Planet Earth

An algorithm is just an algorithm

Gene ExpressionBy Razib KhanApr 24, 2012 1:48 AM

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In the comments below:

You should include a Moroccan or otherwise native North African sample. Without a North African sample West Africans act as proxy for some of that North African ancestry that does exist in Iberia, specially the Western third (Portugal, Galicia, Extremadura, León, etc.) Doing that your analysis would become more precise and you could make better informed claims. I was reading through all the entry and there was no mention to the rather surprising notable West African component in Iberians other than Basques. For my somewhat trained eye it is clear that this is a proxy for North African ancestry and not directly West African ancestry. This is demonstratedly also the case in Canary Islands, at least to a large extent, and, by extension in Cuba (which is nearly identical to your average Canarian), at least Cuba-1. Cuba-2 seems actually admixed at low levels and both seem to have some Amerindian ancestry not existent in Spain.

This is a fair point. I switched computers recently, and the Behar et al. data set I had seems to have become corrupted. So I snatched the Mozabites from the HGDP, and removed the Gujaratis from the previous run. I also added Russians, Druze, and some extra Amerindian groups. At K = 7 this pattern jumped out:

The Mozabites have "swallowed" most of the "African" component in the Iberian populations. But not in the two Cubans. The main objection I would have is that the Northern European groups now show some African, which is likely to be an artifact. It does seem unlikely though that the Cuban African element is due these individuals being Northern European rather than Southwest European. These ADMIXTURE results also align Cuba 1 better with the PCA, where the individual was definitely an outlier. Another illustration that knowledge comes not through blind adherence to methods, but human reflection.

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