Genetic Distance in France and Japan: A Comparative Analysis of FST Values

[Flashball]

the genetic distance, FST, between clusters in France is similar to that in Japan. For example, the FST between the North and Center regions of France is approximately 0.0002, which represents 60% and 80% of the samples in the 3C and SUVIMAX panels, respectively."

The genetic distance, measured by FST, between clusters in France and Japan shows a similar low level of differentiation.

Here's a complete summary based on the data:

France:
https://i.ibb.co/DKFm0sJ/image.png

Northern and Central France:
In the 3C and SUVIMAX panels, the FST between the Northern (NO) and Central (CTR) clusters is around 0.0002. This low value indicates minimal genetic differentiation, with these regions representing between 60% and 80% of the total samples.
Such small FST values suggest that these populations are genetically very close, much like certain clusters in Japan.

Southern France (SW and SE):
For the South-West (SW) and South-East (SE) clusters, FST values with other French regions are slightly higher, ranging from 0.0015 to 0.0040 in the SUVIMAX and 3C panels.
Despite the slight increase, these values are still quite low, indicating weak genetic differentiation even in Southern France.

Comparison with Japan:
When compared to Japan, where FST values between regions like Hokkaido and Kanto-Koshinetsu (around 0.000293) or Kyushu and Okinawa (0.002823) are similarly low, it becomes clear that the genetic differentiation within France is comparable to that within Japan.
Both countries show low FST values, suggesting a relatively homogeneous genetic structure across regions.
https://i.ibb.co/LnYknK3/image.png

Conclusion:
The genetic distances (FST) between regional clusters in France, including both the North/Central and South, are comparable to those observed in Japan. This indicates minimal genetic differentiation within both countries, with some slight variations in the South of France similar to those seen in Japan's Okinawa and Kyushu regions.

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Summary of Genetic Differentiation in Sardinia, France, and Japan:

Sardinia:
Exhibits extremely high genetic differentiation, especially between villages
FST values range from 0.9 to 7.5 between Ogliastra villages
https://i.ibb.co/h24qwv6/image.png

Provincial FST values are lower but still high, ranging from 0.3 to 5.3
Some villages, like Arzana, show remarkable genetic isolation
Clear genetic clusters visible in PCA plot
https://i.ibb.co/PwL74PD/image.png

https://www.readcube.com/articles/supplement?doi=10.1038%2Fs41588-018-0215-8&index=0

France:
Very low genetic differentiation
FST values range from 0.0002 to 0.0049
Little variation between different regions
https://i.ibb.co/hYhFhtM/image.png

Japan:
Extremely low genetic differentiation
FST values range from 0.000229 to 0.003522
Okinawa shows slightly higher differentiation, but still very low overall
https://i.ibb.co/H4MmK4Q/image.png



Surprising Aspects of Sardinian Genetic Differentiation:
The high FST values between geographically close areas in Sardinia are indeed surprising and unusual. This is remarkable for several reasons:
Scale of Differentiation: The FST values between Sardinian villages are orders of magnitude higher than those seen between entire regions of France or Japan. This level of differentiation is typically seen between very distant or long-isolated populations.

Geographic Proximity: Despite the small size of Sardinia, villages that are geographically close show levels of genetic differentiation that would be expected between populations separated by vast distances or major geographical barriers.

Historical Implications: These high FST values suggest a long history of genetic isolation between nearby communities, which is unusual for such a small area. This implies minimal gene flow between villages over many generations, despite their proximity.

Contrast with Mainland Populations: The stark difference between Sardinia's genetic landscape and that of France or Japan highlights how unique Sardinia's population structure is. Mainland populations typically show much more genetic homogeneity due to higher rates of migration and intermarriage between regions.
Microevolutionary Significance: Such high differentiation in a small area makes Sardinia an exceptional case study for understanding the effects of genetic drift, founder effects, and possibly local adaptation in small, isolated populations.

This extreme genetic differentiation in Sardinia, especially given the small geographical distances involved, presents a fascinating anomaly in population genetics. It suggests a complex history of settlement, isolation, and limited gene flow that has resulted in a genetic landscape more diverse and fragmented than what is typically seen in most other human populations.