Human genetic structure in Northwest France provides new insights into West European historical demography

Isabel Alves; Joanna Giemza; Michael G. B. Blum; Carolina Bernhardsson; Stéphanie Chatel; Matilde Karakachoff; Aude Saint Pierre; Anthony F. Herzig; Robert Olaso; Martial Monteil; Véronique Gallien; Elodie Cabot; Emma Svensson; Delphine Bacq; Estelle Baron; Charlotte Berthelier; Céline Besse; Hélène Blanché; Ozvan Bocher; Anne Boland; Stéphanie Bonnaud; Eric Charpentier; Claire Dandine-Roulland; Claude Férec; Christine Fruchet; Simon Lecointe; Edith Le Floch; Thomas E. Ludwig; Gaëlle Marenne; Vincent Meyer; Elisabeth Quellery; Fernando Racimo; Karen Rouault; Florian Sandron; Jean-Jacques Schott; Lourdes Velo-Suarez; Jade Violleau; Eske Willerslev; Yves Coativy; Mael Jézéquel; Daniel Le Bris; Clément Nicolas; Yvan Pailler; Marcel Goldberg; Marie Zins; Hervé Le Marec; Mattias Jakobsson; Pierre Darlu; Emmanuelle Génin; Jean François Deleuze; Richard Redon; Christian Dina

doi:10.1038/s41467-024-51087-1

Human genetic structure in Northwest France provides new insights into West European historical demography

Isabel Alves, Joanna Giemza, Michael G. B. Blum, Carolina Bernhardsson, Stéphanie Chatel, Matilde Karakachoff, Aude Saint Pierre, Anthony F. Herzig, Robert Olaso, Martial Monteil, Véronique Gallien, Elodie Cabot, Emma Svensson, Delphine Bacq, Estelle Baron, Charlotte Berthelier, Céline Besse, Hélène Blanché, Ozvan Bocher, Anne BolandStéphanie Bonnaud, Eric Charpentier, Claire Dandine-Roulland, Claude Férec, Christine Fruchet, Simon Lecointe, Edith Le Floch, Thomas E. Ludwig, Gaëlle Marenne, Vincent Meyer, Elisabeth Quellery, Fernando Racimo, Karen Rouault, Florian Sandron, Jean-Jacques Schott, Lourdes Velo-Suarez, Jade Violleau, Eske Willerslev, Yves Coativy, Mael Jézéquel, Daniel Le Bris, Clément Nicolas, Yvan Pailler, Marcel Goldberg, Marie Zins, Hervé Le Marec, Mattias Jakobsson, Pierre Darlu, Emmanuelle Génin, Jean François Deleuze, Richard Redon^*, Christian Dina

^*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

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Abstract

The demographical history of France remains largely understudied despite its central role toward understanding modern population structure across Western Europe. Here, by exploring publicly available Europe-wide genotype datasets together with the genomes of 3234 present-day and six newly sequenced medieval individuals from Northern France, we found extensive fine-scale population structure across Brittany and the downstream Loire basin and increased population differentiation between the northern and southern sides of the river Loire, associated with higher proportions of steppe vs. Neolithic-related ancestry. We also found increased allele sharing between individuals from Western Brittany and those associated with the Bell Beaker complex. Our results emphasise the need for investigating local populations to better understand the distribution of rare (putatively deleterious) variants across space and the importance of common genetic legacy in understanding the sharing of disease-related alleles between Brittany and people from western Britain and Ireland.

Originalsprog	Engelsk
Artikelnummer	6710
Tidsskrift	Nature Communications
Vol/bind	15
Antal sider	18
ISSN	2041-1723
DOI	https://doi.org/10.1038/s41467-024-51087-1
Status	Udgivet - 2024

Bibliografisk note

Funding Information:
This study received financial support from the Regional Council of Pays-de-la-Loire (VaCaRMe) and the Agence Nationale de la Recherche in France (ANR; FROGH, ANR-16-599-CE12-0033). The PREGO bio-bank was built with the strong support from the Etablissement Fran\u00E7ais du Sang (EFS) and the Centre for Biological Resources (CRB) of CHU Nantes (BB-0033-00040). I.A. received funds from the People Programme (Marie Curie Actions) of the European Union\u2019s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement PCOFUND-GA-2013-609102, through the PRESTIGE programme (PRESTIGE-2017-4-0018) coordinated by Campus France, from Agence Nationale de la Recherche in France (ANR; FROGH, ANR-16-599-CE12-0033) and from Lefoulon Delalande foundation. J.G. and R.R. were supported the Regional Council of Pays-de-la-Loire (GRIOTE) and the ANR (GenSud: ANR-14-CE10-0001). The GAZEL Cohort Study was funded by EDF-GDF and INSERM, and received grants from the \u2018Cohortes Sant\u00E9 TGIR Program\u2019 of the ANR (ANR-08-BLAN-0028), Agence fran\u00E7aise de s\u00E9curit\u00E9 sanitaire de l\u2019environnement et du travail (AFSSET; EST-2008/1/35), CAMIEG (Caisse d\u2019assurance maladie des industries \u00E9lectrique et gazi\u00E8re) and CCAS (Caisse Centrale d\u2019Activit\u00E9s Sociales du Personnel des Industries \u00C9lectriques et Gazi\u00E8res). The extraction and WGS sequencing of blood samples was supported by the Laboratory of Excellence GENMED (ANR; grant no. ANR-10-LABX-0013, PIA: \u201CInvestissements d\u2019Avenir\u201D programme). We also thank the CEPH-Biobank team for their involvement in DNA extractions for the GAZEL cohort. This work was supported by the France G\u00E9nomique National infrastructure, funded as part of the PIA managed by the ANR (contract ANR-10-INBS-09). The authors also wish to thank the Fondation Genavie for its financial support for C.D. We are most grateful to the Genomics & Bioinformatics Core Facilities of Nantes (GenoA & BiRD, Biogenouest) and the Institut Fran\u00E7ais de Bioinformatique (IFB; ANR-11-INBS-0013) for their technical support. This work was supported by the Institut National de Recherches Arch\u00E9ologiques Pr\u00E9ventives (Inrap), funded as part of the days allocated to research.

Publisher Copyright:
© The Author(s) 2024.

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Citationsformater

Alves, I., Giemza, J., Blum, M. G. B., Bernhardsson, C., Chatel, S., Karakachoff, M., Saint Pierre, A., Herzig, A. F., Olaso, R., Monteil, M., Gallien, V., Cabot, E., Svensson, E., Bacq, D., Baron, E., Berthelier, C., Besse, C., Blanché, H., Bocher, O., ... Dina, C. (2024). Human genetic structure in Northwest France provides new insights into West European historical demography. Nature Communications, 15, Artikel 6710. https://doi.org/10.1038/s41467-024-51087-1

Alves, I, Giemza, J, Blum, MGB, Bernhardsson, C, Chatel, S, Karakachoff, M, Saint Pierre, A, Herzig, AF, Olaso, R, Monteil, M, Gallien, V, Cabot, E, Svensson, E, Bacq, D, Baron, E, Berthelier, C, Besse, C, Blanché, H, Bocher, O, Boland, A, Bonnaud, S, Charpentier, E, Dandine-Roulland, C, Férec, C, Fruchet, C, Lecointe, S, Le Floch, E, Ludwig, TE, Marenne, G, Meyer, V, Quellery, E, Racimo, F, Rouault, K, Sandron, F, Schott, J-J, Velo-Suarez, L, Violleau, J, Willerslev, E, Coativy, Y, Jézéquel, M, Le Bris, D, Nicolas, C, Pailler, Y, Goldberg, M, Zins, M, Le Marec, H, Jakobsson, M, Darlu, P, Génin, E, Deleuze, JF, Redon, R & Dina, C 2024, 'Human genetic structure in Northwest France provides new insights into West European historical demography', Nature Communications, bind 15, 6710. https://doi.org/10.1038/s41467-024-51087-1

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abstract = "The demographical history of France remains largely understudied despite its central role toward understanding modern population structure across Western Europe. Here, by exploring publicly available Europe-wide genotype datasets together with the genomes of 3234 present-day and six newly sequenced medieval individuals from Northern France, we found extensive fine-scale population structure across Brittany and the downstream Loire basin and increased population differentiation between the northern and southern sides of the river Loire, associated with higher proportions of steppe vs. Neolithic-related ancestry. We also found increased allele sharing between individuals from Western Brittany and those associated with the Bell Beaker complex. Our results emphasise the need for investigating local populations to better understand the distribution of rare (putatively deleterious) variants across space and the importance of common genetic legacy in understanding the sharing of disease-related alleles between Brittany and people from western Britain and Ireland.",

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AU - Alves, Isabel

AU - Giemza, Joanna

AU - Blum, Michael G. B.

AU - Bernhardsson, Carolina

AU - Chatel, Stéphanie

AU - Karakachoff, Matilde

AU - Saint Pierre, Aude

AU - Herzig, Anthony F.

AU - Olaso, Robert

AU - Monteil, Martial

AU - Gallien, Véronique

AU - Cabot, Elodie

AU - Svensson, Emma

AU - Bacq, Delphine

AU - Baron, Estelle

AU - Berthelier, Charlotte

AU - Besse, Céline

AU - Blanché, Hélène

AU - Bocher, Ozvan

AU - Boland, Anne

AU - Bonnaud, Stéphanie

AU - Charpentier, Eric

AU - Dandine-Roulland, Claire

AU - Férec, Claude

AU - Fruchet, Christine

AU - Lecointe, Simon

AU - Le Floch, Edith

AU - Ludwig, Thomas E.

AU - Marenne, Gaëlle

AU - Meyer, Vincent

AU - Quellery, Elisabeth

AU - Racimo, Fernando

AU - Rouault, Karen

AU - Sandron, Florian

AU - Schott, Jean-Jacques

AU - Velo-Suarez, Lourdes

AU - Violleau, Jade

AU - Willerslev, Eske

AU - Coativy, Yves

AU - Jézéquel, Mael

AU - Le Bris, Daniel

AU - Nicolas, Clément

AU - Pailler, Yvan

AU - Goldberg, Marcel

AU - Zins, Marie

AU - Le Marec, Hervé

AU - Jakobsson, Mattias

AU - Darlu, Pierre

AU - Génin, Emmanuelle

AU - Deleuze, Jean François

AU - Redon, Richard

AU - Dina, Christian

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AB - The demographical history of France remains largely understudied despite its central role toward understanding modern population structure across Western Europe. Here, by exploring publicly available Europe-wide genotype datasets together with the genomes of 3234 present-day and six newly sequenced medieval individuals from Northern France, we found extensive fine-scale population structure across Brittany and the downstream Loire basin and increased population differentiation between the northern and southern sides of the river Loire, associated with higher proportions of steppe vs. Neolithic-related ancestry. We also found increased allele sharing between individuals from Western Brittany and those associated with the Bell Beaker complex. Our results emphasise the need for investigating local populations to better understand the distribution of rare (putatively deleterious) variants across space and the importance of common genetic legacy in understanding the sharing of disease-related alleles between Brittany and people from western Britain and Ireland.

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