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Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland

Furtwängler, Anja, Rohrlach, A. B., Lamnidis, Thiseas C., Papac, Luka, Neumann, Gunnar U., Siebke, Inga, Reiter, Ella, Steuri, Noah, Hald, Jürgen, Denaire, Anthony, Schnitzler, Bernadette, Wahl, Joachim, Ramstein, Marianne, Schuenemann, Verena J., Stockhammer, Philipp W., Hafner, Albert, Lösch, Sandra, Haak, Wolfgang, Schiffels, Stephan, Krause, Johannes·2020·Nature Communications
DOI 10.1038/s41467-020-15560-xPMC PMC7171184
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Abstract

Genetic studies of Neolithic and Bronze Age skeletons from Europe have provided evidence for strong population genetic changes at the beginning and the end of the Neolithic period. To further understand the implications of these in Southern Central Europe, we analyze 96 ancient genomes from Switzerland, Southern Germany, and the Alsace region in France, covering the Middle/Late Neolithic to Early Bronze Age. Similar to previously described genetic changes in other parts of Europe from the early 3rd millennium BCE, we detect an arrival of ancestry related to Late Neolithic pastoralists from the Pontic-Caspian steppe in Switzerland as early as 2860–2460 calBCE. Our analyses suggest that this genetic turnover was a complex process lasting almost 1000 years and involved highly genetically structured populations in this region.

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Fig. 1 Genetic, temporal, and spatial structure of individuals in this study. a Time ranges of calibrated radiocarbon dates of the archaeological sites. b Geographical distribution of the sites and samples sizes per sites in brackets. Map generated with R version 3.4.3 (R Core Team 2017) using the CIA World Data Bank II currently (mid 2003) available from http://www.evl.uic.edu/pape/data/WDB/. c PCA was reconstructed on 1960 modern European individuals of the POPRES dataset and ancient genomes were projected onto it.
Fig. 1 Genetic, temporal, and spatial structure of individuals in this study. a Time ranges of calibrated radiocarbon dates of the archaeological sites. b Geographical distribution of the sites and samples sizes per sites in brackets. Map generated with R version 3.4.3 (R Core Team 2017) using the CIA World Data Bank II currently (mid 2003) available from http://www.evl.uic.edu/pape/data/WDB/. c PCA was reconstructed on 1960 modern European individuals of the POPRES dataset and ancient genomes were projected onto it.CC BY · PubMed Central
Fig. 2 Genetic turnover at the transition to the Central European Bronze Age. a Three-way qpAdm models of the ancient individuals from Switzerland (number of individuals in brackets) sorted by sites in chronological order (bottom to top) with the source populations WHG, steppe pastoralists (Yamnaya Samara) and Anatolia Neolithic. Error bars represent standard error of the proportion of each component. b Relative proportion of the steppe-related ancestry component for each individual in four different regions, calculated with qpAdm and estimates of arrival times (error bars represent the range of C14 dating) and following decrease of the component (dashes lines). Red dots represent female individuals and blue dots male individuals. c An estimate of genetic diversity between individuals before 2700 BCE and after 2700 BCE and sites with individuals from both periods as well as modern European populations (German and French from the HO dataset).
Fig. 2 Genetic turnover at the transition to the Central European Bronze Age. a Three-way qpAdm models of the ancient individuals from Switzerland (number of individuals in brackets) sorted by sites in chronological order (bottom to top) with the source populations WHG, steppe pastoralists (Yamnaya Samara) and Anatolia Neolithic. Error bars represent standard error of the proportion of each component. b Relative proportion of the steppe-related ancestry component for each individual in four different regions, calculated with qpAdm and estimates of arrival times (error bars represent the range of C14 dating) and following decrease of the component (dashes lines). Red dots represent female individuals and blue dots male individuals. c An estimate of genetic diversity between individuals before 2700 BCE and after 2700 BCE and sites with individuals from both periods as well as modern European populations (German and French from the HO dataset).CC BY · PubMed Central
Fig. 3 Estimated admixture times between the Yamnaya-like steppe component and the Middle Neolithic population using DATES software. a Admixture dates of single individuals are plotted against their calC14 dates (horizontal error bars indicate uncertainty in C14 dating and vertical error bars show 95% confidence interval of generation times) and b displayed as time range (C14 dates in red and estimated admixture dates in turquoise). c Admixture dates of grouped individuals according to their regions of origin were calculated (colors as above).
Fig. 3 Estimated admixture times between the Yamnaya-like steppe component and the Middle Neolithic population using DATES software. a Admixture dates of single individuals are plotted against their calC14 dates (horizontal error bars indicate uncertainty in C14 dating and vertical error bars show 95% confidence interval of generation times) and b displayed as time range (C14 dates in red and estimated admixture dates in turquoise). c Admixture dates of grouped individuals according to their regions of origin were calculated (colors as above).CC BY · PubMed Central
Fig. 4 Reconstructed family trees from different sites over time. All relationships between the single individuals were reconstructed from autosomal variants and confirmed by uniparentally inherited markers such as mtDNA haplotype and Y chromosomal haplogroup. Individuals with black outline were available for analysis and individuals with gray outline were not found within the burials and are missing. Same colors indicate identical mtDNA haplotypes and matching Y chromosomal haplogroups.
Fig. 4 Reconstructed family trees from different sites over time. All relationships between the single individuals were reconstructed from autosomal variants and confirmed by uniparentally inherited markers such as mtDNA haplotype and Y chromosomal haplogroup. Individuals with black outline were available for analysis and individuals with gray outline were not found within the burials and are missing. Same colors indicate identical mtDNA haplotypes and matching Y chromosomal haplogroups.CC BY · PubMed Central
Fig. 5 Genetic affinity between the ancient Individuals and the French-, German-, and Italian-speaking regions of Switzerland. Differences in genetic affinity of the ancient individuals from Switzerland to a Swiss–French and Swiss–German, b Swiss–Italian and Swiss–German, and c Swiss–French and Swiss–Italian. Maps generated with R version 3.4.3 (R Core Team 2017) using the CIA World Data Bank II are currently (mid 2003) available from http://www.evl.uic.edu/pape/data/WDB/.
Fig. 5 Genetic affinity between the ancient Individuals and the French-, German-, and Italian-speaking regions of Switzerland. Differences in genetic affinity of the ancient individuals from Switzerland to a Swiss–French and Swiss–German, b Swiss–Italian and Swiss–German, and c Swiss–French and Swiss–Italian. Maps generated with R version 3.4.3 (R Core Team 2017) using the CIA World Data Bank II are currently (mid 2003) available from http://www.evl.uic.edu/pape/data/WDB/.CC BY · PubMed Central

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Citations

Cites

Show all 19 references

Research works printed but not linked: 28

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Cited by

Metadata

Authors
Furtwängler, A., Rohrlach, A. B., Lamnidis, T. C., Papac, L., Neumann, G. U., Siebke, I., Reiter, E., Steuri, N., Hald, J., Denaire, A., Schnitzler, B., Wahl, J., Ramstein, M., Schuenemann, V. J., Stockhammer, P. W., Hafner, A., Lösch, S., Haak, W., Schiffels, S., & Krause, J.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2020-04-20
Volume
11
Issue
1
ISSN
2041-1723
DOI
10.1038/s41467-020-15560-x
PMC
PMC7171184
Cited by
71
References
19
Language
en
Update notices
correction (2020-09-16)
Licence
Funders
  • Max-Planck-Gesellschaft
  • Deutsche Forschungsgemeinschaft (KR 4015/4-1)
  • Heidelberger Akademie der Wissenschaften (Times of Upheaval)

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