The genetic history of France

Abstract

The study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and population structure. Although France occupies a particular location at the western part of Europe and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2184 individuals born in France who were enrolled in two independent population cohorts. Using FineSTRUCTURE, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters correspond closely to geographic, historical, and linguistic divisions of France, and contain different proportions of ancestry from Stone and Bronze Age populations. By modeling the relationship between genetics and geography using EEMS, we were able to detect gene flow barriers that are similar across the two cohorts and correspond to major rivers and mountain ranges. Estimations of effective population sizes also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the 14^th century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in genetic studies of Europe that will be useful to medical geneticists, historians, and archeologists.

Fig. 1. Clustering of the French individuals into six or seven clusters as inferred by FineSTRUCTURE analysis.

(a) 3C Study (770 individuals) and (b) SU.VI.MAX (1414 individuals). The tree structure is shown as well as a map of France with pie-charts giving, for each département, the proportion of individuals belonging to each cluster. Three main rivers of France (Loire, Garonne, and Adour from north to south) are drawn on the maps.

Fig. 2. Estimated effective migration surfaces of France obtained from EEMS.

(a) 3 C and (b) SU.VI.MAX datasets. The color scale reveals low (blue) to high (orange) genetic barriers between populations localized on a grid of 250 demes. Each dot is proportional to the number of populations included.

Fig. 3. Ancestry profiles from the three neighboring European populations inferred by SOURCEFIND.

(a) 3 C and (b) SU.VI.MAX individuals datasets. In each cluster, individuals are ordered according to the latitude of their reported birthplace.

Fig. 4. Relationship between French clusters and three ancient populations: western hunter-gatherers (WHG), early Neolithic farmers (EF), and Steppe pastoralists (SP).

(a) Outgroup f₃-statistics of the form f₃(Mbuti; Ancient population, French clusters) plotted onto the map of France. (b) Ancestry proportions estimated with qpAdm [43] assuming a model where each French cluster results from the mixture of WHG, EF, and SP-related ancestry. Maps were generated using the R statistical package along with ‘maptools’ library.