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. 2020 Jun 9;117(23):12791-12798.
doi: 10.1073/pnas.1918034117. Epub 2020 May 26.

Ancient genomes from present-day France unveil 7,000 years of its demographic history

Samantha Brunel  1 , E Andrew Bennett  1 , Laurent Cardin  1   2 , Damien Garraud  1   2 , Hélène Barrand Emam  3   4 , Alexandre Beylier  5   6 , Bruno Boulestin  7 , Fanny Chenal  4   8 , Elsa Ciesielski  6 , Fabien Convertini  6   8 , Bernard Dedet  6 , Stéphanie Desbrosse-Degobertiere  8 , Sophie Desenne  8   9 , Jerôme Dubouloz  9 , Henri Duday  7 , Gilles Escalon  6   8 , Véronique Fabre  6   8 , Eric Gailledrat  6 , Muriel Gandelin  8   10 , Yves Gleize  7   8 , Sébastien Goepfert  3 , Jean Guilaine  10   11 , Lamys Hachem  8   9 , Michael Ilett  9 , François Lambach  7 , Florent Maziere  6   8 , Bertrand Perrin  3   4 , Suzanne Plouin  4 , Estelle Pinard  8   9 , Ivan Praud  8   9 , Isabelle Richard  8   12 , Vincent Riquier  8   9 , Réjane Roure  6 , Benoit Sendra  6   8 , Corinne Thevenet  8   9 , Sandrine Thiol  8 , Elisabeth Vauquelin  8 , Luc Vergnaud  3   4 , Thierry Grange  13 , Eva-Maria Geigl  13 , Melanie Pruvost  13   7
Affiliations

Ancient genomes from present-day France unveil 7,000 years of its demographic history

Samantha Brunel et al. Proc Natl Acad Sci U S A. .

Abstract

Genomic studies conducted on ancient individuals across Europe have revealed how migrations have contributed to its present genetic landscape, but the territory of present-day France has yet to be connected to the broader European picture. We generated a large dataset comprising the complete mitochondrial genomes, Y-chromosome markers, and genotypes of a number of nuclear loci of interest of 243 individuals sampled across present-day France over a period spanning 7,000 y, complemented with a partially overlapping dataset of 58 low-coverage genomes. This panel provides a high-resolution transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes. Parental lineages and genomic data both revealed demographic patterns in France for the Neolithic and Bronze Age transitions consistent with neighboring regions, first with a migration wave of Anatolian farmers followed by varying degrees of admixture with autochthonous hunter-gatherers, and then substantial gene flow from individuals deriving part of their ancestry from the Pontic steppe at the onset of the Bronze Age. Our data have also highlighted the persistence of Magdalenian-associated ancestry in hunter-gatherer populations outside of Spain and thus provide arguments for an expansion of these populations at the end of the Paleolithic Period more northerly than what has been described so far. Finally, no major demographic changes were detected during the transition between the Bronze and Iron Ages.

Keywords: Neolithic; migration; paleogenomics; population genomics; protohistory.

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Conflict of interest statement

The authors declare no competing interest.

Figures

Fig. 1.
Fig. 1.
Overview of the ancient French dataset. Filled symbols are used for ancient individuals from France whereas open symbols are used for other ancient western Eurasians. The shape of the symbol indicates the geographic origin and the color indicates the time period. (A) Location of the samples included in the study. (B) Principal-component analysis of ancient western Eurasians projected onto the variation of present-day genotypes, restricted to Europe. (C) Ancestry proportion for French individuals ranging from the Mesolithic to the Iron Age established using qpAdm (data from this study and from previoulsy published studies). Each bar represents one individual with the associated mitochondrial DNA haplogroup and Y-chromosome haplogroup (Right). Error bars indicate ±1 SE. Symbols used in A and B are indicated for each individual.
Fig. 2.
Fig. 2.
Genetic affinity between ancient French and either western hunter-gatherers or steppe herders. (A) Boxplot of the D-statistic values of the form D(Mbuti, Test: WHG, Anatolia_Neolithic) for the Early and Middle Neolithic European population with WHGs consisting of Loschbour, ElMiron, GoyetQ2, Villabruna, KO1, and LaBrana to represent better the GoyetQ2 and Villabruna ancestry. (B) D statistics of the form D(Mbuti, Test: WHG, Anatolia_Neolithic) for Early Neolithic individuals of present-day Germany, France, and Iberia. Error bars represent ±1 SE. (C) Boxplot of the D-statistic values of the form D(Mbuti, Test; Yamnaya_Samara, Anatolia_Neolithic) for Late Neolithic and Bronze and Iron Age populations. (D) D statistics of the form D(Mbuti, Test; Yamnaya_Samara, Anatolia_Neolithic) for individuals associated with the Bell Beaker cultural complex. Error bars represent ±1 SE. ALPc, Eastern (Alföld) Linear Pottery Culture; BA, Bronze Age; IA, Iron Age; LNBA, Late Neolithic and Bronze Age; CA, Chalcolithic or Copper Age.
Fig. 3.
Fig. 3.
Frequency of the derived allele for several types of genetic markers in Neolithic French and present-day Europeans. Numbers indicated above the bars correspond to the total number of observations of the derived allele for each variant in the Neolithic population. The color code reflects the function associated with the considered locus. The frequency of the alleles in present-day European populations is indicated in gray. Error bars indicate ±2 SE.
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