Western Eurasia witnessed several large-scale human migrations during the Holocene1-5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.

A Kh Khalikov Institute of Archeology of the Academy of Sciences of the Republic of Tatarstan Kazan Russia

A Kh Margulan Institute of Archaeology Almaty Kazakhstan

Aix Marseille Université CNRS Min Culture UMR 7269 LAMPEA Maison Méditerranéenne des Sciences de l'Homme Aix en Provence France

Anthropology Department University of Utah Salt Lake City UT USA

Archaeology Institute University of Highlands and Islands Orkney UK

ArchaeoScience Globe Institute University of Copenhagen Copenhagen Denmark

ARGEA Consultores SL Madrid Spain

Cabinet of Anthropology Tomsk State University Tomsk Russian Federation

Center for Computational Biology University of California Berkeley CA USA

Center for Egyptological Studies Russian Academy of Sciences Moscow Russian Federation

Centre d'Anthropobiologie et de Génomique de Toulouse CNRS UMR 5500 Université Paul Sabatier Toulouse France

Centre de Recherche en Archéologie Archeosciences Histoire UMR 6869 CNRS Rennes France

Centre for Archaeological Research Toraighyrov University Pavlodar Kazakhstan

Centre for Evolutionary Hologenomics University of Copenhagen Copenhagen Denmark

Centre for the Study of Early Agricultural Societies Department of Cross Cultural and Regional Studies University of Copenhagen Copenhagen Denmark

CIAS Department of Life Sciences University of Coimbra Coimbra Portugal

Collège de France Paris France

Departament de Prehistòria Arqueologia i Història Antiga Universitat de València València Spain

Departamento de Prehistoria y Arqueología Universidad Autónoma de Madrid Madrid Spain

Department of Anthropology Czech National Museum Prague Czech Republic

Department of Anthropology Faculty of Biology Lomonosov Moscow State University Moscow Russian Federation

Department of Anthropology New York University New York NY USA

Department of Archaeology and Ancient History Lund University Lund Sweden

Department of Archaeology and Heritage Studies Aarhus University Aarhus Denmark

Department of Archaeology University of Cambridge Cambridge UK

Department of Archaeology University of Exeter Exeter UK

Department of Biology University of Rome Tor Vergata Rome Italy

Department of Clinical Medicine University of Copenhagen Copenhagen Denmark

Department of Computational Biology University of Lausanne Lausanne Switzerland

Department of Environmental Biology Sapienza University of Rome Rome Italy

Department of Genetics University of Cambridge Cambridge UK

Department of Geological Sciences University of Cape Town Cape Town South Africa

Department of Geology Lund University Lund Sweden

Department of Health and Nature University of Greenland Nuuk Greenland

Department of Health Technology Section of Bioinformatics Technical University of Denmark Kongens Lyngby Denmark

Department of Historical Studies University of Gothenburg Gothenburg Sweden

Department of History and Cultural Heritage University of Siena Siena Italy

Department of History Humanities and Society University of Rome Tor Vergata Rome Italy

Department of History of the Institute of Humanities Ural Federal University Ekaterinburg Russian Federation

Department of History University of Santiago de Compostela Santiago de Compostela Spain

Department of Integrative Biology University of California Berkeley CA USA

Faculty of Archaeology Adam Mickiewicz University in Poznań Poznań Poland

GeoGenetics Group Department of Zoology University of Cambridge Cambridge UK

Georgian National Museum Tbilisi Georgia

Grupo EvoAdapta Departamento de Ciencias Históricas Universidad de Cantabria Santander Spain

HistorieUdvikler Kalundborg Denmark

ICREA University of Barcelona Barcelona Spain

Institute for History of Medicine 1st Faculty of Medicine Charles University Prague Czech Republic

Institute of Archaeology and Ethnography National Academy of Sciences Yerevan Armenia

Institute of Archaeology and Ethnology Polish Academy of Sciences Kraków Poland

Institute of Archaeology Jagiellonian University Kraków Poland

Institute of Archaeology National Academy of Sciences of Ukraine Kyiv Ukraine

Institute of Archeology and Ethnography Siberian Branch of the Russian Academy of Sciences Novosibirsk Russian Federation

Institute of Biological Psychiatry Mental Health Services Copenhagen University Hospital Roskilde Denmark

Institute of Ethnology and Anthropology Russian Academy of Sciences Moscow Russian Federation

Institute of Evolutionary Biology CSIC Universitat Pompeu Fabra Barcelona Spain

Institute of Humanities Ivanovo State University Ivanovo Russian Federation

Institute of Molecular Biology National Academy of Sciences Yerevan Armenia

Institute of Statistical Sciences School of Mathematics University of Bristol Bristol UK

Instituto Internacional de Investigaciones Prehistóricas de Cantabria Universidad de Cantabria Banco Santander Gobierno de Cantabria Santander Spain

IPND Tyumen Scientific Centre Siberian Branch of the Russian Academy of Sciences Tyumen Russian Federation

Janus Pannonius Museum Pécs Hungary

Kostanay Regional University A Baitursynov Kostanay Kazakhstan

Laboratory for Archaeological Chemistry Department of Anthropology University of Wisconsin Madison Madison WI USA

Laboratory for Experimental Traceology Institute for the History of Material Culture of the Russian Academy of Sciences Saint Petersburg Russian Federation

Laboratory of Biological Anthropology Department of Forensic Medicine University of Copenhagen Copenhagen Denmark

Langelands Museum Rudkøbing Denmark

Lipetsk Regional Scientific Public Organisation Archaeological Research Lipetsk Russian Federation

Lundbeck Foundation GeoGenetics Centre Globe Institute University of Copenhagen Copenhagen Denmark

Malmö Museer Malmö Sweden

Margulan Institute of Archaeology Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan Almaty Kazakhstan

MARUM Center for Marine Environmental Sciences and Faculty of Geosciences University of Bremen Bremen Germany

Moesgaard Museum Højbjerg Denmark

Muséum National d'Histoire Naturelle CNRS Université de Paris Musée de l'Homme Paris France

Museum Nordsjælland Hillerød Denmark

Museum of Cultural History University of Oslo Oslo Norway

Museum Østjylland Randers Denmark

Museum Sydøstdanmark Vordingborg Denmark

Museum Vestsjælland Holbæk Denmark

National University of Kyiv Mohyla Academy Kyiv Ukraine

Natural Sciences Museum of Barcelona Barcelona Spain

Neurogenomics Division The Translational Genomics Research Institute Phoenix AZ USA

Nizhny Tagil State Socio Pedagogical Institute Nizhny Tagil Russia

Novo Nordisk Foundation Centre for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark

Paleoecology Laboratory Institute of Plant and Animal Ecology Ural Branch of the Russian Academy of Sciences Ekaterinburg Russian Federation

Peter the Great Museum of Anthropology and Ethnography Russian Academy of Sciences Saint Petersburg Russian Federation

Research Department of Genetics Evolution and Environment University College London London UK

Russian Armenian University Yerevan Armenia

Saryarka Archaeological Institute Buketov Karaganda University Karaganda Kazakhstan

Scientific Research Center Baikal region Irkutsk State University Irkutsk Russian Federation

Sealand Archaeology Kalundborg Denmark

Section for Evolutionary Genomics Globe Institute University of Copenhagen Copenhagen Denmark

Soprintendenza Archeologia Belle Arti e Paesaggio per la Città Metropolitana di Bari Bari Italy

Soprintendenza Archeologia Belle Arti e Paesaggio per la provincia di Cosenza Cosenza Italy

Soprintendenza per i Beni Archeologici delle Marche Ancona Italy

South Ural State University Chelyabinsk Russia

Svendborg Museum Svendborg Denmark

Swiss Institute of Bioinformatics University of Lausanne Lausanne Switzerland

Tårnby Gymnasium og HF Kastrup Denmark

Tbilisi State University Tbilisi Georgia

Terra Ltd Voronezh Russian Federation

The National Museum of Denmark Copenhagen Denmark

The Saxo Institute University of Copenhagen Copenhagen Denmark

The Viking Ship Museum Roskilde Denmark

Trace and Environmental DNA Laboratory School of Molecular and Life Sciences Curtin University Perth Western Australia Australia

UMR 5199 PACEA CNRS Université de Bordeaux Pessac France

UNIARQ University of Lisbon Lisbon Portugal

Västergötlands Museum Skara Sweden

Vendsyssel Historiske Museum Hjørring Denmark

Vesthimmerlands Museum Aars Denmark

Wellcome Sanger Institute Hinxton UK

Zoological Institute of Russian Academy of Sciences Saint Petersburg Russian Federation

Erratum v

Nature. 2024 Feb;626(7997):E3. doi: 10.1038/s41586-024-07044-5. PubMed

Zobrazit více v PubMed

Allentoft ME, et al. Population genomics of Bronze Age Eurasia. Nature. 2015;522:167–172. doi: 10.1038/nature14507. PubMed DOI

Haak W, et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature. 2015;522:207–211. doi: 10.1038/nature14317. PubMed DOI PMC

Lazaridis I, et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature. 2014;513:409–413. doi: 10.1038/nature13673. PubMed DOI PMC

Lazaridis I, et al. Genomic insights into the origin of farming in the ancient Near East. Nature. 2016;536:419–24. doi: 10.1038/nature19310. PubMed DOI PMC

Mathieson I, et al. The genomic history of southeastern Europe. Nature. 2018;555:197–203. doi: 10.1038/nature25778. PubMed DOI PMC

Posth C, et al. Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a late glacial population turnover in Europe. Curr. Biol. 2016;26:827–833. doi: 10.1016/j.cub.2016.01.037. PubMed DOI

Posth C, et al. Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers. Nature. 2023;615:117–126. doi: 10.1038/s41586-023-05726-0. PubMed DOI PMC

Mathieson I, et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature. 2015;528:499–503. doi: 10.1038/nature16152. PubMed DOI PMC

Fu Q, et al. The genetic history of Ice Age Europe. Nature. 2016;534:200–205. doi: 10.1038/nature17993. PubMed DOI PMC

Raghavan M, et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature. 2014;505:87–91. doi: 10.1038/nature12736. PubMed DOI PMC

Villalba-Mouco V, et al. Survival of Late Pleistocene hunter-gatherer ancestry in the Iberian Peninsula. Curr. Biol. 2019;29:1169–1177. doi: 10.1016/j.cub.2019.02.006. PubMed DOI

Brace S, et al. Ancient genomes indicate population replacement in Early Neolithic Britain. Nat. Ecol. Evol. 2019;3:765–771. doi: 10.1038/s41559-019-0871-9. PubMed DOI PMC

de Barros Damgaard P, et al. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science. 2018;360:eaar7711. doi: 10.1126/science.aar7711. PubMed DOI PMC

Saag L, et al. Genetic ancestry changes in Stone to Bronze Age transition in the East European plain. Sci. Adv. 2021;7:eabd6535. doi: 10.1126/sciadv.abd6535. PubMed DOI PMC

Günther T, et al. Population genomics of Mesolithic Scandinavia: investigating early postglacial migration routes and high-latitude adaptation. PLoS Biol. 2018;16:e2003703. doi: 10.1371/journal.pbio.2003703. PubMed DOI PMC

Kashuba N, et al. Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter–gatherers in Scandinavia. Commun. Biol. 2019;2:185. doi: 10.1038/s42003-019-0399-1. PubMed DOI PMC

Zvelebil, M., Domanska, L. & Dennell, R. Harvesting the Sea, Farming the Forest: The Emergence of Neolithic Societies in the Baltic Region (Bloomsbury, 1998).

Jones ER, et al. The Neolithic transition in the Baltic was not driven by admixture with early European farmers. Curr. Biol. 2017;27:576–582. doi: 10.1016/j.cub.2016.12.060. PubMed DOI PMC

Mittnik A, et al. The genetic prehistory of the Baltic Sea region. Nat. Commun. 2018;9:442. doi: 10.1038/s41467-018-02825-9. PubMed DOI PMC

Kislenko, A. & Tatarintseva, N. in Late Prehistoric Exploitation of the Eurasian Steppe (eds Levine, M. et al.) 183–216 (McDonald Institute for Archaeological Research, 1999).

Furholt M. Mobility and social change: understanding the European Neolithic period after the archaeogenetic revolution. J. Archaeol. Res. 2021;29:481–535. doi: 10.1007/s10814-020-09153-x. DOI

Lipson M, et al. Ancient genomes document multiple waves of migration in Southeast Asian prehistory. Science. 2018;361:92–95. doi: 10.1126/science.aat3188. PubMed DOI PMC

Fernandes DM, et al. A genomic Neolithic time transect of hunter-farmer admixture in central Poland. Sci. Rep. 2018;8:14879. doi: 10.1038/s41598-018-33067-w. PubMed DOI PMC

Immel, A. et al. Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry. Commun. Biol.4, 113 (2021). PubMed PMC

Jeong C, et al. The genetic history of admixture across inner Eurasia. Nat. Ecol. Evol. 2019;3:966–976. doi: 10.1038/s41559-019-0878-2. PubMed DOI PMC

Nikitin AG, et al. Interactions between earliest Linearbandkeramik farmers and central European hunter gatherers at the dawn of European Neolithization. Sci. Rep. 2019;9:19544. doi: 10.1038/s41598-019-56029-2. PubMed DOI PMC

Gelabert, P. et al. Social and genetic diversity among the first farmers of Central Europe. Preprint at bioRxiv10.1101/2023.07.07.548126 (2023).

Cassidy LM, et al. Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome. Proc. Natl Acad. Sci. USA. 2016;113:368–373. doi: 10.1073/pnas.1518445113. PubMed DOI PMC

Penske, S. et al. Early contact between late farming and pastoralist societies in southeastern Europe. Nature620, 358–365 (2023). PubMed PMC

Lazaridis I, et al. The genetic history of the Southern Arc: a bridge between West Asia and Europe. Science. 2022;377:eabm4247. doi: 10.1126/science.abm4247. PubMed DOI PMC

Egfjord AF-H, et al. Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark. PLoS One. 2021;16:e0244872. doi: 10.1371/journal.pone.0244872. PubMed DOI PMC

Papac L, et al. Dynamic changes in genomic and social structures in third millennium BCE central Europe. Sci. Adv. 2021;7:eabi6941. doi: 10.1126/sciadv.abi6941. PubMed DOI PMC

Heyd, V. in Rethinking Migrations in Late Prehistoric Eurasia (eds Fernández-Götz, M. et al.) 41–62 (Oxford Univ. Press, 2023).

Allentoft, M. E. et al. 100 ancient genomes show repeated population turnovers in Neolithic Denmark. Nature10.1038/s41586-023-06862-3 (2024). PubMed PMC

Rubinacci S, Ribeiro DM, Hofmeister RJ, Delaneau O. Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat. Genet. 2021;53:412. doi: 10.1038/s41588-021-00788-0. PubMed DOI

The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. 2015;526:68–74. doi: 10.1038/nature15393. PubMed DOI PMC

Leslie S, et al. The fine-scale genetic structure of the British population. Nature. 2015;519:309–314. doi: 10.1038/nature14230. PubMed DOI PMC

Hofmanová Z, et al. Early farmers from across Europe directly descended from Neolithic Aegeans. Proc. Natl Acad. Sci. USA. 2016;113:6886–6891. doi: 10.1073/pnas.1523951113. PubMed DOI PMC

Busby GB, et al. Admixture into and within sub-Saharan Africa. eLife. 2016;5:e15266. doi: 10.7554/eLife.15266. PubMed DOI PMC

Schmitt T. Molecular biogeography of Europe: Pleistocene cycles and postglacial trends. Front. Zool. 2007;4:11. doi: 10.1186/1742-9994-4-11. PubMed DOI PMC

Olalde I, et al. The genomic history of the Iberian Peninsula over the past 8000 years. Science. 2019;363:1230–1234. doi: 10.1126/science.aav4040. PubMed DOI PMC

García-Escárzaga A, et al. Human forager response to abrupt climate change at 8.2 ka on the Atlantic coast of Europe. Sci. Rep. 2022;12:6481. doi: 10.1038/s41598-022-10135-w. PubMed DOI PMC

Narasimhan VM, et al. The formation of human populations in South and Central Asia. Science. 2019;365:eaat7487. doi: 10.1126/science.aat7487. PubMed DOI PMC

Wang C-C, et al. Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions. Nat. Commun. 2019;10:590. doi: 10.1038/s41467-018-08220-8. PubMed DOI PMC

Lipson M, et al. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature. 2017;551:368. doi: 10.1038/nature24476. PubMed DOI PMC

Racimo F, et al. The spatiotemporal spread of human migrations during the European Holocene. Proc. Natl Acad. Sci. USA. 2020;117:8989–9000. doi: 10.1073/pnas.1920051117. PubMed DOI PMC

Martiniano R, et al. The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods. PLoS Genet. 2017;13:e1006852. doi: 10.1371/journal.pgen.1006852. PubMed DOI PMC

Isern N, Zilhão J, Fort J, Ammerman AJ. Modeling the role of voyaging in the coastal spread of the Early Neolithic in the West Mediterranean. Proc. Natl Acad. Sci. USA. 2017;114:897–902. doi: 10.1073/pnas.1613413114. PubMed DOI PMC

Betti L, et al. Climate shaped how Neolithic farmers and European hunter-gatherers interacted after a major slowdown from 6,100 BCE to 4,500 BCE. Nat. Hum. Behav. 2020;4:1004–1010. doi: 10.1038/s41562-020-0897-7. PubMed DOI

Saag L, et al. Extensive farming in Estonia started through a sex-biased migration from the Steppe. Curr. Biol. 2017;27:2185–2193. doi: 10.1016/j.cub.2017.06.022. PubMed DOI

Seguin-Orlando A, et al. Heterogeneous hunter-gatherer and Steppe-related ancestries in Late Neolithic and Bell Beaker genomes from present-day France. Curr. Biol. 2021;31:1072–1083. doi: 10.1016/j.cub.2020.12.015. PubMed DOI

Furholt M. Die Złota-Gruppe in Kleinpolen: Ein Beispiel für die Transformation eines Zeichensystems? Germania. 2008;86:1–28.

Szmyt, M. in A Turning of Ages (ed. Kadrow, S.) 443–466 (Institute of Archaeology and Ethnology, Polish Academy of Sciences, 2000).

Tassi F, et al. Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages. Proc. R. Soc. B. 2017;284:20171540. doi: 10.1098/rspb.2017.1540. PubMed DOI PMC

Nordqvist K, Heyd V. The forgotten child of the wider Corded Ware family: Russian Fatyanovo Culture in context. Proc. Prehist. Soc. 2020;86:65–93. doi: 10.1017/ppr.2020.9. DOI

Kristiansen K, et al. Re-theorising mobility and the formation of culture and language among the Corded Ware Culture in Europe. Antiquity. 2017;91:334–347. doi: 10.15184/aqy.2017.17. DOI

Borzunov, V. A. The neolithic fortified settlements of the Western Siberia and Trans-Urals. Russ. Archaeol.4, 20–34 (2013).

Yu H, et al. Paleolithic to Bronze Age Siberians reveal connections with First Americans and across Eurasia. Cell. 2020;181:1232–1245. doi: 10.1016/j.cell.2020.04.037. PubMed DOI

Okladnikov, A. P. Neolit i Bronzovyi vek Pribaikaliya [Neolithic and Bronze Age of the Baikal region] (AS USSR Publications, 1950).

Merts, V. in Paleodemography and Migration Processes in Western Siberia in Antiquity and the Middle Ages (ed. Kiryushin, Y. F.) 39–42 (Altai State University, 1994).

Merts, V. Periodization of the Holocene Complexes of Northern and Central Kazakhstan Based on the Materials of the Multilayer Site Shiderty 3 (Thesis, Kemerovo State Univ., 2008).

Merts VK. Neolithization processes in the Northeast Kazakhstan. Herald Omsk Univ. Ser. Histor. Stud. 2018;3:99–109.

de Barros Damgaard P, et al. 137 ancient human genomes from across the Eurasian steppes. Nature. 2018;557:369–374. doi: 10.1038/s41586-018-0094-2. PubMed DOI

Librado P, et al. The origins and spread of domestic horses from the Western Eurasian steppes. Nature. 2021;598:634–640. doi: 10.1038/s41586-021-04018-9. PubMed DOI PMC

Huang, Y. et al. The early adoption of East Asian crops in West Asia: rice and broomcorn millet in northern Iran. Antiquity97, 674–689 (2023).

Palamara PF, Lencz T, Darvasi A, Pe’er I. Length distributions of identity by descent reveal fine-scale demographic history. Am. J. Hum. Genet. 2012;91:809–822. doi: 10.1016/j.ajhg.2012.08.030. PubMed DOI PMC

Ringbauer H, Novembre J, Steinrücken M. Parental relatedness through time revealed by runs of homozygosity in ancient DNA. Nat. Commun. 2021;12:5425. doi: 10.1038/s41467-021-25289-w. PubMed DOI PMC

Krzewińska M, et al. Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads. Sci. Adv. 2018;4:eaat4457. doi: 10.1126/sciadv.aat4457. PubMed DOI PMC

Matuzeviciute GM. The possible geographic margin effect on the delay of agriculture introduction in the East Baltic. Eston. J. Archaeol. 2018;22:149–162. doi: 10.3176/arch.2018.2.03. DOI

Piezonka, H. Jäger, Fischer, Töpfer: Wildbeutergruppen mit Früher Keramik in Nordosteuropa im 6. und 5. Jahrtausend v. Chr. (Habelt, 2015).

Oras E, et al. The adoption of pottery by north-east European hunter-gatherers: Evidence from lipid residue analysis. J. Archaeol. Sci. 2017;78:112–119. doi: 10.1016/j.jas.2016.11.010. DOI

Matuzeviciute GM, et al. Archaeobotanical investigations at the earliest horse herder site of Botai in Kazakhstan. Archaeol. Anthropol. Sci. 2019;11:6243–6258. doi: 10.1007/s12520-019-00924-2. DOI

Anthony, D. W. in The Black Sea Flood Question: Changes in Coastline, Climate and Human Settlement (eds Yanko-Hombach, V. et al.) 345–370 (Springer, 2007).

Trautmann M, et al. First bioanthropological evidence for Yamnaya horsemanship. Sci. Adv. 2023;9:eade2451. doi: 10.1126/sciadv.ade2451. PubMed DOI PMC

Anthony DW, et al. The Eneolithic cemetery at Khvalynsk on the Volga River. Praehistor. Zeitschr. 2022;97:22–67. doi: 10.1515/pz-2022-2034. DOI

Kristiansen, K., Kroonen, G. & Willerslev, E. The Indo-European Puzzle Revisited: Integrating Archaeology, Genetics, and Linguistics (Cambridge Univ. Press, 2023).

Damgaard PB, et al. Improving access to endogenous DNA in ancient bones and teeth. Sci. Rep. 2015;5:11184. doi: 10.1038/srep11184. PubMed DOI PMC

Li H, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–2079. doi: 10.1093/bioinformatics/btp352. PubMed DOI PMC

Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–842. doi: 10.1093/bioinformatics/btq033. PubMed DOI PMC

Jónsson H, Ginolhac A, Schubert M, Johnson PLF, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics. 2013;29:1682–1684. doi: 10.1093/bioinformatics/btt193. PubMed DOI PMC

Renaud G, Slon V, Duggan AT, Kelso J. Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biol. 2015;16:224. doi: 10.1186/s13059-015-0776-0. PubMed DOI PMC

Fu Q, et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature. 2014;514:445–449. doi: 10.1038/nature13810. PubMed DOI PMC

Sousa da Mota B, et al. Imputation of ancient human genomes. Nat. Commun. 2023;14:3660. doi: 10.1038/s41467-023-39202-0. PubMed DOI PMC

Skoglund P, Storå J, Götherström A, Jakobsson M. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J. Archaeol. Sci. 2013;40:4477–4482. doi: 10.1016/j.jas.2013.07.004. DOI

Barbera P, et al. EPA-ng: massively parallel evolutionary placement of genetic sequences. Syst. Biol. 2019;68:365–369. doi: 10.1093/sysbio/syy054. PubMed DOI PMC

Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics. 2019;35:4453–4455. doi: 10.1093/bioinformatics/btz305. PubMed DOI PMC

Czech L, Barbera P, Stamatakis A. Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data. Bioinformatics. 2020;36:3263–3265. doi: 10.1093/bioinformatics/btaa070. PubMed DOI PMC

Waples RK, Albrechtsen A, Moltke I. Allele frequency-free inference of close familial relationships from genotypes or low-depth sequencing data. Mol. Ecol. 2019;28:35–48. doi: 10.1111/mec.14954. PubMed DOI PMC

Manichaikul A, et al. Robust relationship inference in genome-wide association studies. Bioinformatics. 2010;26:2867–2873. doi: 10.1093/bioinformatics/btq559. PubMed DOI PMC

Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J. SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One. 2012;7:e37558. doi: 10.1371/journal.pone.0037558. PubMed DOI PMC

Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics. 2014;15:356. doi: 10.1186/s12859-014-0356-4. PubMed DOI PMC

Patterson N, et al. Ancient admixture in human history. Genetics. 2012;192:1065–1093. doi: 10.1534/genetics.112.145037. PubMed DOI PMC

Pickrell JK, et al. The genetic prehistory of southern Africa. Nat. Commun. 2012;3:1143. doi: 10.1038/ncomms2140. PubMed DOI PMC

Shringarpure SS, Bustamante CD, Lange K, Alexander DH. Efficient analysis of large datasets and sex bias with ADMIXTURE. BMC Bioinformatics. 2016;17:218. doi: 10.1186/s12859-016-1082-x. PubMed DOI PMC

Yang, J., Lee, S. H., Goddard, M. E. & Visscher, P. M. GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet.88, 76-82 (2011). PubMed PMC

Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet. 2006;2:e190. doi: 10.1371/journal.pgen.0020190. PubMed DOI PMC

Price AL, et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 2006;38:904–909. doi: 10.1038/ng1847. PubMed DOI

Chang CC, et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015;4:7. doi: 10.1186/s13742-015-0047-8. PubMed DOI PMC

Maier, R. et al. On the limits of fitting complex models of population history to f-statistics. eLife12, e85492 (2023). PubMed PMC

Browning BL, Browning SR. Detecting identity by descent and estimating genotype error rates in sequence data. Am. J. Hum. Genet. 2013;93:840–851. doi: 10.1016/j.ajhg.2013.09.014. PubMed DOI PMC

Browning SR, Browning BL. Accurate non-parametric estimation of recent effective population size from segments of identity by descent. Am. J. Hum. Genet. 2015;97:404–418. doi: 10.1016/j.ajhg.2015.07.012. PubMed DOI PMC

Lawrence M, et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 2013;9:e1003118. doi: 10.1371/journal.pcbi.1003118. PubMed DOI PMC

Greenbaum G, Rubin A, Templeton AR, Rosenberg NA. Network-based hierarchical population structure analysis for large genomic data sets. Genome Res. 2019;29:2020–2033. doi: 10.1101/gr.250092.119. PubMed DOI PMC

Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal. 2006;1695(5):1–9.

Traag VA, Waltman L, van Eck NJ. From Louvain to Leiden: guaranteeing well-connected communities. Sci. Rep. 2019;9:5233. doi: 10.1038/s41598-019-41695-z. PubMed DOI PMC

Lawson DJ, Hellenthal G, Myers S, Falush D. Inference of population structure using dense haplotype data. PLoS Genet. 2012;8:e1002453. doi: 10.1371/journal.pgen.1002453. PubMed DOI PMC

Hellenthal G, et al. A genetic atlas of human admixture history. Science. 2014;343:747–751. doi: 10.1126/science.1243518. PubMed DOI PMC

Soetaert, K., Van den Meersche, K. & van Oevelen, D. limSolve: solving linear inverse models. R version 1.5.7 https://cran.r-project.org/web/packages/limSolve (2009).

Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655–1664. doi: 10.1101/gr.094052.109. PubMed DOI PMC

Cressie, N. & Wikle, C. K. Statistics for Spatio-Temporal Data (John Wiley & Sons, 2015).

Gräler B, Pebesma E, Heuvelink G. Spatio-Temporal Interpolation using gstat. R J. 2016;8:204. doi: 10.32614/RJ-2016-014. DOI

Reimer, P. et al. Laboratory Protocols Used for AMS Radiocarbon Dating at the 14CHRONO Centre. Report No. 5-2015 (English Heritage, 2015).

Brock, F., Higham, T., Ditchfield, P. & Ramsey, C. B. Current pretreatment methods for AMS radiocarbon dating at the Oxford Radiocarbon Accelerator Unit (ORAU). Radiocarbon52, 103–112 (2010).

Beaumont W, Beverly R, Southon J, Taylor RE. Bone preparation at the KCCAMS laboratory. Nucl. Instrum. Methods Phys. Res. B. 2010;268:906–909. doi: 10.1016/j.nimb.2009.10.061. DOI

Reimer P, et al. The IntCal20 Northern Hemisphere Radiocarbon Age Calibration Curve (0–55 cal kBP) Radiocarbon. 2020;62:725–757. doi: 10.1017/RDC.2020.41. DOI

The genetic origin of the Indo-Europeans

The Genetic Origin of the Indo-Europeans