Population genomics of the Viking world

Abstract

The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia during the Viking Age. We also find that several of the members of the only archaeologically well-attested Viking expedition were close family members. By comparing Viking Scandinavian genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci have undergone strong population differentiation during the last millennia. Finally, we are able to trace the allele frequency dynamics of positively selected loci with unprecedented detail, including the lactase persistence allele and various alleles associated with the immune response. We conclude that the Viking diaspora was characterized by substantial foreign engagement: distinct Viking populations influenced the genomic makeup of different regions of Europe, while Scandinavia also experienced increased contact with the rest of the continent.

Full text

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Population genomics of the Viking world 1!
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Ashot!Margaryan1,2,3*,!Daniel!Lawson4*,!Martin!Sikora1*,!Fernando!Racimo1*,!Simon!Rasmussen5,!Ida!3!
Moltke6,! Lara! Cassidy7,! Emil! Jørsboe6,! Andrés! Ingason1,58,59,! Mikkel! Pedersen1,! Thorfinn!4!
Korneliussen1,! Helene! Wilhelmson8,9,! Magdalena! Buś10,! Peter! de! Barros! Damgaard1,! Rui!5!
Martiniano11,!Gabriel!Renaud1,!Claude!Bhérer12,!J.!Víctor!Moreno-Mayar1,13,!Anna! Fotakis3,! Marie!6!
Allen10,! Martyna! Molak14,! Enrico! Cappellini3,! Gabriele! Scorrano3,! Alexandra! Buzhilova15,! Allison!7!
Fox16,!Anders!Albrechtsen6,!Berit!Schütz17,!Birgitte!Skar18,!Caroline!Arcini19,!Ceri!Falys20,!Charlotte!8!
Hedenstierna! Jonson21,! Dariusz! Błaszczyk22,! Denis! Pezhemsky15,! Gordon! Turner-Walker23,! Hildur!9!
Gestsdóttir24,!Inge!Lundstrøm3,!Ingrid!Gustin8,!Ingrid!Mainland25,!Inna!Potekhina26,!Italo!Muntoni27,!10!
Jade!Cheng1,!Jesper!Stenderup1,!Jilong!Ma1,!Julie!Gibson25,!Jüri!Peets28,!Jörgen!Gustafsson29,!Katrine!11!
Iversen5,64,! Linzi! Simpson30,! Lisa! Strand18,! Louise! Loe31,32,! Maeve! Sikora33,! Marek! Florek34,! Maria!12!
Vretemark35,! Mark! Redknap36,! Monika! Bajka37,! Tamara! Pushkina15,! Morten! Søvsø38,! Natalia!13!
Grigoreva39,!Tom! Christensen40,!Ole!Kastholm41,!Otto!Uldum42,!Pasquale! Favia43,!Per!Holck44,!Raili!14!
Allmäe28,! Sabine! Sten45,! Símun! Arge46,! Sturla! Ellingvåg1,! Vayacheslav! Moiseyev47,! Wiesław!15!
Bogdanowicz14,! Yvonne! Magnusson48,! Ludovic! Orlando49,! Daniel! Bradley7,! Marie! Louise! Jørkov50,!16!
Jette! Arneborg40,63,! Niels! Lynnerup50,! Neil! Price21,! M.! Thomas! Gilbert3,51,! Morten! Allentoft1,! Jan!17!
Bill52,! Søren! Sindbæk53,! Lotte! Hedeager54,! Kristian! Kristiansen55,! Rasmus! Nielsen1,56†,! Thomas!18!
Werge1,57,58,59†,!Eske!Willerslev1,60,61,62†!!19!
!20!
1Lundbeck! Foundation! GeoGenetics! Centre,! GLOBE! Institute,! University! of! Copenhagen,! Øster!21!
Voldgade!5-7,!1350!Copenhagen!K,!Denmark.!2Institute!of!Molecular!Biology,!National!Academy!of!22!
Sciences,! 7,! Hasratian! St.,! 0014,! Yerevan,! Armenia.! 3Section! for! Evolutionary! Genomics,! GLOBE!23!
Institute,! University! of! Copenhagen,! Øster! Voldgade! 5-7,! 1350! Copenhagen! K,! Denmark.! 4MRC!24!
Integrative!Epidemiology!Unit,!University!of!Bristol,!Bristol,!UK.!5Novo!Nordisk! Foundation!Center!25!
for! Protein! Research,! Faculty! of! Health! and! Medical! Sciences,! University! of! Copenhagen,!26!
Blegdamsvej!3B,!2200!Copenhagen,!Denmark.!6Department!of!Biology,!The!Bioinformatics!Centre,!27!
University! of! Copenhagen,! 2200! Copenhagen! N,! Denmark.! 7Smurfit! Institute! of! Genetics,! Trinity!28!
College! Dublin,! Dublin.! 8Historical! archaeology,! Department! of! Archaeology! and! Ancient! history,!29!
Lund! University,! PB! 192,! SE! 22100! Lund,! Sweden.! 9Sydsvensk! arkeologi! AB,! PB! 134,! SE! 29122!30!
Kristianstad,! Sweden.! 10Department! of! Immunology,! Genetics! and! Pathology,! Science! for! Life!31!
Laboratory,!Uppsala!University,!751!08!Uppsala,!Sweden.!11Department!of!Genetics,!University!of!32!
Cambridge,!Downing!Street,!Cambridge!CB2!3EH,!UK.!12New!York!Genome!Center,!101!Avenue!of!33!
the! Americas,! New! York,! NY,! USA,! 10013.!13National! Institute! of! Genomic! Medicine! (INMEGEN),!34!
Periférico!Sur!4809,!14610!Mexico!City,!Mexico.!14Museum!and!Institute!of!Zoology,!Polish!Academy!35!
of! Sciences,! Wilcza! 64,! 00-679! Warsaw,! Poland.! 15Anuchin! Research! Institute! and! Museum! of!36!
Anthropology,!Moscow!State!University.!16Manx!National!Heritage,!Kingswood!Grove,!Douglas,!Isle!37!
of! Man,! British! Isles! IM1! 3LY.! 17Upplandsmuseet,! Drottninggatan! 7,! 753! 10! Uppsala,! Sweden.!38!
18NTNU! University! Museum,! Department! of! Archaeology! and! Cultural! History! Norway.!39!
19Arkeologerna.! 20Thames! Valley! Archaeological! Services! (TVAS),! Reading,! UK.! 21Department! of!40!
Archaeology!and!Ancient!History,!Uppsala!University,!Box!626,!751!26!Uppsala,!Sweden.!22Institute!41!
of!Archaeology,!University!of!Warsaw,!ul.!Krakowskie!Przedmieście!26/28,!00-927!Warsaw,!Poland.!42!
23Department! of! Cultural! Heritage! Conservation,! National! Yunlin! University! of! Science! and!43!
Technology,!Douliou,!Taiwan.!24Institute!of!Archaeology,!Iceland.!Bárugata!3,!101!Reykjavík,!Iceland.!44!
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
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25UHI! Archaeology! Institute,! University! of! the! Highlands! and! Islands,! Orkney! College,! Kirkwall,!45!
Orkney,!KW15!1LX.!26Department!of!Bioarchaeology,!Institute!of!Archaeology!of!Natioanal!Academy!46!
of! Sciences! of! Ukraine,! 12! Geroiv! Stalingrada! Ave.! 04210! Kyiv,! Ukraine.! 27Soprintendenza!47!
Archeologia,!Belle!Arti!e!Paesaggio!per!le!Province!di!Barletta!-!Andria!-!Trani!e!Foggia,!Via!Alberto!48!
Alvarez!Valentini,!8!-!71121!Foggia,!Italy.! 28Archaeological! Research! Collection,! Tallinn!University,!49!
Rüütli!10,!Tallinn!10130,!Estonia.!29Jönköping!county!museum,!Jönköping,!Sweden.!30Trinity!College!50!
Dublin.! 31Oxford! Archaeology,! Janus! House,! Osney! Mead,! Oxford! OX2! 0ES,! UK.! 32Heritage! Burial!51!
Services,!Oxford!Archaeology,!Janus!House,!Osney!Mead,!Oxford!OX2!0ES,!UK.!33National!Museum!52!
of! Ireland,! Kildare! Street,! Dublin! 2,! Ireland.! 34Institute! of! Archaeology,! Maria! Curie-Sklodowska!53!
University!in!Lublin,!Pl.!M.!Curie-Sklodowska! 4,! 20-035! Lublin,! Poland.!35Västergötlands!museum,!54!
Box!253,! 532!23!Skara!Sweden.!36National!Museum! Cardiff.!37"Trzy!Epoki"!Archaeological!Service,!55!
Poland.! 38Museum! of! Southwest! Jutland.! 39Institute! for! the! history! of! material! culture,! Russian!56!
Academy!of!Sciences,!Dvotsovaya!Emb.,!18,!Saint-Petersburg,!Russia,!191186.!40National Museum 57!
of Denmark, Frederiksholms Kanal 12, DK-1220 Copenhagen, Denmark.! 41Roskilde Museum, 58!
Museum Organization ROMU, Sankt Ols Stræde 3, DK-4000 Roskilde, Denmark.! 42Langelands 59!
Museum, Jens Winthersvej 12. 5900 Rudkøbing, Langeland, Denmark.!43Department of Humanities, 60!
University of Foggia, Via Arpi, 176, 71121 Foggia, Italy.! 44Department of Molecular Medicine, 61!
Faculty of Medicine, University of Oslo.!45Department of Archaeology and Ancient History, Uppsala 62!
University Campus Gotland.! 46Tjóðsavnið - Faroe Islands National Museum. Kúrdalsvegur 15. 63!
Postboks 1155. FO-110 Tórshavn.! 47Peter the Great Museum of Anthropology and Ethnography 64!
(Kunstkamera), Russian Academy of Science, University Emb, 3, SPb, Russia, 199034.! 48Malmö 65!
Museum, Box 406, 201 24 Malmö, Sweden.! 49Laboratoire d’Anthropobiologie Moléculaire et 66!
d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 67!
Toulouse, France.!50Department of Forensic Medicine, University of Copenhagen, Frederik! V's! vej!68!
11,! 2100! Copenhagen.! 51Department of Natural History, NTNU.! 52Museum of Cultural History, 69!
University of Oslo, P.O.!Box 6762 St. Olavs plass, 0160 Oslo, Norway.!53Centre for Urban Network 70!
Evolutions (UrbNet), Aarhus University, School of Culture and Society, Moesgård Allé 20, building 71!
4215, DK-8270 Højbjerg, Denmark.!54Institute of Archaeology, Conservation and History, Pb. 1019 72!
Blindern, 0315 Oslo, Norway.! 55Department of Historical Studies, University of Gothenburg.!73!
56Departments of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA 94720, USA.!74!
57Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.!58Institute of 75!
Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark.!59The Lundbeck 76!
Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark.! 60Department of 77!
Zoology, University of Cambridge, UK.!61The Danish Institute for Advanced Study,! University! of!78!
Southern! Denmark.! 62The Wellcome Trust Sanger Institute, Cambridge, UK.! 63School of 79!
GeoSciences, University of Edinburgh.! 64Department of Health Technology, Section for 80!
Bioinformatics, Technical University of Denmark, DTU, 2800 Kgs. Lyngby, Denmark 81!
82!
*These!authors!contributed!equally!to!this!work. 83!
†e-mail:!ewillerslev@snm.ku.dk;!Thomas.Werge@regionh.dk;!rasmus_nielsen@berkeley.edu!!84!
!85!
! 86!
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(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
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Abstract 87!
The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one 88!
of the swiftest and most far-flung cultural transformations in global history. During this time 89!
(c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North 90!
America, and left a cultural legacy that persists till today. To understand the genetic structure 91!
and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from 92!
across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern 93!
period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period 94!
preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the 95!
south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. 96!
Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic 97!
structure within Scandinavia, suggesting that regional population differences were already 98!
present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, 99!
Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and 100!
Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia 101!
during the Viking Age. We also find that several of the members of the only archaeologically 102!
well-attested Viking expedition were close family members. By comparing Viking Scandinavian 103!
genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci 104!
have undergone strong population differentiation during the last millennia. Finally, we are able 105!
to trace the allele frequency dynamics of positively selected loci with unprecedented detail, 106!
including the lactase persistence allele and various alleles associated with the immune response. 107!
We conclude that the Viking diaspora was characterized by substantial foreign engagement: 108!
distinct Viking populations influenced the genomic makeup of different regions of Europe, 109!
while Scandinavia also experienced increased contact with the rest of the continent. 110!
! 111!
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(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/703405doi: bioRxiv preprint first posted online Jul. 17, 2019;

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Introduction 112!
Three centuries from approximately 750 to 1050 CE mark a pivotal change for the peoples of 113!
Scandinavia. The maritime transformation commonly known as the Viking Age (VA) altered the 114!
political, cultural and demographic map of Europe in ways that are evident even today. The Vikings 115!
established systems of trade and settlement that stretched from the eastern American seaboard to the 116!
Asian steppe1. They also exported new ideas, technologies, language, beliefs and practices to these 117!
lands. In the process, they gradually developed new socio-political structures, assimilated cultural 118!
influences, and adopted the Christian faith2. 119!
120!
Currently, most of our understanding of the VA is based on written sources and archaeological 121!
evidence. The VA as a historical period has been framed by the first clearly documented raid on 122!
Lindisfarne in 793 CE, and the defeat of a Norwegian army at Stamford Bridge in 1066 CE. More 123!
recent perspectives emphasize long-term, multi-causal social processes with after-effects that varied 124!
greatly by region3–5. Similarly, the notion of a Viking ‘expansion’, implying deliberate drive and 125!
purpose, has been supplemented by the more fluid concept of a ‘diaspora’ that developed over time2. 126!
Under this framework, however, the role of demographic dynamics has remained unclear, as has the 127!
question of whether VA Scandinavia was genetically structured or represented a homogenous 128!
population. Similarly, we still do not know to what extent Vikings mixed with local populations they 129!
encountered and how much foreign ancestry was brought back to Scandinavia. 130!
In order to explore the genomic history of the Viking era, we shotgun sequenced 442 ancient human 131!
remains, from the Bronze Age c. 2400 BC to the Medieval Age c. 1600 AD (Fig. 1). The majority of 132!
these individuals (n=376) were sequenced to between 0.1 and 11X average depth of coverage. The 133!
dataset includes Bronze Age (n=2) and Iron Age (n=10) individuals from Scandinavia; Early Viking 134!
Age (n=43) individuals from Estonia (n=34), Denmark (n=6) and Sweden (n=3); ancient individuals 135!
associated with Norse culture from Greenland (n=23), VA individuals from Denmark (n=78), Faroe 136!
Islands (n=1), Iceland (n=17), Ireland (n=4), Norway (n=29), Poland (n=8), Russia (n=33), Sweden 137!
(n=118), UK (n=42), Ukraine (n=3) as well as medieval individuals from Faroe Islands (n=16), Italy 138!
(n=5), Norway (n=7), Poland (n=2) and Ukraine (n=1). The VA individuals were supplemented with 139!
additional published genomes (n=21) from Sigtuna, in Sweden6. The skeletons originate from major 140!
archaeological sites of VA Scandinavian settlements and activities from Europe to Greenland 141!
(Supplementary Table 1). The data from the ancient individuals were analyzed together with 142!
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previously published data from a total of 3,855 present-day individuals across two reference panels, 143!
and data from 922 individuals of ancient origin (Supplementary Note 6). 144!
145!
Scandinavian genetic ancestry and the beginnings of the Viking era 146!
Although VA Scandinavians shared a common cultural, linguistic and material background, there 147!
was no common word for Scandinavian identity at that time1. The word ‘Viking’ is used in 148!
contemporary sources to mean a ‘pirate’ or ‘sea warrior’2. As such, there is no single ‘Viking world’, 149!
but a coalescence of ‘Viking worlds’ marked by rapidly growing maritime exploration, trade, war 150!
and colonization, following the adoption of deep-sea navigation among the coastal populations of 151!
Scandinavia and the Baltic Sea area7,8. Thus, it is unclear whether the Viking-phenomenon refers to 152!
people with a recently shared genetic background and if foreign influence initiated or accompanied 153!
the transition from the Scandinavian Iron Age into the Viking era. 154!
To assess the genetic relationship of the VA Scandinavians with that of earlier European peoples, we 155!
performed genetic clustering using multi-dimensional scaling (MDS) on a pairwise identity-by-state 156!
(IBS) sharing matrix, as well as latent mixed-ancestry models (Admixture)9. We find that the majority 157!
of our samples broadly cluster within the range of European Bronze Age (BA) and Iron Age (IA) 158!
populations, characterized by an ancestry component that is related to pastoralist populations from 159!
the Pontic-Caspian steppe (Fig. 2a and Extended Data Fig. 2) entering Europe around 5000 BP10,11. 160!
A different dimensionality reduction technique using uniform manifold approximation and projection 161!
(UMAP) revealed additional fine-scale genetic structure. European individuals from the Bronze Age 162!
and onwards are generally distributed within a broad area anchored by four ancestry clusters across 163!
the two UMAP dimensions: Early BA individuals from the Steppe; pre-BA Neolithic Europeans; 164!
Baltic BA individuals; and Scandinavian IA and early VA individuals (Fig. 2b). We observe a wide 165!
range of distributions for VA individuals within this broad area, with notable differences between 166!
geographic regions (Fig. S8.10), indicating complex fine-scale structure among the different groups. 167!
Modelling Scandinavian groups from the BA and onwards as mixtures of three ancestral components 168!
(Mesolithic hunter-gatherers; Anatolian Neolithic; Steppe early BA), again revealed subtle 169!
differences in their composition. We find that the transition from the BA to the IA is accompanied by 170!
a reduction in Neolithic farmer ancestry, with a corresponding increase in both Steppe-like ancestry 171!
and hunter-gatherer ancestry (Extended Data Fig. 6). While most groups show a slight recovery of 172!
farmer ancestry during the VA, there is considerable variation in ancestry across Scandinavia. In 173!
particular, we observe a wide range of ancestry compositions among individuals from Sweden, with 174!
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some groups in southern Sweden showing some of the highest farmer ancestry proportions (40% or 175!
more in individuals from Malmö, Kärda or Öland). Ancestry proportions in Norway and Denmark on 176!
the other hand appear more uniform (Extended Data Fig. 6). Finally, we detect an influx of low levels 177!
of “eastern” ancestry starting in the early VA, mostly constrained among groups from eastern and 178!
central Sweden as well as some Norwegian groups (Extended Data Fig. 6). Testing of putative source 179!
groups for this “eastern” ancestry revealed differing patterns among the Viking Age target groups, 180!
with contributions of either East Asian- or Caucasus-related ancestry (Supplementary Note 10). 181!
Overall, our findings suggest that the genetic makeup of VA Scandinavia derives from mixtures of 182!
three earlier sources: Mesolithic hunter-gatherers, Neolithic farmers, and Bronze Age pastoralists. 183!
Intriguingly, our results also indicate ongoing gene flow from the south and east into Iron Age 184!
Scandinavia. Thus, these observations are consistent with archaeological claims of wide-ranging 185!
demographic turmoil in the aftermath of the Roman Empire with consequences for the Scandinavian 186!
populations during the late Iron Age12,13. We caution, however, that our sampling for the periods 187!
preceding the VA is still sparse, and hence do not provide a full picture of the genetic diversity across 188!
Scandinavia during that period. 189!
190!
Genetic structure within Viking-Age Scandinavia 191!
By the end of the Iron Age in the 8th century CE, Scandinavia formed a patchwork of conflicting and 192!
competing kingdoms with a shared cultural background. For centuries, a political economy based on 193!
raiding, trading and gifts had been common5. However, the cause for the development of this 194!
economic and political system into the more organized maritime society of the Viking era remains 195!
debated5. It is commonly argued that seafaring8,14 contributed to create a densely interlinked 196!
Scandinavia during the Viking era2,15,16. 197!
To disentangle the fine-scale population structure within VA Scandinavia, we performed genotype 198!
imputation on a subset of 300 individuals with sufficient coverage (>0.5X) and inferred genomic 199!
segments shared via identity-by-descent (IBD) within the context of a reference panel of 1,464 200!
present-day Europeans, using IBDseq. We find that VA Scandinavians on average cluster into three 201!
groups according to their geographic origin, shifted towards their respective present-day counterparts 202!
in Denmark, Sweden and Norway (Fig. 3a). Closer inspection of the distributions for the different 203!
groups reveals additional complexity in their genetic structure (Fig. S10.1). We find that the 204!
‘Norwegian’ cluster includes Norwegian IA individuals, who are distinct from both Swedish and 205!
Danish IA individuals which cluster together with the majority of central and eastern Swedish VA 206!
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individuals. Many individuals from southwestern Sweden (e.g. Skara) cluster with Danish present-207!
day individuals from the eastern islands (Funen, Zealand), skewing towards the ‘Swedish’ cluster 208!
with respect to early and more western Danish VA individuals (Jutland). Some individuals have 209!
strong affinity with Eastern Europeans, particularly those from the island of Gotland in eastern 210!
Sweden. The latter likely reflects individuals with Baltic ancestry, as clustering with Baltic BA 211!
individuals is evident in the IBS-UMAP analysis (Fig. 2b) and through f4-statistics (Extended Data 212!
Fig. 4). 213!
To further quantify the within-Scandinavia population structure, we used ChromoPainter17 to identify 214!
long, shared haplotypes among sequenced individuals using a reference panel enriched with 215!
Scandinavian populations (n=1,675 individuals, see Supplementary Notes 6 and 11). Our approach 216!
detects subtle population structure present during the VA in Scandinavia. Supplementary Figures 217!
S11.1-10 and Supplementary Note 11 describe the supervised method that we used to obtain power 218!
to robustly identify local ancestry variation in the presence of sequencing rate variation. We find at 219!
least four major ancestry components in Scandinavia, each with affinities with a present-day 220!
population (Fig. S11.11): a Danish-like, a Swedish-like, a Norwegian-like and a British-like 221!
component. Henceforth, we call this latter component ‘North Atlantic’, and we suspect it may reflect 222!
originally Celtic individuals that occupied the British Isles and were brought into Scandinavia. We 223!
refer to the first three ancestries as ‘Danish-like’, ‘Swedish-like’ and ‘Norwegian-like’, though we 224!
emphasize that the correspondence between these ancestries and present-day inhabitants of the 225!
respective Scandinavian countries is by no means exact or exclusive. During the VA, we mostly find 226!
high levels of Norwegian-like and Swedish-like components in Norway and Sweden, respectively, 227!
while Danish-like and ‘North Atlantic’ components are more widespread within Scandinavia (Fig. 228!
S11.12 and Supplementary Table 6). Notably, the ‘Swedish-like’ component is higher in Salme, 229!
Estonia, than in Sweden, because our sampling scheme included several individuals from the famous 230!
Salme Viking ship burial, of which archaeological and isotopic data suggest a Scandinavian 231!
origin18,19. While in general individuals from most of the Scandinavian VA settlements show mixed 232!
(Danish, Norwegian and Swedish) genetic ancestries, VA individuals from Jutland (Denmark) do not 233!
have significant Swedish-like or Norwegian-like genetic components. Furthermore, gene flow within 234!
Scandinavia appears to be broadly northwards, dominated by Danish Vikings moving into what are 235!
now Norway and Sweden (Table S11.2; see Supplementary Note 11). 236!
Although the majority of the Viking genomes within Scandinavia and abroad show affinities to 237!
Danish, Norwegian, Swedish or British populations, there are some notable exceptions. We identified 238!
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two ancient individuals (VK518 and VK519) originating from northern regions of Norway 239!
(Nordland), which have affinities to present-day Saami. This signal is weaker for VK519, indicating 240!
that he might have also had Norwegian-like ancestors. Given the geographic provenance of these 241!
samples, it was not unexpected to find individuals with Saami-like ancestry among the VA samples. 242!
However, as VK519 is indeed an admixed individual with both Norwegian-like and Saami-like 243!
ancestries, it appears that genetic contacts between these groups were already underway in VA 244!
Norway. 245!
Importantly, present-day country boundaries are not always well reflected in the genetic data. Thus, 246!
the south-western part of Sweden in the VA is genetically more similar to Danish VA populations 247!
than the eastern regions of mainland Sweden (i.e. the area around the Mälaren Valley), likely due to 248!
geographic barriers that prevented gene flow in Sweden. 249!
We quantified genetic diversity in our samples using two measures: conditional nucleotide diversity 250!
(Supplementary Note 9) and variation in inferred ancestry (Supplementary Note 11; Extended Data 251!
Fig. 5 and Fig. S11.13). We find overall high nucleotide diversity among most Viking-Age groups, 252!
with diversity values exceeding those of earlier Neolithic or BA groups, and only slightly lower than 253!
the highly diverse IA individuals from the British Isles (Fig. S9.1). Both measures of diversity vary 254!
significantly across locations. Denmark and Gotland in Sweden have the highest genetic diversity in 255!
the region, suggesting that these regions may have been centers of interaction and trade during this 256!
time. They also possess high diversity in inferred ancestries. North Norway also has high diversity in 257!
inferred ancestry due to its mixture of ‘North Atlantic’ and ‘Norwegian-like’ ancestry. 258!
Interestingly, on Gotland, there are much more Danish-like, British-like and Finnish-like genetic 259!
components than Swedish-like components, supporting the notion that the island may have been 260!
marked by extensive maritime contacts during the VA. Our two Gotland sampling sites, Fröjel and 261!
Kopparsvik, have traditionally been argued to contain non-local individuals20, but recent Sr-isotope 262!
analyses have suggested otherwise21,22. 263!
On Öland in Sweden, we observe high genetic diversity and the most variable patterns of recent 264!
ancestry (Extended Data Fig. 5) in Scandinavia. Sr and O isotope variation in these samples, and 265!
more contemporary samples from Öland have concluded that there is: (i) a high proportion (68%) of 266!
non-locals, (ii) high diversity in geographical origins and (iii) long distance migration23. Thus, the 267!
genetic diversity observed for Öland in the VA fits well with all of these results. 268!
In conclusion, the results for Gotland and Öland agree with the archaeological record, suggesting that 269!
Öland and Gotland were important trading posts from the Roman period onwards24,25. A similar 270!
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pattern is observed at a few archaeological sites from the central Danish islands, such as Langeland, 271!
although at a lower scale. Interestingly, genetic diversity here increases from the early to the late VA, 272!
suggesting increasing interregional interaction. 273!
Our findings do not agree with the view of an overall highly connected population in Viking 274!
Scandinavia 2,8,14–16. Rather, we find clear genetic population structure within Scandinavia. We see 275!
evidence of a few cosmopolitan centers to the south, in southern Sweden and Denmark, where we see 276!
higher diversity of ancestries than in the rest of Scandinavia. These patterns are consistent with a 277!
restricted number of sea routes between the different Scandinavian areas and beyond. 278!
279!
Viking migrations 280!
Viking society is particularly famous for its ship technology, allowing for fast transport of large 281!
numbers of individuals in a single vessel26. These vessels enabled the Vikings not only to carry out 282!
lucrative raids and extended trade routes across Western Eurasia, but also to reach and settle lands in 283!
the North Atlantic27–30. Based on historical and archaeological data, Viking presence extended into 284!
both western and eastern Europe, reaching perhaps as far as the Pontic Steppe and the Middle 285!
East31,32. It is commonly believed that the westward migrations and raids were mainly carried out by 286!
people from what are now Norway and Denmark in the 9th and 10th centuries CE. In contrast to 287!
western movements, eastward expansions are commonly believed to have been carried out by 288!
Swedish Vikings, trading along navigable river systems and overland caravan routes32. Swedish 289!
Vikings (the ‘Rus’) are also credited for being active in the formation of the first Russian state33,34. 290!
Overall, our fine-scale ancestry analysis based on genomic data largely support the Viking expansion 291!
patterns inferred from archaeology (Figs. 3, 4 and S11.12). The eastward movements mainly involved 292!
individuals with Swedish-like ancestry, while the Viking individuals with Norwegian-like ancestry 293!
travelled to Iceland, Greenland, Ireland and the Isle of Man. A Danish-like ancestry component is 294!
more pronounced in present-day England, which is also in accordance with historical records35 and 295!
still visible in place-names34, and modern genetics36,37. Importantly, however, it is currently 296!
impossible for us to distinguish Danish-like ancestry in the British Isles from that of the Angles and 297!
Saxons, who migrated in the 5th-to-6th centuries CE from Jutland and Northern Germany. 298!
Interestingly, the ancient individuals from two execution sites in England (Dorset and Oxford) have 299!
significant local ‘North Atlantic’ ancestry, as well as Danish-like and Norwegian-like ancestries. If 300!
these represent Viking raiding parties coming to grief, as has been suggested38,39, this implies such 301!
forces were composed of individuals from different places of origin. This pattern is also suggested 302!
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by isotopic data from the warrior cemetery in Trelleborg, Denmark40. Similarly, the presence of 303!
Danish-like ancestry in an ancient sample from Gnezdovo (Eastern Europe) indicates that the eastern 304!
migrations were not entirely composed of Vikings from Sweden. 305!
However, in some cases, localities seem to have taken up Viking culture while incorporating little to 306!
no Scandinavian ancestry components, suggesting that the “Viking” identity was not always 307!
necessarily associated with Scandinavian genetic ancestry. Archaeological evidence indicates that the 308!
six higher coverage VA individuals from three different archaeological sites in the Orkney Islands 309!
have Scandinavian cultural links41,42. However, four (VK201, VK202, VK203 and VK207) of these 310!
samples have over 85% “UK” ancestry and are genetically similar to present-day Irish and Scottish 311!
populations (Figs 3a and S10.1, Supplementary Table 6), which is in contrast to the isotopic 312!
evidence43. Haplotype-based analyses corroborate that four of these samples possessed local genetic 313!
ancestries, with little Scandinavian contribution. Only two individuals - VK204 and VK205 314!
- displayed c. 50% Norwegian and Danish ancestries (Supplementary Table 6), respectively, which 315!
may indicate admixture between the locals and Scandinavians on the Orkney Islands during the VA. 316!
The four ancient genomes of Orkney individuals with little Scandinavian ancestry may be the first 317!
ones of Pictish people published to date (Supplementary Note 12). Yet a similar (>80% “UK” 318!
ancestry) individual was found in Ireland (VK545) and five in Scandinavia, implying that Pictish 319!
populations were integrated into Scandinavian culture by the Viking Age. 320!
321!
Gene flow into Scandinavia during the Viking era 322!
Archaeological findings and the written sources support the hypothesis that Viking back migrations 323!
and interaction between the newly settled areas and Scandinavia occurred as part of the process44. 324!
Presumably, if these migrations took place, native ancestry from these areas must have also been 325!
introduced into Scandinavia. We therefore aimed to assess the levels of non-Scandinavian ancestry 326!
emerging in Scandinavia during the VA. 327!
Using fineStructure17, we find that the levels of non-Scandinavian ancestry in the Danish, Norwegian 328!
and Swedish Vikings agree with known trading routes (Supplementary Notes 11 and 12). The most 329!
obvious genetic signals are from Finnish and Baltic sources into the area of what is now modern 330!
Sweden, including Gotland. These ancestries are present at considerably lower levels or are 331!
completely absent in most individuals from Denmark and Norway. A substantial interaction across 332!
the Baltic Sea is also suggested by objects from Finland found in graves in Middle Sweden, albeit 333!
recent Sr-isotope analyses are inconclusive regarding the origin of the buried individuals 45,46. In 334!
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comparison, western regions of Scandinavia have much higher levels of ancestry from the British 335!
Isles, in comparison with the eastern regions of Sweden (Supplementary Notes 11 and 12). We also 336!
observe several individuals (Supplementary Table 6) with large amounts of South European ancestry 337!
in Denmark and southwest Sweden during the Viking period (Fig. 4). No such individuals are found 338!
among our Scandinavian Iron Age samples, though we stress that our sampling for this period is more 339!
limited than for the other two. The discovery of individuals with ancestry from Southern Europe and 340!
the British Isles is the first direct evidence for movement into Scandinavia from these regions. The 341!
directions of interaction marked by these individuals is consistent with the major directions of gene 342!
flows outwards from Scandinavia also seen in the data. 343!
Surprisingly, three individuals from the Kärda site show much higher genetic similarity to Late 344!
Neolithic/Early Bronze Age Danish individuals than to all other VA individuals in the dataset. The 345!
site is located far inland, in south-west Sweden. This similarity is quite unexpected, given that the 346!
samples are AMS-dated to the middle of the VA, and consistent with the presence of Caucasus-related 347!
ancestry inferred in the qpAdm ancestry modelling. Studies of VA burial customs suggest that the 348!
Småland area was characterized by locally confined cultural groups47. The genetic data suggest that 349!
this pattern of cultural isolation was sustained in marked contrast to contemporary coastal and island 350!
communities. Consistent with this hypothesis we find that the individuals from Kärda show a marked 351!
reduction in nucleotide diversity compared to other VA groups (Fig. S9.1), although they also have 352!
high amounts of Southern European ancestry. 353!
354!
Disappearance of the Greenlandic Norse 355!
From around 980 to 1440 CE South-west Greenland was settled by peoples of Scandinavian (Norse) 356!
descent. They likely originated from Icelandic Vikings who established a colony there at the end of 357!
the 9th century CE29,48. It is believed that the Norse also reached Labrador, North America, from 358!
Greenland around 1000, although no permanent settlement was established30. The fate of the Norse 359!
in Greenland remains debated, but probable causes of their disappearance are social or economic 360!
processes in Europe (e.g. political relations within Scandinavia and changed trading systems) and 361!
natural processes, like climatic changes29,49,50. 362!
We see no evidence of long-term inbreeding in the Greenlandic Norse genomes, though we note that 363!
we only have one high-coverage genome from the later period of occupation of Greenland 364!
(Supplementary Note 10; Figs. S10.2 and S10.3). This suggests a depopulation scenario over 365!
approximately 100 years which would be in line with previous demographic models51, as well as the 366!
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archaeology. Indeed, the latter indicates that marginal farms in the Western Settlement and the 367!
northern and southern parts of the Eastern Settlement were abandoned from about 1200 CE, with no 368!
converse intensification of settlement in the central areas. 369!
We also find no evidence of ancestry from local populations from the Western Atlantic (Paleo 370!
Eskimo, Inuit or Native American) in the Norse genomes. This is in accordance with previous 371!
physical anthropological studies of the skeletal remains51. This suggests that either sexual interactions 372!
did not take place or that, if they did, then on a very small and incidental scale with the children 373!
remaining in the native communities. In terms of genetic ancestry of the Greenlandic Norse, we find 374!
evidence of admixture between Scandinavians (mostly from Norway) and individuals from the British 375!
Isles, similar to the first settlers of Iceland52, which supports the archaeological and historical links 376!
between the Greenlandic Norse and the Icelandic Vikings. 377!
378!
Genetic composition of the earliest Viking expedition and kinship findings 379!
Maritime raiding has been a constant of seafaring cultures for millennia. However, the VA is unusual 380!
in that it is partly defined by such activity53. Despite the historical importance of Viking raiding, the 381!
exact nature and composition of these war parties is unknown5. Only one Viking raiding or diplomatic 382!
expedition has left direct archaeological traces, at Salme in Estonia, where 41 Swedish Vikings who 383!
died violently were buried in two boats accompanied by high-status weaponry18,19. Importantly, the 384!
Salme boat-burial predates the first textually documented raid (in Lindisfarne in 793) by nearly half 385!
a century. 386!
Comparing the genomes of 34 individuals from the Salme burial using kinship analyses, we find that 387!
these elite warriors included four brothers buried side by side and a 3rd degree relative of one of the 388!
four brothers (Supplementary Note 4). In addition, members of the Salme group had very similar 389!
ancestry profiles, in comparison to the profiles of other Viking burials (Supplementary Notes 10 and 390!
11). This suggests that this raid was conducted by genetically homogeneous people of high status, 391!
including close kin. Isotope analyses indicate that the crew descended from the Mälaren area in 392!
Eastern Sweden19 thus confirming that the Baltic-Mid-Swedish interaction took place early in the 393!
VA. 394!
Intriguingly, we identified several additional pairs of kin among the other Viking genomes. One is a 395!
pair of 2nd degree male relatives (i.e. half-brothers, nephew-uncle or grandson-grandfather) from two 396!
locations separated by the North Sea: one of the samples (VK279) was excavated in Denmark 397!
(Galgedil site on Funen; this cemetery was also analyzed for strontium with a group of non-locals 398!
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there) while the other individual (VK144) was found in the UK (Oxford site). Another pair of 399!
individuals with 3rd or 4th degree relatedness (e.g. cousins) was discovered in Sweden, namely a male 400!
sample excavated on the island of Öland (VK342) and a female individual from Skämsta, Uppsala 401!
(VK527), some 300-400 kilometers apart. Interestingly, the female from Uppsala (VK527) also had 402!
a brother (VK517), and both siblings display a rare genetic disorder of abnormal skeletal 403!
development: spondyloepiphyseal dysplasia. Given the very low frequency of this disorder, the close 404!
family ties between these individuals were expected by the archaeologists22. Such long-distance 405!
relationships in our dataset underscore the degree of individual-level mobility during the Viking era. 406!
407!
Positive selection in Europe in the last 10,000 years 408!
The availability of hundreds of genomes from the IA and VA - in combination with previously 409!
published Mesolithic, Neolithic and Bronze Age genomes10,11,54,55 - permit us to directly investigate 410!
the role of positive selection using time series of allele frequencies from the last ten millennia of 411!
European history. We looked for SNPs whose allele frequencies changed significantly in the last 412!
10,000 years, using a newly developed method called “neoscan” that is implemented in the Ohana 413!
software package56,57, and that can detect strong allele frequency shifts in time that cannot be 414!
explained by temporal changes in genome-wide genetic ancestry alone (Supplementary Note 14). 415!
Figure 5a shows the resulting likelihood ratio scores in favor of selection looking at the entire 10,000-416!
year period (top, “general” scan), the period up to 4,000 BP (middle, “ancient” scan) and the period 417!
from 4,000 BP up to the present (bottom, “recent” scan). The strongest candidate for selection - 418!
especially in the “recent” scan - is a cluster of SNPs near the LCT gene - a signal that has been 419!
extensively characterized in the past58,59. The rise in frequency of the lactase persistence allele to its 420!
present-day levels in Northern Europe is, however, poorly understood. We know that this rise must 421!
have occurred after the Bronze Age, a time at which this allele was still segregating at low 422!
frequencies10,54. Based on the archaeological record, we also know that VA Scandinavians used a 423!
variety of dairy products as an essential part of their daily food intake. Our dataset allows us, for the 424!
first time, to directly assess the frequency of the lactase persistence allele (at SNP rs4988235, 425!
upstream of the LCT gene) in Scandinavia during the Iron Age and VA, and trace its evolution since 426!
the Bronze Age. 427!
Figure 5b shows that VA groups had very similar allele frequencies at the LCT lactase persistence 428!
SNP to those found in present-day northern European populations. In contrast, the persistence allele 429!
was at low frequencies in Bronze Age Scandinavians, as well as Corded Ware and Bell Beaker 430!
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cultures from central Europe, even though there is evidence for milk consumption in these regions by 431!
that time. The allele frequency in Iron Age samples is at intermediate levels (c. 37.5%), suggesting 432!
this rise in frequency must indeed have occurred during the Iron Age (c. 1500-2500 years ago), but 433!
was largely complete at the onset of the VA. Interestingly, the allele frequency of the allele is much 434!
higher (c. 40%) in the Bronze Age population from the neighboring Baltic Sea region than in Bronze 435!
Age Scandinavia. Given the geographic and cultural proximities between Scandinavia and the Baltic 436!
region, this may suggest gene flow between the two regions resulting in increased frequency of lactase 437!
persistence in Scandinavia during the Iron Age. 438!
Other candidates for selection include previously identified regions like the TLR1/TLR6/TLR10 439!
region, the HLA region, SLC45A2 and SLC22A454. We also find several new candidate regions for 440!
selection in the “ancient” scan, some of which contain SNPs where the selected allele rose in 441!
frequency early in the Holocene but then decreased later on (Supplementary Note 14). These 442!
candidate regions include a region overlapping the DCC gene, which has been implicated in 443!
colorectal cancer60 and another overlapping the AKNA gene, which is involved in the secondary 444!
immune response by regulating CD40 and its ligand61. This highlights the utility of using ancient 445!
DNA to detect signatures of selection that may have been erased by recent selective dynamics. 446!
447!
Pigmentation-associated SNPs 448!
Exploring twenty-two SNPs with large effect associated with eye color and hair pigmentation, we 449!
observe that their frequencies are very similar to those of present-day Scandinavians (Supplementary 450!
Note 13). This suggests that pigmentation phenotype in VA Scandinavians may not have differed 451!
much from the present-day occupants of the region (although see section on complex traits below for 452!
an analysis including alleles of small effect). Nevertheless, it is important to stress that there is quite 453!
a lot of variation in the genotypes of these SNPs across the sequenced samples, and that there is 454!
therefore not a single ‘Viking phenotype’. For example, two of the ancient samples with the highest 455!
coverage have different pigmentation phenotypes: VA individual VK42 from Skara, Sweden has 456!
alleles associated with brown eyes and darker hair coloration while VK1 from Greenland was likely 457!
to have had blue eyes and lighter hair. 458!
459!
Evolution of complex traits in Scandinavia 460!
To search for signals of recent population differentiation of complex traits, we compared genotypes 461!
of Viking age samples with those of a present-day Scandinavian population for a range of trait-462!
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associated SNP markers. We selected 16 traits for which summary statistics from well-powered 463!
genome-wide association studies (GWAS) were available through the GWAS ATLAS 464!
(https://atlas.ctglab.nl)62. For comparison with the Viking age samples we used a random population 465!
subset of the IPSYCH case-cohort study of individuals born in Denmark between 1981-201163. We 466!
derived polygenic risk scores (PRS) for the 16 traits, based on independent genome-wide significant 467!
allelic effects and tested for a difference in the distribution of polygenic scores between the two 468!
groups, correcting for sex and ancestry-sensitive principal components (Supplementary note S15). 469!
We observed a significant difference between the polygenic scores of VA samples and current Danish 470!
population samples for three traits; black hair color (P = 0.00089), standing height (P = 0.019) and 471!
schizophrenia (P = 0.0096) (Extended Data Fig. 5). For all three traits, the polygenic score was higher 472!
in the VA group than in the present-day Danish group. The observed difference in PRS for height and 473!
schizophrenia between the groups did however not remain significant after taking into account the 474!
number of tests. A binomial test of the number of black hair color risk alleles found in higher 475!
frequency in the VA sample and the present-day sample, also returned a significant difference (65/41; 476!
P = 0.025), which suggests that the signal is not entirely driven by a few large-effect loci. 477!
Thus, we only find evidence for systematic changes in combined frequencies of alleles affecting hair 478!
color (and possibly also height and schizophrenia), among all the anthropometric traits and complex 479!
disorders we tested. Also, we cannot conclude whether the observed difference in allele frequencies 480!
are due to selection acting on these alleles between the Viking Age and the present time or to some 481!
other factors (such as more ethnic diversity in the VA sample), nor can we conclude whether a similar 482!
change has occurred in other Nordic populations than the Danish. 483!
484!
Genetic legacy of the Vikings in present-day populations 485!
To test whether present-day Scandinavians share increased ancestry with their respective ancient 486!
Viking counterparts, we first inferred D-statistics of the form D(YRI, ancient; present-day X, present-487!
day DK), which contrast allele sharing of a test ancient individual with a present-day test population 488!
X and present-day Danes. We find subtle but noticeable shifts of ancient individuals towards their 489!
present-day counterparts in the distributions of these statistics (Extended Data Fig. 3). We further 490!
examined variation in present-day populations using fineSTRUCTURE, and then described these 491!
present-day groups by their ancestry from ancient populations (Fig. S11.14). 492!
We find that within Scandinavia, present-day populations are still structured according to the ancient 493!
Viking population groups. The component that we associated as Norwegian-like is present at 45-65% 494!
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in present-day Norway. Similarly, the ancient Swedish-like ancestry is present at 15-30% within 495!
Sweden. Of the four Swedish clusters, one is more related to the ancient Finnish than the Swedish-496!
like ancestry, and a second is more related to Danes and Norwegians. Danish-like ancestry is now 497!
high across the whole region. 498!
Outside of Scandinavia, the genetic legacy of the Vikings is consistent, though limited. A small 499!
component is present in Poland (up to 5%) and the south of Europe. Within the British Isles, it is 500!
difficult to assess how much of the Danish-like ancestry is due to pre-existing Anglo-Saxon ancestry; 501!
however, the Norwegian-like ancestry is consistently around 4%. The Danish-like contribution is 502!
likely to be similar in magnitude and is certainly not larger than 16% as found in Scotland and Ireland. 503!
The lack of strong variation in ancestry from Scandinavia makes sense if the Vikings did not maintain 504!
a diaspora identity over time but instead integrated into the respective societies in which they settled. 505!
The genetic impacts are stronger in the other direction. The ‘British-like’ populations of Orkney 506!
became ‘Scandinavian’ culturally, whilst other British populations found themselves in Iceland and 507!
Norway, and beyond. Present-day Norwegians vary between 12 and 25% in their ‘British-like’ 508!
ancestry, whilst it is still (a more uniform) 10% in Sweden. Separating the VA signals from more 509!
recent population movements is difficult, but these numbers are consistent with our VA estimates. 510!
511!
Discussion 512!
Until now, our main understanding of the VA was largely based on a combination of historical sources 513!
and archaeological evidence. These often characterize the VA as a period of high mobility and 514!
interaction between peoples. Networks of trade were established, connecting distant regions within 515!
Scandinavia through established waterways with significant movement between regions. It has also 516!
been viewed as a time where links were created to regions outside Europe, from the Pontic Steppe in 517!
the east to North America in the west. 518!
Our genomic analyses add complex layers of nuance to this simple picture. We largely reconstruct 519!
the long-argued movements of Vikings outside Scandinavia: Danish Vikings going to Britain, 520!
Norwegian Vikings moving to Ireland, Iceland, and Greenland, and Swedish Vikings sailing east 521!
towards the Baltic and beyond. However, we also see evidence of individuals with ancient Swedish 522!
and Finnish ancestry in the westernmost fringes of Europe, whilst Danish-like ancestry is also found 523!
in the east, defying our modern notions of historical groupings. It is likely that many such individuals 524!
were from communities with mixtures of ancestries, likely thrown together by complex trading, 525!
raiding and settling networks that crossed cultures and the continent. 526!
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Our observations also suggest that the different parts of Scandinavia were not as evenly connected, 527!
as has often been assumed. Despite relatively fast and easy communication between the coastal 528!
regions of Denmark, Norway, and Sweden, we find that clear genetic structure was present in Viking-529!
Age Scandinavia. In fact, our data indicate that Viking Scandinavia consisted of a limited number of 530!
transport zones and maritime enclaves64 where contact was made with Europe, while the remaining 531!
regions had limited external gene flow with the rest of the Scandinavian continent. Some Viking-Age 532!
Scandinavian locations are relatively homogeneous both in terms of genetic diversity and patterns of 533!
ancestry; particularly mid-Norway, Jutland, and the Atlantic settlements, which contain 534!
predominantly Norwegian-like and ‘North Atlantic’ (including pre-Anglo Saxon British) ancestry. 535!
Indeed, one of the clearest vectors of contrast observed in this study is between the strong genetic 536!
variation seen in relatively populous coastal trading communities such as in the islands Gotland and 537!
Öland, and the reduced diversity in less populated (mostly inland) areas in Scandinavia. Such high 538!
genetic heterogeneity, which was likely due to increased population size, extends the urbanization 539!
model of Late Viking Age city of Sigtuna proposed by Krzewińska et al.6 both spatially and further 540!
back in time. 541!
Interestingly, our findings correspond with paleodemographic studies based on place-name evidence 542!
and archaeological distributions suggesting population density was higher in Denmark than elsewhere 543!
in Viking-Age Scandinavia65. Gene flow from Denmark to the north is also paralleled by the linguistic 544!
affinities of the medieval Scandinavian languages: The 12th-century Icelandic law text Grágás states 545!
that the common language of Swedes, Norwegians, Icelanders, and Danes was dǫnsk tunga (‘Danish 546!
tongue’)66. It appears that the formation of large-scale trading and cultural networks that spread 547!
people, goods and warfare took time to affect the heartlands of Scandinavia, which received much 548!
more restricted gene flow, retaining pre-existing genetic differences between Scandinavian 549!
populations. This pattern of behavior seems to prevail from the beginning of the Viking diaspora to 550!
its end at the beginning of the medieval period. 551!
Our findings also show that Vikings are not simply a direct continuation of the Scandinavian Iron 552!
Age groups. Rather than simple continuity, we observe foreign gene flow from the south and east 553!
into Scandinavia, starting in the Iron Age, and continuing throughout the duration of the Viking 554!
period from an increasing number of sources. Our findings also contradict the myth of the Vikings as 555!
peoples of pure local Scandinavian ancestry. In fact, we found many Viking Age individuals with 556!
high levels of foreign ancestry, both within and outside Scandinavia, suggesting ongoing gene flow 557!
with different peoples across Europe. Indeed, it appears that some foreign peoples contributed more 558!
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genetic ancestry to Scandinavia during this period than the Vikings contributed to them which could 559!
partially be due to smaller effective population size of the VA Scandinavians as opposed to their 560!
continental and British neighbors. 561!
562!
Acknowledgements 563!
This work was supported by the Mærsk Foundation, the Lundbeck Foundation, the Novo Foundation, 564!
the Danish National Research Foundation, KU2016, and the Wellcome Trust (grant nos. 565!
WT104125MA). The authors thank the iPSYCH Initiative, funded by the Lundbeck Foundation 566!
(grant nos. R102-A9118 and R155-2014-1724), for supplying SNP frequency estimates from the 567!
present-day Danish population for comparison with Viking Age samples. EW would like to thank St. 568!
John’s College, Cambridge for providing an excellent environment for scientific thoughts and 569!
collaborations. SR was supported by the Novo Nordisk Foundation (NNF14CC0001). FR was 570!
supported by a Villum Young Investigator Award (project no. 000253000). The authors are grateful 571!
to Marisa Corrente for providing access to the skeletal remains from Cancarro and Nunzia M. 572!
Mangialardi and Marco Maruotti for the useful suggestion. G.S. and E.C. were supported by a Marie 573!
Skłodowska-Curie Individual Fellowship “PALAEO-ENEO”, a project funded by the European 574!
Union EU Framework Programme for Research and Innovation Horizon 2020 (Grant Agreement 575!
number 751349). RM was supported by an EMBO Long-Term Fellowship (ALTF 133-2017). We 576!
thank Mattias Jakobsson and Anders Götherström for providing preliminary access to the sequencing 577!
data of 23 Viking Age samples from Sigtuna; L. Vinner, A. Seguin-Orlando, K. Magnussen, L. 578!
Petersen and C. Mortensen at the Danish National Sequencing Centre for producing the analysed 579!
sequences; P.V. Olsen and T. Brand for technical assistance in the laboratories. We thank Richard M. 580!
Durbin and James H. Barrett for comments and suggestions. 581!
582!
! 583!
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
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747!
748!
749!
Fig. 1: Map of the “Viking World” from 8th till 11th centuries. Different symbols on the map (a) 750!
correspond to ancient sites of a specific age/culture. The ancient samples are divided into the 751!
following five broad categories: Bronze Age (BA) - c. 2500 BC - 900 BC; Iron Age (IA) - c. 900 BC 752!
to 700 CE; Early Viking Age (EVA) - c. 700 to 800 CE; VA - c. 800 to 1100 CE; Medieval - c. 1100 753!
to 1600 CE. b, All ancient individuals from this study (n=442) and published VA samples (n=21) 754!
from Sigtuna6 are categorized based on their spatio-temporal origin. 755!
756!
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/703405doi: bioRxiv preprint first posted online Jul. 17, 2019;

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25!
757!
758!
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766!
Fig. 2: Genetic structure of VA samples. a, Multidimensional scaling (MDS) plot based on a 767!
pairwise identity-by-state (IBS) sharing matrix of the VA and other ancient samples (Supplementary 768!
Table 3). b, Uniform manifold approximation and projection (UMAP) analysis of the same dataset 769!
as in plot (a). 770!
771!
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
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26!
772!
773!
774!
775!
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786!
Fig. 3: Genetic structure and diversity of ancient samples. a, Uniform manifold approximation 787!
and projection (UMAP) analysis of the ancient and modern Scandinavian individuals based on the 788!
first 10 dimensions of MDS using identity-by-descent (IBD) segments of imputed individuals. Large 789!
symbols indicate median coordinates for each group. b, Genetic diversity in major Scandinavian VA 790!
populations. Plots next to the map show MDS analysis based on a pairwise IBS sharing matrix. Here 791!
“Norway” represents all the sites from Norway. The scale is identical for all the plots. 792!
793!
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
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Fig. 4: Spatiotemporal patterns of Viking and non-Viking ancestry in Europe during the IA, 816!
EVA and VA. UK = ‘British-like’ / ‘North Atlantic’ ancient ancestry component. Sweden = 817!
‘Swedish-like’ ancient ancestry component. Denmark = ‘Danish-like’ ancient ancestry component. 818!
Norway = ‘Norwegian-like’ ancient ancestry component. Italy = ‘Southern European-like’ ancestry 819!
component. See Table S11.2 for statistical tests. The ‘Swedish-like’ ancestry is the highest in present-820!
day Estonia due to the ancient samples from the Salme ship burial, which originated from the Mälaren 821!
Valley of Sweden, according to archaeological sources. 822!
823!
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
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28!
824!
825!
Fig. 5: Positive selection in Europe. a, Manhattan plots of the likelihood ratio scores in favor of 826!
selection looking at the entire 10,000-year period (top, “general” scan), the period up to 4,000 BP 827!
(middle, “ancient” scan) and the period from 4,000 BP up to the present (bottom, “recent” scan). The 828!
highlighted SNPs have a score larger than the 99.9% quantile of the empirical distribution of log-829!
likelihood ratios, and have at least two neighboring SNPs (+/- 500kb) with a score larger than the 830!
same quantile. b, Frequencies of the derived ‘A’ allele rs4988235 SNP responsible for lactase 831!
persistence in humans for different Viking-Age groups, present-day populations from the 1000 832!
Genomes Project as well as relevant Bronze Age population panels. The numbers at the top of the 833!
bars denote the sample size on which the allele frequency estimates are based. 834!
835!
836!
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
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29!
Extended Data Figures 837!
838!
Extended Data Fig. 1: Viking Age archaeological sites. 839!
840!
841!
842!
Examples of a few archaeological Viking Age sites and samples used in this study. a, Salme II ship 843!
burial site of Early Viking Age excavated in present-day Estonia: schematic representation of 844!
skeletons (upper left-hand corner image) and aerial images of skeletons (upper right-hand corner and 845!
lower images). b, Ridgeway Hill mass grave dated to the 10th or 11th century, located on the crest of 846!
Ridgeway Hill, near Weymouth, on the South coast of England. Around 50 predominantly young 847!
adult male individuals were excavated. c, The site of Balladoole: around AD 900, a Viking was buried 848!
in an oak ship at Balladoole, Arbory in the south east of the Isle of Man. d, Viking Age archaeological 849!
site in Varnhem, Sweden: Schematic map of the church foundation (left) and the excavated graves 850!
(red markings) at the early Christian cemetery in Varnhem; foundations of the Viking Age stone 851!
church in Varnhem (middle) and the remains of a 182 cm long male individual (no. 17) buried in a 852!
lime stone coffin close to the church foundations (right). 853!
854!
855!
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
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30!
Extended Data Fig. 2: Model-based clustering analysis 856!
857!
858!
859!
Admixture plot (K=2 to K=5) for 517 ancient individuals spanning 60 different populations. This 860!
figure is a subset of most relevant individuals and populations from Figure S7.2, see Supplementary 861!
Note 7 for details. 862!
863!
864!
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31!
Extended Data Fig. 3: Symmetry tests of genetic affinity of ancient individuals 865!
with contemporary populations. 866!
867!
868!
869!
Panels show D-statistics of the form D(YRI,Y; X,Denmark), which contrast allele sharing of an 870!
ancient individual Y with either contemporary population X or Denmark. Plot symbols show point 871!
estimates, and density plots distributions across all individuals per analysis group. 872!
873!
874!
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
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32!
Extended Data Fig. 4: Symmetry tests for genetic affinity with Baltic Bronze 875!
Age 876!
877!
878!
Panels show f4-statistics of the form f4(Mbuti,Baltic_BA;Y, Salme.SG_EVA), which contrast allele 879!
sharing of Baltic_BA with either a test individual Y or Salme.SG_EVA. a, point estimates and error 880!
bars (± 3 standard errors) for each target individual, aggregated by analysis group. Individuals with 881!
significant f4-statistics (|Z| ≥ 3) are indicated without transparency and respective sample IDs. b, as 882!
in (a), with density plot for distributions across all individuals per analysis group. 883!
884!
885!
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33!
Extended Data Fig. 5: Ancestry diversity of different population groups 886!
887!
888!
Diversity of different labels (i.e. sample locations combined with historical age) are shown as a 889!
function of their sample size. The Diversity measure is the Kullback-Leibler divergence from the 890!
label means, capturing the diversity of a group with respect to the average of that group; see text for 891!
details. Larger values are more diverse, though a dependence on sample size is expected. The 892!
simulation expectation for the best-fit to the data (0=0.2) is shown. 893!
894!
895!
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
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34!
Extended Data Fig. 6: Ancestry modelling using qpAdm 896!
897!
898!
899!
a, Ternary plots of ancestry proportions for a three-way model of Mesolithic hunter-gatherer 900!
(Loschbour.SG_M), Neolithic farmer (Barcin.SG_EN) and Bronze Age Steppe herders 901!
(Yamnaya.SG_EBA). b, Bar plots with ancestry proportions as in (a), with error bars indicating 902!
standard errors and transparency/text colors indicating p-value for model fit (no transparency/black: 903!
p ≥ 0.05; light transparency/blue: 0.05 > p ≥ 0.01; strong transparency/red: p ≤ 0.01). c, Ancestry 904!
proportions of four-way models including additional putative source groups for target groups for 905!
which three-way fit was rejected (p ≤ 0.01); transparency/text colors as in (b) 906!
907!
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35!
Extended Data Fig. 7: Polygenic risk scores 908!
909!
910! 911!
Polygenic risk scores (PRS) for 16 complex human traits in Viking Age samples from Denmark, Sweden and 912!
Norway compared against a reference sample of >20,000 Danish-ancestry individuals randomly drawn from 913!
all individuals born in Denmark in 1981-2011. The PRS is in each case based on allelic effects for >100 914!
independent genome-wide significant SNPs from recent GWAS of the respective traits. Only PRS for black 915!
hair colour is significantly different between the groups after taking account of multiple testing, although PRS 916!
for height and schizophrenia are considerably elevated as well in the Viking Age samples. 917!
918!
919!
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
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36!
Extended Data Fig. 8: Kinship analysis of ancient samples from Sandoy Church 920!
2 site in Faroe Islands. 921!
922!
923! 924!
a, Reconstruction of four most likely pedigree networks for one (Family-1) of the three families in 925!
Sandoy Church 2 site in Faroe Islands. b, Five most likely pedigree networks for the Family-2: the 926!
most “parsimonious” network (top left) is likely to represent the true family relationship between the 927!
individuals (i.e. grandparents and grandsons) based on the burial pattern of the graves as shown at 928!
the bottom image (c). Ages of the individuals are approximate to help pedigree reconstructions. Blue 929!
diamond shapes and lines in each possible pedigree reconstruction represent the same individual. 930!
931!
932!
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The copyright holder for this preprint. http://dx.doi.org/10.1101/703405doi: bioRxiv preprint first posted online Jul. 17, 2019;