Abstract
We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes1,2,3,4 with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians3, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations’ deep relationships and show that early European farmers had ∼44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages.
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Accession codes
Primary accessions
European Nucleotide Archive
Data deposits
The aligned sequences are available through the European Nucleotide Archive under accession number PRJEB6272. The fully public version of the Human Origins dataset can be found at (http://genetics.med.harvard.edu/reichlab/Reich_Lab/Datasets.html). The full version of the dataset (including additional samples) is available to researchers who send a signed letter to D.R. indicating that they will abide by specified usage conditions (Supplementary Information section 9).
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Acknowledgements
We thank the 1,615 volunteers from 147 diverse populations who donated DNA samples and whose genetic data are newly reported in this study. We are grateful to C. Beall, N. Bradman, A. Gebremedhin, D. Labuda, M. Nelis and A. Di Rienzo for sharing DNA samples; to D. Weigel, C. Lanz, V. Schünemann, P. Bauer and O. Riess for support and access to DNA sequencing facilities; to P. Johnson for advice on contamination estimation; to G. Hellenthal for help with the ChromoPainter software; and to P. Skoglund for sharing graphics software. We thank K. Nordtvedt for alerting us to newly discovered Y-chromosome SNPs. We downloaded the POPRES data from dbGaP at (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000145.v4.p2) through dbGaP accession number phs000145.v1.p2. We thank all the volunteers who donated DNA. We thank the staff of the Unità Operativa Complessa di Medicina Trasfusionale, Azienda Ospedaliera Umberto I, Siracusa, Italy for assistance in sample collection; and The National Laboratory for the Genetics of Israeli Populations for facilitating access to DNA. We thank colleagues at the Applied Genomics at the Children’s Hospital of Philadelphia, especially H. Hakonarson, C. Kim, K. Thomas, and C. Hou, for genotyping samples on the Human Origins array. J.Kr., A.M. and C.P. are grateful for support from DFG grant number KR 4015/1-1, the Carl-Zeiss Foundation and the Baden Württemberg Foundation. S.P., G.R., Q.F., C.F., K.P., S.C. and J.Ke. acknowledge support from the Presidential Innovation Fund of the Max Planck Society. G.R. was supported by an NSERC fellowship. J.G.S. acknowledges use of the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by NSF grant number OCI-1053575. E.B. and O.B. were supported by RFBR grants 13-06-00670, 13-04-01711, 13-04-90420 and by the Molecular and Cell Biology Program of the Presidium, Russian Academy of Sciences. B.M. was supported by grants OTKA 73430 and 103983. A.Saj. was supported by a Finnish Professorpool (Paulo Foundation) Grant. The Lithuanian sampling was supported by the LITGEN project (VP1-3.1-ŠMM-07-K-01-013), funded by the European Social Fund under the Global Grant Measure. A.S. was supported by Spanish grants SAF2011-26983 and EM 2012/045. O.U. was supported by Ukrainian SFFS grant F53.4/071. S.A.T. was supported by NIH Pioneer Award 8DP1ES022577-04 and NSF HOMINID award BCS-0827436. K.T. was supported by an Indian CSIR Network Project (GENESIS: BSC0121). L.S. was supported by an Indian CSIR Bhatnagar Fellowship. R.V., M.M., J.P. and E.M. were supported by the European Union Regional Development Fund through the Centre of Excellence in Genomics to the Estonian Biocentre and University of Tartu and by an Estonian Basic Research grant SF0270177As08. M.M. was additionally supported by Estonian Science Foundation grant number 8973. J.G.S. and M.S. were supported by NIH grant GM40282. P.H.S. and E.E.E. were supported by NIH grants HG004120 and HG002385. D.R. and N.P. were supported by NSF HOMINID award BCS-1032255 and NIH grant GM100233. D.R. and E.E.E. are Howard Hughes Medical Institute investigators. This project has been funded in part with federal funds from the National Cancer Institute, National Institutes of Health, under contract HHSN26120080001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government. This Research was supported in part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.
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B.B., E.E.E., J.Bu., M.S., S.P., J.Ke., D.R. and J.Kr. supervised the study. I.L., N.P., A.M., G.R., S.M., K.K., P.H.S., J.G.S., S.C., M.L., Q.F., H.L., C.dF., K.P., W.H., M.Met., M.Mey. and D.R. analysed genetic data. F.H., E.F., D.D., M.F., J.-M.G., J.W., A.C. and J.Kr. obtained human remains. A.M., C.E., R.Bo., K.I.B., S.S., C.P., N.R. and J.Kr. processed ancient DNA. I.L., N.P., S.N., N.R., G.A., H.A.B., G.Ba., E.B., O.B., R.Ba., G.Be., H.B.-A., J.Be., F.Be., C.M.B., F.Br., G.B.J.B., F.C., M.C., D.E.C.C., D.Cor., L.D., G.vD., S.D., J.-M.D., S.A.F., I.G.R., M.G., M.H., B.M.H., T.H., U.H., A.R.J., S.K.-Y., R.Kh., E.K., R.Ki., T.K., W.K., V.K., A.K., L.L., S.L., T.L., R.W.M., B.M., E.M., J.Mol., J.Mou., K.N., D.N., T.N., L.O., J.P., F.P., O. P., V.R., F.R., I.R., R.R., H.S., A.Saj., A.Sal., E.B.S., A.Tar., D.T., S.T., I.U., O.U., R.Va., M.Vi., M.Vo., C.A.W., L.Y., P.Z., T.Z., C.C., M.G.T., A.R.-L., S.A.T., L.S., K.T., R.Vi., D.Com., R.S., M.Met., S.P. and D.R. assembled the genotyping dataset. I.L., N.P., D.R. and J.Kr. wrote the manuscript with help from all co-authors.
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U.H. is an employee of Illumina, T.L. is an employee of Amgen, and J.M. is an employee of 23andMe.
Extended data figures and tables
Extended Data Figure 1 Photographs of analysed ancient samples.
a, Loschbour skull. b, Stuttgart skull, missing the lower right M2 we sampled. c, Excavation at Kanaljorden in Motala, Sweden. d, Motala 1 in situ.
Extended Data Figure 2 Pairwise sequential Markovian coalescent (PSMC) analysis.
a, Inference of population size as a function of time, showing a very small recent population size over the most recent period in the ancestry of Loschbour (at least the last 5–10 thousand years). b, Inferred time since the most recent common ancestor from the PSMC for chromosomes 20, 21, 22 (top to bottom); Stuttgart is plotted on top and Loschbour at bottom.
Extended Data Figure 3 ADMIXTURE analysis (K = 2 to K = 20).
Ancient samples (Loschbour, Stuttgart, Motala_merge, Motala12, MA1, and LaBraña) are on the left.
Extended Data Figure 4 ANE ancestry is present in both Europe and the Near East but WHG ancestry is restricted to Europe, which cannot be due to a single admixture event.
On the x axis we present the statistic f4(Test, Stuttgart; MA1, Chimp), which measures where MA1 shares more alleles with a test population than with Stuttgart. It is positive for most European and Near Eastern populations, consistent with ANE (MA1-related) gene flow into both regions. On the y axis we present the statistic f4(Test, Stuttgart; Loschbour, Chimp), which measures whether Loschbour shares more alleles with a test sample than with Stuttgart. Only European populations show positive values of this statistic, providing evidence of WHG (Loschbour-related) admixture only in Europeans.
Extended Data Figure 5 MA1 is the best surrogate for ANE for which we have data.
Europeans share more alleles with MA1 than with Karitiana, as we see from the fact that in a plot of f4(Test, BedouinB; MA1, Chimp) and f4(Test, BedouinB; Karitiana, Chimp), the European cline deviates in the direction of MA1, rather than Karitiana (the slope is > 1 and European populations are above the line indicating inequality of these two statistics).
Extended Data Figure 6 The differential relatedness of west Eurasians to Stuttgart (EEF), Loschbour (WHG), and MA1 (ANE) cannot be explained by two-way mixture.
We plot on a West Eurasian map the statistic f4(Test, Chimp; A1, A2), where A1 and A2 are a pair of the three ancient samples representing the three ancestral populations of Europe. a, In both Europe and the Near East/Caucasus, populations from the south have more relatedness to Stuttgart than those from the north where ANE influence is also important. b, Northern European populations share more alleles with Loschbour than with Stuttgart, as they have additional WHG ancestry beyond what was already present in EEF. c, We observe a striking contrast between Europe west of the Caucasus and the Near East in degree of relatedness to WHG. In Europe, there is a much higher degree of allele sharing with Loschbour than with MA1, which we ascribe to the 60–80% WHG/(WHG + ANE) ratio in most Europeans that we report in Supplementary Information section 14. In contrast, the Near East has no appreciable WHG ancestry but some ANE ancestry, especially in the northern Caucasus. (Jewish populations are marked with a square in this figure to assist in interpretation as their ancestry is often anomalous for their geographic regions.)
Extended Data Figure 7 Evidence for Siberian gene flow into far north-eastern Europe.
Some north-eastern European populations (Chuvash, Finnish, Russian, Mordovian, Saami) share more alleles with Han Chinese than with other Europeans who are arrayed in a cline from Stuttgart to Lithuanians/Estonians in a plot of f4(Test, BedouinB; Han, Mbuti) against f4(Test, BedouinB; MA1, Mbuti).
Supplementary information
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Lazaridis, I., Patterson, N., Mittnik, A. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014). https://doi.org/10.1038/nature13673
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DOI: https://doi.org/10.1038/nature13673
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