Parallel palaeogenomic transects reveal complex genetic history of early European farmers - Nature
- ️Reich, David
- ️Wed Nov 08 2017
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References
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Acknowledgements
We thank I. Lazaridis, P.-R. Loh, I. Mathieson, I. Olalde, E. Palkopoulou, N. Patterson and P. Skoglund for helpful comments and suggestions; J. Krause for providing the Stuttgart sample for which we generated a new library in this study; A. Whittle and A. Bayliss from The Times of Their Lives project for providing the radiocarbon date for sample VEJ5a; and B. Havasi (Balaton Museum), G. V. Székely (Katona József Museum), C. Farkas (Dobó István Museum), B. Nagy (Herman Ottó Museum), I. Pap, A. Kustár, T. Hajdu (Hungarian Natural History Museum), J. Ódor (Wosinsky Mór Museum), E. Nagy (Janus Pannonius Museum), P. Rácz (King St Stephen Museum), L. Szathmáry (Debrecen University), N. Kalicz, V. Voicsek, O. Vajda-Kiss, V. Majerik and I. Ko˝vári for assistance with samples. This work was supported by the Australian Research Council (grant DP130102158 to B.L. and W.H.), Hungarian National Research, Development and Innovation Office (K 119540 to B.M.), German Research Foundation (Al 287/7-1, 10-1 and 14-1 to K.W.A.), FEDER and Ministry of Economy and Competitiveness of Spain (BFU2015-64699-P to C.L.-F.), National Science Foundation (HOMINID grant BCS-1032255 to D.R.), National Institutes of Health (NIGMS grant GM100233 to D.R.), and Howard Hughes Medical Institute (D.R.).
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Mark Lipson and Anna Szécsényi-Nagy: These authors contributed equally to this work.
Authors and Affiliations
Department of Genetics, Harvard Medical School, Boston, 02115, Massachusetts, USA
Mark Lipson, Swapan Mallick, Nadin Rohland, Kristin Stewardson, Matthew Ferry, Megan Michel, Jonas Oppenheimer, Nasreen Broomandkhoshbacht, Eadaoin Harney, Susanne Nordenfelt & David Reich
Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, 1097, Hungary
Anna Szécsényi-Nagy, Annamária Pósa, Balázs Stégmár, Balázs Gusztáv Mende, Kitti Köhler, Krisztián Oross, Mária Bondár, Tibor Marton, Anett Osztás, János Jakucs, Gábor Serlegi & Eszter Bánffy
Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, 02142, Massachusetts, USA
Swapan Mallick & David Reich
Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, 55128, Germany
Victoria Keerl, Ruth Bollongino & Joachim Burger
Howard Hughes Medical Institute, Harvard Medical School, Boston, 02115, Massachusetts, USA
Kristin Stewardson, Matthew Ferry, Megan Michel, Jonas Oppenheimer, Nasreen Broomandkhoshbacht, Eadaoin Harney & David Reich
Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, 5005, South Australia, Australia
Bastien Llamas, Alan Cooper & Wolfgang Haak
Móra Ferenc Museum, Szeged 6720, Hungary
Tibor Paluch & Ferenc Horváth
Herman Ottó Museum, Miskolc 3529, Hungary
Piroska Csengeri & Judit Koós
Institute of Archaeological Sciences, Eötvös Loránd University, Budapest, 1088, Hungary
Katalin Sebők, Alexandra Anders & Pál Raczky
Laczkó Dezso˝ Museum, Veszprém 8200, Hungary
Judit Regenye
Balaton Museum, Keszthely 8360, Hungary
Judit P. Barna
Department of Archaeological Excavations and Artefact Processing, Hungarian National Museum, Budapest, 1088, Hungary
Szilvia Fábián
Jósa András Museum, Nyíregyháza 4400, Hungary
Zoltán Toldi
Déri Museum, Debrecen 4026, Hungary
Emese Gyöngyvér Nagy & János Dani
Department of Biological Anthropology, Szeged University, Szeged 6726, Hungary
Erika Molnár & György Pálfi
Department of Biochemistry and Medical Chemistry, University of Pécs, Pécs, 7624, Hungary
László Márk
Imaging Center for Life and Material Sciences, University of Pécs, Pécs, 7624, Hungary
László Márk
Szentágothai Research Center, University of Pécs, Pécs, 7624, Hungary
László Márk, Béla Melegh & Zsolt Bánfai
PTE-MTA Human Reproduction Research Group, Pécs, 7624, Hungary
László Márk
Department of Medical Genetics and Szentágothai Research Center, University of Pécs, Pécs 7624, Hungary
Béla Melegh & Zsolt Bánfai
Dobó István Castle Museum, Eger, 3300, Hungary
László Domboróczki
Department of Geography, Prehistory, and Archaeology, University of the Basque Country, Investigation Group IT622-13, Vitoria-Gasteiz 01006, Spain
Javier Fernández-Eraso & José Antonio Mujika-Alustiza
CRONOS SC, Burgos 09007, Spain
Carmen Alonso Fernández & Javier Jiménez Echevarría
Department of Prehistoric Archaeology, Free University of Berlin, Berlin 14195, Germany
Jörg Orschiedt
Curt-Engelhorn-Centre Archaeometry gGmbH, Mannheim 68159, Germany
Jörg Orschiedt
Commission for Westphalian Antiquities, Westphalia-Lippe Regional Association, Münster, 48157, Germany
Kerstin Schierhold
State Office for Heritage Management and Archaeology Saxony-Anhalt and State Heritage Museum, Halle 06114, Germany
Harald Meller
Environment Institute, University of Adelaide, Adelaide, South Australia, 5005, Australia
Alan Cooper
Romano-Germanic Commission, German Archaeological Institute, Frankfurt am Main 60325, Germany
Eszter Bánffy
Center of Natural and Cultural History of Man, Danube Private University, Krems-Stein 3500, Austria
Kurt W. Alt
Department of Biomedical Engineering, University of Basel, Allschwil 4123, Switzerland
Kurt W. Alt
Institute for Integrative Prehistory and Archaeological Science, University of Basel, Basel 4055, Switzerland
Kurt W. Alt
Institute of Evolutionary Biology (CSIC-UPF), Barcelona 08003, Spain
Carles Lalueza-Fox
Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
Wolfgang Haak
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- Anna Szécsényi-Nagy
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- Swapan Mallick
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- Balázs Stégmár
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- Szilvia Fábián
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- Gábor Serlegi
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- Zoltán Toldi
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- Emese Gyöngyvér Nagy
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- Erika Molnár
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Contributions
A.S.-N., J.B., E.B., K.W.A., C.L.-F., W.H. and D.R. designed and supervised the study. B.G.M., K.K., K.O., M.B., T.M., A.O., J.J., T.P., F.H., P.C., J.K., K.Se., A.A., P.R., J.R., J.P.B., S.F., G.S., Z.T., E.G.N., J.D., E.M., G.P., L.M., B.M., Z.B., L.D., J.F.-E., J.A.M.-A., C.A.F., J.J.E., R.B., J.Or., K.Sc., H.M., A.C., J.B., E.B., K.W.A., C.L.-F. and W.H. provided samples and assembled archaeological and anthropological information. A.S.-N., A.P., B.S., V.K., N.R., K.St., M.F., M.M., J.Op., N.B., E.H., S.N. and B.L. performed laboratory work. M.L., A.S.-N., S.M. and D.R. analysed genetic data. M.L., A.S.-N. and D.R. wrote the manuscript with input from all coauthors.
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Correspondence to Mark Lipson, Anna Szécsényi-Nagy or David Reich.
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Extended data figures and tables
Extended Data Figure 1 First two principal components from the PCA.
We computed the principal components (PCs) for a set of 782 present-day western Eurasian individuals genotyped on the Affymetrix Human Origins array (background grey points) and then projected ancient individuals onto these axes. A close-up omitting the present-day Bedouin population is shown.
Extended Data Figure 2 Scaffold admixture graph used for modelling the European Neolithic populations.
Dotted lines denote admixture events. Neolithic Anatolians, LB1 and KO1 are modelled as admixed, with basal Eurasian ancestry, deeper European hunter-gatherer ancestry and FEF ancestry, respectively. European test populations were fitted as a mixture of FEF and ancestry related to one or two of the four WHG individuals (here VIL-related as an example). See Supplementary Information section 6 for details.
Extended Data Figure 3 Examples of ALDER weighted linkage disequilibrium decay curves.
Weighted linkage disequilibrium (LD) curves are shown as a function of genetic distance d, using Neolithic Anatolians and WHG as references, for four individuals: BAM17b (Starčevo Early Neolithic), CB13 (Iberia Early Neolithic), Bla8 (Blätterhöhle hunter-gatherer) and KO1. The results shown here use helper individuals M11-363 (Neolithic Anatolian), L11-322 (Neolithic Anatolian), BIC and LB1, respectively, and have fitted dates (blue curves) of 3.8 ± 1.2, 18.3 ± 6.0, 13.1 ± 2.7 and 21.6 ± 8.8 generations (compared to final individual-level dates of 4.5 ± 1.9, 17.5 ± 3.5, 12.1 ± 2.9 and 21.0 ± 7.0 generations; see Supplementary Information section 7). Note that the x-axis scales are different for the four plots.
Extended Data Figure 4 Hunter-gatherer ancestry as a function of latitude and longitude for Neolithic individuals.
a, b, Early and Middle Neolithic Hungary. c, d, Late Neolithic and Chalcolithic Hungary. e, f, Iberia. HG, hunter-gatherer; Protob., Protoboleráz.
Extended Data Figure 5 Germany and Iberia time series and simulated data.
a, Dates of admixture. b, Hunter-gatherer ancestry proportions, normalized to the total of the most recent (rightmost) population. Symbols are as in Figs 1, 2 and indicate population-level mean ± 2 s.e.m. Yellow dashed lines represent continuous admixture simulations: from top to bottom, diminishing 5% per generation, diminishing 3%, diminishing 1% and uniform. Green solid lines represent pulse-plus-continuous admixture simulations: from top to bottom, all hunter-gatherer ancestry in a pulse at time zero; three-quarters of final hunter-gatherer ancestry in an initial pulse followed by uniform continuous gene flow; half in initial pulse and half continuous; and one-quarter in initial pulse.
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Lipson, M., Szécsényi-Nagy, A., Mallick, S. et al. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature 551, 368–372 (2017). https://doi.org/10.1038/nature24476
Received: 01 March 2017
Accepted: 06 October 2017
Published: 08 November 2017
Issue Date: 16 November 2017
DOI: https://doi.org/10.1038/nature24476