October 13, 2010

Clustering European Populations with ADMIXTURE

Here is the result of running ADMIXTURE for K=6 using 275K SNPs on the combined HGDP+HapMap European populations + the CHB Chinese sample from HapMap. (Only the larger HapMap Tuscan sample was included, rather than the smaller HGDP one).

Using a large number of K in closely related populations makes convergence quite harder, but the end result does correspond to several identifiable clusters.

yellow: Northern European
green: "Adygei"
red: "Sardinian"
purple: "Basque"
light and dark blue: Chinese

It's interesting that the Chinese split before some Europeans do. Interestingly, one of the two Chinese components (light blue) is the one represented in Russians, so this split probably reflects some type of northern/southern differentiation in Chinese, as the east Eurasian component in Russians was introduced from northern Finno-Ugric speakers.

Here are the admixture proportions:

It would be interesting to add the Xing et al. dataset into the mix, however, there is little overlap between all three datasets, rendering the aggregate quite useless for such fine-level work.

4 comments:

onur said...

The Chinese components in Utah Whites (CEU) and the French and the Chinese-2 component in the Adygei are in negligible quantities and would probably not show up in a different setting, they are probably entirely to do with the limitations of the ADMIXTURE software. As to the Chinese-1 component in North Russians from Vologda (who are probably mostly descended from the assimilated Finno-Ugric locals) and the Adygei, there is something real there, but as long as intermediate populations like Central Asians (including Mongols), Siberians and South Asians aren't included (we can also include West Asians for more clarity), we cannot say whether it is connected with China or East Asia or Mongoloids in general.

Dienekes said...

but as long as intermediate populations like Central Asians (including Mongols), Siberians and South Asians aren't included (we can also include West Asians for more clarity), we cannot say whether it is connected with China or East Asia or Mongoloids in general.

Inclusion of these populations would not alter the fact that whatever component these Russians have _is_ somehow connected to China/East Asia/Mongoloids as it is pulling them away from Europeans and towards China/East Asia/Mongoloids.

The same effect can be achieved by a small number of pure Mongoloids, or a larger number of Caucasoid-Mongoloid Central Asians, or a third race between Caucasoids and Mongoloids. In all these cases "something" more similar to Mongoloids than Caucasoids are was added to these Russians to move them in that direction.

onur said...

Dieneke, that was essentially what I was trying to say: many things are possible to explain this situation.

Ponto said...

It should be stressed that the Russians being used are North Russians and the results do not apply to the west Russians.

I would appreciate some sort of recap or synopsis of the possible admixture in West Eurasians and other groups based on the Admixture runs done by dienekes. I am not sure but are the Adygei supposed to be some sort of proxy for SE Europeans.