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.

UPDATE:

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.

Ancestry, admixture and selection in Bolivian and Totonac populations

BMC Genetics 2012, 13:39 doi:10.1186/1471-2156-13-39

Genetic analysis of ancestry, admixture and selection in Bolivian and Totonac populations of the New World

W Scott Watkins, Jinchuan Xing, Chad Huff, David J Witherspoon, Yuhua Zhang, Ugo A Perego, Scott R Woodward and Lynn B Jorde

Abstract (provisional) 
Background

Populations of the Americas were founded by early migrants from Asia, and some have experienced recent genetic admixture. To better characterize the native and non-native ancestry components in populations from the Americas, we analyzed 815,377 autosomal SNPs, mitochondrial hypervariable segments I and II, and 36 Y-chromosome STRs from 24 Mesoamerican Totonacs and 23 South American Bolivians.

Results and conclusions

We analyzed common genomic regions from native Bolivian and Totonac populations to identify 324 highly predictive Native American ancestry informative markers (AIMs). As few as 40-50 of these AIMs perform nearly as well as large panels of random genome-wide SNPs for predicting and estimating Native American ancestry and admixture levels. These AIMs have greater New World vs. Old World specificity than previous AIMs sets. We identify highly-divergent New World SNPs that coincide with high-frequency haplotypes found at similar frequencies in all populations examined, including the HGDP Pima, Maya, Colombian, Karitiana, and Surui American populations. Some of these regions are potential candidates for positive selection. European admixture in the Bolivian sample is approximately 12%, though individual estimates range from 0-48%. We estimate that the admixture occurred ~360-384 years ago. Little evidence of European or African admixture was found in Totonac individuals. Bolivians with pre-Columbian mtDNA and Ychromosome haplogroups had 5-30% autosomal European ancestry, demonstrating the limitations of Y-chromosome and mtDNA haplogroups and the need for autosomal ancestry informative markers for assessing ancestry in admixed populations.

Link