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Ancient genomes indicate population replacement in Early Neolithic Britain

Abstract

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 bc, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500–2500 bc. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 bc.

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Data availability

BAM files (one file per library, before realigning around InDels; see Supplementary Table 1) have been deposited at the European Nucleotide Archive under study accession PRJEB31249.

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Competing interests

The authors declare no competing interests.

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Change history

  • 08 May 2019

    In the version of this Article originally published, there were errors in the colour ordering of the legend in Fig. 5b, and in the positions of the target and surrogate populations in Fig. 5c. This has now been corrected. The conclusions of the study are in no way affected. The errors have been corrected in the HTML and PDF versions of the article.

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Acknowledgements

The authors would like to thank the Longleat Estate, T. Lord at Lower Winskill Farm, B. Chandler at Torquay Museum, A. Chamberlain at the University of Manchester, L. Wilson and G. Mullan at the University of Bristol Spelaeological Society, E. Walker, A. Gwilt and J. Deacon at the National Museum of Wales, A. Maxted at Brighton Museum, M. Lahr at the Duckworth Laboratory, B. Lane at Wells Museum, M. Smith at Bournemouth University, D. Rice at the Museum of Gloucester and R. Kruszynski at the Natural History Museum for providing access to samples. In addition, Y.D. wishes to thank J. Blöcher, A. Scheu, C. Sell and J. Burger for discussions on the bioinformatic pipeline, and V. Link for help with ATLAS. M.G.T. and I.B. were supported by a Wellcome Trust Investigator Award (project No. 100713/Z/12/Z). S.C. was supported by the Natural Environment Research Council (NE/K500987/1). L.v.D acknowledges financial support from the Newton Trust (grant No. MR/P007597/1). R.M. was supported by an EMBO Long-Term Fellowship (No. ALTF 133-2017). D.R. was supported by a NIH grant (No. GM100233), by NSF HOMINID (No. BCS-1032255) and by an Allen Discovery Center of the Paul Allen Foundation, and is a Howard Hughes Medical Institute investigator. C.S. is supported by the Calleva Foundation and the Human Origins Research Fund. S.W. was supported by the US National Institute of Justice (grant No. 2014-DN-BX-K031).

Author information

I.B. and M.G.T. conceived the project. Y.D., S.B., Z.F., O.C. and T.B. contributed to the project design. S.B., Y.D., T.B., L.v.D, N.R., S.M., I.O., M.F., M.M., J.O., N.B., K.S., R.M., S.C. and S.W. generated and analysed data. I.B., M.G.T., Y.D., S.B., T.B., M.K., S.W., G.H., I.A., R.S., O.C., A.S., M.P.P., C.S. and D.R. contributed to the sampling strategy and the interpretation of results. I.B., M.G.T., Y.D., S.B. and T.B. wrote the paper, with contributions from all other authors.

Competing interests

The authors declare no competing interests.

Correspondence to Mark G. Thomas or Ian Barnes.

Supplementary information

Supplementary Information

Supplementary Notes 1–7 and Supplementary Figs. 1–23

Reporting Summary

Supplementary Data 1

Summary of sequencing data per individual with relevant metadata

Supplementary Data 2

Functional variation

Supplementary Data 3

Admixture dates

Supplementary Data 4

Pairwise comparison of WHG admixture proportions

Supplementary Data 5

Y-chromosomal lineages

Supplementary Data 6

New radiocarbon dates and stable isotopes

Supplementary Data 7

Chronological model outputs

Supplementary Data 8

SOURCEFIND inferred proportions of ancient ancestry

Supplementary Data 9

SOURCEFIND inferred proportions of modern ancestry

Supplementary Data 10

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Fig. 1: Map of sample locations.
Fig. 2: Principal component analysis of modern and ancient West Eurasians.
Fig. 3: WHG and ANF ancestry components of British and Central European Neolithic populations.
Fig. 4: Affinities of British and continental Neolithic populations.
Fig. 5: Patterns of haplotype sharing across high-coverage aDNA samples.