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

Author

Listed:
  • Isabel Alves

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax
    Université de Strasbourg, CNRS, GMGM)

  • Joanna Giemza

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Michael G. B. Blum

    (Univ. Grenoble Alpes)

  • Carolina Bernhardsson

    (Uppsala University)

  • Stéphanie Chatel

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Matilde Karakachoff

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax
    Nantes Université, CHU Nantes, Pôle Hospitalo-Universitaire 11: Santé Publique, Clinique des données, INSERMCIC 1413)

  • Aude Pierre

    (Univ Brest, Inserm, EFS, UMR 1078, GGB)

  • Anthony F. Herzig

    (Univ Brest, Inserm, EFS, UMR 1078, GGB)

  • Robert Olaso

    (Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH)
    Labex GenMed)

  • Martial Monteil

    (Nantes Université, CNRS, Ministère de la Culture, CReAAH, LARA)

  • Véronique Gallien

    (INRAP - Institut national de recherches archéologiques préventives
    Moyen-Age)

  • Elodie Cabot

    (INRAP - Institut national de recherches archéologiques préventives
    Faculté de Médecine Site Nord)

  • Emma Svensson

    (Uppsala University)

  • Delphine Bacq

    (Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH)
    Labex GenMed)

  • Estelle Baron

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Charlotte Berthelier

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Céline Besse

    (Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH)
    Labex GenMed)

  • Hélène Blanché

    (CEPH)

  • Ozvan Bocher

    (Univ Brest, Inserm, EFS, UMR 1078, GGB)

  • Anne Boland

    (Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH)
    Labex GenMed)

  • Stéphanie Bonnaud

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Eric Charpentier

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Claire Dandine-Roulland

    (Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH)
    Labex GenMed)

  • Claude Férec

    (Univ Brest, Inserm, EFS, UMR 1078, GGB
    CHRU Brest)

  • Christine Fruchet

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Simon Lecointe

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Edith Floch

    (Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH)
    Labex GenMed)

  • Thomas E. Ludwig

    (Univ Brest, Inserm, EFS, UMR 1078, GGB
    CHRU Brest)

  • Gaëlle Marenne

    (Univ Brest, Inserm, EFS, UMR 1078, GGB)

  • Vincent Meyer

    (Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH))

  • Elisabeth Quellery

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Fernando Racimo

    (University of Copenhagen)

  • Karen Rouault

    (Univ Brest, Inserm, EFS, UMR 1078, GGB
    CHRU Brest)

  • Florian Sandron

    (Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH)
    Labex GenMed)

  • Jean-Jacques Schott

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Lourdes Velo-Suarez

    (Univ Brest, Inserm, EFS, UMR 1078, GGB)

  • Jade Violleau

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Eske Willerslev

    (University of Copenhagen
    University of Cambridge)

  • Yves Coativy

    (Université de Bretagne Occidentale)

  • Mael Jézéquel

    (Université de Bretagne Occidentale)

  • Daniel Bris

    (Université de Bretagne Occidentale)

  • Clément Nicolas

    (Université Paris 1 Panthéon-Sorbonne, Centre Malher, 9 rue Malher)

  • Yvan Pailler

    (Université de Brest, Université de Nantes, Université de Rennes 2, Institut Universitaire Européen de la Mer)

  • Marcel Goldberg

    (Université Paris Cité, “Population-based Cohorts Unit”, INSERM, Paris Saclay University, UVSQ)

  • Marie Zins

    (Université Paris Cité, “Population-based Cohorts Unit”, INSERM, Paris Saclay University, UVSQ)

  • Hervé Marec

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Mattias Jakobsson

    (Uppsala University)

  • Pierre Darlu

    (Université de Paris Cité)

  • Emmanuelle Génin

    (Univ Brest, Inserm, EFS, UMR 1078, GGB
    CHRU Brest)

  • Jean-François Deleuze

    (Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH)
    Labex GenMed
    CEPH)

  • Richard Redon

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

  • Christian Dina

    (Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax)

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.

Suggested Citation

  • Isabel Alves & Joanna Giemza & Michael G. B. Blum & Carolina Bernhardsson & Stéphanie Chatel & Matilde Karakachoff & Aude Pierre & Anthony F. Herzig & Robert Olaso & Martial Monteil & Véronique Gallie, 2024. "Human genetic structure in Northwest France provides new insights into West European historical demography," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51087-1
    DOI: 10.1038/s41467-024-51087-1
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    as
    1. Joscha Gretzinger & Duncan Sayer & Pierre Justeau & Eveline Altena & Maria Pala & Katharina Dulias & Ceiridwen J. Edwards & Susanne Jodoin & Laura Lacher & Susanna Sabin & Åshild J. Vågene & Wolfgang , 2022. "Author Correction: The Anglo-Saxon migration and the formation of the early English gene pool," Nature, Nature, vol. 611(7934), pages 3-3, November.
    2. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    3. Wolfgang Haak & Iosif Lazaridis & Nick Patterson & Nadin Rohland & Swapan Mallick & Bastien Llamas & Guido Brandt & Susanne Nordenfelt & Eadaoin Harney & Kristin Stewardson & Qiaomei Fu & Alissa Mittn, 2015. "Massive migration from the steppe was a source for Indo-European languages in Europe," Nature, Nature, vol. 522(7555), pages 207-211, June.
    4. Yali Xue & Massimo Mezzavilla & Marc Haber & Shane McCarthy & Yuan Chen & Vagheesh Narasimhan & Arthur Gilly & Qasim Ayub & Vincenza Colonna & Lorraine Southam & Christopher Finan & Andrea Massaia & H, 2017. "Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations," Nature Communications, Nature, vol. 8(1), pages 1-7, August.
    5. Iñigo Olalde & Selina Brace & Morten E. Allentoft & Ian Armit & Kristian Kristiansen & Thomas Booth & Nadin Rohland & Swapan Mallick & Anna Szécsényi-Nagy & Alissa Mittnik & Eveline Altena & Mark Lips, 2018. "Erratum: The Beaker phenomenon and the genomic transformation of northwest Europe," Nature, Nature, vol. 555(7697), pages 543-543, March.
    6. Rui Martiniano & Anwen Caffell & Malin Holst & Kurt Hunter-Mann & Janet Montgomery & Gundula Müldner & Russell L. McLaughlin & Matthew D. Teasdale & Wouter van Rheenen & Jan H. Veldink & Leonard H. va, 2016. "Genomic signals of migration and continuity in Britain before the Anglo-Saxons," Nature Communications, Nature, vol. 7(1), pages 1-8, April.
    7. Ashot Margaryan & Daniel J. Lawson & Martin Sikora & Fernando Racimo & Simon Rasmussen & Ida Moltke & Lara M. Cassidy & Emil Jørsboe & Andrés Ingason & Mikkel W. Pedersen & Thorfinn Korneliussen & Hel, 2020. "Population genomics of the Viking world," Nature, Nature, vol. 585(7825), pages 390-396, September.
    8. Iain Mathieson & Iosif Lazaridis & Nadin Rohland & Swapan Mallick & Nick Patterson & Songül Alpaslan Roodenberg & Eadaoin Harney & Kristin Stewardson & Daniel Fernandes & Mario Novak & Kendra Sirak & , 2015. "Genome-wide patterns of selection in 230 ancient Eurasians," Nature, Nature, vol. 528(7583), pages 499-503, December.
    9. Joscha Gretzinger & Duncan Sayer & Pierre Justeau & Eveline Altena & Maria Pala & Katharina Dulias & Ceiridwen J. Edwards & Susanne Jodoin & Laura Lacher & Susanna Sabin & Åshild J. Vågene & Wolfgang , 2022. "The Anglo-Saxon migration and the formation of the early English gene pool," Nature, Nature, vol. 610(7930), pages 112-119, October.
    10. John Novembre & Toby Johnson & Katarzyna Bryc & Zoltán Kutalik & Adam R. Boyko & Adam Auton & Amit Indap & Karen S. King & Sven Bergmann & Matthew R. Nelson & Matthew Stephens & Carlos D. Bustamante, 2008. "Genes mirror geography within Europe," Nature, Nature, vol. 456(7219), pages 274-274, November.
    11. Iosif Lazaridis & Nick Patterson & Alissa Mittnik & Gabriel Renaud & Swapan Mallick & Karola Kirsanow & Peter H. Sudmant & Joshua G. Schraiber & Sergi Castellano & Mark Lipson & Bonnie Berger & Christ, 2014. "Ancient human genomes suggest three ancestral populations for present-day Europeans," Nature, Nature, vol. 513(7518), pages 409-413, September.
    12. Daniel John Lawson & Garrett Hellenthal & Simon Myers & Daniel Falush, 2012. "Inference of Population Structure using Dense Haplotype Data," PLOS Genetics, Public Library of Science, vol. 8(1), pages 1-16, January.
    13. Clare Bycroft & Ceres Fernandez-Rozadilla & Clara Ruiz-Ponte & Inés Quintela & Ángel Carracedo & Peter Donnelly & Simon Myers, 2019. "Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    14. Ross P. Byrne & Wouter van Rheenen & Leonard H. van den Berg & Jan H. Veldink & Russell L. McLaughlin, 2020. "Dutch population structure across space, time and GWAS design," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    15. John Novembre & Toby Johnson & Katarzyna Bryc & Zoltán Kutalik & Adam R. Boyko & Adam Auton & Amit Indap & Karen S. King & Sven Bergmann & Matthew R. Nelson & Matthew Stephens & Carlos D. Bustamante, 2008. "Genes mirror geography within Europe," Nature, Nature, vol. 456(7218), pages 98-101, November.
    16. Iñigo Olalde & Selina Brace & Morten E. Allentoft & Ian Armit & Kristian Kristiansen & Thomas Booth & Nadin Rohland & Swapan Mallick & Anna Szécsényi-Nagy & Alissa Mittnik & Eveline Altena & Mark Lips, 2018. "The Beaker phenomenon and the genomic transformation of northwest Europe," Nature, Nature, vol. 555(7695), pages 190-196, March.
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