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Post by Admin on Jun 4, 2019 22:34:41 GMT
Discussion
By analyzing ancient mitochondrial genomes, we show that people from the eastern and western Corded Ware culture were genetically differentiated. Individuals associated with the eastern Corded Ware culture (from present day Poland and the Czech Republic) shared close maternal genetic affinity with individuals associated with the Yamnaya horizon while the genetic differentiation between individuals associated with the western Corded Ware culture (from present-day Germany) and the Yamnaya horizon was more extensive. This decreasing cline of steppe related ancestry from east to west likely reflect the direction of the steppe migration. It also indicates that more people with steppe-related ancestry, likely both females and males, contributed to the formation of the population associated with the eastern Corded Ware culture. Similarly, closer genetic affinity to populations associated with Yamnaya horizon can be observed in Baltic Corded Ware groups, which confirms earlier indications of a direct migrations from the steppe not only to the west but also to the north, into the eastern Baltic region18,19,55. The mitochondrial data further suggests that with increased distance from the source populations of the steppe, the contribution of local people increase, which is seen as an increase of maternal lineages of Neolithic farmer ancestry in individuals associated with the western Corded Ware culture.
Among the analyzed samples, we identified two Catacomb culture-associated individuals (poz220 and poz221) belonging to hg X4. They are the first ancient individuals assigned to this particular lineage. Haplogroup X4 is rare among present day populations and has been found only in one individual each from Central Europe, Balkans, Anatolia and Armenia56,57. Moreover, we have reported mtDNA haplotypes that might be associated with the migration from the steppe and point to genetic continuity in the north Pontic region from Bronze Age until the Iron Age. These haplotypes were assigned to hgs U5, U4, U2 and W3. MtDNA hgs U5a and U4, identified in this study among Yamnaya, Late Eneolithic and Corded Ware culture-associated individuals, have previously been found in high frequencies among northern and eastern hunter-gatherers19,23,28,55,58,59. Moreover, they appeared in the north Pontic region in populations associated with Mesolithic (hg U5a)45, Eneolithic (Post-Stog) (hg U4)24, Yamnaya (hgs U5, U5a)24, Catacomb (hgs U5 and U5a)24 and Iron Age Scythians (hg U5a)60, suggesting genetic continuity of these particular mtDNA lineages in the Pontic region from, at least, the Bronze Age. Hgs U5a and U4-carrying populations were also present in the eastern steppe, along with individuals from the Yamnaya culture from Samara region14,17, the Srubnaya23 and the Andronovo from Russia14. Interestingly, hg U4c1 found in the Yamnaya individual (poz224) has so-far been found only in two Bell Beaker- associated individuals61 and one Late Bronze Age individual from Armenia14, which might suggest a steppe origin for hg U4c1. A steppe origin can possibly also be assigned to hg U4a2f, found in one individual (poz282) but not reported in any other ancient populations to date, and to U5a1- the ancestral lineage of U5a1b, reported for individual poz232, which was identified not only in Corded Ware culture-associated population from central and eastern Europe55,61 but also in representatives of Catacomb culture from the north Pontic region24, Yamnaya from Bulgaria and Russia17,46, Srubnaya23 and Andronovo62-associated groups. Hg U2e, reported for Late Eneolithic individual (poz090), was also identified in western Corded Ware culture-associated individual23 and in succeeding Sintashta14, Potapovka and Andronovo23 groups, suggesting possible genetic continuity of U2e1 in the western part of the north Pontic region.
Hgs W3a1 and W3a1a, found in two Yamnaya individuals from this study (poz208 and poz222), were also identified in Yamnaya-associated individuals from the Russia Samara region17 and later in Únětice and Bell Beaker groups from Germany61,63, supporting the idea of an eastern European steppe origin of these haplotypes and their contribution to the Yamnaya migration toward the central Europe. The W3a1 lineage was not identified in Neolithic times and, thus, we assume that it appeared in the steppe region for the first time during the Bronze Age. Notably, hgs W1 and W5, which predate the Bronze Age in Europe, were found only in individuals associated with the early Neolithic farmers from Starčevo in Hungary (hg W5)64, early Neolithic farmers from Anatolia (hg W1-T119C)23, and from the Schöningen group (hg W1c)61 and Globular Amphora culture from Poland (hg W5)45.
This study is the first to present mitochondrial genome data from the population associated with Corded Ware culture from the south-eastern part of present-day Poland. As this area is geographically close to the steppe region, it provides us with a better picture of the early steppe migration between 3,000 and 2,500 BC. Although our results indicate a contribution of females as well as males to the formation of populations associated with eastern Corded Ware culture, more detailed studies of X chromosome data are needed to clearly resolve female and male migrations, especially between the western Pontic steppe and the eastern part of the North European Plain.
Conclusions
Ancient mitochondrial genome data from the western Pontic region and, for the first time, from the south-eastern part of present day Poland, show close genetic affinities between populations associated with the eastern Corded Ware culture and the Yamnaya horizon. This indicates that females had also participated in the migration from the steppe. Furthermore, greater mtDNA differentiation between populations associated with the western Corded Ware culture and the Yamnaya horizon points to an increased contribution of individuals with a maternal Neolithic farmer ancestry with increasing geographic distance from the steppe region, forming the population associated with the western Corded Ware culture. Among the analyzed samples, we identified, for the first time in ancient populations, two Catacomb culture-associated individuals belonging to the now-rare mtDNA hg X4.
Scientific Reports 8, Article number: 11603 (2018)
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Post by Admin on Oct 10, 2019 18:03:06 GMT
Abstract The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330–1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26–3.24× coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial ‘Bergsgraven’. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic–Caspian steppe herders, as well as smaller components originating from hunter–gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.  1. Introduction An influential wave of migration into central Europe from the Pontic–Caspian steppe occurred ca 3000 before common era (BCE) [1,2]. The Yamnaya expansion brought new genetic ancestry to Neolithic Europe, which still today is a part of the genetic variation [3]. Northwest of the Yamnaya complex, we find the Corded Ware Culture (CWC) complex that was distributed over central and northern Europe between 3000/2800 and 2300/2000 BCE (see electronic supplementary material) [4,5]. The impact of the Yamnaya migration on the formation of the CWC complex continues to be debated ([4] with comments in [5,6]). Genetic signals of migration and admixture have been found in central Europe, Scandinavia, and to the east of the Baltic Sea [1,2,7–9]. However, the development took different paths in different regions and it is not clear exactly how the migrations affected the demographic development and population history at the fringes of the European continent [5,6]. In Sweden, the CWC complex has been labelled the (Swedish-Norwegian) Boat Axe or Battle Axe Culture (BAC). The material manifestation of BAC, starting around 3000/2800 BCE [10], was distributed in Scandinavia up to modern-day Middle Sweden and southern Norway and on the eastern side of the Baltic Sea up to the southwestern parts of Finland (e.g. [11–13]). How the BAC/CWC complex dispersed into the Baltic countries and Fennoscandia has been extensively debated (e.g. [12,14–18]), especially in association with a process of migration or of cultural diffusion and local development [11,12,16,19,20]. Earlier archaeological research viewed the BAC/CWC complex as a society with common cultural and social practices and stressed the uniformity of burial customs, pottery design and typology, and the boat-shaped battle axes (e.g. [12,15,21]). Recently, it has been argued that these views were too simplistic, and regional patterns and traits within the BAC/CWC complex have been highlighted (e.g. [4–6,11,22]).  While previous archaeogenetic research has studied individuals connected with the BAC/CWC cultural complexes in some regions around the Baltic Sea [1,2,7–9,23], the character of the migration patterns and the temporal and regional dynamics within the CWC area as well as the BAC introduction into Scandinavia are yet to be explored. To achieve a better understanding of these population dynamics and the BAC introduction to Scandinavia, we investigated the demographic development in the CWC area around the Baltic Sea, in the third millennium BCE, by sequencing DNA from 11 prehistoric individuals from (modern-day) Sweden, Estonia, and Poland. By comparing the genetic profiles of the newly sequenced individuals to individuals from different regions of the CWC area and from different kinds of cultural contexts, we investigate ancestry and admixture to paint a more detailed picture of the demographic processes that took place across the CWC area, with a specific focus on the onset and subsequent dynamics of the BAC in Scandinavia. 2. Results |
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Post by Admin on Oct 11, 2019 18:24:12 GMT
2. Results (a) Genome sequencing, quality assessment, and genetic results We generated and analysed genome sequence shotgun data from 11 individuals originating in northeastern Europe dated to 3300–1660 cal BCE (electronic supplementary material, table S1). Five individuals were excavated from CWC contexts: two from Obłaczkowo, Poland, one from Karlova, Estonia, and two from the CWC-related BAC burial Bergsgraven in Linköping, Sweden. The six additional individuals were from other archaeological contexts in Sweden: five from megalithic burial structures primarily associated with Funnel Beaker Culture (FBC) (two from Rössberga in Västergötland and three from Öllsjö in Scania) and one from a Pitted Ware Culture (PWC) context (Ajvide on Gotland). Radiocarbon dating showed that the three individuals from the Öllsjö megalithic tomb derived from later burials, where oll007 (2860–2500 cal BCE) overlaps with the time interval of the BAC, and oll009 and oll010 (1930–1650 cal BCE) fall within the Scandinavian Late Neolithic and Early Bronze Age (table 1; electronic supplementary material, table S1 and figure S2). Genome-wide sequence coverages range from 0.1 to 3.2×, and the sequence data for all individuals exhibit characteristic properties of ancient DNA: short fragment size and cytosine deamination at the ends of fragments (e.g. [24]) (table 1; electronic supplementary material, figure S5). Estimates of mitochondrial contamination [25] were low, less than 2% for all 11 individuals, as was the estimated nuclear contamination on the X-chromosome in males [26,27] (less than 1.2%) (table 1; electronic supplementary material, table S3). Five individuals were genetically determined to be males, and six were females, based on the fraction of sequence fragments mapping to the different sex chromosomes [28] (table 1).
Table 1. Information on the 11 ancient individuals investigated in this study, including radiocarbon dates, average read length, average genome coverage, average mtDNA coverage, mtDNA and Y-chromosome haplogroups, biological sex, and contamination estimates based on mtDNA and on the X-chromosome in males.
sample site/grave country context date cal BCE (95% CI) Av. RL nu cov MT cov MT hg Y hg biol sex cont est MT (%) cont est X (%)
ber1 Bergsgraven Sweden BAC 2620–2470 84.5 3.24 1344 U4c1a R1a-Z283 XY 0.19 0.80
ber2 Bergsgraven Sweden BAC 2640–2480 74.4 0.48 443 N1a1a1a1 — XX 0.26 —
oll007 Ölljsö Sweden Megalithica 2860–2500 77.4 1.24 86 H1c — XX 0.44 —
oll009 Ölljsö Sweden Megalithica 1930–1750 99.7 1.01 325 H6a1b3 n.a. XY 1.97 0.32
oll010 Öllsjö Sweden Megalithica 1880–1660 87.7 0.26 96 X2b11 — XX 1.83 —
kar1 Karlova Estonia CWC 2440–2140 61.9 2.35 2481 H1f1a — XX 0.79 —
ajv54 Ajvide Sweden PWC 2900–2680 89.3 0.91 510 U5b1d2 n.a. XY 1.24 0.58
ros3 Rössberga Sweden FBC 3330–2930 64.1 0.37 30 K1b1a1 — XX 0.40 —
ros5 Rössberga Sweden FBC 3090–2920 97.9 0.85 106 J1c5 IJ-M429* XY 0.19 0.28
poz44 Obłaczkowo Poland CWC 2870–2580 86.6 0.11 253 U3a'c — XX 0.29 —
poz81 Obłaczkowo Poland CWC 2880–2630 84.4 1.87 172 U4b1b2 R1a-M417 XY 1.32 1.15
Megalithic contexts mean that the individuals are from the FBC-associated megalithic tomb, but constitute secondary burials and have radiocarbon dates associated with the BAC time period (oll007) or the Scandinavian Late Neolithic and Bronze Age (oll009 and oll010).  The individuals from BAC and CWC contexts, including oll007 from a megalithic burial, displayed U4 and U5 mitochondrial DNA (mtDNA) lineages, previously associated with Stone Age hunter–gatherers [29–34], and H1, N1a, and U3 lineages, associated with Neolithic farmers [1,32,35,36] (table 1; electronic supplementary material, table S4). This broadly coincides with the wide variety of mtDNA lineages found in other individuals from CWC contexts (e.g. [2,32]). However, the U3 and N1a lineages, which were found here (poz44 and ber2), have not been reported from individuals excavated in CWC contexts. The two males in our dataset (ber1 and poz81) belonged to Y-chromosome R1a haplogroups (table 1; electronic supplementary material, table S5), as do the majority of males (16/24) from the previously published CWC contexts (Viby in Sweden, Ardu and Kunila in Estonia, Gyvakarai and Spiginas in Lithuania, Bergrheinfeld and Esperstedt in Germany, and Brandýsek in the Czech Republic) [1,2,7,31,32,37], while a smaller fraction belonged to R1b [3/24] or I2a [3/24] lineages (Tiefbrunn and Esperstedt in Germany, Pikutkowo and Łęki Małe in Poland, and Brandýsek in the Czech Republic) [2,23,32,37]. The R1a haplogroup has not been found among Neolithic farmer populations nor in hunter–gatherer groups in central and western Europe, but it has been reported from eastern European hunter–gatherers and Eneolithic groups [1,31,32]. Individuals from the Pontic–Caspian steppe, associated with the Yamnaya Culture, carry mostly R1b and not R1a haplotypes [1,2,31,32]. Three individuals had enough data for investigating the LCT gene-region (electronic supplementary material, table S6), and one of these individuals (kar1) carried at least one allele (-13910 C->T) associated with lactose tolerance, while the other two individuals (ber1 and poz81) carried at least one ancestral variant each, consistent with previous observations of low levels of lactose tolerance variants in the Neolithic [1,2,33,38] and a slight increase among individuals from CWC contexts [32]. The individuals further displayed a mixed appearance with both light and dark hair and brown and blue eyes (electronic supplementary material, table S6). Stable carbon and nitrogen isotope values for the individuals from modern-day Sweden show a terrestrial diet except for the Ajvide individual (electronic supplementary material, table S1 and figure S3). Strontium isotope data for the two individuals in Bergsgraven have differing signals, indicating recent migration of at least one of the individuals to the area (electronic supplementary material, table S2 and figure S4). |
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Post by Admin on Oct 12, 2019 18:08:35 GMT
(b) Exploratory analyses To investigate the genomic ancestry of the 11 individuals from this study in context with other ancient individuals, we projected them onto the PC1–PC2 space of 60 modern-day Western Eurasian populations (figure 1a) [40] together with 272 relevant prehistoric individuals who have been previously reported (electronic supplementary material, table S7). We further used an unsupervised clustering approach [41] to examine the broad-scale genomic affinities (electronic supplementary material, figure S6).  Figure 1. (a) Principal component analysis of modern Europeans (grey) and projected ancient Europeans. The full list of ancient samples with sample IDs, the associated culture or time period followed, and two-letter International Organization for Standardization codes for country can be found in table 1 and electronic supplementary material, table S7. (b) Geographical range of BAC/CWC and admixture modelling with qpAdm of BAC/CWC individuals in a three-source model: Anatolian Neolithic (orange), European hunter–gatherers (blue), and Yamnaya steppe herders (green). Individuals marked with an asterisk lived after the BAC/CWC time period. Map source: Sjögren et al. [39], published CC-BY. The broad continental pattern that appears confirms previous results (figure 1a) [3]: (i) a clear separation between Early and Middle Neolithic farmers and Mesolithic hunter–gatherers from all over Europe [1,30,32–34,42,43], (ii) substructure among the hunter–gatherers roughly corresponding to an east–west gradient [1,8,29,31,32], with an exception in Scandinavia [29], and (iii) most Late Neolithic and Bronze Age individuals overlapping with modern-day central and northern Europeans due to admixture with incoming groups related to the Yamnaya herders from the Pontic steppe [1,32]. In Scandinavia, we see a clear separation between individuals from the three different archaeological complexes, the FBC, PWC, and BAC, with individuals associated with the farming FBC (including the Rössberga individuals reported here) grouping with other Middle Neolithic farmer groups (figure 1a). Neolithic foragers associated with the Pitted Ware Culture (including ajv54) were genetically similar to Mesolithic Scandinavian hunter–gatherers with some trend towards farming groups, likely due to admixture between the two groups [9,29,33]. The individuals associated with BAC (including the two individuals from Bergsgraven) show a clear association with individuals from other CWC contexts elsewhere in Europe. Notably, the oll007 individual from the megalithic site at Öllsjö (southern Sweden), who was not directly associated with any CWC-related artefacts but overlaps with CWC chronologically, clusters with individuals from CWC contexts, as do the two individuals with later dates (oll009 and oll010) from the same site. Similar to the BAC individuals, the newly sequenced individuals from the present-day Karlova in Estonia and Obłaczkowo in Poland appear to have strong genetic affinities to other individuals from BAC and CWC contexts across the Baltic Sea region [1,2,7,8,23,31,32] (figure 1a). Some individuals from CWC contexts, including the two from Obłaczkowo, cluster closely with the potential source population of steppe-related ancestry, the Yamnaya herders. Notably, these individuals appear to be those with the earliest radiocarbon dates among all genetically investigated individuals from CWC contexts. Overall, for CWC-associated individuals, there is a clear trend of decreasing affinity to Yamnaya herders with time (figure 2).  Figure 2. Correlation between f4(Chimp, LBK, YAM, X), where X is a CWC or BAC individual, and the date (BCE) of each individual (table 1 and [1,2,7,8,23,31,32,37]). This statistic measures shared drift between CWC and Linear Pottery Culture (LBK) as opposed to YAM and should increase with the higher proportion of Neolithic farmer ancestry in CWC and BAC. The pattern is not driven by spurious affinities between single nucleotide polymorphism (SNP) capture or shotgun data (electronic supplementary material, figures S9 and S10). Ages on the x-axis correspond to the mid-point of the interval for the date of each sample as reported in their original publication (electronic supplementary material, tables S7 and S8). (Online version in colour.) |
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Post by Admin on Oct 13, 2019 18:53:01 GMT
(c) Admixture modelling of Corded Ware Culture To investigate the spread of CWC-related people into Scandinavia and obtain a clearer picture of the ancestry proportions found in individuals associated with the CWC and the BAC, we conducted a supervised modelling of their ancestry from three sources: Anatolian farmers, western European hunter–gatherers, and Yamnaya steppe herders. We estimated ancestry under this three-source model per individual using qpAdm [1]. The geographical pattern of ancestry is shown in figure 1b. This approach confirms that most ancestry in all CWC individuals originates from a group related to Yamnaya steppe herders (green), while smaller contributions from Western hunter–gatherers (blue) and Neolithic farmers (orange) are also widespread (figure 1b). Individuals from BAC contexts in (modern-day) Sweden also show this pattern, with a large genetic component tracing its ancestry to Yamnaya steppe herders and with small ancestry components related to Neolithic farmers and hunter–gatherers. The other individuals who were contemporary with BAC but had unclear cultural contexts, and who were buried in the Ölljsö megalith constructed many hundred years earlier (oll007), or found as a stray find (Ölsund) [9], show the same genetic profile as individuals from typical BAC contexts in other parts of Sweden. Although the individuals associated with the BAC (including the oll007, oll009, oll010, and Olsund) have a large proportion of steppe ancestry, it is relatively low compared with most other individuals from CWC contexts. The female (kar1) from the Karlova CWC burial in Estonia shows similar patterns, also displaying slightly less steppe ancestry than other CWC-associated individuals from Estonian sites [2,7]. By contrast, the CWC individuals from Obłaczkowo in Poland (poz44 and poz81) show an extremely high proportion of steppe ancestry (greater than 90%), which is different from the later CWC-associated individuals excavated in Pikutkowo (Poland) [23], but similar to some other CWC-associated individuals from Germany, Lithuania, and Latvia [2,8,31]. Interestingly, these individuals with a large fraction of steppe ancestry have typically been dated to more than 2600 BCE, making them among the earliest CWC individuals genetically investigated. This observation, i.e. early CWC individuals resembled (genetically) Yamnaya-associated individuals, while later CWC groups show higher levels of European Neolithic farmer ancestry (Pearson's correlation coefficient: −0.51, p = 0.006) (figure 2), suggests an initial dispersal that occurred rapidly.  Figure 3. Admixture graph modelling BAC as a mix of a CWC source and an admixed Middle Neolithic group (worst |Z| < 1.68). CWC individuals from modern-day Poland (CWC_PL) chosen here, other groups shown in electronic supplementary material, figures S7 and S8. WHG, western hunter-gatherers; EHG, eastern hunter-gatherers. The sub-Saharan African Mbuti were used as an outgroup for this analysis. (d) Admixture modelling of Battle Axe Culture The positioning in the principal component analysis (PCA) (figure 1a) and the admixture modelling results (figure 1b) suggest ancestry from three different main ancestral groups in BAC: Anatolian farmers, European hunter–gatherers, and Yamnaya steppe herders. Direct candidates for contributions to BAC are the Scandinavian Middle Neolithic PWC and FBC plus a third population carrying high proportions of Yamnaya-related ancestry (YAM), like CWC. We used an explicit model to investigate contributions from predefined ancestral groups (qpWave of ADMIXTOOLS) [1,44] to model the BAC genetic make-up. We found that the BAC-associated individuals can be modelled as a combination of genetic material from these three groups (p = 0.80). In addition to the three-source model, two models only using two sources were consistent with the data: the best fitting two-source model was FBC + YAM (p = 0.86), while YAM + PWC would also fit the data (although trending toward low p-values; p = 0.07). These observations suggest that—to our statistical resolution—a direct PWC contribution to BAC is not needed in a model, but actual PWC admixture might have been small or there may have been indirect PWC contributions through PWC first mixing with FBC [34] who later contributed ancestry to BAC. Notably, using only the CWC population as the single source for BAC was consistent with the data in all cases (p > 0.05, except when using CWC-associated individuals from Latvia, CWC_LV), showing that the BAC individuals in Sweden could not have emerged without migrations from other CWC groups. To find out if BAC represents an admixed group that came into Scandinavia or if (at least some of) the admixture took place in Scandinavia, we investigated the relationship among the Scandinavian BAC group and various CWC groups from other geographical areas by constructing admixture graphs (figure 3). The BAC groups fit as a sister group to the CWC-associated group from Estonia (CWC_EE, electronic supplementary material, figure S8) but not as a sister group to the CWC groups from Poland (CWC_PL, figure 3) or Lithuania (CWC_LT, electronic supplementary material) (|Z| > 3), indicating some differences in ancestry between these CWC groups and BAC (CWC from Latvia, CWC_LV, and the CWC group from Germany, CWC_DE, had to be excluded from this analysis due to the number of SNPs being too low, see electronic supplementary material). Supervised admixture modelling suggests that BAC may be the CWC-related group with the lowest YAM-related ancestry and with more ancestry from European Neolithic groups (figure 1b). Consequently, models, where BAC is an admixed group between a CWC group and additional ancestry from a group carrying ancestry-related European Neolithic groups, were consistent with the data for all three tested CWC groups (|Z| < 2.3, figure 3; electronic supplementary material, figures S7 and S8). Two potential scenarios were consistent with the data to explain the emergence of BAC in Scandinavia: (i) direct migration of CWC groups from the eastern Baltic or (ii) a migration of CWC groups from the southern Baltic Sea region mixing with FBC groups in Scandinavia. Future archaeogenetic studies could fill geographical and chronological gaps by including more samples that should help to distinguish between the scenarios. |
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