Data Table1). By modelling the Saqqaq individual as a mixture of Ancient Palaeo-Siberians (rep-resented by Kolyma1) and East Asians (represented by the Devil’s Gate Cave individuals), we estimate that the Saqqaq individual con-tains around 20% East Asian ancestry (Extended Data Fig.7a, b, Supplementary Information6, Supplementary Table5). Individuals from the Uelen and Ekven Neo-Eskimo sites (dated to 2.7–1.6ka), located on the Siberian shore of the Bering Sea, cluster closely with contemporary Inuit individuals (Fig.1, Extended Data Fig.8a). We fit them as a mixture of 69% Ancient Palaeo-Siberian (Kolyma1) and 31% Native American ancestry (represented by the Anzick individual associated with Clovis assemblages), thereby documenting a ‘reverse’ gene flow across the Bering Sea (from northwestern North America to northeastern Siberia). This is consistent with linguistic evidence for a back-migration into Siberia of a population speaking a language from the Eskimo–Aleut family (Extended Data Table1; Extended Data Fig.7, Supplementary Information6, 9, Supplementary Table5). The source population of this gene flow post-dates the divergence of the USR1 individual from other Native Americans (at about 20.9ka21), as the individuals at Ekven share more alleles with ancient Native Americans (individuals Anzick-1 and Kennewick Man) than with Ancient Beringians (USR1); this confirms previous results from present-day Inuits24 (Extended Data Table1). Using linkage-disequilibrium-based admixture dating25 with the Saqqaq and Anzick-1 individuals as source populations, we find a significant signal of admixture linkage dise-quilibrium, with an estimated date of 100–200generations before the age of theindividuals (Supplementary Information6). Although these estimates show considerable uncertainty (owing to the limited sam-ple size and genomic coverage), they nevertheless indicate that gene flow from Native Americans into Siberia took place possibly as early as about 5ka (about 100 generations before the earliest individual from Uelen and Ekven), well after the disappearance of Beringia. Finally, we investigated the genetic affinity between North American populations who speak Na-Dene languages (including Athabascans) and Siberian populations26, which has previously been suggested to relate either to gene flow from a Palaeo-Eskimo source27 or to an unknown source population that was more closely related to Koryaks21. We find that the Kolyma1 individual is a better proxy for this source population than the Saqqaq individual, using both admixture graph modelling (Supplementary Information6) and chromosome-painting symmetry tests (Extended Data Fig.5); this provides additional evidence against a genetic contribution from a migration of Palaeo-Eskimos (Saqqaq) to contemporary speakers of Na-Dene languages. The Holocene archaeological record of northeast Siberia is marked by further changes in material culture. We used a temporal transect of ancient Siberians from about 6ka to 500years ago to investi-gate whether these cultural transitions were associated with genetic changes. We find that, in a principal component analysis of present-day non-African populations, most contemporary Siberian populations are arranged along two separate genetic clines. The majority of individuals (referred to as ‘Neo-Siberians’) lie on an east–west cline that is stretched out along principal component 1, between European individuals at one end and East Asian individuals at the other (Fig.1). A secondary cline between East Asians and Native Americans along principal component 2 includes speakers of Palaeo-Siberian languages and Inuit populations (Extended Data Fig.8c). Estimated mixture proportions show that Ancient Palaeo-Siberian ancestry (Kolyma1) was common in other Siberian regions until the early Bronze Age (Extended Data Fig.7),
|
|
|
Post by Admin on Dec 20, 2021 19:03:10 GMT
Fig. 3 | Genetic legacy of ancient Eurasians. a, Worldwide map of top haplotype donations inferred by chromopainter. Coloured symbols represent a modern recipient population; the colour and shape indicate the donor population that contributes the highest fraction of haplotypes to that recipient population. Geographical locations of donor populations used in this analysis (modern Africans and ancient Eurasians) are indicated by the corresponding larger symbols with a black outline added. Extended regions of shared top donors are visualized by spatial interpolation of the respective donor population colour. b, Major hypothesized migrations into northeast Siberia. Arrows indicate putative migrations that gave rise to ANS (left), Ancient Palaeo-Siberians (middle) and Neo-Siberians (right). Key sample locations for the respective time slice are indicated with symbols. Small blue arrows in the middle panel indicate possible ANS admixture scenarios: (1) admixture in southern Siberia and (2) admixture in Beringia. but thereafter was largely restricted to the northeast; this is exemplified by an individual from Ol’skaya dated to 3ka, who closely resembles present-day Koryaks and Itelmen. Using present-day Even individuals to represent Neo-Siberians in our demographic model, we find evi-dence for a divergence from East Asians at about 20ka, with only low levels (about 4%) of Ancient Palaeo-Siberian gene flow at around 13ka (Fig.2, Supplementary Information7). Thus, our data provide evi-dence for a second major population turnover in northeastern Siberia in which Neo-Siberians expanding northwards largely replaced Ancient Palaeo-Siberians; this pattern is also evident in chromosome-painting analyses of present-day populations (Fig.3). A notable exception are the Ket (an isolated population that speaks a Yeniseian language), who have previously been described as rich in ‘Ancestral North Eurasian’ ances-try and as having genetic links to Palaeo-Eskimos26. The Ket fall on a secondary cline parallel to Neo-Siberians in the chromosome-paint-ing analysis, and carry about 40% Ancient Palaeo-Siberian ancestry (Extended Data Figs.8c, 7). Our findings are consistent with the pro-posed linguistic link between the Yeniseian-speaking Ket and Na-Dene-speaking Athabascan populations (Supplementary Information9), likely through shared ancestry with an Ancient Palaeo-Siberian meta-population that was more widespread across northern Eurasia before the expansion of Neo-Siberian peoples. Our Holocene transect reveals additional complexity in recent times, with evidence for further episodes of gene flow and local population replacements. A notable example is found in the Lake Baikal region in southern Siberia; here, the genomes from Ust’Belaya and neighbouring Neolithic and Bronze Age sites show a succession of three distinct genetic ancestries over an approximately 6,000-year period. The earliest individuals show predominantly East Asian ancestry (represented by individuals from Devil’s Gate Cave) (Fig.1, Extended Data Figs.7, 8, followed by a resurgence of Ancient Palaeo-Siberian ancestry (up to about 50% ancestry) in the early Bronze Age, as well as the influence of West Eurasian steppe ancestry (about 10% ancestry from individ-uals associated with the Afanasievo culture) (Extended Data Fig.7, Supplementary Table5). This is consistent with previous reports of gene flow from an unknown AncestralNorthEurasian-related source into Lake Baikal hunter-gatherers28. Our results suggest a southward expansion of Ancient Palaeo-Siberians as a possible source. This is consistent with the replacement of Y chromosome lineages observed at Lake Baikal, from predominantly haplogroup N in the Neolithic to haplogroup Q during the early Bronze Age28. Finally, the most recent individual from Ust’Belaya (about 600years old) falls along the Neo-Siberian cline and is similar to the Young Yana individual from north-eastern Siberia (about 760years old), demonstrating the geographical extent of the Neo-Siberian demographic expansion in the recent past. We show that most populations on the Neo-Siberian cline can be modelled as predominantly East Asian, with varying proportions of West Eurasian steppe ancestry; the largest proportions of this latter ancestry are observed among Altaian populations, both of the present day and in more-recent Bronze Age and Iron Age archaeological con-texts (Extended Data Fig.7, Supplementary Table5). Together, these findings demonstrate considerable population movement and admix-ture throughout southern and eastern Siberia during the Holocene, in which groups dispersed in multiple directions—but without clear evidence of the wholesale population replacement seen earlier in the Pleistocene.
|
|
|
Post by Admin on Dec 20, 2021 19:49:05 GMT
Finally, we investigated the geographical extent of these processes of population flux across northern Eurasia. The notable spatial pattern of Ancestral Palaeo-Siberian and East Asian ancestry in present-day populations (Fig.3) suggests that Ancient Palaeo-Siberian ancestry was once widespread, probably as far west as the Ural Mountains. At the western edge of northern Eurasia, genetic and strontium-isotope data from ancient individuals at the Levänluhta site (Supplementary Information1) document the presence of Saami ancestry in south-western Finland in the late Holocene, at about 1.5ka. This ancestry component is currently limited to the northern fringes of the region, which mirrors the pattern that is observed for Ancient Palaeo-Siberian ancestry in northeastern Siberia. However, although the ancient Saami individuals contain ancestry from an eastern source, we find that this is modelled better by East Asians than by Ancient Palaeo-Siberians, which suggests that the influence of Ancient Palaeo-Siberians prob-ably did not extend across the Ural Mountains into western Eurasia (Extended Data Fig.7, Supplementary Table5). East–west gene flow continued to shape the gene pool of the Finnish population into the very recent past. We observe West Eurasian admixture in present-day Saami; by contrast, present-day Finns have greater Siberian ancestry than the ancient Levänluhta individual (Extended Data Table1), who may represent the Scandinavian component in the dual-origin (Uralic and Scandinavian) gene pool of Finns today.
Our findings reveal that the population history of northeastern Siberia is far more complex than previously inferred from the contemporary genetic record. It involved, at a minimum, three major population expansions and subsequent large-scale replacements during the late Pleistocene and early Holocene, with smaller-scale population fluxes since then. These three major waves are also clearly documented in the archaeological record. The initial movement into the region repre-sents a now-extinct ANS population diversifying at about 38ka, soon after the basal split between West Eurasians and East Asians, which is represented by the archaeological culture found at Yana RHS4,29. This finding is consistent with other studies that have shown that this period was a time of rapid expansion of early modern humans across Eurasia13. The arrival of people who carried ancestry from East Asia and their admixture with descendants of the ANS lineage at about 20–18ka led to the formation of the Ancient Palaeo-Siberian and Native American lineages. In the archaeological record, this is reflected by the spread of a microblade technology that accompanies the post-LGM contraction of the once-extensive mammoth steppe10. This group was, in turn, largely replaced by Neo-Siberians in the early to mid-Holocene. Our data suggest that the Neo-Siberians received ANS-related ancestry indirectly through admixture with Ancient Palaeo-Siberian groups at about 13ka, and possibly later from Bronze Age groups from the central Asian steppe after around 5ka. A signal of Australasian ancestry that has been observed at a very low frequency in some modern and ancient South American populations30–32 is not evident in any of the ancient Siberian or Beringian samples sequenced here, or in previous studies21. We find that—despite the complex pattern of population admixture throughout the past 40,000 years—the first inhabitants of northeastern Siberia (represented by the Yana RHS individuals) were not the direct ancestors of either Native Americans or present-day Siberians, although traces of their genetic legacy can be observed in ancient and modern genomes across America and northern Eurasia. These earliest ancient Siberians (the ANS) are known from a handful of other ancient genomes (those of the Mal’ta and Afontova Gora individuals); they are the descendants of one of the early modern human populations that diversified as Eurasia was first settled by our species, and are thus highly distinct. The ANS were later partially assimilated with a group with East Asian affinity who formed the Ancient Palaeo-Siberians (represented by Kolyma1); this group also probably once had a wide geographical distribution across northern Eurasia. The genetic legacy of Ancient Palaeo-Siberians among present-day Siberians is more limited, being restricted to groups in northeastern Siberia. Importantly, this legacy is also evident in the Americas, which implies that the majority of Native American genetic ancestry is likely to have originated in northeastern Siberia rather than south-central Siberia, as has beeninferred from modern mitochondrial and Y chromosome DNA33. The Neo-Siberians, who occupy much of the range that was previously inhabited by ANS-related and Ancient Palaeo-Siberian groups, represent a more recent arrival that originated further south. The replacement processes we have revealed for the northeastern portion of Siberia are mirrored in far-western Eurasia by the regional displacement and admixture of the Saami people during the late Holocene. This suggests that simi-lar processes probably took place in many other parts of the northern hemisphere.
|
|
|
Post by Admin on Dec 20, 2021 20:21:30 GMT
Extended Data Fig. 1 | Geographical, chronological and archaeological context for the earliest human remains discovered in northern Siberia. a, Map of known 14C-dated anatomically modern human fossils of late Pleistocene and early Holocene age (yellow dots) found in Siberia54,82–87. Yellow star, Yana RHS site; red triangle, Denisova Cave, which has yielded Neanderthal and Denisovan remains88,89; white line, reconstructed maximum ice sheet extent at about 60ka; blue filling, ice sheet extent during the LGM, around 20ka (refs 90,91); potentially glaciated areas are cross-hatched. b, General view of the Northern Point excavation area at the Yana RHS site4. c, Cultural layer in H29 unit in which the human tooth was found. d, Cryolithological profile for Northern Point of YanaRHS92. e, Human tooth found during the excavations in unit 2V26 shown in occlusal and lateral view (e1); human tooth found in unit X26 shown in occlusal view (e2); and human tooth found in unit H29 shown in occlusal and lateral view (e3). The samples e2 (Yana2 genome) and e3 (Yana1 with high-coverage (25.6×) genome sequence) are used in this study. In the key for d (bottom): 1, sand with small pebbles; 2, sandy silt; 3, clayey-sand silt; 4, sandy-clayey silt; 5, interbedding of clayey silt bands and sandy-clayey silt with beds and lenses of peat; 6, soil–vegetation layer; 7, cultural layer; 8, polygonal ice wedges; 9, boundary of seasonally active layer; 10, location of bones of Pleistocene animals sampled for 14 dating; 11, location of 14 samples of plant remains; 12, radiocarbon date and laboratory code. Extended Data Fig. 2 | Y chromosome phylogeny. Maximum likelihood tree of Y chromosome sequences for modern and ancient individuals, with major haplogroups highlighted. Numbers on internal nodes show bootstrap support values from 100 replicates for nodes with bootstrap values<100.
|
|
|
Post by Admin on Dec 20, 2021 21:04:27 GMT
Extended Data Fig. 3 | Genetic affinities of Yana RHS individuals. a–c,Geographical heat maps depicting the outgroup-f3 statistics for Yana1 (a), Tianyuan (b) and Sunghir3 (c) individuals with 167 worldwide populations. d, f4-statistics contrasting allele sharing of Yana RHS individuals and other selected Upper Palaeolithic groups with early West Eurasians (represented by the Kostenki 14 individual) or East Asians (represented by the Tianyuan individual). e, f4-statistics for highlighting groups with affinities to both early West Eurasians and East Asians (joined with dashed lines). Error bars indicate±3 s.e., obtained using a block jackknife (Methods). f, Admixture graph models of ancient and modern populations for western Eurasia (left) and East Asia and the Americas (right). Newly reported individuals are highlighted with a coloured background. Early Upper Palaeolithic individuals were modelled allowing for a possible additional Neanderthal contribution to account for higher levels of Neanderthal ancestry (dotted lines). Extended Data Fig. 4 | Relatedness and identity-by-descent. a, Kinship coefficient and R1 ratio (number of double-heterozygous (Aa/Aa) sites divided by the total number of discordant genotypes) for newly reported ancient groups with multiple individuals per site. b, Number and length of homozygosity-by-descent (HBD) segments in ancient and modern individuals. Grey ellipses indicate 95% confidence region obtained from simulations of 100 haploid genomes of indicated effective population size. c, Distribution of total identity-by-descent (IBD) lengths for simulations of varying effective population sizes. Observed values for pairs from the Sunghir and Yana individuals are indicated by dashed lines.
|
|