Genomic and strontium isotope variation reveal immigration patterns in a Viking Age town

The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10th to 12th century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration

The genetic history of Scandinavia from the Roman Iron Age to the present

The authors acknowledge support from the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation and the Swedish Research Council, and SNIC/Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We used resources from projects SNIC 2022/23-132, SNIC 2022/22-117, SNIC 2022/23-163, SNIC 2022/22-299, and SNIC 2021-2-17. This research was supported by the Swedish Research Council project ID 2019-00849_VR and ATLAS (Riksbankens Jubileumsfond). Part of the modern dataset was supported by a research grant from Science Foundation Ireland (SFI), grant number 16/RC/3948, and co-funded under the European Regional Development Fund and by FutureNeuro industry partners.Peer reviewedPublisher PD

Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers

Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains a contentious idea. Population-genomic data from 11 Scandinavian Stone Age human remains suggest that hunter-gatherers had lower genetic diversity than that of farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer-related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone Age foraging groups were historically in low numbers, likely owing to oscillating living conditions or restricted carrying capacity, and that they were partially incorporated into expanding farming groups

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57× coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans.Günther T., Malmström H., Svensson E.M., Omrak A., Sánchez-Quinto F, Kılınç G.M., Krzewinska M., Eriksson G., Fraser M., Edlund H., Munters A.R., Coutinho A., Simões L.G., Vicente M., Sjölander A., Sellevold B.J., Jørgensen R., Claes P., Shriver M.D., Valdiosera C., Netea M.G., Apel J., Lidén K., Skar B., Storå J., Götherström A., Jakobsson M., ''Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation'', PLoS Biology, vol. 16, no. 1, pp. e2003703, 22 pp., January 9, 2018.status: publishe

The Demographic Development of the First Farmers in Anatolia

The archaeological documentation of the develop-ment of sedentary farming societies in Anatolia isnot yet mirrored by a genetic understanding of thehuman populations involved, in contrast to thespread of farming in Europe [1–3]. Sedentary farmingcommunities emerged in parts of the Fertile Crescentduring the tenth millennium and early ninth millen-nium calibrated (cal) BC and had appeared in centralAnatolia by 8300 cal BC [4]. Farming spread intowest Anatolia by the early seventh millennium calBC and quasi-synchronously into Europe, althoughthe timing and process of this movement remain un-clear. Using genome sequence data that we gener-ated from nine central Anatolian Neolithic individuals,we studied the transition period from early Aceramic(Pre-Pottery) to the later Pottery Neolithic, whenfarming expanded west of the Fertile Crescent. Wefind that genetic diversity in the earliest farmerswas conspicuously low, on a par with Europeanforaging groups. With the advent of the PotteryNeolithic, genetic variation within societies reachedlevels later found in early European farmers. Our re-sults confirm that the earliest Neolithic central Anato-lians belonged to the same gene pool as the firstNeolithic migrants spreading into Europe. Further,genetic affinities between later Anatolian farmersand fourth to third millennium BC Chalcolithic southEuropeans suggest an additional wave of Anatolianmigrants, after the initial Neolithic spread but beforethe Yamnaya-related migrations. We propose thatthe earliest farming societies demographicallyresembled foragers and that only after regionalgene flow and rising heterogeneity did the farmingpopulation expansions into Europe occur.WoSScopusPubMe

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57× coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500–6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east–west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans

Information on the seven SHGs investigated in this study, including cal BP (corrected for the marine reservoir effect, given as a range of two standard deviations), average genome coverage, average mt coverage, mt and Y chromosome haplogroups, and contamination estimates based on the mt, the X-chromosome for males and the autosomes.

<p>Information on the seven SHGs investigated in this study, including cal BP (corrected for the marine reservoir effect, given as a range of two standard deviations), average genome coverage, average mt coverage, mt and Y chromosome haplogroups, and contamination estimates based on the mt, the X-chromosome for males and the autosomes.</p

Genetic diversity in prehistoric Europe.

<p>(A) RoH for the six prehistoric humans that have been sequenced to >15× genome coverage, (Kotias is a hunter-gatherer from the Caucasus region [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref035" target="_blank">35</a>], NE1 is an early Neolithic individual from modern-day Hungary [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref027" target="_blank">27</a>], the other individuals are described in the text), compared to all modern-day non African individuals from the 1000 Genomes Project [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref032" target="_blank">32</a>]. (B) LD decay for five prehistoric populations each represented by two individuals (eastern SHGs: SF [SF9 and SF12], western SHGs: Hum [Hum1 and Hum2], CHGs [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref035" target="_blank">35</a>]: [Kotias and Satsurblia], WHGs [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref018" target="_blank">18</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref035" target="_blank">35</a>] [Loschbour and Bichon], and early Neolithic Hungarians [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref027" target="_blank">27</a>]: EN_Hungary [NE1 and NE6]). LD was scaled in each distance bin by using the LD for two modern populations [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref032" target="_blank">32</a>] as 0 (TSI) and as 1 (PEL). LD was calculated from the covariance of derived allele frequencies of two haploid individuals per population (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s012" target="_blank">S7 Text</a>). Error bars show two standard errors estimated during 100 bootstraps across SNP pairs. (C) Effective population size over time as inferred by PSMC’ [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref044" target="_blank">44</a>] for four prehistoric humans with high genome coverage. The dashed lines show the effective population sizes for selected modern-day populations. All curves for prehistoric individuals were shifted along the x-axis according to their radiocarbon date. <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s005" target="_blank">S4 Fig</a>. shows 100 bootstrap replicates per individual. Data shown in this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s015" target="_blank">S1 Data</a>. BP, before present; CHG, Caucasus hunter-gatherer; LD, linkage disequilibrium; PEL, modern-day Peruvian individual; PSMC’, pairwise sequentially Markovian coalescent; RoH, runs of homozygosity; SHG, Scandinavian hunter-gatherer; TSI, modern-day Tuscan individual; WHG, western hunter-gatherer.</p

Migration scenarios into postglacial Scandinavia.

<p>Maps showing potential migration routes into Scandinavia. Scenario (a) shows a migration related to the Ahrensburgian tradition from the south (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s006" target="_blank">S1 Text</a>). Scenarios (b), (c), and (d) show different possible routes into Scandinavia for the EHG ancestry. The scenarios are discussed in the text and the scenario most consistent with genetic data and stone tools is a combination of routes (a) and (b). All maps were plotted using the R package rworldmap [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref028" target="_blank">28</a>]. EHG, eastern hunter-gatherer.</p

Adaptation to high-latitude environments.

<p>(A) Plot of similarity between Mesolithic allele frequency and FIN allele frequency in contrast to difference to TSI allele frequency using the statistic D_sel. The figure shows all positive Z scores representing the number of standard deviations each SNP deviates from the mean. The green-highlighted SNPs are all located in the <i>TMEM131</i> gene. The plot was made with qqman [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.ref049" target="_blank">49</a>]. (B) Derived allele frequencies for three pigmentation-associated SNPs (<i>SLC24A5</i>, <i>SLC45A2</i>, which are associated with skin pigmentation, and <i>OCA2/HERC2</i>, which is associated with eye pigmentation). The dashed line connecting EHG and WHG represents potential allele frequencies if SHG were a linear combination of admixture between EHG and WHG. The solid horizontal line represents the derived allele frequency in SHG. The blue symbols representing SHGs were set on the average genome-wide WHG and EHG mixture proportion (on x-axis) across all SHGs, and the thick black line represents the minimum and maximum admixture proportions across all SHGs. Dashed horizontal lines represent modern European populations (CEU). The <i>p</i>-values were estimated from simulations of SHG allele frequencies based on their genome-wide ancestry proportions (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s014" target="_blank">S9 Text</a>). Data shown in this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003703#pbio.2003703.s015" target="_blank">S1 Data</a>. CEU, Utah residents with Central European ancestry; EHG, eastern hunter-gatherer; FIN, modern-day Finnish individual; SHG, Scandinavian hunter-gatherer; TSI, modern-day Tuscan individual; WHG, western hunter-gatherer.</p