The Genetic Prehistory Of The Baltic Sea Region
ARTICLEDOI: 10.1038/s41467-018-02825-9OPENThe genetic prehistory of the Baltic Sea region1234567890():,;Alissa Mittnik 1,2, Chuan-Chao Wang1,3, Saskia Pfrengle2, Mantas Daubaras4, Gunita Zariņa5,Fredrik Hallgren 6, Raili Allmäe7, Valery Khartanovich8, Vyacheslav Moiseyev8, Mari Tõrv9, Anja Furtwängler2,Aida Andrades Valtueña1, Michal Feldman1, Christos Economou10, Markku Oinonen 11, Andrejs Vasks5,Elena Balanovska12, David Reich13,14,15, Rimantas Jankauskas 16, Wolfgang Haak1,17, Stephan Schiffels 1 &Johannes Krause 1,2While the series of events that shaped the transition between foraging societies and foodproducers are well described for Central and Southern Europe, genetic evidence fromNorthern Europe surrounding the Baltic Sea is still sparse. Here, we report genome-wide DNAdata from 38 ancient North Europeans ranging from 9500 to 2200 years before present.Our analysis provides genetic evidence that hunter-gatherers settled Scandinavia via tworoutes. We reveal that the first Scandinavian farmers derive their ancestry from Anatolia1000 years earlier than previously demonstrated. The range of Mesolithic Western huntergatherers extended to the east of the Baltic Sea, where these populations persisted withoutgene-flow from Central European farmers during the Early and Middle Neolithic. The arrivalof steppe pastoralists in the Late Neolithic introduced a major shift in economy and mediatedthe spread of a new ancestry associated with the Corded Ware Complex in Northern Europe.1 Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany. 2 Institute for Archaeological Sciences,Archaeo- and Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany. 3 Department of Anthropology and Ethnology Xiamen University 361005Xiamen, China. 4 Department of Archaeology, Lithuanian Institute of History, 01108 Vilnius, Lithuania. 5 Institute of Latvian History University of Latvia Riga,LV-1050, Latvia. 6 The Cultural Heritage Foundation, 72212 Västerås, Sweden. 7 Archaeological Research Collection, Tallinn University, 10130 Tallinn, Estonia.8 Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS St. Petersburg, Russia 199034. 9 Institute of History and Archaeology,University of Tartu, 50090 Tartu, Estonia. 10 Archaeological Research Laboratory, Stockholm University, 11418 Stockholm, Sweden. 11 Finnish Museum ofNatural History - LUOMUS, University of Helsinki, 00014 Helsinki, Finland. 12 Research Centre for Medical Genetics, Moscow, 115478, Russia. 13 Departmentof Genetics, Harvard Medical School, Boston, MA 02115, USA. 14 Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. 15 Howard HughesMedical Institute, Harvard Medical School, Boston, MA 02115, USA. 16 Department of Anatomy, Histology and Anthropology, Vilnius University, 03101Vilnius, Lithuania. 17 School of Biological Sciences The University of Adelaide Adelaide, SA 5005, Australia. Correspondence and requests for materials shouldbe addressed to A.M. (email: mittnik@shh.mpg.de) or to J.K. (email: krause@shh.mpg.de)NATURE COMMUNICATIONS (2018)9:442 DOI: 10.1038/s41467-018-02825-9 www.nature.com/naturecommunications1
ARTICLENATURE COMMUNICATIONS DOI: 10.1038/s41467-018-02825-9Recent studies of ancient human genomes have revealed acomplex population history of modern Europeans involving at least three major prehistoric migrations1–6, influenced by climatic conditions, the availability of resources, thespread of technological and cultural innovations, and possiblydiseases7, 8. However, the archaeological record of the very northof the European subcontinent surrounding today’s Baltic Seashows a history distinct to that of Central and Southern Europewhich has not yet been comprehensively studied on a genomiclevel.Settlement of the Eastern Baltic and Scandinavia by mobileforagers started after the retreat of the glacial ice sheets around11,000 years before present9. To the west and south, huntergatherers sharing a common genetic signature (Western HunterGatherers or WHG; Supplementary Note 1 provides a glossary ofabbreviations and archaeological terms) already occupied wideranges of Europe for several millennia1, 2, 5, 10, 11. From further tothe east, in the territory of today’s Russia, remains of Mesolithicforagers have been studied (Eastern Hunter-Gatherers or EHG)2, 4. They derived part of their ancestry, referred to as AncientNorth Eurasian (ANE) ancestry, from a population related to theUpper Palaeolithic Mal’ta boy found in Siberia (MA1)6, 12. LateMesolithic foragers excavated in central Sweden, which have beencalled Scandinavian Hunter-Gatherers (SHG)1, 2, were modelledas admixed between WHG and EHG6. Archaeological evidencefor the settlement of Scandinavia suggests both a route throughsouthern Scandinavia and a route along the northern coast ofFennoscandia13. Foraging groups that inhabited the eastern coastand larger islands of the Baltic Sea as well as the Eastern Balticinland during the 8th and 7th millennium calibrated radiocarbonyears before Common Era (calBCE) developed a dual habitationsystem, establishing more permanent settlements than their surrounding contemporaries while remaining partially mobile14, 15.The following Early Neolithic period, starting around 6000calBCE, saw the transition from foraging to a sedentary agricultural lifestyle with the expansion of farmers out of Anatoliainto Central and Southern Europe1, 4, 6, 16, 17. This developmentreached southern Scandinavia at around 4000 calBCE withfarmers of the so-called Early Neolithic Funnel Beaker Culture(EN TRB; from German Trichterbecher) who gradually introduced cultivation of cereals and cattle rearing. At the transition tothe northern Middle Neolithic, around 3300 calBCE, an intensification of agriculture occurred in Denmark and in westerncentral Sweden accompanied by the erection of megaliths. Settlements in eastern central Sweden increasingly concentratedalong the coast, where the economy shifted towards the marineresources. Early pottery of these coastal hunter-gatherers, knownas the Pitted Ware Culture (PWC), resembles the Funnel beakersin shape. Analysis of ancient genomes from PWC and megalithicMiddle Neolithic TRB (MN TRB) context in central Sweden hasshown that the PWC individuals retain the genetic signature ofMesolithic hunter-gatherers while the TRB farmers’ ancestry canmainly be traced back to Central European farmers, albeit withsubstantial admixture from European hunter-gatherers18–20. Asthese TRB individuals date to a period one millennium after theinitial Neolithization in southern Scandinavia, the questionremains whether the first introduction of farming around 4000BCE was driven by newcomers or by local groups involving latergene-flow from Central European farmers.The production and use of pottery, in Central and SouthernEurope often seen as part of the ‘Neolithic package’, was alreadycommon among foragers in Scandinavia during the precedingMesolithic Ertebølle phase. Similarly, in the Eastern Baltic, whereforaging continued to be the main form of subsistence until atleast 4000 calBCE15, ceramics technology was adopted beforeagriculture, as seen in the Narva Culture and Combed Ceramic2NATURE COMMUNICATIONS (2018)9:442Culture (CCC). Recent genome-wide data of Baltic potteryproducing hunter-gatherers revealed genetic continuity with thepreceding Mesolithic inhabitants of the same region as well asinfluence from the more northern EHG21, 22, but did not revealconclusively whether there was a temporal, geographical or cultural correlation with the affinity to either WHG or EHG.The transition from the Late (Final) Neolithic to the EarlyBronze Age (LNBA) is seen as a major transformative period inEuropean prehistory, accompanied by changes in burial customs,technology and mode of subsistence as well as the creation of newcross-continental networks of contact seen in the emergence ofthe pan-European Corded Ware Complex (CWC, ca. 2900–2300calBCE) in Central2 and north-eastern Europe21. Studies ofancient genomes have shown that those associated with the CWCwere closely related to the pastoralists of the Yamnaya Culturefrom the Pontic-Caspian steppe, introducing a genetic component that was not present in Europe previously2, 3. This geneticcomponent is hypothesized to have spread in the subsequentmillennia throughout Europe and can be seen in today’s European populations in a decreasing north-east to south-westgradient.Intriguingly, modern Eastern Baltic populations carry thehighest proportion of WHG ancestry of all Europeans1, supporting the theory that the hunter-gatherer population of thisregion left a lasting genetic impact on subsequent populations23.Here, we investigate the modes of cultural and economictransitions experienced by the prehistoric populations surrounding the Baltic Sea. Were the changes seen in the EasternBaltic Neolithic, which did not involve the introduction of agriculture, driven by contact with neighbouring groups and if so canwe identify these? Was the earliest practice of farming in southernScandinavia a development by a local population or did it involvemigration from the South? How did the unique genetic signatureof modern Eastern Baltic populations come to be?We present novel genome-wide data from 38 ancient individuals from the Eastern Baltic, Russia and Sweden spanning 7000years of prehistory, covering the transition from a mobile huntergatherer to a sedentary agricultural lifestyle, as well as theadoption of bronze metallurgy. We show that the settlement ofScandinavia by hunter-gatherers likely took place via at least tworoutes, and that the first introduction of farming was broughtabout by the movement of the Central European farmers into theregion at around 4000 calBCE. In the Eastern Baltics, foragingremained the dominant economy among interconnected northeastern hunter-gatherer groups that did not experience admixturefrom European farmers until around 3000 calBCE, when a shifttowards agro-pastoralism came about through migrations fromthe Pontic-Caspian steppe.ResultsSamples and archaeological background. The skeletal remainsstudied here were recovered from 25 archaeological sites in theterritory of modern Lithuania, Latvia, Estonia, ArchangelskOblast and Karelia (north-western Russia) and Sweden datingfrom around 7500 to 200 calBCE (Fig. 1, Supplementary Note 2,Supplementary Data 1). In total, we analyzed DNA from 106human remains. A total of 41 samples with good DNA preservation were selected for deeper shotgun sequencing or SNPcapture (Supplementary Data 1). In the latter case, we enrichedsamples for a panel of around 1.24 million single nucleotidepolymorphisms (SNPs) via in-solution capture4, 24. After qualitycontrol, genome-wide data from 38 individuals, with an averagecoverage of 0.02–8.8-fold on targeted SNPs, were included infurther analysis. DOI: 10.1038/s41467-018-02825-9 www.nature.com/naturecommunications
ARTICLENATURE COMMUNICATIONS DOI: 10.1038/s41467-018-02825-9Yuzhnyy Oleni nisPlinkaigalisTurlojiskeEHGBaltic MesolithicSHGBaltic EMN NarvaEarly Neolithic TRBBaltic MN CCCBaltic LNScandinavia LNBABaltic Bronze Age80007000600050004000300020001000BCEFig. 1 Sampling locations and dating of 38 ancient Northern European samples introduced in this study. Chronology based on calibrated radiocarbon datesor relative dating, see Supplementary Note 2. Map generated with QGIS 2.18.2 (http://www.qgis.org/) using the Natural Earth data set (http://www.naturalearthdata.com) for the basemapThe 38 final samples fall into nine broad groups (Table 1): first,two Mesolithic hunter-gatherers from north-western Russia (ca.7500–5000 calBCE); secondly, an individual (5720–5560 calBCE)from the lake burial site of Motala, Sweden, adding to thepreviously published six SHG individuals from this site4; twoMesolithic hunter-gatherers from Lithuania (ca. 6440–5740calBCE) associated with the Kunda Culture (referred to as BalticMesolithic), whose archaeological assemblages found in Lithuania, Latvia, Estonia and adjacent parts of Russia.Twelve individuals were associated with pottery-producingforager cultures. Ten of them from Lithuania and Estonia (ca.5460–3820 calBCE) were assigned to the Narva Culture thatoccupied the Eastern Baltic region from the Late Mesolithic to theMiddle Neolithic (Baltic EMN Narva) and two individuals fromEstonia were associated with the CCC that was spread across thenorthern part of the Eastern Baltic by the Middle Neolithic (BalticMN CCC; dated to ca. 3800–3360 calBCE).Five individuals from Lithuania and Estonia were dated to theLate Neolithic (Baltic LN; ca. 3260–1750 calBCE). For theindividual Gyvakarai1, we present genome-wide data at 7.6-foldaverage coverage from shotgun sequencing.Fourteen samples from Latvia and Lithuania were attributed tothe Baltic Bronze Age (Baltic BA) and date to ca. 1230–230calBCE.We supplemented our dataset of ancient Eastern Baltic sampleswith recently published data from 13 individuals spanning theMesolithic to Late Neolithic in Latvia21 and Estonia22, andmerged data from identical individuals where they overlappedNATURE COMMUNICATIONS (2018)9:442with the latter. We present the first data from the southernmostregion of the Eastern Baltic (the territory of modern-dayLithuania), the Early Neolithic of Estonia and the Eastern BalticBronze Age.From southern Sweden, we analyzed one farmer (3950–3650calBCE) from the EN TRB, the earliest agricultural population inScandinavia for which there exists no genetic data to date. Onesample from northern Sweden (Scandinavia LNBA Olsund, ca.2570–2140 calBCE) dates to the Late Neolithic but was foundwithout associated archaeological assemblages. The data wereanalyzed in context with published data from the ScandinavianMiddle Neolithic to Bronze Age3, 19 as well as other ancient andmodern genome-wide datasets described below.Affinities of northern Mesolithic hunter-gatherers. To gain anoverview of the broad genetic affinities of our samples, we projected all 38 ancient genome-wide datasets, as well as previouslypublished ancient samples4, 6, 19, 21, 22, using a principal component analysis (PCA), constructed from 1007 modern individuals from a diverse set of West Eurasian contemporarypopulations, and used the same individuals to investigate modelbased clustering using ADMIXTURE. We see that the Mesolithicforagers of Northern Europe fall into three distinct clusters,associated with EHG, SHG and WHG, respectively, as evidencedby their position on the PCA (Fig. 2a), similar composition ofancestral genetic clusters in ADMIXTURE analysis (Fig. 2b,Supplementary Fig. 4) and in sharing most genetic drift since DOI: 10.1038/s41467-018-02825-9 www.nature.com/naturecommunications3
ARTICLENATURE COMMUNICATIONS DOI: 10.1038/s41467-018-02825-9Table 1 Information on ancient samples for which we report the nuclear data in this studySample nameUzOO7795.4% CI calibrated radiocarbon age (calBCE)/contextual dating (BCE)5500–5000 BCEPopulationlabelEHGPopovo27500–5000 BCEEHGMotalaAA5722–5564 calBCESHGDonkalnis46000–5740 calBCESpiginas46440–6230 calBCEDonkalnis15500/5300–3100/2900 BCEDonkalnis75460–4940 calBCEVeibri44900–4720 calBCEKivisaare34730–4540 calBCESpiginas14440–4240 calBCEDonkalnis64720–4530 calBCEKretuonas14460–3820 calBCEKretuonas54450–4340 calBCEKretuonas45500/5300–3100/2900 BCEKretuonas25500/5300–3100/2900 BCETamula13630–3360 calBCETamula33800–3640 calBCEBalticMesolithicBalticMesolithicBaltic EMNNarvaBaltic EMNNarvaBaltic EMNNarvaBaltic EMNNarvaBaltic EMNNarvaBaltic EMNNarvaBaltic EMNNarvaBaltic EMNNarvaBaltic EMNNarvaBaltic EMNNarvaBaltic MNCCCBaltic MNCCCEN TRBSaxtorp51643945–3647 linkaigalis241Olsund2580–2340 calBCE2620–2470 calBCE2130–1750 calBCE3260–2630 calBCE2860–2410 calBCE2573–2140 s209Kivutkalns215Kivutkalns222930–810 calBCE1010–800 calBCE2100/2000–600 BCE1230–920 calBCE800–545 calBCE730–390 calBCE730–400 calBCE800–545 calBCE810–560 calBCE800–545 calBCE730–390 calBCE405–230 calBCE790–535 calBCE805–515 calBCEBaltic LNBaltic LNBaltic LNBaltic LNBaltic LNScandinaviaLNBABaltic BABaltic BABaltic BABaltic BABaltic BABaltic BABaltic BABaltic BABaltic BABaltic BABaltic BABaltic BABaltic BABaltic BASite locationYuzhnyy Oleni Ostrov,Karelia, RussiaPopovo, Archangelsk,RussiaKanaljorden, Motala,SwedenDonkalnis, LithuaniaGeneticsexFSNPs overlapping1240k set530434Average coverage on1240k 064U4dF565080.055U5a2dM220050.021U5b2c1Spiginas, LithuaniaF6638851.122U4a2Donkalnis, LithuaniaF472280.045U5b1Donkalnis, LithuaniaM4587380.758U5a2d1Veibri, EstoniaF5427331.047U5b1Kivisaare, EstoniaM1765330.186U4a1n/aSpiginas, LithuaniaM9625846.106H11aI2a1a2a1aDonkalnis, LithuaniaF9339976.030U5a2eKretuonas 1B, LithuaniaF2976960.367U5b1Kretuonas 1B, LithuaniaM1925230.204U5b2bKretuonas 1B, LithuaniaF9933198.792U5b1b1aKretuonas 1B, LithuaniaM6342691.282U5b2bTamula, EstoniaF1602700.168U5a1d2bTamula, EstoniaM1532190.160U4d2Kvärlöv, Saxtorp, Skåne,SwedenKunila, EstoniaGyvakarai, LithuaniaSpiginas, LithuaniaPlinkaigalis, LithuaniaPlinkaigalis, LithuaniaÖlsund, Hälsingland,SwedenTurlojiškė, LithuaniaTurlojiškė, LithuaniaTurlojiškė, LithuaniaTurlojiškė, LithuaniaKivutkalns, LatviaKivutkalns, LatviaKivutkalns, LatviaKivutkalns, LatviaKivutkalns, LatviaKivutkalns, LatviaKivutkalns, LatviaKivutkalns, LatviaKivutkalns, LatviaKivutkalns, oups are based on the most downstream defining mutation covered and might not reflect the true haplogroup, see Supplementary Note 3**Data merged with published data from this individual [22]divergence from Africa as shown by outgroup f3-statistics (Supplementary Fig. 1). Based on these results, our Mesolithic Russianforagers fall within the EHG cluster formed by previously published samples4 and are grouped as EHG in subsequent analyses.ADMIXTURE shows that EHG carry a genetic component(green component in Fig. 2b) that is maximized in huntergatherers from the Caucasus (CHG) and shared with Neolithicfarmers from Iran and Steppe populations from the Bronze Age,suggesting some common ancestry for these populations,consistent with previous results21.Despite their geographical vicinity to EHG, the two EasternBaltic individuals associated with the Mesolithic Kunda Cultureshow a very close affinity to WHG in all our analyses (Fig. 2,Supplementary Figs. 1 and 2), with a significant contributionfrom ANE, as revealed by negative admixture f3 results involvinga Palaeolithic hunter-gatherer from Switzerland, most closelyrelated to WHG, and populations containing ANE ancestry(Supplementary Table 1). This is additionally confirmed by Dstatistics of the form D(Baltic Mesolithic, WHG; X, Mbuti) forpopulations X with ANE ancestry, which are significant andamong the highest in EHG (Z 6.2; Supplementary Table 2).Using the qpWave/qpAdm framework, we modelled the Baltic4NATURE COMMUNICATIONS (2018)9:442Mesolithic hunter-gatherers as a two-way mixture between EHGand WHG (Fig. 3), which reveals a difference in mixtureproportions between the more northern individuals from theLatvian site21 (65–76% WHG with 24–35% EHG; SupplementaryTable 3) and the samples from the Lithuanian sites to the south(88–100% WHG with 0–12% EHG; Supplementary Table
the east, in the territory of today’s Russia, remains of Mesolithic foragers have been studied (Eastern Hunter-Gatherers or EHG) 2, 4. They derived part of their ancestry, referred to as Ancient North Eurasian (ANE) ancestry, from a population related to the Upper Palaeolithic Mal’ta boy found in Siberia (MA1)6, 12. Late
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