November 24, 2012

Assessment of Totonac and Bolivian samples using 'globe13'

I was on the lookout for some Affy 6.0 samples recently, and I discovered the data of the recent Watkins et al. (2012) paper, so I decided to run them through my globe13 calculator. A total of 49,233 SNPs were in common between that and my globe13 set, which is not much, but ought to be sufficient to discover the main features of these two population samples.

It appears that both samples are mainly "Amerindian", with the Bolivian sample having some more European admixture than the Totonac one.

Here are the population portraits, clearly showing that the "European" admixture in Bolivians comes from a subset of individuals.
For comparison, here are the ADMIXTURE results from the original paper that appear quite similar to my own. (Note that the individual ordering is probably not the same as my own):

The Mediterranean/North_European ratio of my own analysis suggests the likely "southern" (probably Spanish) origin of the European admixture in these populations.


I also combined the two Amerindian populations with HGDP Karitiana, Sardinian, and French to calculate f3-statistics. Here are the significant ones:

So, admixture in the Bolivian sample is confirmed, while in the Totonac one it is not. I do think it's possible that the Totonac might have a little European admixture though which might be masked by their history of drift. Also notice the evidence for admixture in the French using all three Amerindian samples, with lowest f3(French; Amerindian, Sardinian) using the Karitiana reference.


Acid said...

Nice! ;)

Is it possible to have population portraits for project participants? Thanks.

Dienekes said...

Project participants have their raw numbers, so they don't need portraits, or they can make their own in Excel or something if they want to visualize their proportions.

Mark D said...

It surprises me that Totonac, a Mexican people, would show less admixture than Bolivians. I suspect this has naturally to do with sampling small groups of individuals, or possibly the result of determining beforehand which individuals have the least amount of acknowledged European ancestry. Both countries, as a whole, have a wide range of admixture, but it does not occur across all regions, groups or economic classes. There is considerable variation, and I'm sure one can find a sample of native Bolivians with no European admixture.