Genetic population structure across Brittany and the downstream Loire basin

[J. Ketch]

https://www.biorxiv.org/content/10.1101/2022.02.03.478491v1


Abstract
European genetic ancestry originates from three main ancestral populations - Western hunter-gatherers, early European farmers and Yamnaya Eurasian herders - whose edges geographically met in present-day France. Despite its central role to our understanding of how the ancestral populations interacted and gave rise to modern population structure, the population history of France has remained largely understudied. Here, we analysed 856 high-coverage whole-genome sequences along with genome-wide genotyping data of 3,234 present-day individuals from the northern half of France and merged them with publicly available present-day and ancient Europe-wide genotype datasets. We also analysed, for the first time, the whole-genome sequences of six medieval individuals (300-1100 CE) from Western France to gain insights into the genetic impact of what is commonly known as the Migration Period in Europe. We found extensive fine-scale population structure across Brittany and the downstream Loire basin, emphasizing the need for investigating local populations to better understand the distribution of rare and putatively deleterious variants across space. Overall, we observed an increased population differentiation between the northern and southern sides of the river Loire, which are characterised by different proportions of steppe vs. Neolithic-related ancestry. Samples from Western Brittany carry the largest levels of steppe ancestry and show high levels of allele sharing with individuals associated with the Bell Beaker complex, levels that are only comparable with those found in populations lying on the northwestern edges of Europe. Together, our results imply that present-day individuals from Western Brittany retain substantial legacy of the genetic changes that occurred in Northwestern Europe following the arrival of the Bell Beaker people c. 2500 BCE. Such genetic legacy may explain the sharing of disease-related alleles with other present-day populations from Western Britain and Ireland.

Basically re-affirms the close genetic links between Bretons and Irish/Welsh/Cornish, but stops short of discussing exactly how much ancestry comes from Ancient Britain. Does say that Migration Period Britons are unlikely to be the main explanation for the closeness with Insular Celts though, but a much older connection instead, which I agree with.
https://i.postimg.cc/MKXjhZnt/Capturebrz.jpg

[J.S.]

Mostly Western Breton cluster. There is a clear shift between West Brittany, East-Brittany which is a Gallo-Roman speaking area and South Loire also Gallo-Roman speaking area.





Genetic continuity since mediaeval times
To disentangle the sources of ancestry contributing to the modern French genetic makeup, we merged our WGS data with the largest available compilation of ancient (>3000 samples including ~400 ancient Vikings) and modern samples (>5000) (47,48). In addition, we sequenced six individuals with dates ranging from the 4th to the 12th century CE, from Pays-de- la-Loire (Fig. 4a) to increase our resolution in detecting changes in ancestry during the Mediaeval Period. PCA resulting from projecting the ancient individuals onto the principal component space of modern variation shows that most of the samples fall well within the distribution of present-day French (Fig. S4.1). Out of the six individuals, one (fra009, Table S4.1) likely represents a migrant with genetic affinities to present-day North Africans. This individual, dated from the 5th-6th century CE, was found in an archaeological site located in an ancient town likely built during the Roman period (see SOM, Supplementary archaeological details). Trading networks involving this town may explain the presence of North African migrants so far north. To test whether French Mediaeval samples from the 3-4th century CE and samples from the 6-7th century CE significantly differ in their genetic affinities to other ancient European populations we computed the f4-statistics of the form f4(Mbuti, ancient European sample; sLoire_France_3-4cCE, sLoire_France_6-7cCE). We found no significant differences in allele sharing between individuals from early (300-550 CE, fra001 and fra004) and later Mediaeval Period (600-700 CE, fra016 and fra017, Table S4.2). Therefore, we considered individuals from both periods to represent the same population and refer to them as “Mediaeval French”.
To check for ancestry changes since the Mediaeval Period, we tested whether Mediaeval French individuals are a good proxy source for the ancestry of present-day Northwestern French. To do so we used the modelling approach implemented in qpAdm (49) and we tested one-way models (i.e., genetic continuity) using the five Mediaeval French individuals as surrogate source population for the present-day French. Our results support genetic continuity between the eight present-day French populations (WBR, EBP, SLO, NOR, HAU, GRA, CEN and NOU) and Mediaeval French (P > 0.05, Table 1). qpAdm modelling results are consistent with the PCA showing that Mediaeval French from Pays-de-la-Loire fall within the distribution of modern individuals from the same region.

https://i.imgur.com/R3qcvwU.png
https://i.imgur.com/7ukIyw0.png

Eastern Brittany is closer to the Central cluster than to Western Brittany and South Loire claim as part of historical Brittany is closer to Nouvelle Aquitaine than the two other Briton cluster's.

[Nurzat]

how French are actually different populations that got Frenchified. by the results below, French in Brittany look Celtic, French in Corsica look Italo-Sardinian, French in Aquitaine look Basque, French in Alsace look Germanic, French in Normandy look Germanic; only Central and Southern France look Gallo-Roman:


Eurogenes 'K13 updated'

Target: French_Brittany
Distance: 0.5349% / 0.53493398 | R6P
32.6 Irish_Connacht
18.6 Norwegian
15.0 German_Bavaria_Lower/Middle_Franconia
13.0 Spanish_Valencia
10.7 German_Schleswig-Holstein
10.1 Basque_France


Target: French_Aquitaine
Distance: 0.5255% / 0.52550899 | R6P
71.1 Basque_France
14.2 Spanish_Galicia
7.5 German_Frisian
7.2 Sardinian



Target: French_Corsica
Distance: 0.1728% / 0.17281684 | R6P
33.2 Swiss_Italian
26.7 Italian_Umbria
22.4 Sardinian
11.9 Italian_Molise
5.8 Lebanese_Christian


Target: French_Alsace
Distance: 0.1604% / 0.16035832 | R6P
31.1 German_South_Hesse
17.2 German_North_Hesse
16.3 German_Rhineland-Palatinate_East_of_Rhine
15.6 Austrian_Lower_Austria
10.2 German_County_Glatz
9.6 Italian_Veneto


Target: French_Normandy
Distance: 0.1770% / 0.17700091 | R6P
44.0 German_Rhineland-Palatinate
20.6 German_Lower_Saxony_South
11.6 Basque_France
8.9 Norwegian
7.5 Swedish_Norrland
7.4 Swiss_French


Target: French_Provence
Distance: 0.1020% / 0.10202830 | R6P
34.0 Spanish_Valencia
20.2 Italian_Trentino
18.6 Greek_Andros
15.8 German_Rhineland-Palatinate
7.9 German_Rhineland-Palatinate_East_of_Rhine
3.5 Jew_Morroco


Target: French_Central
Distance: 0.0828% / 0.08278774 | R6P
29.0 German_Bavaria_Proper
17.6 German_South_Hesse
17.1 Spanish_Andalusia
14.2 Spanish_Aragon
13.8 Norwegian
8.3 Spanish_Cantabria

[J.S.]

how French are actually different populations that got Frenchified. by the results below, French in Brittany look Celtic, French in Corsica look Italo-Sardinian, French in Aquitaine look Basque, French in Alsace look Germanic, French in Normandy look Germanic; only Central and Southern France look Gallo-Roman:


Eurogenes 'K13 updated'



Authors of the study claim genetic continuity since Early Medieval Times but, of course, someone needs to come with the K13 panel...to show what the truth is.
The fact you include Corsica, in what is supposed to be a conclusive demonstration, show how biased you are. By the way, Corsica is as relevant as the French Western indies in terms of genetic continuity since Bronze, iron or Medieval times.

nb:

Here, we analysed 856 high-coverage whole-genome sequences along with genome-wide genotyping data of 3,234 present-day individuals from the northern half of France and merged them with publicly available present-day and ancient Europe-wide genotype datasets.


Cohort description
Project PREGO (“Population de référence du Grand Ouest”, www.vacarme-project.org) collected the DNA of 5,707 healthy persons originating from western France (Pays de la Loire and Brittany regions). Individuals were recruited during 295 blood drives organized by the French Blood Service (EFS in French) carried out between February 2014 and March 2017, with a mean of 19 donors per blood drive. Blood drives were spatially and temporally sampled in order to obtain a coverage as homogeneous as possible of the nine départements included in the study. Priority was given to blood drives taking place in rural areas. Participants should be native of western France. Individuals’ birthplace was assessed by the place of birth of the four grandparents.
Only individuals whose four grandparents were born in western France and preferably within a radius of 30 km were included in this study. From the 3,234 individuals included in the present study, 25%, 50% and 75% have their grandparents born 3.25, 6.38 and 12.33 kms from each other, respectively.

The FranceGenRef study aims to describe patterns of population diversity across metropolitan France at the beginning of the 20th century. Thus, individuals were sampled based on the birthplace of their grandparents, whose distance should not exceed 30 kilometres. FranceGenRef includes a total of 862 individuals satisfying the aforementioned criteria and sampled under the scope of three different studies:

[Nurzat]

Authors of the study claim genetic continuity since Early Medieval Times but, of course, someone needs to come with the K13 panel...to show what the truth is.
The fact you include Corsica, in what is supposed to be a conclusive demonstration, show how biased you are. By the way, Corsica is as relevant as the French Western indies in terms of genetic continuity since Bronze, iron or Medieval times.

nb:

Here, we analysed 856 high-coverage whole-genome sequences along with genome-wide genotyping data of 3,234 present-day individuals from the northern half of France and merged them with publicly available present-day and ancient Europe-wide genotype datasets.


Cohort description
Project PREGO (“Population de référence du Grand Ouest”, www.vacarme-project.org) collected the DNA of 5,707 healthy persons originating from western France (Pays de la Loire and Brittany regions). Individuals were recruited during 295 blood drives organized by the French Blood Service (EFS in French) carried out between February 2014 and March 2017, with a mean of 19 donors per blood drive. Blood drives were spatially and temporally sampled in order to obtain a coverage as homogeneous as possible of the nine départements included in the study. Priority was given to blood drives taking place in rural areas. Participants should be native of western France. Individuals’ birthplace was assessed by the place of birth of the four grandparents.
Only individuals whose four grandparents were born in western France and preferably within a radius of 30 km were included in this study. From the 3,234 individuals included in the present study, 25%, 50% and 75% have their grandparents born 3.25, 6.38 and 12.33 kms from each other, respectively.

The FranceGenRef study aims to describe patterns of population diversity across metropolitan France at the beginning of the 20th century. Thus, individuals were sampled based on the birthplace of their grandparents, whose distance should not exceed 30 kilometres. FranceGenRef includes a total of 862 individuals satisfying the aforementioned criteria and sampled under the scope of three different studies:

K13 doesn't disprove continuity in each region. Alsace has always been Germanic until it went to French, Normandy, well, even the name says it, Brittany as well, until recently fully Breton, for Aquitaine it's nothing unusual to have a high degree of similarity to the Basques. so it leaves Central and Southern France (minus Corsica) to be Gallo-Roman/French-proper.

[J.S.]

K13 doesn't disprove continuity in each region. Alsace has always been Germanic until it went to French, Normandy, well, even the name says it, Brittany as well, until recently fully Breton, for Aquitaine it's nothing unusual to have a high degree of similarity to the Basques. so it leaves Central and Southern France (minus Corsica) to be Gallo-Roman/French-proper.

Come one...Alsace has always been German?! Actually, in France, there is one thing we know for sure as a roman speaking country, language is not equal to genetic. The name Normandy does not mean anything other way, French should speak german and, by the way, according to the study, there is no noticeable impact of Viking migration to France, even in Normandy. Brittany is half Gallo-Roman, since the begining of it existence, that is the main point of the study and here is the conclusion about Aquitaine(NOU Nouvelle Aquitaine):
Interestingly, ancient Spanish reported as Celtiberians or from the Mediaeval period do not generally fit contemporary French (with the exception of NOU) and only Spanish individuals associated with the Germanic invasions, especially individuals associated with Visigoth or Carolingian archaeological remains, are suitable proxies for contemporary French ancestry
https://i.imgur.com/AbBBQkj.png
Almost 90% of the French Territory is a Gallo-Roman speaking area.
https://i.imgur.com/9kt5zL6.png
https://i.imgur.com/cfxlMq5.png

Another interesting thing concerning the Southern-French Spanish-like profile, Spanish-North and Basque included in the study share more drift with France_Low_Steppe_Beaket than with Iberia_Beaker.

[Flashball]

Come one...Alsace has always been German?! Actually, in France, there is one thing we know for sure as a roman speaking country, language is not equal to genetic. The name Normandy does not mean anything other way, French should speak german and, by the way, according to the study, there is no noticeable impact of Viking migration to France, even in Normandy. Brittany is half Gallo-Roman, since the begining of it existence, that is the main point of the study and here is the conclusion about Aquitaine(NOU Nouvelle Aquitaine):
https://i.imgur.com/AbBBQkj.png
Almost 90% of the French Territory is a Gallo-Roman speaking area.
https://i.imgur.com/9kt5zL6.png
https://i.imgur.com/cfxlMq5.png

Another interesting thing concerning the Southern-French Spanish-like profile, Spanish-North and Basque included in the study share more drift with France_Low_Steppe_Beaket than with Iberia_Beaker.

this