Abstract
Present-day people from England and Wales have more ancestry derived from early European farmers (EEF) than did people of the Early Bronze Age1. To understand this, here we generated genome-wide data from 793 individuals, increasing data from the Middle to the Late Bronze Age and Iron Age in Britain by 12-fold, and western and central Europe by 3.5-fold. Between 1000 and 875 bc, EEF ancestry increased in southern Britain (England and Wales) but not northern Britain (Scotland) due to incorporation of migrants who arrived at this time and over previous centuries, and who were genetically most similar to ancient individuals from France. These migrants contributed about half the ancestry of people of England and Wales from the Iron Age, thereby creating a plausible vector for the spread of early Celtic languages into Britain. These patterns are part of a broader trend of EEF ancestry becoming more similar across central and western Europe in the Middle to the Late Bronze Age, coincident with archaeological evidence of intensified cultural exchange2,3,4,5,6. There was comparatively less gene flow from continental Europe during the Iron Age, and the independent genetic trajectory in Britain is also reflected in the rise of the allele conferring lactase persistence to approximately 50% by this time compared to approximately 7% in central Europe where it rose rapidly in frequency only a millennium later. This suggests that dairy products were used in qualitatively different ways in Britain and in central Europe over this period.
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Data availability
The raw data are available as aligned sequences (.bam files) through the European Nucleotide Archive under accession number PRJEB47891. The newly generated genotype data are available as a Supplementary Data file. The previously published data co-analysed with our newly reported data can be obtained as described in the original publications, which are all referenced in Supplementary Table 3; a compiled dataset that includes the merged genotypes used in this paper is available as the Allen Ancient DNA Resource at https://reich.hms.harvard.edu/allen-ancient-dna-resourceaadr-downloadable-genotypes-present-day-and-ancient-dna-data. Any other relevant data are available from the corresponding authors on reasonable request.
Code availability
This study uses publicly available software, which we fully reference.
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Acknowledgements
We thank P. Csengeri, T. de Rider, M. Giesen, E. Melis, A. Parkin and A. Schmitt for their contribution to sample selection and collection of archaeological data; R. Crellin, J. Koch, K. Kristiansen and G. Kroonen for comments on the manuscript; A. Williamson for manually revising Y chromosome haplogroup determinations and making corrections to nine; and M. Lee for assistance with data entry. This work was funded in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 834087; the COMMIOS Project to I.A.). M.N. was supported by the Croatian Science Fund grant (HRZZ IP-2016-06-1450). P.V., M.Dobeš and Z.V. were supported by the Ministry of Culture of the Czech Republic (DKRVO 2019-2023/7.I.c, 00023272). M.E. was supported by Czech Academy of Sciences award Praemium Academiae. M.Dobisíková and A.Danielisová were supported by the grant RVO 67985912 of the Institute of Archaeology of the Czech Academy of Sciences. M.G.B.F. was funded by The Leverhulme Trust via a Doctoral Scholarship scheme awarded to M.Pala and M.B.R. Support to M.Legge came from the South, West & Wales Doctoral Training Partnership. M.G.’s osteological analyses were funded by Culture Vannin. A.S.-N. was supported by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences. T.H., T.S. and K.K.’s work was supported by a grant from the Hungarian Research, Development and Innovation Office (project number: FK128013). We acknowledge support for radiocarbon dating and stable isotope analyses as well as access to skeletal material from Manx National Heritage and A. Fox. Dating analysis was funded by Leverhulme Trust grant RPG-388. M.G.T. and I.B. were supported by a Wellcome Trust Investigator Award (project 100713/Z/12/Z). I.O. was supported by a Ramón y Cajal grant from Ministerio de Ciencia e Innovación, Spanish Government (RYC2019-027909-I). The research directed at Harvard was funded by NIH grants GM100233 and HG012287, by John Templeton Foundation grant 61220, by a gift from Jean-François Clin, and by the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation. D.R. is also an Investigator of the Howard Hughes Medical Institute.
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D.J.K., B.Cunliffe, N.R., R.Pinhasi, I.A. and D.R. supervised the study. T.B., L.Büster, C.-E.F., O.Cheronet, S.B., B.A., T.A., K.A., L.A., A.Ash, C.B.-D., A.Barclay, L.Bartosiewicz, K.B., Z.B., J.Blažek, M.Bodružić, P.Boissinot, C.Bonsall, P.Bradley, M.Brittain, A.Brookes, F.B., L.Brown, R.Brunning, C.Budd, J.Burmaz, S.Canet, S.C.-C., M.Č.-B., A.Chamberlain, S.Chauvin, S.Clough, N.Č., A.Coppa, O.Craig, M.Č., V.C., S.Czifra, A.Danielisová, R.D., A.Davis, P.d.J., J.D., C.D., P.W.D., M.Dizdar, M.Dobeš, M.Dobisíková, L.Domboróczki, G.D., A.Đukić, C.J.E., M.E., C.E., J.E., M.F.-G., S.Filipović, A.Fitzpatrick, H.F., C.F., A.Fox, Z.G., M.G., M.R.G.M., B.G.-R., A.G., K.G., D.Habermehl, T.H., D.Hamilton, J.Harris, C.H., J.Hendriks, B.H., G.H., M.H., G.I., E.I., A.M.J., M.B.K., K.K., R.A.K., A.Khreisheh, V.Kiss, J.K., M.K., L.M.K., P.F.K., A.Kozubová, G.K., V.Kulcsár, C.L.P., M.Legge, M.Leivers, L.L., O.L.-C., T.L., D.L., J.L., A.B.M.-A., P.M., D.M., A.Maxted, L.McIntyre, J.McKinley, K.McSweeney, B.M., B.G.M., M.Menđušić, M.Metlička, S.Meyer, K.Mihovilić, L.Milasinovic, S.Minnitt, J.Moore, G.Morley, G.Mullan, M.Musilová, B.N., R.N., M.N., M.Pala, M.Papworth, C.Paresys, R.Patten, D.P., K.Pesti, A.P., K.Petriščáková, C.Pichon, C.Pickard, Z.P., T.D.P., S.R., R.R., B.R., D.T.R., M.B.R., A.R., J.R., P.S., A.Šefčáková, A.Sheridan, S.S., K.Somogyi M.Šmolíková, Á.Somogyvári, M.Stephens, G.S., A.S.-N., T.S., J.Tabor, C.T.M., R.Terry, B.T., M.T.-N., J.F.T.-M., J.Trapp, R.Turle, F.U., M.v.d.H., P.V., B.V., Z.V., C.W., P.Ware, P.Wilkinson, L.W., R.W., E.Y., J.Z., A.Ž., C.L.-F., P.H., B.Cunliffe, M.Lillie, R.Pinhasi and I.A. excavated or curated samples and provided archaeological contextualization. T.B., O.Cheronet, M.Bleasdale, N.A., E.A., S.B., N.B., K.C., F.C., B.Culleton, E.C., L.Demetz, K.S.D.C., D.M.F., M.G.B.F., S.Freilich, A.Kearns, A.M.L., K.Mandl, M.Michel, G.B.M., J.O., K.T.Ö., L.Q., C.S., K.Stewardson, J.N.W., F.Z., C.J.E., D.J.K. and N.R. generated the data through sample preparation or laboratory work. N.P., M.I., L.Büster, C.-E.F., I.O., H.R., A.Akbari, O.Cheronet, M.Bleasdale, R.Bernardos, H.G., I.L., M.Mah, S.Mallick, A.Micco, Z.Z. and D.R. curated and analysed the data. N.P., M.I., T.B., L.Büster, C.-E.F., I.O., M.Bleasdale, I.A. and D.R. wrote substantial sections of the paper.
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Extended data figures and tables
Extended Data Fig. 1 Post-MBA Britain was not a mix of earlier British populations.
a, qpAdm p-values for modelling British groups as a mix of Neolithic and Chalcolithic/EBA populations from England and Wales or Scotland (outgroups OldAfrica, OldSteppe, Turkey_N, CzechRepublic.Slovakia.Germany_3800.to.2700BP, Netherlands_C.EBA, Poland_Globular_Amphora, Spain.Portugal_4425.to.3800BP, CzechRepublic.Slovakia.Germany_4465.to.3800.BP, Sardinia_4100.to.2700BP, Sardinia_8100.to.4100BP, Spain.Portugal_6500.to.4425BP). We highlight p<0.05 (yellow) or p<0.005 (red). Both sources and target populations in this analysis remove outlier individuals (“Filter 2” in Supplementary Table 5); we obtain qualitatively similar results when outlier individuals are not removed (not shown). b, To obtain insight into the source of the new ancestry in Britain in the IA, we computed f4(England.and.Wales_IA, α(England.and.Wales_N) + (1-α)(England.Wales_C.EBA); R1, R2) for different (R1, R2) population pairs. If England.and.Wales_IA is a simple mixture of England.and.Wales_N and England.and.Wales_C.EBA without additional ancestry, then for some mixture proportion the statistic will be consistent with zero for all (R1, R2 pairs). When (R1, R2) = (OldAfrica, OldSteppe) feasible Z-scores (Z1 in the plot) are observed when α∼0.85, showing that ~85% ancestry from England.and.Wales_C.EBA ancestry is needed to contribute the observed proportion of Steppe ancestry in England.and.Wales_IA. However, when (R1, R2) is (Balkan_N, Sardinian_8100.to.4100BP), we get infeasible Z-scores (Z2) of <−6 across the range where Z1 is remotely feasible. Thus, Iron Age people from England and Wales must have ancestry from an additional population deeply related to Sardinian Early Neolithic groups.
Extended Data Fig. 2 By-individual analysis of the British time transect.
Version of Fig. 3 with the time transect extended into the Neolithic, and adding in individuals from Scotland. We plot mean estimates of EEF ancestry and one standard error bars from a Block Jackknife for all individuals in the time transect that pass basic quality control, that fit to a three-way admixture model (EEF + WHG + Yamnaya) at p>0.01 using qpAdm, and for the Neolithic period that fit a two-way admixture model (EEF + WHG) at p>0.01. Individuals that fit the main cluster of their time are shown in blue (southern Britain) and green (Scotland), while red and orange respectively show outliers at the ancestry tails (identified either as p<0.005 based on a qpWave test from the main cluster of individuals from their period and |Z|>3 for a difference in their EEF ancestry proportion from the period, or alternatively p<0.1 and |Z|>3.5). The averages for the main clusters in both southern Britain and Scotland in each archaeological period (Neolithic, C/EBA, MBA, LBA and IA) are shown in dashed lines.
Extended Data Fig. 3 Changes in the size of the mate pool over time.
Close kin unions were rare at all periods as reflected in the paucity of individuals harbouring >50 centimorgans (cM) of their genome in runs of homozygosity (ROH) of >12 cM (red dots in top panel). The number of ROH of size 4–8 cM per individual (bottom panel) reflects the rate at which distant relatives have children, providing information about the sizes of mate pools (Ne) averaged over the hundreds of years prior to when individuals lived; thus, the broad trend of an approximately fourfold drop in Ne from the Neolithic to the IA is robust, but we may miss fluctuations on a time scale of centuries. The thick black lines represent the mean Ne obtained by fitting a mathematical model of a Gaussian process with a 600-year smoothing kernel (gray area 95% confidence interval). The horizontal grey lines show period averages from maximum likelihood which can differ from the mean obtained through the mathematical modelling if the counts do not conform well to a Gaussian process. We interrupt the fitted line for periods with too little data for accurate inference (<10 individuals in a 400-year interval centered on the point).
Extended Data Fig. 4 Frequency change over time at two phenotypically important alleles.
Present-day frequencies are shown by the red dashed lines; sample sizes for each period are labelled at the bottom of each plot; and we show means along with 95% confidence intervals (Supplementary Table 8). (a–d/Top) Lactase persistence allele at rs4988235. (e–h/Bottom) Light skin pigmentation allele at rs16891982. In Britain the rise in frequency of the lactase persistence allele occurred earlier than in central Europe. This analysis is based on direct observation of alleles; imputation results are qualitatively consistent (Fig. 4b).
Extended Data Fig. 5 Y chromosome haplogroup frequency changes over time.
Estimated frequency of the characteristically British Y chromosome haplogroup R1b-P312/L21/M529 in all individuals for which we are able to make a determination and which are not first-degree relatives of a higher coverage individual in the dataset. Sample sizes for each period are labelled at the bottom, and we show means and one standard error bars from a binominal distribution. The frequency increases significantly from ~0% in the whole island Neolithic, to 89±4% in the whole island C/EBA. It declines non-significantly to 79±9% in the MBA and LBA (from this time onward restricting to England and Wales because of the autosomal evidence of a change in EEF ancestry in the south but not the north). It further declines to 68±4% in the IA, a significant reduction relative to the C/EBA (P=0.014 by a two-sided chi-square contingency test). There is additional reduction from this time to the present, when the proportion is 43±3% in Wales and the west of England (P=5x10−6 for a reduction relative to the IA), and 14±2% in the center and east of England (P=3x10−32 for a reduction relative to the IA).
Extended Data Fig. 6 Version of Fig. 3a contrasting Kent to the rest of southern Britain.
We show the period 2450-1 BCE. Each point corresponds to a single individual and we show means and one standard error bars from a Block Jackknife. All the high EEF outliers during the M-LBA are from Kent—the part of the island closest to France—and in addition all the individuals from 1000-875 BCE from the group of samples showing the ramp-up from MBA to IA levels of EEF ancestry are from Kent (5 from Cliffs End Farm and 3 from East Kent Access Road). This suggests the possibility that this small region was the gateway for migration to Britain during the M-LBA. Further sampling from the rest of Britain during the M-LBA is critical in order to understand the dynamics of how this ancestry spread more broadly. However, the fact that the only sample from the second half of the LBA that is not from Kent—I12624 from Blackberry Field in Potterne in Wiltshire at 950-750 BCE—already has a proportion of EEF ancestry typical of the IA in southern Britain—suggests that this ancestry began spreading more broadly by the second half of the LBA.
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Patterson, N., Isakov, M., Booth, T. et al. Large-scale migration into Britain during the Middle to Late Bronze Age. Nature 601, 588–594 (2022). https://doi.org/10.1038/s41586-021-04287-4
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DOI: https://doi.org/10.1038/s41586-021-04287-4
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