Genetic analysis of ancestry in Bolivian and Mesoamerican Totonac populations

[curupira]

Genetic analysis of ancestry, admixture and selection in Bolivian and Totonac populations of the New World. Interesting, since I have not often found autosomal studies on Bolivia.

BMC Genet. 2012 May 20;13:39. doi: 10.1186/1471-2156-13-39.

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 Y-chromosome 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.

http://www.ncbi.nlm.nih.gov/pubmed/22606979

Most New World Totonac and Bolivian individuals are clustered and have smaller estimated distances to the HapMap CHB/JPT than to the CEU or YRI:



Another study, from 2013:

PLoS One. 2013;8(3):e58980. doi: 10.1371/journal.pone.0058980. Epub 2013 Mar 20.
The genetic legacy of the pre-colonial period in contemporary Bolivians.

Only a few genetic studies have been carried out to date in Bolivia. However, some of the most important (pre)historical enclaves of South America were located in these territories. Thus, the (sub)-Andean region of Bolivia was part of the Inca Empire, the largest state in Pre-Columbian America. We have genotyped the first hypervariable region (HVS-I) of 720 samples representing the main regions in Bolivia, and these data have been analyzed in the context of other pan-American samples (>19,000 HVS-I mtDNAs). Entire mtDNA genome sequencing was also undertaken on selected Native American lineages. Additionally, a panel of 46 Ancestry Informative Markers (AIMs) was genotyped in a sub-set of samples. The vast majority of the Bolivian mtDNAs (98.4%) were found to belong to the main Native American haplogroups (A: 14.3%, B: 52.6%, C: 21.9%, D: 9.6%), with little indication of sub-Saharan and/or European lineages; however, marked patterns of haplogroup frequencies between main regions exist (e.g. haplogroup B: Andean [71%], Sub-Andean [61%], Llanos [32%]). Analysis of entire genomes unraveled the phylogenetic characteristics of three Native haplogroups: the pan-American haplogroup B2b (originated ∼21.4 thousand years ago [kya]), A2ah (∼5.2 kya), and B2o (∼2.6 kya). The data suggest that B2b could have arisen in North California (an origin even in the north most region of the American continent cannot be disregarded), moved southward following the Pacific coastline and crossed Meso-America. Then, it most likely spread into South America following two routes: the Pacific path towards Peru and Bolivia (arriving here at about ∼15.2 kya), and the Amazonian route of Venezuela and Brazil southwards. In contrast to the mtDNA, Ancestry Informative Markers (AIMs) reveal a higher (although geographically variable) European introgression in Bolivians (25%). Bolivia shows a decreasing autosomal molecular diversity pattern along the longitudinal axis, from the Altiplano to the lowlands. Both autosomes and mtDNA revealed a low impact (1-2%) of a sub-Saharan component in Bolivians.

http://www.ncbi.nlm.nih.gov/pubmed/23527064

[Maguzanci]

Do you find it surprising that Totonac (supposedly pure Native Americans) and Bolivians don't cluster with CHB/JPT but intermediate between them and CEU?

[Zanzibar]

So I decided to do some modifications to the PCA to show the West Eurasian shiftedness of Totonacs and Bolivians.



Comparing with this with the simplification of the same PCA to show the Amerindian % of the samples



As you can see in the modified PCA, the Totonac cluster who are on average 100% Amerindian are around ~ 28 to 31% Western shifted (by my estimation in their position between CHB/JPT and CEU) while the Bolivian cluster who have substantial Euro admix are around 44 to 53% Western shifted. There are however, several Bolivians who are less Euro admixed and closer to Totonac cluser while there is one Bolivian outlier on PCA who has the highest~ 48% Euro admix.