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The genomic history of southeastern Europe


Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west–east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.

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Figure 1: Geographic and genetic structure of 216 analysed individuals.
Figure 2: Structure and change in hunter-gatherer-related populations.
Figure 3: Structure and change in northwestern-Anatolian-Neolithic-related populations.

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We thank D. Anthony, I. Lazaridis and M. Lipson for comments on the manuscript, B. Llamas, A. Cooper and A. Furtwängler for contributions to laboratory work, R. Evershed for contributing 14C dates and F. Novotny for assistance with samples. Support for this project was provided by the Human Frontier Science Program fellowship LT001095/2014-L to I.M., by DFG grant AL 287 / 14-1 to K.W.A.; by Irish Research Council grant GOIPG/2013/36 to D.F.; by the NSF Archaeometry program BCS-1460369 to D.J.K. for AMS 14C work; by MEN-UEFISCDI grant, Partnerships in Priority Areas Program – PN II (PN-II-PT-PCCA-2013-4-2302) to C.L.; by Croatian Science Foundation grant IP-2016-06-1450 to M.N. and I.J.; by European Research Council grant ERC CoG 724703 and Deutsche Forschungsgemeinschaft DFG FOR2237 to K.H.; by ERC starting grant ADNABIOARC (263441) to R.P.; and by US National Science Foundation HOMINID grant BCS-1032255, US National Institutes of Health grant GM100233, the Howard Hughes Medical Institute and an Allen Discovery Center grant from the Paul Allen Foundation to D.R.

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Authors and Affiliations



S.A.-R., A.S.-N., S.Vai., S.A., K.W.A., R.A., D.A., A.A., N.A., K.B., M.B.G., H.B., M.B., A.Bo., Y.B., A.Bu., J.B., S.C., N.J.C., R.C., M.C., C.C., D.G.D., N.E., M.Fr., B.Gal., G.G., B.Ge., T.Ha., V.H., K.H., T.Hi., S.I., I.J., I.Ka., D.Ko., A.K., D.La., M.La., C.L., M.Le., K.L., D.L.V., D.Lo., I.L., M.Ma., F.M., K.M., H.M., M.Me., P.M., V.M., V.P., T.D.P., A.Si., L.S., M.Š., V.S., P.S., A.St., T.S., M.T.-N., C.T., I.V., F.Va., S.Vas., F.Ve., S.Ve., E.V., B.V., C.V., J.Z., S.Z., P.W.S., G.C., R.K., D.C., G.Z., B.Gay., M.Li., A.G.N., I.P., A.P., D.B., C.B., J.K., R.P. and D.R. assembled and interpreted archaeological material. C.P., A.S.-N., N.R., N.B., F.C., O.C., D.F., M.Fe., B.Gam., G.G.F., W.H., E.H., E.J., D.Ke., B.K.-K., I.Ku., M.Mi., A.M., K.N., M.N., J.O., S.P., K.Si., K.St. and S.Vai. performed laboratory work. I.M., C.P., A.S.-N., S.M., I.O., N.P. and D.R. analysed data. D.J.K., S.T., D.B. and C.B. interpreted 14C dates. J.K., R.P. and D.R. supervised analysis or laboratory work. I.M. and D.R. wrote the paper with input from all co-authors.

Corresponding authors

Correspondence to Iain Mathieson, Ron Pinhasi or David Reich.

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The authors declare no competing financial interests.

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Reviewer Information Nature thanks C. Renfrew, A. Scally and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Figure 1 Principal components analysis of ancient individuals.

Points for 486 ancient individuals are projected onto principal components defined by 777 present-day west Eurasian individuals (grey points). This differs from Fig. 1b in that the plot is not cropped and the present-day individuals are shown.

Extended Data Figure 2 Supervised ADMIXTURE analysis.

Supervised ADMIXTURE analysis modelling each ancient individual (one per row), as a mixture of populations represented by clusters that are constrained to contain northwestern-Anatolian Neolithic (grey), Yamnaya from Samara (yellow), EHG (pink) and WHG (green) populations. Dates in parentheses indicate approximate range of individuals in each population. This differs from Fig. 1d in that it contains some previously published samples7,9,10,19,23,26 and includes sample identification numbers.

Extended Data Figure 3 Unsupervised ADMIXTURE analysis.

Unsupervised ADMIXTURE plot from k = 4 to 12 on a dataset consisting of 1,099 present-day individuals and 476 ancient individuals. We show newly reported ancient individuals and some previously published individuals7,10,19,22,23,26 for comparison.

Extended Data Figure 4 Genetic spatial structure in hunter-gatherers.

We infer the estimated effective migration surface62, a model of genetic relatedness in which individuals move in a random direction from generation to generation on an underlying grid, such that genetic relatedness is determined by distance. The migration parameter, m, defining the local rate of migration, varies on the grid and is inferred. This plot shows log10(m), scaled relative to the average migration rate, which is arbitrary. Thus log10(m) = 2, for example, implies that the rate of migration at this point on the grid is 100 times higher than average. To restrict the model as much as possible to hunter-gatherer populations, the migration surface is inferred using data from 116 individuals that date to earlier than approximately 5000 bc and have no northwestern-Anatolian-Neolithic-related ancestry. Although the migration surface is sensitive to sampling and fine-scale features may not be interpretable, the migration ‘barrier’ (region of low migration) running north-to-south and separating populations with primarily WHG ancestry from those with primarily EHG ancestry seems to be robust, and consistent with inferred admixture proportions. This analysis suggests that Mesolithic hunter-gatherer population structure was clustered and not smoothly clinal (that is, genetic differentiation did not vary consistently with distance). Superimposed on this background, pie charts show the WHG, EHG and CHG ancestry proportions inferred for populations used to construct the migration surface. This represents another way of visualizing the data in Fig. 2, Supplementary Table 3.1.3; we use two population models if they fit with P > 0.01, and three population models otherwise. Pie charts with only a single colour are those that were fixed to be the source populations.

Extended Data Figure 5 Sex bias in hunter-gatherer admixture.

The log-likelihood surfaces for the proportion of female (x axis) and male (y axis) ancestors that are hunter-gatherer-related for the combined populations analysed in Fig. 3c, and the two populations with the strongest evidence for sex bias. Numbers in parentheses, number of individuals in each group. The log-likelihood scale ranges from 0 to −10, in which 0 is the feasible point with the highest likelihood.

Supplementary information

Life Sciences Reporting Summary (PDF 72 kb)

Supplementary Information

This file contains Supplementary Notes 1-3. (PDF 11029 kb)

Supplementary Data

This file contains Supplementary Tables 1-5. Supplementary Table 1 shows the details of ancient individuals analysed in this study, Supplementary Table 2 shows the key D-statistics to support statements about population history, Supplementary Table 3 shows the qpAdm models with 7-population outgroup set, Supplementary Table 4 shows the qpAdm models with extended 14-population outgroup set, Supplementary Table 5 shows the qpAdm models for Neolithic populations for chromosome X and Supplementary Table 6 shows the additional 14C dating information. (XLSX 268 kb)

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Mathieson, I., Alpaslan-Roodenberg, S., Posth, C. et al. The genomic history of southeastern Europe. Nature 555, 197–203 (2018).

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