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.
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.