Genomic insights into the origin of farming in the ancient Near East

Journal name:
Nature
Volume:
536,
Pages:
419–424
Date published:
DOI:
doi:10.1038/nature19310
Received
Accepted
Published online

Abstract

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter–gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter–gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter–gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

At a glance

Figures

  1. Genetic structure of ancient West Eurasia.
    Figure 1: Genetic structure of ancient West Eurasia.

    a, Sampling locations and times in six regions. Sample sizes for each population are given below each bar. E, Early; M, Middle; L, Late; HG, hunter–gatherer; N, Neolithic; ChL, Chalcolithic; BA, Bronze Age; IA, Iron Age. b, Principal components analysis of 991 present-day West Eurasians (grey points) with 278 projected ancient samples (excluding the Upper Palaeolithic Ust’-Ishim, Kostenki14, and MA1). To avoid visual clutter, population labels of present-day individuals are shown in Extended Data Fig. 1.

  2. Basal Eurasian ancestry explains the reduced Neanderthal admixture in West Eurasians.
    Figure 2: Basal Eurasian ancestry explains the reduced Neanderthal admixture in West Eurasians.

    Basal Eurasian ancestry estimates are negatively correlated to a statistic measuring Neanderthal ancestry f4(Test, Mbuti; Altai, Denisovan).

  3. Genetic differentiation and its marked decrease over time in West Eurasia.
    Figure 3: Genetic differentiation and its marked decrease over time in West Eurasia.

    Pairwise FST distribution among populations belonging to four successive time slices in West Eurasia; the median (red) and range of FST is shown.

  4. Modelling ancient West Eurasians, East Africans, East Eurasians and South Asians.
    Figure 4: Modelling ancient West Eurasians, East Africans, East Eurasians and South Asians.

    a, All the ancient populations can be modelled as mixtures of two or three other populations and up to four proximate sources (marked in colour). Mixture proportions inferred by qpAdm are indicated by the incoming arrows to each population. Green rectangles represent sets of more than one population. Multiple admixture solutions are consistent with the data for some populations, and while only one solution is shown here, Supplementary Information, section 7 presents the others. b, A flat representation of the graph showing mixture proportions from the four proximate sources.

  5. Principal components analysis of 991 present-day West Eurasians.
    Extended Data Fig. 1: Principal components analysis of 991 present-day West Eurasians.

    The PCA analysis is performed on the same set of individuals as are reported in Fig. 1b, using EIGENSOFT. Here, we colour the samples by population (to highlight the present-day populations) instead of using grey points as in Fig. 1b (where the goal is to highlight ancient samples).

  6. Genetic structure in ancient West Eurasian populations across time and decline of genetic differentiation over time.
    Extended Data Fig. 2: Genetic structure in ancient West Eurasian populations across time and decline of genetic differentiation over time.

    a, ADMIXTURE model-based clustering analysis of 2,583 present-day humans and 281 ancient samples; we show the results only for ancient samples for K = 11 clusters. b, Pairwise FST between 19 Ancient West Eurasian populations (arranged in approximate chronological order), and select present-day populations.

  7. Outgroup f3(Mbuti; X, Y) for pairs of ancient populations.
    Extended Data Fig. 3: Outgroup f3(Mbuti; X, Y) for pairs of ancient populations.

    The dendrogram is plotted for convenience and should not be interpreted as a phylogenetic tree. Areas of high shared genetic drift are ‘yellow’ and include from top-right to bottom-left along the diagonal: early Anatolian and European farmers; European hunter–gatherers, Steppe populations and populations admixed with steppe ancestry; populations from the Levant from the Epipalaeolithic (Natufians) to the Bronze Age; populations from Iran from the Mesolithic to the Late Neolithic.

  8. Reduction of genetic differentiation in West Eurasia over time.
    Extended Data Fig. 4: Reduction of genetic differentiation in West Eurasia over time.

    We measure differentiation by FST. Each column of the 5 × 5 matrix of plots represents a major region and each row the earliest population with at least two individuals from each major region.

  9. West Eurasian related admixture in East Africa, Eastern Eurasia and South Asia.
    Extended Data Fig. 5: West Eurasian related admixture in East Africa, Eastern Eurasia and South Asia.

    a, Levantine ancestry in Eastern Africa in the Human Origins dataset. b, Levantine ancestry in different Eastern African population in the dataset from Pagani et al. (2012); the remainder of the ancestry is a clade with Mota, a ~4,500 year old sample from Ethiopia49. c, EHG ancestry in Eastern Eurasians. d, Afontova Gora (AG2)-related ancestry in Eastern Eurasians; the remainder of their ancestry is a clade with Onge. e, Mixture proportions for South Asian populations showing that they can be modelled as having West Eurasian-related ancestry similar to that in populations from both the Eurasian steppe and Iran.

  10. Inferred position of ancient populations in West Eurasian PCA according to the model of Fig. 4.
    Extended Data Fig. 6: Inferred position of ancient populations in West Eurasian PCA according to the model of Fig. 4.
  11. Admixture from ghost populations using ‘cline intersection’.
    Extended Data Fig. 7: Admixture from ghost populations using ‘cline intersection’.

    af, We model each Test population (purple) as a mixture (pink) of a fixed reference population (blue) and a ghost population (orange) residing on the cline defined by two other populations (red and green) according to the visualization method of Supplementary Information, section 10. a, Early/Middle Bronze Age steppe populations are a mixture of Iran_ChL and a population on the WHG→SHG cline. b, Scandinavian hunter–gatherers (SHG) are a mixture of WHG and a population on the Iran_ChL→Steppe_EMBA cline. c, Caucasus hunter–gatherers (CHG) are a mixture of Iran_N and both WHG and EHG. d, Late Neolithic/Bronze Age Europeans are a mixture of the preceding Europe_MNChL population and a population with both EHG and Iran_ChL ancestry. e, Somali are a mixture of Mota49 and a population on the Iran_ChL→Levant_BA cline. f, Eastern European hunter–gatherers (EHG) are a mixture of WHG and a population on the Onge→Han cline.

  12. Admixture from a ‘ghost’ ANE population into both European and Eastern Eurasian ancestry.
    Extended Data Fig. 8: Admixture from a ‘ghost’ ANE population into both European and Eastern Eurasian ancestry.

    EHG, and Upper Palaeolithic Siberians Mal’ta 1 (MA1) and Afontova Gora 2 (AG2) are positioned near the intersection of clines formed by European hunter–gatherers (WHG, SHG, EHG) and Eastern non-Africans in the space of outgroup f3-statistics of the form f3(Mbuti; Papuan, Test) and f3(Mbuti; Switzerland_HG, Test).

Tables

  1. No evidence for admixture related to sub-Saharan Africans in Natufians
    Extended Data Table 1: No evidence for admixture related to sub-Saharan Africans in Natufians
  2. Admixture f3-statistics
    Extended Data Table 2: Admixture f3-statistics

Accession codes

Primary accessions

European Nucleotide Archive

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Author information

  1. These authors jointly supervised this work.

    • Ron Pinhasi &
    • David Reich

Affiliations

  1. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Iosif Lazaridis,
    • Nadin Rohland,
    • Swapan Mallick,
    • Kristin Stewardson,
    • Eadaoin Harney,
    • Qiaomei Fu &
    • David Reich
  2. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

    • Iosif Lazaridis,
    • Swapan Mallick,
    • Nick Patterson &
    • David Reich
  3. The Zinman Institute of Archaeology, University of Haifa, Haifa 3498838, Israel

    • Dani Nadel
  4. Department of Anthropology, Whitman College, Walla Walla, Washington 99362, USA

    • Gary Rollefson
  5. Department of Archaeology, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada

    • Deborah C. Merrett
  6. Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Swapan Mallick,
    • Kristin Stewardson,
    • Eadaoin Harney &
    • David Reich
  7. School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland

    • Daniel Fernandes,
    • Mario Novak,
    • Beatriz Gamarra,
    • Kendra Sirak,
    • Sarah Connell &
    • Ron Pinhasi
  8. CIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal

    • Daniel Fernandes
  9. Institute for Anthropological Research, Zagreb 10000, Croatia

    • Mario Novak
  10. Department of Anthropology, Emory University, Atlanta, Georgia 30322, USA

    • Kendra Sirak
  11. Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA

    • Eadaoin Harney
  12. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany

    • Qiaomei Fu
  13. Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China

    • Qiaomei Fu
  14. Department of Biology and Evolution, University of Ferrara, Ferrara I-44121, Italy

    • Gloria Gonzalez-Fortes
  15. Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK

    • Eppie R. Jones
  16. J.M. van Nassaulaan 9, Santpoort-Noord 2071 VA, The Netherlands

    • Songül Alpaslan Roodenberg
  17. Department of Prehistory and Archaeology, University of Miskolc, Miskolc-Egyetemváros 3515, Hungary

    • György Lengyel
  18. French National Centre for Scientific Research, UMR 7041, Nanterre Cedex 92023, France

    • Fanny Bocquentin
  19. Institute of Archaeology and Ethnology, National Academy of Sciences of the Republic of Armenia, Yerevan 0025, Republic of Armenia

    • Boris Gasparian
  20. University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, Pennsylvania 19104, USA

    • Janet M. Monge &
    • Michael Gregg
  21. Israel Antiquities Authority, Jerusalem 91004, Israel

    • Vered Eshed &
    • Ahuva-Sivan Mizrahi
  22. Department of Anthropology, University of Winnipeg, Winnipeg, Manitoba R3B 2E9, Canada

    • Christopher Meiklejohn
  23. Netherlands Institute in Turkey, Istanbul 34433, Turkey

    • Fokke Gerritsen
  24. Faculty of Biology, Alexandru Ioan Cuza University of Iasi, Iasi 700505, Romania

    • Luminita Bejenaru
  25. Department of Internal Medicine and Dermatology, Clinic of Endocrinology and Nephrology, Leipzig 04103, Germany

    • Matthias Blüher,
    • Michael Stumvoll &
    • Anke Tönjes
  26. Generation Scotland, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK

    • Archie Campbell &
    • Shona M. Kerr
  27. RCSI Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland

    • Gianpiero Cavalleri &
    • Edmund Gilbert
  28. Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain

    • David Comas
  29. Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8199 - EGID, Lille F-59000, France

    • Philippe Froguel &
    • Loic Yengo
  30. Imperial College London, Department of Genomics of Common Disease, London Hammersmith Hospital, London W12 0HS, UK

    • Philippe Froguel
  31. Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany

    • Peter Kovacs
  32. Max Planck Institute for the Science of Human History, Jena 07745, Germany

    • Johannes Krause
  33. School of History, Newman Building, University College Dublin, Belfield, Dublin 4, Ireland

    • Darren McGettigan
  34. Genealogical Society of Ireland, Dún Laoghaire, County Dublin, Ireland

    • Michael Merrigan &
    • Seamus O'Reilly
  35. Department of Anthropology, Binghamton University, State University of New York, New York 13902, USA

    • D. Andrew Merriwether &
    • Michel Shamoon-Pour
  36. Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK

    • Martin B. Richards
  37. Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia 27100, Italy

    • Ornella Semino &
    • Antonio Torroni
  38. Institutul de Cercetari Biologice, Iaşi 700505, Romania

    • Gheorghe Stefanescu
  39. Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH8 9AG, UK

    • James F. Wilson
  40. MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK

    • James F. Wilson
  41. Center of Excellence in Applied Biosciences, Yerevan State University, Yerevan 0025, Republic of Armenia

    • Nelli A. Hovhannisyan

Contributions

R.P. and D.R. conceived the idea for the study. D.N., G.R., D.C.M., S.C., S.A.R., G.L., F.B., B.Gas., J.M.M., M.G., V.E., A.M., C.M., F.G., N.A.H. and R.P. assembled skeletal material. N.R., D.F., M.N., B.Gam., K.Si., S.C., K.St., E.H., Q.F., G.G.-F., E.R.J., R.P. and D.R. performed or supervised ancient DNA wet laboratory work. L.B, M.B., A.C., G.C., D.C., P.F., E.G., S.M.K., P.K., J.K., D.M., M.M., D.A.M., S.O., M.B.R., O.S., M.S.-P., G.S., M.S., A.Tön., A.Tor., J.F.W., L.Y. and D.R. assembled present-day samples for genotyping. I.L, N.P. and D.R. developed methods for data analysis. I.L., S.M., Q.F., N.P. and D.R. analysed data. I.L., R.P. and D.R. wrote the manuscript and supplements.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:

Reviewer Information

Nature thanks O. Bar-Yosef, G. Coop and the other anonymous reviewer(s) for their contribution to the peer review of this work.

The aligned sequences are available through the European Nucleotide Archive under accession number PRJEB14455. Fully public subsets of the analysis datasets are at http://genetics.med.harvard.edu/reichlab/Reich_Lab/Datasets.html. The complete dataset (including present-day humans for which the informed consent is not consistent with public posting of data) is available to researchers who send a signed letter to D.R. indicating that they will abide by specified usage conditions (Supplementary Information, section 2).

Author details

Extended data figures and tables

Extended Data Figures

  1. Extended Data Figure 1: Principal components analysis of 991 present-day West Eurasians. (385 KB)

    The PCA analysis is performed on the same set of individuals as are reported in Fig. 1b, using EIGENSOFT. Here, we colour the samples by population (to highlight the present-day populations) instead of using grey points as in Fig. 1b (where the goal is to highlight ancient samples).

  2. Extended Data Figure 2: Genetic structure in ancient West Eurasian populations across time and decline of genetic differentiation over time. (333 KB)

    a, ADMIXTURE model-based clustering analysis of 2,583 present-day humans and 281 ancient samples; we show the results only for ancient samples for K = 11 clusters. b, Pairwise FST between 19 Ancient West Eurasian populations (arranged in approximate chronological order), and select present-day populations.

  3. Extended Data Figure 3: Outgroup f3(Mbuti; X, Y) for pairs of ancient populations. (296 KB)

    The dendrogram is plotted for convenience and should not be interpreted as a phylogenetic tree. Areas of high shared genetic drift are ‘yellow’ and include from top-right to bottom-left along the diagonal: early Anatolian and European farmers; European hunter–gatherers, Steppe populations and populations admixed with steppe ancestry; populations from the Levant from the Epipalaeolithic (Natufians) to the Bronze Age; populations from Iran from the Mesolithic to the Late Neolithic.

  4. Extended Data Figure 4: Reduction of genetic differentiation in West Eurasia over time. (177 KB)

    We measure differentiation by FST. Each column of the 5 × 5 matrix of plots represents a major region and each row the earliest population with at least two individuals from each major region.

  5. Extended Data Figure 5: West Eurasian related admixture in East Africa, Eastern Eurasia and South Asia. (315 KB)

    a, Levantine ancestry in Eastern Africa in the Human Origins dataset. b, Levantine ancestry in different Eastern African population in the dataset from Pagani et al. (2012); the remainder of the ancestry is a clade with Mota, a ~4,500 year old sample from Ethiopia49. c, EHG ancestry in Eastern Eurasians. d, Afontova Gora (AG2)-related ancestry in Eastern Eurasians; the remainder of their ancestry is a clade with Onge. e, Mixture proportions for South Asian populations showing that they can be modelled as having West Eurasian-related ancestry similar to that in populations from both the Eurasian steppe and Iran.

  6. Extended Data Figure 6: Inferred position of ancient populations in West Eurasian PCA according to the model of Fig. 4. (339 KB)
  7. Extended Data Figure 7: Admixture from ghost populations using ‘cline intersection’. (246 KB)

    af, We model each Test population (purple) as a mixture (pink) of a fixed reference population (blue) and a ghost population (orange) residing on the cline defined by two other populations (red and green) according to the visualization method of Supplementary Information, section 10. a, Early/Middle Bronze Age steppe populations are a mixture of Iran_ChL and a population on the WHG→SHG cline. b, Scandinavian hunter–gatherers (SHG) are a mixture of WHG and a population on the Iran_ChL→Steppe_EMBA cline. c, Caucasus hunter–gatherers (CHG) are a mixture of Iran_N and both WHG and EHG. d, Late Neolithic/Bronze Age Europeans are a mixture of the preceding Europe_MNChL population and a population with both EHG and Iran_ChL ancestry. e, Somali are a mixture of Mota49 and a population on the Iran_ChL→Levant_BA cline. f, Eastern European hunter–gatherers (EHG) are a mixture of WHG and a population on the Onge→Han cline.

  8. Extended Data Figure 8: Admixture from a ‘ghost’ ANE population into both European and Eastern Eurasian ancestry. (118 KB)

    EHG, and Upper Palaeolithic Siberians Mal’ta 1 (MA1) and Afontova Gora 2 (AG2) are positioned near the intersection of clines formed by European hunter–gatherers (WHG, SHG, EHG) and Eastern non-Africans in the space of outgroup f3-statistics of the form f3(Mbuti; Papuan, Test) and f3(Mbuti; Switzerland_HG, Test).

Extended Data Tables

  1. Extended Data Table 1: No evidence for admixture related to sub-Saharan Africans in Natufians (246 KB)
  2. Extended Data Table 2: Admixture f3-statistics (714 KB)

Supplementary information

Excel files

  1. Supplementary Table 1 (65 KB)

    This file contains Supplementary Data Table 1.

  2. Supplementary Table 2 (23 KB)

    This file contains Supplementary Data Table 2.

  3. Supplementary Table 3 (60 KB)

    This file contains Supplementary Data Table 3.

PDF files

  1. Supplementary Information (9.8 MB)

    This file contains Supplementary Text, Data and References – see contents page for details.

Additional data