Population genomics of post-glacial western Eurasia

Morten E Allentoft ^1,2, Martin Sikora ³, Alba Refoyo-Martínez ⁴

¹Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. morten.allentoft@curtin.edu.au.
²Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia. morten.allentoft@curtin.edu.au.
³Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. martin.sikora@sund.ku.dk.
⁴Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
⁵Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden.
⁶Sealand Archaeology, Kalundborg, Denmark.
⁷GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
⁸Department of Genetics, University of Cambridge, Cambridge, UK.
⁹Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark.
¹⁰Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
¹¹Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
¹²Department of Integrative Biology, University of California, Berkeley, CA, USA.
¹³Research Department of Genetics, Evolution and Environment, University College London, London, UK.
¹⁴Department of Archaeology, University of Cambridge, Cambridge, UK.
¹⁵Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark.
¹⁶Muséum National d'Histoire Naturelle, CNRS, Université de Paris, Musée de l'Homme, Paris, France.
¹⁷The National Museum of Denmark, Copenhagen, Denmark.
¹⁸Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
¹⁹Centre for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark.
²⁰Anthropology Department, University of Utah, Salt Lake City, UT, USA.
²¹Center for Computational Biology, University of California, Berkeley, CA, USA.
²²Department of Geology, Lund University, Lund, Sweden.
²³Tårnby Gymnasium og HF, Kastrup, Denmark.
²⁴Department of Archaeology and Heritage Studies, Aarhus University, Aarhus, Denmark.
²⁵Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark.
²⁶Vendsyssel Historiske Museum, Hjørring, Denmark.
²⁷Terra Ltd., Voronezh, Russian Federation.
²⁸Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA.
²⁹Department of Archaeology, University of Exeter, Exeter, UK.
³⁰Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.
³¹Department of Anthropology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation.
³²Department of Environmental Biology, Sapienza University of Rome, Rome, Italy.
³³Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Saint Petersburg, Russian Federation.
³⁴CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
³⁵UNIARQ, University of Lisbon, Lisbon, Portugal.
³⁶Kostanay Regional University A. Baitursynov, Kostanay, Kazakhstan.
³⁷Vesthimmerlands Museum, Aars, Denmark.
³⁸Grupo EvoAdapta, Departamento de Ciencias Históricas, Universidad de Cantabria, Santander, Spain.
³⁹Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
⁴⁰Natural Sciences Museum of Barcelona (MCNB), Barcelona, Spain.
⁴¹Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain.
⁴²Department of Biology, University of Rome Tor Vergata, Rome, Italy.
⁴³Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Banco Santander, Gobierno de Cantabria, Santander, Spain.
⁴⁴Centre de Recherche en Archéologie, Archeosciences, Histoire (CReAAH), UMR-6869 CNRS, Rennes, France.
⁴⁵Georgian National Museum, Tbilisi, Georgia.
⁴⁶Tbilisi State University, Tbilisi, Georgia.
⁴⁷IPND, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences, Tyumen, Russian Federation.
⁴⁸Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain.
⁴⁹Department of Geological Sciences, University of Cape Town, Cape Town, South Africa.
⁵⁰Laboratory for Archaeological Chemistry, Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA.
⁵¹Department of Anthropology, New York University, New York, NY, USA.
⁵²Institute of Humanities, Ivanovo State University, Ivanovo, Russian Federation.
⁵³Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russian Federation.
⁵⁴Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan.
⁵⁵South Ural State University, Chelyabinsk, Russia.
⁵⁶A. Kh. Khalikov Institute of Archeology of the Academy of Sciences of the Republic of Tatarstan, Kazan, Russia.
⁵⁷Margulan Institute of Archaeology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty, Kazakhstan.
⁵⁸The Saxo Institute, University of Copenhagen, Copenhagen, Denmark.
⁵⁹Museum Østjylland, Randers, Denmark.
⁶⁰Soprintendenza Archeologia Belle Arti e Paesaggio per la Città Metropolitana di Bari, Bari, Italy.
⁶¹UMR 5199 PACEA, CNRS, Université de Bordeaux, Pessac, France.
⁶²A.Kh. Margulan Institute of Archaeology, Almaty, Kazakhstan.
⁶³Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv, Ukraine.
⁶⁴National University of Kyiv-Mohyla Academy, Kyiv, Ukraine.
⁶⁵Collège de France, Paris, France.
⁶⁶Svendborg Museum, Svendborg, Denmark.
⁶⁷ICREA, University of Barcelona, Barcelona, Spain.
⁶⁸ARGEA Consultores SL, Madrid, Spain.
⁶⁹Museum Sydøstdanmark, Vordingborg, Denmark.
⁷⁰Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland.
⁷¹Department of Archaeology and Ancient History, Lund University, Lund, Sweden.
⁷²Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l'Homme, Aix-en-Provence, France.
⁷³Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.
⁷⁴Russian-Armenian University, Yerevan, Armenia.
⁷⁵HistorieUdvikler, Kalundborg, Denmark.
⁷⁶Department of History and Cultural Heritage, University of Siena, Siena, Italy.
⁷⁷Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5500, Université Paul Sabatier, Toulouse, France.
⁷⁸Soprintendenza per i Beni Archeologici delle Marche, Ancona, Italy.
⁷⁹Västergötlands Museum, Skara, Sweden.
⁸⁰Cabinet of Anthropology, Tomsk State University, Tomsk, Russian Federation.
⁸¹Department of History, Humanities and Society, University of Rome Tor Vergata, Rome, Italy.
⁸²Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poznań, Poland.
⁸³Institute of Archaeology, Jagiellonian University, Kraków, Poland.
⁸⁴Zoological Institute of Russian Academy of Sciences, Saint Petersburg, Russian Federation.
⁸⁵Department of Anthropology, Czech National Museum, Prague, Czech Republic.
⁸⁶Department of Health and Nature, University of Greenland, Nuuk, Greenland.
⁸⁷The Viking Ship Museum, Roskilde, Denmark.
⁸⁸Archaeology Institute, University of Highlands and Islands, Orkney, UK.
⁸⁹Scientific Research Center "Baikal region", Irkutsk State University, Irkutsk, Russian Federation.
⁹⁰Laboratory for Experimental Traceology, Institute for the History of Material Culture of the Russian Academy of Sciences, Saint Petersburg, Russian Federation.
⁹¹Janus Pannonius Museum, Pécs, Hungary.
⁹²Langelands Museum, Rudkøbing, Denmark.
⁹³Soprintendenza Archeologia, Belle Arti e Paesaggio per la provincia di Cosenza, Cosenza, Italy.
⁹⁴Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russian Federation.
⁹⁵Department of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russian Federation.
⁹⁶Centre for the Study of Early Agricultural Societies, Department of Cross-Cultural and Regional Studies, University of Copenhagen, Copenhagen, Denmark.
⁹⁷Museum Nordsjælland, Hillerød, Denmark.
⁹⁸Museum Vestsjælland, Holbæk, Denmark.
⁹⁹Museum of Cultural History, University of Oslo, Oslo, Norway.
¹⁰⁰ArchaeoScience, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
¹⁰¹Department of History, University of Santiago de Compostela, Santiago de Compostela, Spain.
¹⁰²Lipetsk Regional Scientific Public Organisation "Archaeological Research", Lipetsk, Russian Federation.
¹⁰³Institute of Archaeology and Ethnography, National Academy of Sciences, Yerevan, Armenia.
¹⁰⁴Center for Egyptological Studies, Russian Academy of Sciences, Moscow, Russian Federation.
¹⁰⁵Moesgaard Museum, Højbjerg, Denmark.
¹⁰⁶Nizhny Tagil State Socio-Pedagogical Institute, Nizhny Tagil, Russia.
¹⁰⁷Institute for History of Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic.
¹⁰⁸Centre for Archaeological Research, Toraighyrov University, Pavlodar, Kazakhstan.
¹⁰⁹Malmö Museer, Malmö, Sweden.
¹¹⁰Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK.
¹¹¹Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
¹¹²Wellcome Sanger Institute, Hinxton, UK.
¹¹³Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
¹¹⁴Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. ew482@cam.ac.uk.
¹¹⁵GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. ew482@cam.ac.uk.
¹¹⁶MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany. ew482@cam.ac.uk.

⁰Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. morten.allentoft@curtin.edu.au.

Nature +

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January 10, 2024

View abstract on PubMed

Summary

Ancient human genome sequencing reveals a genomic divide in Western Eurasia. Migrations, including the Yamnaya expansion, caused major population turnovers and reshaped genetic diversity across the continent.

Area Of Science

Paleogenomics
Human Evolution
Population Genetics

Background

Western Eurasia experienced significant human migrations throughout the Holocene.
Understanding the genetic impact of these movements is crucial for reconstructing population history.

Purpose Of The Study

To investigate the cross-continental genetic effects of Holocene human migrations in Eurasia.
To analyze ancient genomes from Mesolithic and Neolithic periods to identify population dynamics.

Main Methods

Shotgun sequencing of 317 ancient genomes from northern and western Eurasia.
Imputation with published data to generate over 1,600 diploid genotypes.
Analysis of genomic data to identify ancestry shifts and relatedness patterns.

Main Results

A 'great divide' genomic boundary was identified between the Black Sea and the Baltic.
Mesolithic populations were genetically distinct east and west of this boundary.
Neolithization led to substantial ancestry replacement in the west but not the east.
Yamnaya-related ancestry spread around 5,000 BP, causing a second major population turnover across Eurasia.
Hunter-gatherers from the Middle Don region contributed ancestry to the Yamnaya.

Conclusions

Prehistoric migrations profoundly and lastingly impacted Eurasian genetic diversity.
The Yamnaya expansion played a key role in reshaping the genetic landscape of Western Eurasia.
Distinct Mesolithic populations and differential responses to Neolithization shaped early Eurasian genetic structure.

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