An important division separates Northern from Southern France. It may coincide with the von Wartburg line, which divides France into “Langue d’Oïl” part (influenced by Germanic speaking) and “Langue d’Oc” part (closer to Roman speaking). This border has changed through centuries and our North-South limit is close to the limit as it was estimated in the IXth century. This border also follows the Loire River, which has long been a political and cultural border between kingdoms/counties in the North and in the South. Regions with strong cultural particularities tend to separate. This is for example the case for Aquitaine in the South-West which duchy has long represented a civilization on its own. The Brittany region is also detected as a separate entity in both datasets. This could be explained both by its position at the end of the continent where it forms a peninsula and, by its history since Brittany has been an independent political entity (Kingdom and, later, duchy of Bretagne), with stable borders, for a long time.
The extreme South-West regions show the highest differentiation to neighbor clusters. . . . This cluster is likely due to a higher proportion of possibly Basque individuals . . . . which overlap with HGDP Basque defined individuals. The FST between the south-west and the other French clusters were markedly higher than the FST between remaining French clusters. . . . [T]hese values are comparable to what we observed between the Italian and the British heritage clusters (FST=0.0035). . . . We also observe that the broad-scale genetic structure of France strikingly aligns with two major rivers of France “La Garonne” and “La Loire”. At a finer-scale, the “Adour” river partition the SW to the SO cluster. . . .
While historical, cultural and political borders seem to have shaped the genetic structure of modern-days France, exhibiting visible clusters, the population is quite homogeneous with low FST values between-clusters . . . . We find that each cluster is genetically close to the closest neighbor European country, which is in line with a continuous gene flow at the European level. However, we observe that Brittany is substantially closer to British Isles population than North of France, in spite of both being equally geographically close. Migration of Britons in what was at the time Armorica (and is now Brittany) may explain this closeness. These migrations may have been quite constant during centuries although a two waves model is generally assumed. A first wave would have occurred in the Xth century when soldiers from British Isles were sent to Armorica whereas the second wave consisted of Britons escaping the Anglo-Saxon invasions. . . .
Studying the evolution of French population size based on genetic data, we observe a very rapid increase in the last generations. This observation is in line with what has been seen in European populations. We also observe, in most cases, a depression during a period spanning from 12 to 22 generations ago. This may correspond to a period spanning from 1300 to 1700. Indeed, this period was characterized by a deep depression in population size due to a long series of plague events. While the population size in kingdom of France was estimated to be 20 million in 1348, it dropped down to 12,415 million in 1400, followed by an uneven trajectory to recover the 20 million at the end of Louis XIVth reign (1715). However, the decrease we observe in the genetic data does seem to affect mainly the Northern part of France, and for instance is mainly observed in the NO cluster. We see no reason for this trend based on historical records except perhaps the last plague epidemics in 1666-1670 that was limited to the North of France. Alternatively, a more spread population in the South (which is in general hilly or mountainous) may explain a lower impact of these dramatic episodes. Plague is expected to have had a very strong impact on the population demography in the past as some epidemics led to substantial reduction in the population sizes.