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Nature
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137 ancient human genomes from across the Eurasian steppes

Naturevolume 557, pages369–374 (2018)Cite this article

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AnAuthor Correction to this article was published on 30 August 2018

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Abstract

For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third centurybc, forming the Hun traditions in the fourth–fifth centuryad, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry.

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Fig. 1: Cultural and geographical presentation of the ancient samples.
Fig. 2: Principal component analyses.
Fig. 3: QpAdm results depicting the changes in ancestry across time in Central Asia.
Fig. 4: Summary map.

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Change history

  • 30 August 2018

    with In this Article, Angela M. Taravella and Melissa A. Wilson Sayres have been added to the author list (associated with: School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ, USA). The author list and Author Information section have been corrected online.

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Acknowledgements

We thank K. Magnussen, L. Petersen, C. Mortensen and A. Seguin-Orlando at the Danish National Sequencing Centre for producing the analysed sequences; P. Reimer and S. Hoper at the 14Chrono Center Belfast for providing accelerator mass spectrometry dating; S. Hackenbeck for discussing palaeodietary reconstructions; D. Christiansen Appelt, B. Heyerdahl, the Explico Foundation team, J. Isakova, B. Daulet, A. Tairov, N. Abduov, B. Tudiyarov, V. Volkov, M. Akchurin, I. Baimukhan, N. Namdakov, Y. Yusupov, E. Ramankulov, A. Nurgaziyev and A. Kusaev for important assistance in fieldwork; J. Stenderup, P. V. Olsen and T. Brand for technical assistance in the laboratory; all involved archaeologists, historians and geographers from Kazakhstan: A. Suslov, I. Erofeeva, E. Nurmaganbetov, B. Kozhakhmetov, N. Loman, Y. Parshin, S. Ladunskiy, M. Bedelbaeva, A. Marcsik, O. Gábor, M. Půlpán, Y. Kubeev, R. Zhumashev, K. Omarov, S. Kasymov and U. Akimbayeva; P. Rodzianko for creating the initial contact between P.d.B.D., S.E. and E.U.; and S. Jacobsen and J. O’Brien for translating and proofreading Russian contributions. E.W. thanks St. John’s College, Cambridge for support and for providing an environment facilitating scientific discussions. B.Boldg. thanks the Taylor Family-Asia Foundation Endowed Chair in Ecology and Conservation Biology. The project was funded by the Danish National Research Foundation (E.W.), the Lundbeck Foundation (E.W.) and KU2016 (E.W.).

Reviewer information

Nature thanks T. Higham, D. Anthony, B. Shapiro, R. Dennell and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Author information

Author notes

  1. Kasper Nielsen

    Present address: Carlsberg Research Laboratory, Copenhagen, Denmark

Authors and Affiliations

  1. Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

    Peter de Barros Damgaard, Gabriel Renaud, Thorfinn Korneliussen, J. Víctor Moreno-Mayar, Ashot Margaryan, Morten E. Allentoft, Ludovic Orlando, Rasmus Nielsen, Martin Sikora & Eske Willerslev

  2. Eco-anthropologie et Ethnobiologie, Muséum national d’Histoire naturelle, CNRS, Université Paris Diderot, Paris, France

    Nina Marchi & Evelyne Heyer

  3. Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark

    Simon Rasmussen, Anders Gorm Pedersen & Kasper Nielsen

  4. Leiden University Centre for Linguistics, Leiden University, Leiden, The Netherlands

    Michaël Peyrot

  5. Department of Zoology, University of Cambridge, Cambridge, UK

    Thorfinn Korneliussen, Mikkel Winther Pedersen & Eske Willerslev

  6. Department of Biology, Stanford University, Stanford, CA, USA

    Amy Goldberg

  7. Buketov Karaganda State University, Saryarka Archaeological Institute, Karaganda, Kazakhstan

    Emma Usmanova, Valeriy Loman, Evgeniy Dmitriev, Valeriy Evdokimov, Alexey Kukushkin, Igor Kukushkin & Victor Varfolomeev

  8. Shejire DNA, Almaty, Kazakhstan

    Nurbol Baimukhanov & Gabit Baimbetov

  9. Department of Archaeology, Conservation and History, University of Oslo, Oslo, Norway

    Lotte Hedeager

  10. Department of Theory and Methods, Institute of Archaeology Russian Academy of Sciences, Moscow, Russia

    Gennady Afanasiev

  11. Department of History, Kyrgyzstan-Turkey Manas University, Bishkek, Kyrgyzstan

    Kunbolot Akmatov, Ashyk Alpaslan & Tabaldiev Kubatbek

  12. National Academy of Sciences of Kyrgyzstan, Bishkek, Kyrgyzstan

    Almaz Aldashev

  13. Department of History, Irkutsk State University, Irkutsk, Russia

    Vladimir I. Bazaliiskii

  14. A. Kh. Margulan Institute of Archaeology, Almaty, Kazakhstan

    Arman Beisenov & Egor Kitov

  15. Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, Mongolia

    Bazartseren Boldbaatar

  16. Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia

    Bazartseren Boldgiv & Sainbileg Undrakhbold

  17. Departament of Biology and Ecology, Tuvan State University, Kyzyl, Russia

    Choduraa Dorzhu

  18. The Explico Foundation, Floro, Norway

    Sturla Ellingvag

  19. Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar, Mongolia

    Diimaajav Erdenebaatar & Enkhbayar Mijiddorj

  20. Department of Biology and Biotechnology, Hashemite University, Zarqa, Jordan

    Rana Dajani

  21. Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, USA

    Rana Dajani

  22. Unit for Environmental Archaeology and Materials Science, National Museum of Denmark, Copenhagen, Denmark

    Karin M. Frei

  23. Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St. Petersburg, Russia

    Andrey Gromov & Vyacheslav Moiyesev

  24. Archaeological Expertise LLC, Almaty, Kazakhstan

    Alexander Goryachev & Dmitriy Voyakin

  25. Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Hakon Hakonarson

  26. Republican Scientific Center of Immunology, Ministry of Public Health, Tashkent, Uzbekistan

    Tatyana Hegay

  27. Department of Bioengineering, Bioinformatics and Molecular Biology, Russian-Armenian University, Yerevan, Armenia

    Zaruhi Khachatryan & Levon Yepiskoposyan

  28. Complex Research Institute of the Russian Academy of Sciences, Grozny, Russia

    Ruslan Khaskhanov

  29. Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia

    Egor Kitov

  30. Kostanay Regional Local History Museum, Kostanay, Kazakhstan

    Alina Kolbina

  31. Centre for Baltic and Scandinavian Archaeology, Schleswig, Germany

    Nina Lau

  32. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia

    Ashot Margaryan

  33. Saxo-Institute, University of Copenhagen, Copenhagen, Denmark

    Inga Merkyte

  34. Center for Archaeological Research, S. Toraighyrov Pavlodar State University, Pavlodar, Kazakhstan

    Ilya V. Mertz & Viktor K. Mertz

  35. The State Historical and Cultural Reserve-Museum (ISSYK), Almaty, Kazakhstan

    Gulmira Mukhtarova, Bekmukhanbet Nurmukhanbetov & Turaly Tulegenov

  36. Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia

    Z. Orozbekova

  37. University of Arizona, Laboratory of Tree-Ring Research, Tucson, AZ, USA

    Irina Panyushkina

  38. Institute of Archaeology of the Slovak Academy of Sciences, Nitra, Slovakia

    Karol Pieta & Tereza Štolcová

  39. Institute for History of Medicine and Foreign Languages, First Faculty of Medicine, Charles University, Prague, Czech Republic

    Václav Smrčka

  40. Archaeological Laboratory, Kostanay State University, Kostanay, Kazakhstan

    Irina Shevnina & Andrey Logvin

  41. Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden

    Karl-Göran Sjögren & Kristian Kristiansen

  42. Institute of History and Cultural Heritage of National Academy of Sciences, Bishkek, Kyrgyzstan

    Kadicha Tashbaeva

  43. Institute of Problems Development of the North Siberian Branch of the Russian Academy of Sciences, Tyumen, Russia

    Alexander Tkachev

  44. Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada

    Andrzej Weber

  45. Institute of History, Archaeology and Ethnology, Far-Eastern Branch of the Russian Academy of Sciences, Ulan-Ude, Russia

    Nikolay Kradin

  46. Institute of Mongolian, Buddhist, and Tibetan Studies, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude, Russia

    Nikolay Kradin

  47. Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, Université de Toulouse, Université Paul Sabatier, Toulouse, France

    Ludovic Orlando

  48. Departments of Integrative Biology and Statistics, University of Berkeley, Berkeley, CA, USA

    Rasmus Nielsen

  49. Wellcome Trust Sanger Institute, Hinxton, UK

    Eske Willerslev

  50. School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ, USA

    Angela M. Taravella & Melissa A. Wilson Sayres

Authors
  1. Peter de Barros Damgaard
  2. Nina Marchi
  3. Simon Rasmussen
  4. Michaël Peyrot
  5. Gabriel Renaud
  6. Thorfinn Korneliussen
  7. J. Víctor Moreno-Mayar
  8. Mikkel Winther Pedersen
  9. Amy Goldberg
  10. Emma Usmanova
  11. Nurbol Baimukhanov
  12. Valeriy Loman
  13. Lotte Hedeager
  14. Anders Gorm Pedersen
  15. Kasper Nielsen
  16. Gennady Afanasiev
  17. Kunbolot Akmatov
  18. Almaz Aldashev
  19. Ashyk Alpaslan
  20. Gabit Baimbetov
  21. Vladimir I. Bazaliiskii
  22. Arman Beisenov
  23. Bazartseren Boldbaatar
  24. Bazartseren Boldgiv
  25. Choduraa Dorzhu
  26. Sturla Ellingvag
  27. Diimaajav Erdenebaatar
  28. Rana Dajani
  29. Evgeniy Dmitriev
  30. Valeriy Evdokimov
  31. Karin M. Frei
  32. Andrey Gromov
  33. Alexander Goryachev
  34. Hakon Hakonarson
  35. Tatyana Hegay
  36. Zaruhi Khachatryan
  37. Ruslan Khaskhanov
  38. Egor Kitov
  39. Alina Kolbina
  40. Tabaldiev Kubatbek
  41. Alexey Kukushkin
  42. Igor Kukushkin
  43. Nina Lau
  44. Ashot Margaryan
  45. Inga Merkyte
  46. Ilya V. Mertz
  47. Viktor K. Mertz
  48. Enkhbayar Mijiddorj
  49. Vyacheslav Moiyesev
  50. Gulmira Mukhtarova
  51. Bekmukhanbet Nurmukhanbetov
  52. Z. Orozbekova
  53. Irina Panyushkina
  54. Karol Pieta
  55. Václav Smrčka
  56. Irina Shevnina
  57. Andrey Logvin
  58. Karl-Göran Sjögren
  59. Tereza Štolcová
  60. Angela M. Taravella
  61. Kadicha Tashbaeva
  62. Alexander Tkachev
  63. Turaly Tulegenov
  64. Dmitriy Voyakin
  65. Levon Yepiskoposyan
  66. Sainbileg Undrakhbold
  67. Victor Varfolomeev
  68. Andrzej Weber
  69. Melissa A. Wilson Sayres
  70. Nikolay Kradin
  71. Morten E. Allentoft
  72. Ludovic Orlando
  73. Rasmus Nielsen
  74. Martin Sikora
  75. Evelyne Heyer
  76. Kristian Kristiansen
  77. Eske Willerslev

Contributions

E.W. initiated and led the study. P.d.B.D., E.W., E.U. and E.H. designed the study. P.d.B.D. and N.M. produced the data. P.d.B.D., N.M., S.R., M.S., G.R., T.Ko., A.Gol., M.W.P., A.G.P. and K.N. analysed or assisted in analysis of data. A.M.T. and M.A.W.S. provided an overview of major Y-chromosomal haplogroups in Supplementary Information Section 8. P.d.B.D., E.W. and K.K. interpreted results with considerable input from M.S., R.N., M.P., N.K., S.R., L.O., M.E.A. and J.V.M.-M. P.d.B.D., E.W., K.K., M.P. and S.R. wrote the manuscript with considerable input from N.K., L.H., M.S., R.N., M.E.A., L.O. and J.V.M.-M., with contributions from all authors. P.d.B.D., M.E.A., L.O., E.U., N.B., V.L., G.A., K.A., A.Ald., A.Alp., G.B., V.I.B., A.B., B.Boldb., B.Boldg., C.D., S.E., D.E., R.D., E.D., V.E., K.M.F., A.Gor., A.Gr., H.H., T.H., Z.K., R.K., E.K., A.Ko., T.Ku., A.Ku., I.K., N.L., A.M., V.K.M., I.V.M., I.M., E.M., V.M., G.M., B.N., Z.O., I.P., K.P., V.S., I.S., A.L., K.-G.S., T.S., K.T., A.T., T.T., D.V., L.Y., S.U., V.V., A.W. and E.H. excavated, curated, sampled and/or described analysed skeletons; all authors contributed to final interpretation of data.

Corresponding author

Correspondence toEske Willerslev.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 Analyses of Iron Age clusters.

a, PCA of Iron Age nomads and ancestral sources, explaining the diversity between them using 74 individuals at 242,406 autosomal single nucleotide polymorphism (SNP) positions.b, PCA of Iron Age nomads alone using 29 individuals at 242,406 autosomal SNP positions.c, PCA of Xiongnu, ‘Western’ Xiongnu, Tian Shan Huns, Nomads Hun Period, and Tian Shan Sakas, using 39 individuals at 242,406 autosomal SNP positions.d, Model-based clustering atK = 7 illustrating differences in ancestral proportions. Labelled individuals: A, Andronovo; B, Neolithic European (Europe_EN, ina); C, Baikal hunter-gatherers; D, Neolithic Iranian (Iran_N, ina). Here we illustrate the admixture analyses withK = 7 as it approximately identifies the major component of relevance (Anatolian/European farmer component, Caucasian ancestry, EHG-related ancestry and East Asian ancestry). The asterisk indicates an individual flagged as a genetic outlier.d, e, Results for model-based clustering analysis atK = 7. Here we illustrate the admixture analyses withK = 7 as it approximately identifies the major component of relevance (Anatolian/European farmer component, Caucasian ancestry, EHG-related ancestry and East Asian ancestry). Paneld is focused on the Iron Age, whilee is focused on the transition to the Hun period.

Extended Data Fig. 2 Illustration of shared ancestry between Neolithic farmers and Iron Age nomads.

Results for model-based clustering analysis atK = 7, plotting only one individual from relevant groups, to illustrate shared ancestry between Neolithic farmers from Europe, Late Bronze Age nomads and Iron Age nomads, not shared with Early Bronze Age nomads. MBLA, Middle-to-Late Bronze Age; Neo, Neolithic.

Extended Data Fig. 3 Illustration of gene flow into Hungarian Scythians.

We represent allD(Test, Mbuti; Andronovo, Hungarian Scythians) that deviate significantly from 0 (that is, higher than 3× the standard errors). The reported numbers are theD-statistics and the 3 standard errors were plotted as error bars. The number of individuals per population can be found in Supplementary Tables 3,4.

Extended Data Fig. 4 Illustration of negative admixturef3 statistics for Iron Age populations.

Plot showsf3(Bronze Age Test 1, Bronze Age Test 2; Iron Age Test). The reported numbers are of thef3 statistics, and the 3 standard errors were plotted as errors bars. The number of individuals per population can be found in Supplementary Table 3.

Extended Data Fig. 5 Illustration of West Eurasian gene flow into groups forming the Xiongnu culture.

We represent allD(Test, Mbuti; ‘Western’ Xiongnu, Xiongnu) that deviate significantly from 0 (that is, higher than 3× the standard errors). The reported numbers are theD-statistics and the 3 standard errors were plotted as error bars. The number of individuals per population can be found in Supplementary Tables 3,4.

Extended Data Fig. 6 Illustration of West Eurasian ancestry in early Tian Shan Huns.

We represent allD(Test, Mbuti; Tian Shan Huns, Xiongnu) that deviate significantly from 0 (that is, higher than 3× the standard errors). The reported numbers are theD-statistics and the 3 standard errors were plotted as error bars. The number of individuals per population can be found in Supplementary Tables 3,4.

Extended Data Fig. 7 Analyses of Xiongnu and Hun period population clusters.

a, PCA of Xiongnu, ‘Western’ Xiongnu, Tian Shan Huns, Hun-period nomads, Tian Shan Sakas, Kangju and Wusun, including 49 individuals analysed at 242,406 autosomal SNP positions.b, Results for model-based clustering analysis atK = 7. Here we illustrate the admixture analyses withK = 7 as it approximately identifies the major component of relevance (Anatolian/European farmer component, Caucasian ancestry, EHG-related ancestry and East Asian ancestry). Individual A is a southern Siberian individual associated with the Andronovo culture.

Extended Data Fig. 8 Analyses of Turk- and Medieval-period population clusters.

a, PCA of Tian Shan Hun, Turk, Kimak, Kipchack, Karakhanid and Golden Horde, including 28 individuals analysed at 242,406 autosomal SNP positions.b, Results for model-based clustering analysis atK = 7. Here we illustrate the admixture analyses withK = 7 as it approximately identifies the major component of relevance (Anatolian/European farmer component, Caucasian ancestry, EHG-related ancestry and East Asian ancestry).

Extended Data Fig. 9 Maximum likelihood phylogenetic reconstruction ofY. pestis.

This tree reveals the basal position of the Tian Shan sample (0.ANT5, DA101,ad 186) compared to the Justinian plague sample (0.ANT4, A120,ad 536). These two samples are shown in orange italics. Other ancient plague samples included in the tree are Bronze Age samples (0.PRE1 and 0.PRE2) and a Black Death sample (1.PRE1). Numbers on nodes indicate bootstrap support (not all of which are shown, for clarity) and certain branches have been collapsed for clarity. Branch lengths are substitutions per site.

Extended Data Fig. 10 Analyses of sex-specific contributions to Iron Age populations.

Estimates of the male and female contributions from each source populations (left column) to each of the four admixed populations (right column) using a previously published method40. For each admixed population, we compared the observed mean autosomal and X-chromosomal ancestry, estimated in qpAdm, to that calculated under a constant admixture model on a grid of sex-specific contribution parameters ranging from 0 to 1 in 0.025 increments using a Euclidean distance. The logarithms of the ratio of male to female contribution parameters that produce the smallest 0.1% of distances from the data are plotted, with the full range of parameter values in grey, the middle 50% in black, and the median value in red. The dashed line indicates equal male and female contributions.

Supplementary information

Supplementary Information

This files contains Section 1 (Archaeological background for Iron Age to Medieval steppe cultures), Section 2 (Linguistic history of the steppe), Section 3 (Data generation and analyses), Section 4 (Site descriptions and individual outgroup-f3 statistics), Section 5 (Modern dataset), Section 6 (Comparing ancient DNA preservation in the mineral and organic phases of tooth cementum), Section 7 (Plague genome reconstructions), Section 8 (Y-chromosomal analyses), Section 9 (Sarmatians and Alan), Section 10 (Mitogenomes) and Section 11 (Radiocarbon dating)

Supplementary Table 1

Basic mapping statistics

Supplementary Table 2

Overview of ancient samples. This table includes radiocarbon dating and calibration, geographical coordinates and genetic gender.

Supplementary Table 3

Population label and sample size overview. This table provides a fast contextualization of population labels used here.

Supplementary Table 4

Information on present-day dataset. This includes geographical coordinates coupled to the full presentation of ancestral proportions estimated using qpAdm with a set of 5 outgroups: Mbuti, Ust'Ishim, Clovis, Kostenki14 and Switzerland HG. Number of individuals per modelled population can be found in Supplementary Table 3. See Supplementary Information section 3 for description of qpAdm analyses.

Supplementary Table 5

QpAdm modelling of Iron Age Scythians. We here compare different sets of sources, ie. Andronovo, Sintashta and Yamnaya and a set of 7 outgroups (Mbuti, Ust'Ishim, Clovis, Kostenki14, Switzerland_HG, Natufian and MA1). Red colors reflect a failed model. Note that for Tagar where MA1 was used a source, the outgroup was replaced with EHG. Number of individuals per modelled population can be found in Supplementary Table 3. See Supplementary Section 3 for description of qpAdm analyses.

Supplementary Table 6

Fst values between the Iron Age Scythian groups. Number of individuals per modelled population can be found in Supplementary Table 3.

Supplementary Table 7

QpAdm modelling of Kangju and Wusun. We here use a set of 7 outgroups (Mbuti, Ust'Ishim, Clovis, Kostenki14, Switzerland_HG, Natufian and MA1). Number of individuals per modelled population can be found in Supplementary Table 3. See Supplementary Information section 3 for description of qpAdm analyses.

Supplementary Table 8

Authentication assessment. Damage parameters, contamination estimates and mitogenome haplogroup assignment. See Supplementary Information sections 3 and 10 for exhaustive description of sample analyses.

Supplementary Table 9

Confident Y-chromosomal haplogroup assignment.

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Damgaard, P.d.B., Marchi, N., Rasmussen, S.et al. 137 ancient human genomes from across the Eurasian steppes.Nature557, 369–374 (2018). https://doi.org/10.1038/s41586-018-0094-2

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  1. Canadelectrochim

    This is the history of the world and should be away from any effect of the present day politics.
    These authors believe that the great Scythian were an ancient Iranian people or Persian are
    mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry.
    How can the present day Turkish-speaking groups who are Caucasian be of Asian ancestry.

  2. TanaReplied toCanadelectrochim

    Present day Turkish-speaking groups include a wide range of ethnicities from Russian Altai mountains, Baikal lake up to Turkey. They are a mixture of mostly Asian and some Caucasian ancestry. If you mean modern Turkish people from Turkey, they have Semitic and Caucasian influence, yes, but they originate from Central Asian steppes, where they moved from in Middle Ages.

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