Population genomics of the Viking world

Abstract

The maritime expansion of Scandinavian populations during the Viking Age (about ad 750–1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci—including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response—in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.

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Fig. 1: Overview of the Viking Age genomic dataset.
Fig. 2: Genetic structure of Viking Age samples.
Fig. 3: Genetic structure and diversity of ancient samples.
Fig. 4: Spatiotemporal patterns of Viking and non-Viking ancestry in Europe during the Iron Age, Early Viking Age and Viking Age.

Data availability

Sequence data are available at the European Nucleotide Archive under accession number PRJEB37976.

Code availability

Functions for calculating f-statistics are available as an R package at GitHub (https://github.com/martinsikora/admixr).

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Acknowledgements

This work was supported by the Mærsk Foundation, the Lundbeck Foundation, the Novo Nordisk Foundation, the Danish National Research Foundation, University of Copenhagen (KU2016) and the Wellcome Trust (grant no. WT104125MA). E.W. thanks St John’s College, Cambridge for providing an excellent environment for scientific thoughts and collaborations. S.R. was supported by the Novo Nordisk Foundation (NNF14CC0001). F.R. was supported by a Villum Fonden Young Investigator Award (project no. 00025300). G.S. and E.C. were supported by a Marie Skłodowska-Curie Individual Fellowship ‘PALAEO-ENEO’, a project funded by the European Union EU Framework Programme for Research and Innovation Horizon 2020 (grant agreement number 751349). R.M. was supported by an EMBO Long-Term Fellowship (ALTF 133-2017). M.C. is supported by the Canada Research Chairs Program (231256), the Canada Foundation for Innovation (36801) and the British Columbia Knowledge Development Fund (962-805808). I. Moltke was supported by a YDUN grant from Independent Research Fund Denmark (DFF-4090-00244) and a Villum Fonden Young Investigator Award (project no. 19114). N.P. and C.H.J. are supported by the Swedish Research Council (2015-00466). N.G. was supported by the Program of Fundamental Scientific Research of the State Academies of Sciences, Russian Federation, state assignment no. 0184-2019-0006. D.G.B. and L.M.C. were supported by Science Foundation Ireland/Health Research Board/Wellcome Trust award no. 205072. We thank the iPSYCH Initiative, funded by the Lundbeck Foundation (grant numbers R102-A9118 and R155-2014-1724), for supplying SNP frequency estimates from the present-day Danish population for comparison with Viking Age samples; M. Jakobsson and A. Götherström for providing preliminary access to the sequencing data of 23 Viking Age samples from Sigtuna; M. Corrente for providing access to the skeletal remains from Cancarro; and N. M. Mangialardi and M. Maruotti for the useful suggestions; Greenland National Museum and Archives, as well as the Gotland Museum, for permission to sample their skeletons; J. Kavanagh for providing information on his excavation, and L. Buckley, D. Keating and B. Ó Donnabháin for analysing the remains; R. Breward and J. Murden from the Dorset County Museum for allowing access to their assemblage for DNA sampling; J. Hansen and M. B. Henriksen at Odense Bys Museer for allowing sampling of skeletal material from Hessum and Galjedil; Moesgaard Museum for allowing sampling of skeletal material from Hesselbjerg; C. Bertilsson, P. Lingström, B. Lundberg, K. Lidén and J. Andersson for their help in sampling the ancient human remains; L. Drenzel for permission to sample the human remains; C. Ödman for suggesting relevant material for this study; Ł. Stanaszek, M. Zaitz and the Regional Museum in Cedynia for providing samples; L. Vinner, A. Seguin-Orlando, K. Magnussen, L. Petersen, C. Mortensen and M. J. Jacobsen at the Danish National Sequencing Centre for producing the analysed sequences; P. S. Olsen and T. Brand for technical assistance in the laboratories; R. M. Durbin and J. H. Barrett for comments and suggestions; and J. Wilson, J. Jesch, E. Harlitz-Kern and F. Martín Racimo for their feedback.

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E.W. initiated and led the study. E.W., A.M., D.J.L., Martin Sikora, F.R., R.N., K.K., L.H., S.M.S., J.B., N.P., T.W., A.I., M.E.A., M.W.P., N.L., J.A., I. Moltke and A.A. designed the study. A.M., P.d.B.D., L.M.C., M.M.B., A.K.F., I.L. and J.S. produced the data. A.M., D.J.L., Martin Sikora, F.R., S.R., I. Moltke, R.N., T.W., L.M.C., E.J., A.I., M.W.P., T.K., R.M., G.R., C.B., J.V.M.-M., H.M., A.A., J.C., K.H.I. and M.E.A. analysed or assisted in analysis of data. E.W., A.M., D.J.L., Martin Sikora, F.R., S.M.S., K.K., L.H., R.N., M.C. and A.I. interpreted the results with considerable input from I. Moltke, M.E.A., M.W.P., T.K., H.W., R.M., G.R., T.W., C.H.J., J.A., N.L., N.P., J.B., A.A., M.T.P.G., L.O. and other authors. E.W., A.M., D.J.L., Martin Sikora, F.R., S.M.S., K.K. and L.H. wrote the manuscript with considerable input from M.C., J.B., N.P., I. Moltke, N.L., A.I., R.M., E.J., J.A., M.L.J., C.H.J., M.W.P., M.E.A., G.R. and M.M., with contributions from all authors. A.M., L.M.C., M.W.P., H.W., M.M.B., P.d.B.D., A.K.F., M.A., R.A., M.M., E.C., G.S., A.B., A.F., B. Schütz, B. Skar, C.A., C.F., D.B., D.P., G.T.-W., H.G., I.L., I.G., I. Mainland, I.P., I.M.M., J.M., J. Gibson, J.P., J. Gustafsson, L. Simpson, L. Strand, L.L., Maeve Sikora, M.F., M.V., M.R., M.B., T.P., M. Søvso, N.G., T.C., O.K., O.U., P.F., P.H., S.S., S.V.A., S.E., V.M., W.B., Y.M., P.P., M.D.J., A.P., D.G.B., M.L.J., J.A., N.L., N.P., M.T.P.G., M.E.A., J.B. and E.W. excavated, curated, sampled and/or described analysed skeletons.

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Correspondence to Rasmus Nielsen or Thomas Werge or Eske Willerslev.

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The authors declare no competing interests.

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Peer review information Nature thanks James Barrett, Wolfgang Haak and Pontus Skoglund their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Fig. 1 Viking Age archaeological sites.

Examples of a few archaeological Viking Age sites and samples used in this study. a, Salme II ship burial site of the Early Viking Age, excavated in present-day Estonia: schematic of skeletons (top left) and aerial images of skeletons (top right, and bottom). b, Ridgeway Hill mass grave dated to the tenth or eleventh century ad, located on the crest of Ridgeway Hill near Weymouth, on the south coast of England (reproduced with permission from Dorset County Council/Oxford Archaeology). Around 50 predominantly young adult male individuals were excavated. c, The site of Balladoole, around ad 900, a Viking was buried in an oak ship at Balladoole (Arbory) in the south east of the Isle of Man. d, Viking Age archaeological site in Varnhem, in Skara municipality (Sweden). Schematic map of the church foundation (left) and the excavated graves (red markings) at the early Christian cemetery in Varnhem; foundations of the Viking Age stone church in Varnhem (middle) and the remains of a 182-cm-long male individual (no. 17) buried in a lime stone coffin close to the church foundations (right).

Extended Data Fig. 2 Model-based clustering analysis.

Admixture plot (K = 2 to K = 5) for 567 ancient individuals, spanning 71 populations. This figure is a subset of the most relevant individuals and populations from Supplementary Fig. 7.2; see Supplementary Note 7 for further details. This plot consists of 378 ancient samples from this study; Viking Age samples from Sigtuna (Sweden)10 (n = 21), Iceland18 (n = 22) and other ancient comparative groups (n = 146).

Extended Data Fig. 3 Fine-scale population structure.

The point cloud at the top centre shows an alternative view of the UMAP result from Fig. 2b, with all ancient individuals coloured on the basis of analysis group. The framed panels surrounding the point cloud highlight particular ancestry clusters (as indicated), with labels and larger symbols corresponding to the median coordinates for the respective group. Similarly, the larger bottom panel shows median group coordinates for the large central point cloud, which includes the vast majority of European individuals from the Bronze Age onwards.

Extended Data Fig. 4 Ancestry modelling for distal sources.

a, Contrasting allele-sharing between Anatolian farmers (Barcin_EN) and Steppe pastoralists (Yamnaya_EBA) for European individuals from the Bronze Age and later. Violin plots showing distributions of statistics f4(YRI,test individual;Barcin_EN,Yamnaya_EBA) for n = 515 individuals with a minimum of 1,000,000 SNPs with genotypes and groups with at least 2 such individuals. b, Ancestry proportions of analysis groups from the Bronze Age and later inferred using qpAdm. Target groups were modelled using three distal sources representing European hunter-gatherer (Loschbour_M), Anatolian farmer (Barcin_EN) and Steppe pastoralist (Yamnaya_EBA) ancestry. Sample sizes for target groups can be found in Supplementary Table 10. Error bars indicate standard error obtained from qpAdm. c, Ancestry proportions of analysis groups for which the three-source model was rejected using qpAdm (P < 0.05). Target groups were modelled including one additional distal source representing either Steppe hunter-gatherer (Botai_EBA), Caucasus hunter-gatherer (CaucasusHG_M) or East-Asian-related (XiongNu_IA) ancestry.

Extended Data Fig. 5 Ancestry modelling for proximate sources.

a, Testing for continuity between European Iron Age and later Viking Age and Medieval groups. Coloured squares depict whether a particular target group (row) can be modelled using a single source group (column). P values for f4 rank of 0 (corresponding to a single source group) were obtained using qpAdm with a set of 15 outgroups, which included European Bronze Age groups that preceded the source groups. Sample sizes for target groups can be found in Supplementary Table 12. b, Two-way admixture ancestry proportions of target groups for which a single source was rejected (P ≤ 0.05). Target groups were modelled using additional proximate Bronze and Iron Age sources. Sample sizes for target groups can be found in Supplementary Table 13. For both a and b, only ancient groups containing at least 3 individuals with a minimum of 1,000,000 SNPs with genotypes are plotted. c, Contrasting allele-sharing between populations of present-day Denmark and other populations. Violin plots showing distributions of statistics f4(YRI,test individual;panel population,Denmark) for n = 489 individuals with a minimum of 50,000 SNPs with genotypes and groups with at least 2 such individuals. Median values for distributions are indicated with horizontal lines.

Extended Data Fig. 6 Ancestry diversity of different population groups.

Diversity of different labels (that is, sample locations combined with historical age) are shown as a function of their sample size. The diversity measure is the Kullback–Leibler divergence from the label means, capturing the diversity of a group with respect to the average of that group (see Supplementary Note 11 for details). Larger values are more diverse, although a dependence on sample size is expected. The simulation expectation for the best fit to the data (0 = 0.2) is shown.

Extended Data Fig. 7 Polygenic risk scores.

Polygenic risk scores (PRS) for 16 complex human traits in 148 Viking Age samples from Denmark, Sweden and Norway, compared against a reference sample of 20,551 Danish-ancestry individuals randomly drawn from all individuals born in Denmark in 1981–2005. The PRS is in each case based on allelic effects for >100 independent genome-wide significant SNPs from recent genome-wide association studies of the respective traits and standardised to a mean of 0 and standard deviation of 1 in the entire sample. Difference in PRS was estimated in a linear regression correcting for sex and 25 principal components of overall genetic structure. The plotted BETA indicates the coefficient for the test-group (Viking Age sample) PRS compared to that of the Danish comparison sample, with error bars indicating the 95% confidence interval of BETA, and P indicating the two-tailed P value of the corresponding t-test (not corrected for number of tests). Only PRS for black hair colour is significantly different between the groups after taking account of multiple testing.

Extended Data Fig. 8 Positive selection in Europe.

a, Manhattan plots of the likelihood ratio scores in favour of selection looking at the entire 10,000-year period (top, general scan), the period up to 4,000 years before present (middle, ancient scan) and the period from 4,000 years before present up to the present day (bottom, recent scan). The highlighted SNPs have a score larger than the 99.9% quantile of the empirical distribution of log-likelihood ratios, and have at least two neighbouring SNPs (± 500 kb) with a score larger than the same quantile. n = 1,185 genomes are used in the selection scan. b, Frequencies of the derived A allele rs4988235 SNP responsible for lactase persistence in humans for different Viking Age groups, present-day populations from the 1000 Genomes Project as well as relevant Bronze Age population panels. The numbers at the top of the bars denote the sample size on which the allele frequency estimates are based.

Supplementary information

Supplementary Information

This file contains Supplementary Notes 1-15, including and Supplementary Figures, Supplementary Tables and Supplementary References.

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Supplementary Tables

This file contains Supplementary Tables 1-13.

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Margaryan, A., Lawson, D.J., Sikora, M. et al. Population genomics of the Viking world. Nature 585, 390–396 (2020). https://doi.org/10.1038/s41586-020-2688-8

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