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Post by Admin on May 12, 2022 19:33:15 GMT
Deep population structure of western Eurasians Our study comprises the largest genomic dataset on European hunter-gatherers to date, including 113 imputed hunter-gatherer genomes of which 79 were sequenced in this study. Among them, we report a 0.83X genome of an Upper Palaeolithic (UP) skeleton from Kotias Klde Cave in Georgia, Caucasus (NEO283), directly dated to 26,052 - 25,323 cal BP (95%). In the PCA of all non-African individuals, it occupies a position distinct from other previously sequenced UP individuals, shifted towards west Eurasians along PC1 (Supplementary Note 3d). Using admixture graph modelling, we find that this Caucasus UP lineage derives from a mixture of predominantly West Eurasian UP hunter-gatherer ancestry (76%) with ∼24% contribution from a “basal Eurasian” ghost population, first observed in West Asian Neolithic individuals29 (Extended data Fig. 5A). Models attempting to reconstruct major post-LGM clusters such as European hunter-gatherers and Anatolian farmers without contributions from this Caucasus UP lineage provided poor admixture graph fits or were rejected in qpAdm analyses (Extended data Fig. 5B,C). These results thus suggest a central role of the descendants related to this Caucasus UP lineage in the formation of later West Eurasian populations, consistent with recent genetic data from the nearby Dzudzuana Cave, also in Georgia30. Fig 5. The genetic legacy of Stone Age ancestry in modern populations. From top left clockwise: Neolithic Farmer, Yamnaya, Caucasus hunter-gatherer, Eastern hunter-gatherer, Western hunter-gatherer. Panels show average admixture proportion in modern individuals per country estimated using NNLS (large maps), average per county within the UK (top left insert), and PCA (PC2 vs PC1) of admixture proportions, with the top 10 highest countries by admixture fraction labelled and PCA loadings for that ancestry. We performed supervised admixture modelling using a set of twelve possible source clusters representing Mesolithic hunter-gatherers from the extremes of the HG cline, as well as temporal or geographical outgroups of deep Eurasian lineages (Fig 2A). We replicate previous results of broad-scale genetic structure correlated to geography in European hunter-gatherers after the LGM17, while also revealing novel insights into their fine-scale structure. Ancestry related to southern European hunter-gatherers (source: Italy_15000BP_9000 BP) predominates in western Europe. This includes Denmark, where our 28 sequenced and imputed hunter-gatherer genomes derive almost exclusively from this cluster, with remarkable homogeneity across a 5,000 year transect (Fig. 3A). In contrast, hunter-gatherer individuals from the eastern and far northern reaches of Europe show the highest proportions of Russian hunter-gatherer ancestry (source: RussiaNW_11000BP_8000BP; Fig. 2B, D), with genetic continuity until ∼5,000 BP in Russia. Ancestry related to Mesolithic hunter-gatherer populations from Ukraine (source: Ukraine_10000BP_4000BP) is carried in highest proportions in hunter-gatherers from a geographic corridor extending from south-eastern Europe towards the Baltic and southern Scandinavia. Swedish Mesolithic individuals derive up to 60% of their ancestry from that source (Fig. 2C). Our results thus indicate northwards migrations of at least three distinct waves of hunter-gatherer ancestry into Scandinavia: a predominantly southern European source into Denmark; a source related to Ukrainian and south-eastern European hunter-gatherers into the Baltic and southern Sweden; and a northwest Russian source into the far north, before venturing south along the Atlantic coast of Norway31 (Fig. 2). These movements are likely to represent post glacial expansions from refugia areas shared with many plant and animal species32, 33. Despite the major role of geography in shaping European hunter-gatherer structure, we also document more complex local dynamics. On the Iberian Peninsula, the earliest individuals, including a ∼9,200-year-old hunter-gatherer (NEO694) from Maira (eastern Spain), sequenced in this study, show predominantly southern European hunter-gatherer ancestry with a minor contribution from UP hunter-gatherer sources (Fig. 3). In contrast, later individuals from Northern Iberia are more similar to hunter-gatherers from eastern Europe, deriving ∼30-40% of their ancestry from a source related to Ukrainian hunter-gatherers34, 35. The earliest evidence for this gene flow is observed in a Mesolithic individual from El Mazo, Spain (NEO646) that was dated, calibrated and reservoir-corrected to c. 8,200 BP (8365-8182 cal BP, 95%) but context-dated to slightly older (8550-8330 BP, see36). The younger date coincides with some of the oldest Mesolithic geometric microliths in northern Iberia, appearing around 8,200 BP at this site36. In southern Sweden, we find higher amounts of southern European hunter-gatherer ancestry in late Mesolithic coastal individuals (NEO260 from Evensås; NEO679 from Skateholm) than in the earlier Mesolithic individuals from further inland, suggesting either geographic genetic structure in the Swedish Mesolithic population or a possible eastward expansion of hunter-gatherers from Denmark, where this ancestry prevailed (Fig. 3). An influx of southern European hunter-gatherer-related ancestry in Ukrainian individuals after the Mesolithic (Fig. 3) suggests a similar eastwards expansion in south-eastern Europe17. Interestingly, two herein reported ∼7,300-year-old imputed genomes from the Middle Don River region in the Pontic-Caspian steppe (Golubaya Krinitsa, NEO113 & NEO212) derive ∼20-30% of their ancestry from a source cluster of hunter-gatherers from the Caucasus (Caucasus_13000BP_10000BP) (Fig. 3). Additional lower coverage (non-imputed) genomes from the same site project in the same PCA space (Fig. 1D), shifted away from the European hunter-gatherer cline towards Iran and the Caucasus. Our results thus document genetic contact between populations from the Caucasus and the Steppe region as early as 7,300 years ago, providing documentation of continuous admixture prior to the advent of later nomadic Steppe cultures, in contrast to recent hypotheses, and also further to the west than previously reported17, 37.
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Post by Admin on May 12, 2022 22:00:18 GMT
Major genetic transitions in Europe Previous ancient genomics studies have documented multiple episodes of large-scale population turnover in Europe within the last 10,000 years6, 11, 14, 16, 17, 20, 21, 34, 38–41. The 317 genomes reported here fill important knowledge gaps, particularly in northern and eastern Europe, allowing us to track the dynamics of these events at both continental and regional scales. Our analyses reveal profound differences in the spatiotemporal Neolithisation dynamics across Europe. Supervised admixture modelling (“deep” set) and spatiotemporal kriging42 document a broad east-west distinction along a boundary zone running from the Black Sea to the Baltic. On the western side of this “Great Divide”, the Neolithic transition is accompanied by large-scale shifts in genetic ancestry from local hunter-gatherers to Neolithic farmers with Anatolian-related ancestry (Boncuklu_10000BP; Fig. 3; Extended Data Fig. 4, 6). The arrival of Anatolian-related ancestry in different regions spans an extensive time period of over 3,000 years, from its earliest evidence in the Balkans (Lepenski Vir) at ∼8,700 BP17 to c. 5,900 BP in Denmark. On the eastern side of this divide, no ancestry shifts can be observed during this period. In the East Baltic region (see also43), Fig 6. Patterns of co-ancestry. (A)-(D) Panels show within-cluster genetic relatedness over time, measured either as the total length of genomic segments shared IBD between individuals (A, B) or the proportion of individual genomes found in a run of homozygosity f(ROH) (C,D). Results for both measures are shown separately for individuals from western (A, C) or eastern Eurasia (B, D). Small grey dots indicate estimates for individual pairs (A, B) or individuals (C, D), with larger coloured symbols indicating median values within genetic clusters. (E) Distribution of ROH lengths for 39 individuals with evidence for recent parental relatedness (>50 cM total in ROHs > 20 cM). Ukraine and Western Russia local hunter-gatherer ancestry prevails until ∼5,000 BP without noticeable input of Neolithic Anatolian-related farmer ancestry (Fig. 3; Extended Data Fig. 4, 6). This Eastern genetic continuity is in remarkable congruence with the archaeological record showing persistence of pottery-using hunter-gatherer-fisher groups in this wide region, and delayed introduction of cultivation and husbandry by several thousand years (Supplementary Note 5). From approximately 5,000 BP, an ancestry component appears on the eastern European plains in Early Bronze Age Steppe pastoralists associated with the Yamnaya culture and it rapidly spreads across Europe through the expansion of the Corded Ware complex (CWC) and related cultures20, 21. We demonstrate that this “steppe” ancestry (Steppe_5000BP_4300BP) can be modelled as a mixture of ∼65% ancestry related to herein reported hunter-gatherer genomes from the Middle Don River region (MiddleDon_7500BP) and ∼35% ancestry related to hunter-gatherers from Caucasus (Caucasus_13000BP_10000BP) (Extended data Fig. 4). Thus, Middle Don hunter-gatherers, who already carry ancestry related to Caucasus hunter-gatherers (Fig. 2), serve as a hitherto unknown proximal source for the majority ancestry contribution into Yamnaya genomes. The individuals in question derive from the burial ground Golubaya Krinitsa (Supplementary Note 3). Material culture and burial practices at this site are similar to the Mariupol-type graves, which are widely found in neighbouring regions of Ukraine, for instance along the Dnepr River. They belong to the group of complex pottery-using hunter-gatherers mentioned above, but the genetic composition at Golubaya Krinitsa is different from the remaining Ukrainian sites (Fig 2A, Extended data Fig. 4). We find that the subsequent transition of the Late Neolithic and Early Bronze Age European gene pool happened at a faster pace than during the Neolithisation, reaching most parts of Europe within a ∼1,000-year time period after first appearing in eastern Baltic region ∼4,800 BP (Fig. 3). In line with previous reports we observe that beginning c. 4,200 BP, steppe-related ancestry was already dominant in samples from France and the Iberian peninsula, while it reached Britain only 400 years later11, 38, 44. Strikingly, because of the delayed Neolithisation in Southern Scandinavia these dynamics resulted in two episodes of large-scale genetic turnover in Denmark and southern Sweden within a 1,000-year period (Fig. 3). We next investigated fine-grained ancestry dynamics underlying these transitions. We replicate previous reports11, 16, 17, 21, 41, 45, 46 of widespread, but low-level admixture between Neolithic farmers and local hunter-gatherers resulting in a resurgence of HG ancestry in many regions of Europe during the middle and late Neolithic (Extended data Fig. 7). Estimated hunter-gatherer ancestry proportions among early Neolithic people rarely exceed 10%, with notable exceptions observed in individuals from south-eastern Europe (Iron Gates), Sweden (Pitted Ware Culture) as well as herein reported early Neolithic genomes from Portugal (western Cardial), estimated to harbour 27% – 43% Iberian hunter-gatherer ancestry (Iberia_9000BP_7000BP). The latter result, suggesting extensive first-contact admixture, is in agreement with archaeological inferences derived from modelling the spread of farming along west Mediterranean Europe47. Individuals associated with Neolithic farming cultures from Denmark show some of the highest overall hunter-gatherer ancestry proportions (up to ∼25%), mostly derived from Western European-related hunter-gatherers (EuropeW_13500BP_8000BP) supplemented with marginal contribution from local Danish groups in some individuals (Extended data Fig. 7D; Supplementary Note 3f). We estimated the timing of the admixture using the linkage-disequilibrium-based method DATES48 at ∼6,000 BP. Both lines of evidence thus suggest that a significant part of the hunter-gatherer admixture observed in Danish Neolithic individuals occurred already before the arrival of the incoming Neolithic people in the region (Extended data Fig. 7), and further imply Central Europe as a key region in the resurgence of HG ancestry. Interestingly, the genomes of two ∼5,000-year-old Danish male individuals (NEO33, NEO898) were entirely composed of Swedish hunter-gatherer ancestry, and formed a cluster with Pitted Ware Culture (PWC) individuals from Ajvide on the Baltic island of Gotland (Sweden)49–51. Of the two individuals, NEO033 also displays an outlier Sr-signature (Fig. 4), potentially suggesting a non-local origin matching his unusual ancestry. Overall, our results demonstrate direct contact across the Kattegat and Öresund during Neolithic times (Extended Data Fig. 3, 4), in line with archaeological finds from Zealand (east Denmark) showing cultural affinities to PWC on the Swedish west coast52–55.
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Post by Admin on May 13, 2022 18:33:13 GMT
Fig 7. Genome-wide selection scan for trait associated variants. A) Manhattan plot of p-values from selection scan with CLUES, based on a time-series of imputed aDNA genotype probabilities. Twenty-one genome-wide significant selection peaks highlighted in grey and labelled with the most significant gene within each locus. Within each sweep, SNPs are positioned on the y-axis and coloured by their most significant marginal ancestry. Outside of the sweeps, SNPs show p-values from the pan-ancestry analysis and are coloured grey. Red dotted lines indicate genome-wide significance (p < 5e-8), while the grey dotted line shows the Bonferroni significance threshold, corrected for the number of tests (p < 1.35e-6). B) Detailed plots for three genome-wide significant sweep loci: (i) MCM6, lactase persistence; (ii) SLC45A2, skin pigmentation; and (iii) FADS2, lipid metabolism. Rows show results for the pan-ancestry analysis (ALL) plus the four marginal ancestries: Western hunter-gatherers (WHG), Eastern hunter-gatherers (EHG), Caucasus hunter-gatherers (CHG) and Anatolian farmers (ANA). The first column of each loci shows zoomed Manhattan plots of the p-values for each ancestry (significant SNPs sized by their selection coefficients), and column two shows allele trajectories for the top SNPs across all ancestries (grey shading for the marginal ancestries indicates approximate temporal extent of the pre-admixture population). Further, we find evidence for regional stratification in early Neolithic farmer ancestries in subsequent Neolithic groups. Specifically, southern European early farmers appear to have provided major genetic ancestry to mid- and late Neolithic groups in Western Europe, while central European early farmer ancestry is mainly observed in subsequent Neolithic groups in eastern Europe and Scandinavia (Extended data Fig. 7D-F). These results are consistent with distinct migratory routes of expanding farmer populations as previously suggested8. For example, similarities in material culture and flint mining activities could suggest that the first farmers in South Scandinavia originated from or had close social relations with the central European Michelsberg Culture56. The second continental-wide and CWC-mediated transition from Neolithic farmer ancestry to Steppe-related ancestry was found to differ markedly between geographic regions. The contribution of local Neolithic farmer ancestry to the incoming groups was high in eastern, western and southern Europe, reaching >50% on the Iberian Peninsula (“postNeol” set; Extended Data Fig. 4, 6B, C)34. Scandinavia, however, portrays a dramatically different picture, with a near-complete replacement of the local Neolithic farmer population inferred across all sampled individuals (Extended data Fig. 7B, C). Following the second transition, Neolithic Anatolian-related farmer ancestry remains in Scandinavia, but the source is now different. It can be modelled as deriving almost exclusively from a genetic cluster associated with the Late Neolithic Globular Amphora Culture (GAC) (Poland_5000BP_4700BP; Extended data Fig. 4). Strikingly, after the Steppe-related ancestry was first introduced into Europe (Steppe_5000BP_4300BP), it expanded together with GAC-related ancestry across all sampled European regions (Extended data Fig. 7I). This suggests that the spread of steppe-related ancestry throughout Europe was predominantly mediated through groups that were already admixed with GAC-related farmer groups of the eastern European plains. This finding has major implications for understanding the emergence of the CWC. A stylistic connection from GAC ceramics to CWC ceramics has long been suggested, including the use of amphora-shaped vessels and the development of cord decoration patterns57. Moreover, shortly prior to the emergence of the earliest CWC groups, eastern GAC and western Yamnaya groups exchanged cultural elements in the forest-steppe transition zone northwest of the Black Sea, where GAC ceramic amphorae and flint axes were included in Yamnaya burials, and the typical Yamnaya use of ochre was included in GAC burials58, indicating close interaction between the groups. Previous ancient genomic data from a few individuals suggested that this was limited to cultural influences and not population admixture59. However, in the light of our new genetic evidence it appears that this zone, and possibly other similar zones of contact between GAC and Yamnaya (or other closely-related steppe/forest-steppe groups) were key in the formation of the CWC through which steppe-related ancestry and GAC-related ancestry co-dispersed far towards the west and the northcf. 60. This resulted in regionally diverse situations of interaction and admixture61, 62 but a significant part of the CWC dispersal happened through corridors of cultural and demic transmission which had been established by the GAC during the preceding period63, 64.
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Post by Admin on May 13, 2022 21:33:37 GMT
Fine-scale structure and multiproxy analysis of Danish transect We present a detailed and continuous sequence of multiproxy data from Denmark, from the Early Mesolithic Maglemose, via the Kongemose and Late Mesolithic Ertebølle epochs, the Early and Middle Neolithic Funnel Beaker Culture and the Single Grave Culture, to Late Neolithic and Bronze Age individuals (Fig. 4). To integrate multiproxy data from as many skeletons as possible we made use of non-imputed data for the admixture analyses (Supplementary Note S3d) which were not restricted to the >0.1X coverage cut-off used elsewhere. This provided genetic profiles from 100 Danish individuals (Fig 4), spanning c. 7,300 years from the earliest known skeleton in Denmark (the Mesolithic “Koelbjerg Man” (NEO254, 10,648-10,282 cal. BP, 95% probability interval) and formerly known as the “Koelbjerg Woman”65), to a Bronze Age skeleton from Hove Å (NEO946) dated to 3322-2967 cal. BP (95%). Two temporal shifts in genomic admixture proportions confirm the major population genetic turnovers (Fig. 4) that was inferred from imputed data (Fig. 3). The multiproxy evidence, however, unveils the dramatic concomitant changes in all investigated phenotypic, environmental and dietary parameters (Fig. 4).
During the Danish Mesolithic, individuals from the Maglemose, Kongemose and Ertebølle cultures displayed a remarkable genetic homogeneity across a 5,000 year transect deriving their ancestry almost exclusively from a southern European source (source: Italy_15000BP_9000BP) that later predominates in western Europe (Fig. 2). These cultural transitions occurred in genetic continuity, apparent in both autosomal and uniparental markers, which rules out demic diffusion and supports the long-held assumption of a continuum of culture and populatione.g. 66–68. Genetic predictions indicate blue eye pigmentation with high probability in several individuals throughout the duration of the Mesolithic (Supplementary Note 4f), consistent with previous findings 11, 20, 45. In contrast, none of the analysed Mesolithic individuals displayed high probability of light hair pigmentation. Height predictions for Mesolithic individuals generally suggest slightly lower or perhaps less variable genetic values than in the succeeding Neolithic period. However, we caution that the relatively large genetic distance to modern individuals included in the GWAS panel make these scores poorly applicable to Mesolithic individuals (Supplementary Note 4c) and are dependent on the choice of GWAS filters used. Unfortunately, only a fraction of the 100 Danish skeletons included were suitable for stature estimation by actual measurement, why these values are not reported.
Stable isotope δ13C values in collagen inform on the proportion of marine versus terrestrial protein, while δ15N values reflect the trophic level of protein sources69, 70. Both the Koelbjerg Man and the second earliest human known from Denmark, (Tømmerupgårds Mose – not part of the present study; see71) showed more depleted dietary isotopic values, representing a lifestyle of inland hunter-fisher-gatherers of the early Mesolithic forest. A second group consisted of coastal fisher-hunter-gatherers dating to the late half of the Maglemose epoch onwards (Supplementary Figs. S10.1 and S10.2). During this period global sea-level rise gradually changed the landscape of present-day Denmark from an interior part of the European continent to an archipelago, where all human groups had ample access to coastal resources within their annual territories. Increased δ13C and δ15N values imply that from the late Maglemose marine foods gradually increased in importance, to form the major supply of proteins in the final Ertebølle period71,cf. 72. Interestingly, rather stable 87Sr/86Sr isotope ratios throughout the Mesolithic indicate limited mobility, in agreement with the evidence for genetic continuity reported here and modelled in previous work73, 74 Fig. 3, and/or dietary sources from homogeneous environments.
The arrival of Neolithic farmer-related ancestry at c. 5,900 BP in Denmark resulted in a population replacement with very limited genetic contribution from the local hunter-gatherers. The shift is abrupt and brings changes in all the measured parameters. This is a clear case of demic diffusion, which settles a long-standing debate concerning the neolithisation process in Denmark15, 56, 75, 76, at least at a broader population level. The continuing use of coastal kitchen middens well into the Neolithic77, 78 remains, however, an enigma, although this may represent sites where local remnants of Mesolithic groups survived in partly acculturated form, or it could be middens taken over by the newcomers. Concomitant shifts in both autosomal and uniparental genetic markers show that the migration by incoming farmers was not clearly sex-biased but more likely involved nuclear family units. Diet shifted abruptly to terrestrial sources evidenced by δ13C values around -20 ‰ and δ15N values around 10 ‰ in line with archaeological evidence that domesticated crops and animals were now providing the main supply of proteins (Supplementary Note 6). Isotope values remained stable at these levels throughout the following periods, although with somewhat greater variation after c. 4,500 BP. However, five Neolithic and Early Bronze Age individuals have δ13C and δ15N values indicating intake of high trophic marine food. This is most pronouncedly seen for NEO898 (Svinninge Vejle) who was one of the two aforementioned Danish Neolithic individuals displaying typical Swedish PWC hunter-gatherer ancestry. A higher variability in 87Sr/86Sr values can be seen with the start of the Neolithic and this continues in the later periods, which suggests that the Neolithic farmers in Denmark consumed food from more diverse landscapes and/or they were more mobile than the preceding hunter-gatherers (Supplementary Note 11). The Neolithic transition also marks a considerable rise in frequency of major effect alleles associated with light hair pigmentation79, whereas polygenic score predictions for height are generally low throughout the first millennium of the Neolithic (Funnel Beaker epoch), echoing previous findings based on a smaller set of individuals45, 80.
We do not know how the Mesolithic Ertebølle population disappeared. Some may have been isolated in small geographical pockets of brief existence and/or adapted to a Neolithic lifestyle but without contributing much genetic ancestry to subsequent generations. The most recent individual in our Danish dataset with Mesolithic WHG ancestry is “Dragsholm Man” (NEO962), dated to 5,947-5,664 cal. BP (95%) and archaeologically assigned to the Neolithic Funnel Beaker farming culture based on his grave goods81, 82. Our data confirms a typical Neolithic diet matching the cultural affinity but contrasting his WHG ancestry. Thus, Dragsholm Man represents a local person of Mesolithic ancestry who lived in the short Mesolithic-Neolithic transition period and adopted a Neolithic culture and diet. A similar case of very late Mesolithic WHG ancestry in Denmark was observed when analysing human DNA obtained from a piece of chewed birch pitch dated to 5,858– 5,661 cal. BP (95%)83.
The earliest example of Anatolian Neolithic ancestry in our Danish dataset is observed in a bog skeleton of a female from Viksø Mose (NEO601) dated to 5,896-5,718 cal. BP (95%) (and hence potentially contemporaneous with Dragsholm Man) whereas the most recent Danish individual showing Anatolian ancestry without any Steppe-related ancestry is NEO943 from Stenderup Hage, dated to 4,818-4,415 cal. BP (95%). Using Bayesian modelling we estimate the duration between the first appearance of Anatolian ancestry to the first appearance of Steppe-related ancestry in Denmark to be between 876 and 1100 years (95% probability interval, Supplementary Note 9) indicating that the typical Neolithic ancestry was dominant for less than 50 generations in Denmark. From this point onwards the steppe-ancestry was introduced, signalling the rise of the late Neolithic Corded Ware derived cultures in Denmark (i.e. Single Grave Culture), followed by the later Neolithic Dagger epoch and Bronze Age cultures. While this introduced a major new component in the Danish gene pool, it was not accompanied by apparent shifts in diet. Our complex trait predictions indicate an increase in “genetic height” occurring concomitant with the introduction of Steppe-related ancestry, which is consistent with Steppe individuals (e.g., Yamnaya) being genetically taller on average45 and with previous results from other European regions80, 84.
These major population turnovers were accompanied by significant environmental changes, as apparent from high-resolution pollen diagrams from Lake Højby in Northwest Zealand reconstructed using the Landscape Reconstruction Algorithm (LRA85 (Supplementary Note 8). While the LRA has previously been applied at low temporal resolution regional scale e.g. 86, 87, and at local scale to Iron Age and later pollen diagrams e.g. 88, 89, this is the first time this quantitative method is applied at local scale to a pollen record spanning the Mesolithic and Neolithic periods in Denmark. Comparison with existing pollen records show that the land cover changes demonstrated here reflect the general vegetation development in eastern Denmark, while the vegetation on the sandier soils of western Jutland maintains a more open character throughout the sequence (Supplementary Note 12). We find that during the Mesolithic (i.e. before c. 6,000 BP) the vegetation was dominated by primary forest trees (Tilia, Ulmus, Quercus, Fraxinus, Alnus etc.). The forest composition changed towards more secondary, early successional trees (Betula and then Corylus) in the earliest Neolithic, but only a minor change in the relationship between forest and open land is recorded. From c. 5,650 BP deforestation intensified, resulting in a very open grassland-dominated landscape. This open phase was short-lived, and secondary forest expanded from 5,500 to 5,000 BP, until another episode of forest clearance gave rise to an open landscape during the last part of the Funnel Beaker epoch. We thus conclude that the agriculture practice was characterised by repeated clearing of the forest with fire, followed by regrowth. This strategy changed with the onset of the Single Grave Culture, when the forest increased again, but this time dominated by primary forest trees, especially Tilia and Ulmus. This reflects the development of a more permanent division of the landscape into open grazing areas and forests. In contrast, in western Jutland this phase was characterised by large-scale opening of the landscape, presumably as a result of human impact aimed at creating pastureland90.
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Post by Admin on May 14, 2022 17:51:22 GMT
Finally, we investigated the fine-scale genetic structure in southern Scandinavia after the introduction of Steppe-related ancestry using a temporal transect of 38 Late Neolithic and Early Bronze Age Danish and southern Swedish individuals. Although the overall population genomic signatures suggest genetic stability, patterns of pairwise IBD-sharing and Y-chromosome haplogroup distributions indicate at least three distinct ancestry phases during a ∼1,000-year time span: i) An early stage between ∼4,600 BP and 4,300 BP, where Scandinavians cluster with early CWC individuals from Eastern Europe, rich in Steppe-related ancestry and males with an R1a Y-chromosomal haplotype (Extended data Fig. 8A, B); ii) an intermediate stage until c. 3,800 BP, where they cluster with central and western Europeans dominated by males with distinct sub-lineages of R1b-L51 (Extended data Fig. 8C, D; Supplementary Note 3b) and includes Danish individuals from Borreby (NEO735, 737) and Madesø (NEO752) with distinct cranial features (Supplementary Note 6); and iii) a final stage from c. 3,800 BP onwards, where a distinct cluster of Scandinavian individuals dominated by males with I1 Y-haplogroups appears (Extended data Fig. 8E). Using individuals associated with this cluster (Scandinavia_4000BP_3000BP) as sources in supervised ancestry modelling (see “postBA”, Extended data Fig. 4), we find that it forms the predominant source for later Iron- and Viking Age Scandinavians, as well as ancient European groups outside Scandinavia who have a documented Scandinavian or Germanic association (e.g., Anglo-Saxons, Goths; Extended data Fig. 4). Y-chromosome haplogroup I1 is one of the dominant haplogroups in present-day Scandinavians,s, and we document its earliest occurrence in a ∼4,000-year-old individual from Falköping in southern Sweden (NEO220). The rapid expansion of this haplogroup and associated genome-wide ancestry in the early Nordic Bronze Age indicates a considerable reproductive advantage of individuals associated with this cluster over the preceding groups across large parts of Scandinavia. Fig 8. Fig 8. Selection at the MAPT / 17q21.31 inversion locus. A) Results for the pan-ancestry analysis (ALL) plus the four marginal ancestries: Western hunter-gatherers (WHG), Eastern hunter-gatherers (EHG), Caucasus hunter-gatherers (CHG) and Anatolian farmers (ANA). Grey shading for the marginal ancestries indicates approximate temporal extent of the pre-admixture population. B) Haplotypes of the 17q21.31 locus: the ancestral (non-inverted) H1 17q21.31 and the inverted H2 haplotype. Duplications of the KANSL1 gene have occurred independently on both lineages yielding H1D and H2D haplotypes. C) Frequency of the 17q21.31 inversion and duplication haplotypes across modern-day global populations (Human Genome Diversity Project 119). D) Change in the frequency of the 17q21.31 inversion haplotype through time. Hunter-gatherer resilience east of the Urals In contrast to the significant number of ancient hunter-gatherer genomes from western Eurasia studied to date, genomic data from hunter-gatherers east of the Urals remain sparse. These regions are characterised by an early introduction of pottery from areas further east and are inhabited by complex hunter-gatherer-fisher societies with permanent and sometimes fortified settlements (Supplementary Note 5; 91). Here, we substantially expand the knowledge on ancient Stone Age populations of this region by reporting new genomic data from 38 individuals, 28 of which date to pottery-associated hunter-gatherer contexts e.g. 92 between 8,300-5,000 BP (Supplementary Table II).The majority of these genomes form a previously only sparsely sampled 48, 93 “Neolithic Steppe” cline spanning the Siberian Forest Steppe zones of the Irtysh, Ishim, Ob, and Yenisei River basins to the Lake Baikal region (Fig. 1C; Extended Data Fig. 2A, 3E). Supervised admixture modelling (using the “deep” set of ancestry sources) revealed contributions from three major sources in these hunter gatherers from east of Urals: early West Siberian hunter-gatherer ancestry (SteppeC_8300BP_7000BP) dominated in the western Forest Steppe; Northeast Asian hunter-gatherer ancestry (Amur_7500BP) was highest at Lake Baikal; and Paleosiberian ancestry (SiberiaNE_9800BP) was observed in a cline of decreasing proportions from northern Lake Baikal westwards across the Forest Steppe (Extended Data Fig. 4, 9). 93
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