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137 ancient human genomes from across the Eurasian steppes

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.

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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

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.

Correspondence to Eske Willerslev.

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 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.

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.

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.

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.

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.

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.

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.

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).

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.

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)

Reporting Summary

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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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.
Extended Data Fig. 1: Analyses of Iron Age clusters.
Extended Data Fig. 2: Illustration of shared ancestry between Neolithic farmers and Iron Age nomads.
Extended Data Fig. 3: Illustration of gene flow into Hungarian Scythians.
Extended Data Fig. 4: Illustration of negative admixture f3 statistics for Iron Age populations.
Extended Data Fig. 5: Illustration of West Eurasian gene flow into groups forming the Xiongnu culture.
Extended Data Fig. 6: Illustration of West Eurasian ancestry in early Tian Shan Huns.
Extended Data Fig. 7: Analyses of Xiongnu and Hun period population clusters.
Extended Data Fig. 8: Analyses of Turk- and Medieval-period population clusters.
Extended Data Fig. 9: Maximum likelihood phylogenetic reconstruction of Y. pestis.
Extended Data Fig. 10: Analyses of sex-specific contributions to Iron Age populations.

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