Abstract
The Linearbandkeramik (LBK) Neolithic communities were the first to spread farming across large parts of Europe. We report genome-wide data for 250 individuals: 178 individuals from whole-cemetery surveys of the Alföld Linearbankeramik Culture eastern LBK site of Polgár-Ferenci-hát, the western LBK site of Nitra Horné Krškany and the western LBK settlement and massacre site of Asparn-Schletz, as well as 48 LBK individuals from 16 other sites and 24 earlier Körös and Starčevo individuals from 17 more sites. Here we show a systematically higher percentage of western hunter-gatherer ancestry in eastern than in western LBK sites, showing that these two distinct LBK groups had different genetic trajectories. We find evidence for patrilocality, with more structure across sites in the male than in the female lines and a higher rate of within-site relatives for males. At Asparn-Schletz we find almost no relatives, showing that the massacred individuals were from a large population, not a small community.
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Data availability
All sequencing data are freely available at the European Nucleotide Archive with the accession number PRJEB64177. All the data used for comparison with the data produced in this study are available in the Allen Ancient DNA Resource63.
Code availability
We can provide the full code used in this project upon request.
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Acknowledgements
We dedicate this paper to the memory of Tibor Paluch, who passed away while it was being written. This study followed principles for ethical DNA research on human remains47. We thank the authorities and sample stewards, including museums, museum curators and archaeologists; N. Adamski, R. Bernardos and K. Stewardson for help with sample handling and sample preparation; and Z. Zhang for bioinformatics support. Ancient DNA data generation and analysis were supported by the National Institutes of Health (grant nos GM100233 and HG012287), the John Templeton Foundation (grant no. 61220), a gift from J.-F. Clin, the Howard Hughes Medical Institute and the Allen Discovery Center programme, a Paul G. Allen Frontiers Group advised programme of the Paul G. Allen Family Foundation. The physical anthropology and archaeological work were supported by a grant from the Hungarian Research, Development, and Innovation Office (project no. FK128013) (T. Hajdu), the Bolyai Scholarship of the Hungarian Academy of Sciences (T. Hajdu) and the New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund (TSZ, T. Hajdu). Z.T. was supported by the Ministry of Culture via institutional funding for the long-term conceptual development of the Moravian Museum research organization (DKRVO, MK000094862). M.N. was supported by the Croatian Science Foundation (HRZZ IP-2016-06-1450). C.L. was funded by a grant from the Romanian Ministry of Research, Innovation, and Digitisation (41PFE/30.12.2021) within PNCDI III. M. Kuhlwilm was supported by the Vienna Science and Technology Fund (WWTF) (10.47379/VRG20001). We thank L. Buster for critical comments. The author-accepted version of this article, that is, the version not reflecting proofreading and editing and formatting changes following the article’s acceptance, is subject to the Howard Hughes Medical Institute (HHMI) Open Access to Publications policy, as HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author-accepted manuscript can be made freely available under a CC BY 4.0 license immediately upon publication.
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P.G., R. Pinhasi, P.B., D.H., M.T.-N., A. Anders and D.R. conceived the study. M.T.-N., A. Anders, F.P., A.S., M.D., J.P., C.L., T.P., M.K.Š., M.S., Ž.B., F.N., L.D.S., L.S., O.C.-L., T. Hajdu, F. Zoltán, P.M., E.G.N., Z.M.V., A.M.H., L.A.H., K.T.B., L.D., T.S., J.J., M.Š., S.S., K.T., P.C., I.P., R. Patay, B.H., C.S., G.L., Z.T., D.B., M.R., M.N., J.D., T. Haga, J.B., P.R., K.S., Z.F., M. Krošláková, A.P. and B.V. provided the samples. K.T.Ö., F. Zalzala, J.N.W., J.O., B.Z., K.M., E.C., M.F., K.C., O.C., D.M.F., C.S., K.B., F.C., G.B.M., L.Q., N.B., D.K., S.F., V.O., E.H., N.R., A.M.L. and M. Mah performed the experiments. P.G., X.H., P.B., I.O., M. Kuhlwilm, S.S., H.R., A. Akbari, P.F.P., O.C., M.H., S.M., A.M., I.L., R.F. and A.K. analysed the data. P.G., R. Pinhasi, P.B. and D.R. wrote the manuscript with input from all authors.
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Extended data
Extended Data Fig. 1 Principal Component Analysis (PCA).
PCA performed with 879 modern Eurasian individuals in which the ancient individuals were projected. The modern individuals have been removed from the image. The PCA shows the clustering of the LBK and the position of individuals along the X axis, indicating differential WHG affinities and showing that WHG (represented by two Körös culture outliers with entirely WHG ancestry) are more closely related to ALPC. Three individuals: I6914 (Austria_LBK) and I1507, I497 (Köros) are outliers.
Extended Data Fig. 2 qpWave plots.
qpWave plots to test for individual differentiation, with each population represented in one plot. Grey colour means results were highly significant (not consistent with being genetically homogeneous). The number after the name of each individual relates is the point estimate of WHG ancestry from qpAdm. A) ALPC individuals. Individuals I21898, I10349, I21902, I18660, I10350, I18656, I18695, I4186, I1499, I21714, and I2377 are labelled in our analysis as ALPC outliers with high WHG ancestry. Individuals: I21828, I21830, I10351, I10352, I10353, I18657, I21767, 17933, I1500, I2380, I3537, I17455, I18636, I29883, I18641 and I4187 are labelled in our analysis as ALPC outliers with low WHG ancestry. B) Austria LBK Individuals: Individuals I27785, I25349, I6913, I6912 and I24028 are labelled in our analysis as outliers with high WHG ancestry. C) Germany LBK Individuals, D) Slovakia LBK Individuals: Individual I18144 is labelled in our analysis as an outlier with high WHG ancestry. E) Transdanubia_Hungary LBK Individuals: individuals I1882 and I1883 are labelled in our analysis as outliers with high WHG ancestry. We used qpWave from admixtools to perform the plots, each square represents the two-sided p-value of every single test.
Extended Data Fig. 3 Parental haplogroups.
A,B, Distribution of the Y chromosome and mtDNA haplogroups per population. The Y-axis represents the number of individuals.
Extended Data Fig. 4 Isotopic data.
Isotope data from Pólgar-Ferenci-hát. Here we plot the ratio δ13C/δ15N. Each dot represents one individual and the colour denotes the family.
Extended Data Fig. 5 Runs of Homozygosity.
ROH distribution in the dataset. A)LBK individuals, B) ALPC individuals, C) Koros and Starcevo individuals. Individuals with more than 400,000 SNPs and the assessed ROH. Individuals in the ALPC group show a higher rate of close-kin unions (as reflected in the presence of ROH segments >20 cM) than the rest of the dataset.
Extended Data Fig. 6 Natural selection in Neolithic.
Tests for positive selection in the ALPC and LBK population, made with qqman66. The red lines indicate the top 0.05% cutoff. (A) Normalized iHS scores in ALPC. (B) Normalized iHS scores in LBK. (C) Normalized unphased iHS scores in ALPC. (D) Normalized unphased iHS scores in LBK. (E) Normalized nSL scores in ALPC. (F) Normalized nSL scores in LBK. (G) Normalized unphased nSL scores in ALPC. (H) Normalized unphased nSL scores in LBK.
Extended Data Fig. 7 Correspondence between the ancestry in ALPC and LBK segments with the selection scan values.
Each dot represents a region of 0.2 cM of the genome, in the Y-axis we display the average WHG ancestry of the region, and in the X-axis the average selection scores from candidate SNPs within the region (Supplementary Table 11). We show the two-sided Spearman correlation coefficients and p-value.
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Gelabert, P., Bickle, P., Hofmann, D. et al. Social and genetic diversity in first farmers of central Europe. Nat Hum Behav 9, 53–64 (2025). https://doi.org/10.1038/s41562-024-02034-z
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DOI: https://doi.org/10.1038/s41562-024-02034-z
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