Article | Published:

137 ancient human genomes from across the Eurasian steppes

Naturevolume 557pages369374 (2018) | Download Citation

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 century bc, forming the Hun traditions in the fourth–fifth century ad, 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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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.

References

  1. 1.

    Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).

  2. 2.

    Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015).

  3. 3.

    Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015).

  4. 4.

    Chlenova, N. L. in The Archaeol ogy of th e Steppes: Methods and Strategies (ed. Genito, B.) 499–540 (Istituto Universitario Orientale, Naples, 1994).

  5. 5.

    Grakov, B. N., Yelagina, N. G. & Yatsenko, I. V. The Early Iron Age (Moscow State Univ. Press, Moscow, 1977).

  6. 6.

    Kristiansen, K. Europe Before History (Cambridge Univ. Press, Cambridge, 2000).

  7. 7.

    Parzinger, H. Die Frühen Völker Eurasiens: vom Neolithikum bis zum Mittelalter (CH Beck, München, 2006).

  8. 8.

    Alekseev, A. in The Golden Deer of Eurasia: Scythian and Sarmatian Treasures from the Russian Steppes (eds Aruz, J. et al.) 41–47 (The Metropolitan Museum of Art, New York, 2006).

  9. 9.

    Yablonsky, L. in The Golden Deer of Eurasia: Scythian and Sarmatian Treasures from the Russian Steppes (eds Aruz, J. et al.) 24–31 (The Metropolitan Museum of Art, New York, 2006).

  10. 10.

    Bashilov, V. A. & Yablonsky, L. T. in Kurgans, Ritual Sites, and Settlements: Eurasian Bronze and Iron Age (eds Davis-Kimball, J. et al.) 9–12 (Archaeopress, Oxford, 2000).

  11. 11.

    Unterländer, M. et al. Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe. Nat. Commun. 8, 14615 (2017).

  12. 12.

    Frachetti, M. D. Multiregional emergence of mobile pastoralism and nonuniform institutional complexity across Eurasia. Curr. Anthropol. 53, 2–38 (2012).

  13. 13.

    Kohl, P. L. Shared social fields: evolutionary convergence in prehistory and contemporary practice. Am. Anthropol. 110, 495–506 (2008).

  14. 14.

    Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).

  15. 15.

    Dybo, A. V. Lingvističeskie kontakty rannix tjurkov. Leksičeskij fond (Vostočnaja Literatura, Moscow, 2007).

  16. 16.

    Keyser-Tracqui, C., Crubézy, E. & Ludes, B. Nuclear and mitochondrial DNA analysis of a 2,000-year-old necropolis in the Egyin Gol Valley of Mongolia. Am. J. Hum. Genet. 73, 247–260 (2003).

  17. 17.

    Keyser-Tracqui, C., Crubézy, E., Pamzsav, H., Varga, T. & Ludes, B. Population origins in Mongolia: genetic structure analysis of ancient and modern DNA. Am. J. Phys. Anthropol. 131, 272–281 (2006).

  18. 18.

    Kim, K. et al. A western Eurasian male is found in 2000-year-old elite Xiongnu cemetery in Northeast Mongolia. Am. J. Phys. Anthropol. 142, 429–440 (2010).

  19. 19.

    Pohl, W. in A Companion to Ethnicity in the Ancient Mediterranean (ed. McInerney, J.) 555–568 (Wiley Blackwell, Chichester, 2014).

  20. 20.

    De la Vaissière, É. Huns et Xiongnu. Cent. Asiat. J. 49, 3–26 (2005).

  21. 21.

    Mallory, J. P. In Search of the Indo-Europeans. Language, Archaeology and Myth (Thames & Hudson, London, 1989).

  22. 22.

    Sinor, D. in The Cambridge History of Early Inner Asia (ed. Sinor, D.) 285–316 (Cambridge Univ. Press, Cambridge, 1990).

  23. 23.

    Findley, C. V. The Turks in World History (Oxford Univ. Press, Oxford, 2004).

  24. 24.

    Kradin, N. in Xiongnu Archaeology: Multidisciplinary Perspectives of the First Steppe Empire in Inner Asia (eds Brosseder, U. & Miller, B. K.) 77–96 (Universität Bonn, Bonn, 2011).

  25. 25.

    Golden, P. B. An Introduction to the History of the Turkic Peoples: Ethnogenesis and State-Formation in Medieval and Early Modern Eurasia and the Middle East (Harrassowitz, Wiesbaden, 1992).

  26. 26.

    Hildinger, E. Warriors of the Steppe: a Military History of Central Asia, 500 bc to 1700 ad (Da Capo Press, Cambridge, 1997).

  27. 27.

    Kradin, N. N. & Skrynnikova, T. D. Imperiya Imperija Chingis Čingis-Khana Xana [The Genghis Khan Empire] (Vostočnaja Literatura, Moscow, 2006).

  28. 28.

    Little, L. K. Plague and the End of Antiquity: the Pandemic of 541–750 (Cambridge Univ. Press, Cambridge, 2007).

  29. 29.

    Wagner, D. M. et al. Yersinia pestis and the plague of Justinian 541–543 ad: a genomic analysis. Lancet Infect. Dis. 14, 319–326 (2014).

  30. 30.

    Cui, Y. et al. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc. Natl Acad. Sci. USA 110, 577–582 (2013).

  31. 31.

    Rasmussen, S. et al. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell 163, 571–582 (2015).

  32. 32.

    Sun, Y.-C. C., Jarrett, C. O., Bosio, C. F. & Hinnebusch, B. J. Retracing the evolutionary path that led to flea-borne transmission of Yersinia pestis. Cell Host Microbe 15, 571–582 (2015).

  33. 33.

    Kuz’mina, E. E. The Origin of the Indo-Iranians (Brill, Leiden, 2007).

  34. 34.

    Tremblay, X. Irano-Tocharica et Tocharo-Iranica. Bull. Sch. Orient. Afr. Stud. 68, 421–449 (2005).

  35. 35.

    Nichols, J. in Language Contact in Times of Globalization (eds Hasselblatt, C. et al.) 177–195 (Rodopi, Amsterdam, 2011).

  36. 36.

    Johanson, L. in The Turkic Languages (eds Johanson, L. & Csató, É. Á.) 81–125 (Routledge, London, 1998).

  37. 37.

    Johanson, L. in The Handbook of Language Contact (ed. Hickey, R.) 652–672 (Wiley-Blackwell, Chichester, 2010).

  38. 38.

    Janhunen, J. Manchuria: an Ethnic History (The Finno-Ugrian Society, Helsinki, 1996).

  39. 39.

    Doerfer, G. Türkische und Mongolische Elemente im Neupersischen 1–4 (Harrassowitz, Wiesbaden, 1963–1975).

  40. 40.

    Goldberg, A. et al. Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations. Proc. Natl Acad. Sci. USA 114, 2657–2662 (2017).

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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

    • Kasper Nielsen

    Present address: Carlsberg Research Laboratory, Copenhagen, Denmark

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

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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.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Eske Willerslev.

Extended data figures and tables

  1. 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 at K = 7 illustrating differences in ancestral proportions. Labelled individuals: A, Andronovo; B, Neolithic European (Europe_EN, in a); C, Baikal hunter-gatherers; D, Neolithic Iranian (Iran_N, in a). Here we illustrate the admixture analyses with K = 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. de, Results for model-based clustering analysis at K = 7. Here we illustrate the admixture analyses with K = 7 as it approximately identifies the major component of relevance (Anatolian/European farmer component, Caucasian ancestry, EHG-related ancestry and East Asian ancestry). Panel d is focused on the Iron Age, while e is focused on the transition to the Hun period.

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

    Results for model-based clustering analysis at K = 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.

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

    We represent all D(Test, Mbuti; Andronovo, Hungarian Scythians) that deviate significantly from 0 (that is, higher than 3× the standard errors). The reported numbers are the D-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.

  4. Extended Data Fig. 4 Illustration of negative admixture f3 statistics for Iron Age populations.

    Plot shows f3(Bronze Age Test 1, Bronze Age Test 2; Iron Age Test). The reported numbers are of the f3 statistics, and the 3 standard errors were plotted as errors bars. The number of individuals per population can be found in Supplementary Table 3.

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

    We represent all D(Test, Mbuti; ‘Western’ Xiongnu, Xiongnu) that deviate significantly from 0 (that is, higher than 3× the standard errors). The reported numbers are the D-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.

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

    We represent all D(Test, Mbuti; Tian Shan Huns, Xiongnu) that deviate significantly from 0 (that is, higher than 3× the standard errors). The reported numbers are the D-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.

  7. 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 at K = 7. Here we illustrate the admixture analyses with K = 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.

  8. 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 at K = 7. Here we illustrate the admixture analyses with K = 7 as it approximately identifies the major component of relevance (Anatolian/European farmer component, Caucasian ancestry, EHG-related ancestry and East Asian ancestry).

  9. Extended Data Fig. 9 Maximum likelihood phylogenetic reconstruction of Y. 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.

  10. 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

  1. 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)

  2. Reporting Summary

  3. Supplementary Table 1

    Basic mapping statistics

  4. Supplementary Table 2

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

  5. Supplementary Table 3

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

  6. 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.

  7. 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.

  8. Supplementary Table 6

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

  9. 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.

  10. 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.

  11. Supplementary Table 9

    Confident Y-chromosomal haplogroup assignment.

About this article

Publication history

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DOI

https://doi.org/10.1038/s41586-018-0094-2

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