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Genetic map of Europe; genes vary as a function of distance

Gene Expression
By Razib Khan
Sep 1, 2008 6:29 AMJul 13, 2023 4:00 PM

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My post The Genetic Map of Europe drew a lot of interest, but there's even a cooler paper on the same topic out, Genes mirror geography within Europe:

...Despite low average levels of genetic differentiation among Europeans, we find a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans. The results emphasize that when mapping the genetic basis of a disease phenotype, spurious associations can arise if genetic structure is not properly accounted for. In addition, the results are relevant to the prospects of genetic ancestry testing; an individual's DNA can be used to infer their geographic origin with surprising accuracy--often to within a few hundred kilometres.

Again, great maps. First, check out this plotting of the two largest independent dimensions of genetic variation. Note the rough correspondence to the geography of Europe in terms of spatial relations. This should be no surprise considering that for all practical purposes marriage networks move across two dimensions and drop off in likelihood as a function of distance. In other words, it is common sense that relatedness between groups would drop as a function of distance. Do note the small sample sizes for some groups, the N for Denmark, Finland, Latvia, Slovakia and Ukraine is 1, while Italy and the United Kingdom have N's of 200 or more .

Click here for full sized figure No big surprise, but it greats really cool when you zoom in as they do in B of Figure 1 for Switzerland.

Note the intersection between various language based ethnicities across national boundaries, as well the fact that that Swiss themselves occupy a central position on the plot of genetic variation. Finally, they took the data of genetic variation and projected back onto the map of Europe the location of the individuals in their sample. Check out the results....

It's not perfect, but think that it is nevertheless an impressive prediction based on their data set. At Gene Expression Classic p-ter notes:

The method the authors develop for predicting an individual's country of origin from genetics are only a beginning for this kind of application of genetic data. They note that the SNP chip used in the study only includes common variation, while rare variants are likely to be much more geographically restricted (and thus more informative in this kind of analysis). The limits to the resolution of these sorts of methods are likely to be very fine indeed; the authors note that, even with this panel, they're able to distinguish with some confidence individuals that are from the German, Italian, and French-speaking parts of Switzerland. With full resequencing data, it's likely that even the precise village of origin of an individual will be predictable from genetics alone.

I don't need to connect the dots here in terms of the power of these sorts of methodologies. Imagine if you could figure out what town a criminal's ancestors were likely from based on DNA alone? Additionally, with our better understanding of how genetic variation maps onto phenotype we are getting where we can imagine constructing a physical image of someone based purely on DNA. For those interested in genealogy these techniques are going to be a gold mine, and for those who are going to be providing these techniques to interested parties there's some gold to be had. The point that Europe has little diversity is also something that bears noting, when they get to non-European populations they'll hopefully be plucking some lower hanging fruit. Europeans aren't the only ones interested in their genealogy, the the black American have in historical genetics has an obvious underpinning. The possibility of extremely detailed knowledge of one's geographic origin would be very valuable to some of these people. Of course the devil is in the details, black Americans are compound, while an Italian family in Calabria might have been resident in the region for centuries. But one can at least start on this project at this point in terms of feasibility, and the basic outline of how one will go about doing it will already in place. Also, see Popgen Ramblings. And New Scientist has some quotes from the researchers in the study:

"It tells us that geography matters," says John Novembre, a population geneticist at the University of California, Los Angeles, who led one of the studies. Despite language, immigration and intermarriage, genetic differences between Europeans are almost entirely related to where they were born. This, however, does not mean that the citizens of each European nation represent miniature races. "The genetic diversity in Europe is very low. There isn't really much," says Manfred Kayser, a geneticist at Erasmus University Rotterdam in the Netherlands, who led the other study. ... The map was so accurate that when Novembre's team placed a geopolitical map over their genetic "map", half of the genomes landed within 310 kilometres of their country of origin, while 90% fell within 700 km. Both teams found that southern Europeans boast more overall genetic diversity than Scandinavians, British and Irish.

Related: Also see Not Exactly Rocket Science.

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