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torsdag 4. juli 2013

La Braña and modern World variation II

I have done a new analysis of the La Braña, now using ADMIXTURE with only 4k SNP's (both LD pruned and MAF 0.05 filtered in PLINK) and over 2200 samples worldwide from different reference sets and because of the large sample size it was possible to increase the numbers of K up to 8. As a caution please remember that compared to earlier analysis the number of SNP's are very low and so the resolution is low and the individual variation large especially for the minority components compared to earlier analysis linked and unlinked, but by pooling individuals into populations this is to some extent made more even.

As we can see from the enclosed admixture bars the La Braña appears (given the considerations above) to have a very high level of North European like affiliation similar to the ones we see from the northernmost populations in Europe and is consistent with earlier analysis but ADMIXTURE is here not able to differentiate between them as Chromopainter-Finestructure did. The Middle-Eastern like admixture is close to 0 very different from the modern Iberian peninsula populations who reach levels up to 34%.

We further see that the Central Asian like admixture is close to zero similar to todays Iberian populations and Saamis (please note that the CA admixture in the Saami is due to only 1 individual, the rest shows close to 0 admixture), so is the affiliation to Siberians and Native Americans.

The implication of this result may be that large part of Europe was populated by hunter gatherers who mostly resembled todays North-Europeans and especially the Saamis. Later Middle-Eastern farmers moved westward and northwards. Their genetic impact was minimal in the fringe populations in the far north. Later Central-Asian like populations moved west from the east but their genetic impact was minimal in the Iberian populations and among Saamis in Fennoscandia. The Finns, Mordovians and especially the Saami on the other appears to have received considerable Siberian like admixture from the arctic.

First in alphabetical order:

Then in order of North-European (NE) admixture:

Then in order of Middle-East (ME) admixture:

Then in order of Central-Asian (CA) admixture:
Then in order of Siberian (SIB) admixture:

This ADMIXTURE study appears to show similartity to the study of Hughe 2011.

4 kommentarer:

  1. What you call "Central Asian-like admixture" is in reality a Caucasian-like admixture. There is unfortunately no Central Asian population in this analysis and the component that you call "Central Asian", or in the abbreviated form "CA", peaks in the populations of the Caucasus (Lezgins and Georgians).

  2. Onur: You have misunderstood the analysis. It is a worldwide analysis but I have only presented the results for the European populations. The CA component peaks among Kalash and surrounding populations. This component is also seen in large amount in Caucasus. In earlier 289k haplotype based Chromopainter-Finestructure analysis there is similar affiliation between these Central-Asian populations and the Caucasus.

  3. Thanks for the clarification, Anders. Could you post the full results of the analysis or give link to them?

  4. "Later Central-Asian like populations moved west from the east but their genetic impact was minimal in the Iberian populations and among Saamis in Fennoscandia."

    This is nonsense.

    Central Asians like the Kalash have suffered founder effects and extreme genetic drift, so they create a component which peaks in Central Asia, but also shows up in the populations that are ancestral to this component.

    So there was no post-Ice Age migration from Central Asia to the Caucasus or Eastern Europe. The migrations went the other way; from Eastern Europe and West Asia to Central Asia. See here...

    The same thing can be seen very clearly via the phylogeography of R1a, which expanded from Eastern Europe to Central Asia.

    This is a pretty sloppy effort on your part. You need to understand these concepts before writing about them.