Genetic map of Europe again
On the heels of the previous paper describing the “genetic map of europe” comes a new paper that makes the same general observation that genetic data contain information about geography. These authors also develop a model that does reasonably well at predicting the country of origin of an individual based on genetics alone.
It’s worth considering why this is possible. A previous paper by some of these same authors proved that under a simple isolation by distance model, the first two principal components of genetic data are perpendicular in geographic space. So it appears that this basic model is a decent approximation to Europe; further work will likely refine the ways, which are likely to be interesting, that this model doesn’t fit the data.
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.
Labels: Genetics, Population genetics
Slovaks are genetically Italian?
As this progresses, it would be interesting to look at what geographic features lessen and increase gene flow — for example, do mountain ranges pose barriers while navigable rivers increase intermarriage? For example, culturally, the Pyrenees seem like a strong barrier while the Rhine, while militarily significant in case of war as a defensive barrier, functions in peacetime to unify both banks of the river.
Makes me wonder who the Romansh in Switzerland would cluster with relatively speaking.
with italians more, right?
Slovaks are genetically Italian?
i think they just have a small sample size of slovaks; that’s probably not a reliable result.
here are the low N’s
bosnia 9
croatia 8
greece 8
russia 6
scotland 5
cyprus 4
macedonia 4
turkey 4
albania 3
norway 3
bulgaria 2
kosovo 2
slovenia 2
denmark 1
finland 1
latvia 1
slovakia 1
ukraine 1
from supplemental:
Individual 13011 was born in Slovakia but has no observed grandparental or language information.
don’t want to make shit up, but what the fuck, slovakia was part of the austro-hungarian empire which included parts of northern italy, right? ;-)
Some time ago I read a report in a Turkish site that a Turkish geneticist had shown that the Belgians were members of a Turkish tribe. How they had battled their way all across Europe was unknown. Of course, he forgot that the Ankara area was the center of Galatia (as in Paul’s Letter to the Galatians)and that Galatia meant Little Gaul and that their ancestors had come from Gaul before the Roman period. And of course, the Belgae were a Gaulish tribe. The sample sizes here are ridiculously small. Go to http://www.kirkpinar.jp and take a look at the most prominent Turkish Pehlevans (olive oil wrestlers) and figure out where their ancestors came from (some look Greek, some look English and Irish, French, German, one looks like Abraham Lincoln.)
while the Rhine, while militarily significant in case of war as a defensive barrier, functions in peacetime to unify both banks of the river.
1) to my knowledge for most of the period after the fall of rome the northern portions of the rhine weren’t a major political boundary. it was the heartland of western germany and the low countries.
2) during the roman period it was obviously a political limit…but, as you note, during peacetime it serves as a conduit, not barrier. the germans on the other side of the rhine were in close touch with groups right within the empire as evidenced by cultural influences. the rhine was mainly a barrier for armed men bent on war or mass tribal movements. OTOH, i suspect it wasn’t a big issue if you wanted to get a wife from the other side of the river.
Did anyone find it strange that on the map of Europe in the image displayed on this post that there was no area marked England? they had a section with an abbreviation for Scotland and the overall area of Britain was given an abbreviation meaning Great Britain but no area was marked England.This makes no sense to me.
So if the PC map and the real map match so well, does it mean that there has been no mass migration in Europe (other than limited, homogeneous diffusion) for a very long time?
(Also, do they plan to include any Basques?)
does it mean that there has been no mass migration in Europe (other than limited, homogeneous diffusion) for a very long time?
depends on what you mean as a “mass migration.” e.g., the folk wandering of the vandals, alans and suevii was only a small proportion of the population of the roman provinces they traversed, but it was at least on the order of tens of thousands, probably more. also, what about the 3rd, 4th, etc. PC components?
So if the PC map and the real map match so well, does it mean that there has been no mass migration in Europe (other than limited, homogeneous diffusion) for a very long time?
no, I don’t think the behavior of PCA in different situations is well-enough known to make that conclusion. isolation by distance is sufficient for the matching of the real map and the PC map, but it’s probably not necessary. it’s mostly unknown how different types of migration affect PCA.
It’s unfortunate that the map doesn’t show more than just European populations.
Besides just curiosity for seeing those other relations… seeing non-European populations often gives me a better feel for how “big” the distances on the “genetic map” really are.
– Charles Iliya Krempeaux
http://changelog.ca/
for PCA analyses of a worldwide set of human populations, see here
http://www.sciencemag.org/cgi/content/abstract/319/5866/1100
Does anyone know a good, non-technical explanation of PCA in general, and its use in genomics in particular? I just looked up the Wiki article on PCA and found it completely unintelligible to anyone (including me) without advanced knowledge of mathematics.
David,
You can find a good non-mathematical explanation in this book: Measuring Intelligence.
Darth: thanks. Oddly enough, I already have that book, but I didn’t recall what it said about PCA! At least it doesn’t go straight into talking about eigenvectors, which causes my eyes to glaze over instantly.
John Costello:
I’m going back 55+ years to remember–but I think they were Belgii (vs Belgae) and I’m certain the correct adjective is “Gallic” (vs Gaulish).
Julius Caesar described them as the “fiercest” of the tribes of Gaul.