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

Abstract

BackgroundPopulations 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 ConclusionsWe 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.

The E180splice mutation in the GHR gene causing Laron syndrome: Witness of a Sephardic Jewish exodus from the Iberian Peninsula to the New World?

“…The origin of haplogroup R is located in Central to West Asia, although a precise region has not yet been determined. The R1b branch is the most abundant haplotype identified in South American countries [Guerra et al, ; Francez et al, ; Watkins et al, ], consistent with historical accounts of male admixture in colonies of Spain and Portugal, where this haplogroup is common [Adams et al, ]. However, the haplogroups E1 and J, also found in our patients, are infrequently observed in the Iberian Peninsula.…”

The Genetic Legacy of the Pre-Colonial Period in Contemporary Bolivians

“…Given the way in which the LACE panel was designed (in order to balance the informative content of the different AIMS included in the panel), it seems logical to believe that the Indels panel would tend to over-estimate the proportion of European ancestry in Bolivians. Note, however, that the genome-wide study of Watkins et al [24] carried out in few Bolivians estimated a higher European component (12%) compared to the LACE. Further genome-wide studies on a larger Bolivian sample will allow better estimates of continental ancestries to be obtained.…”

“…These authors found that most of the Bolivians have a main Native American component (ranging from 90% to 98%), with the exception of the Yungas province, showing a dominant African nature. Recently, Watkins et al [24] carried out a genome-wide analysis of 28 Bolivians, and although the results agreed with Galanter et al in that Bolivian genomes have predominant Native American features, they estimated a higher European component (12%) in these peoples.…”

Ancestry, admixture and fitness in Colombian genomes

“…Whole genome sequences for 60 admixed Colombians from Medellin were taken from the 1000 Genomes Project 26 27 . Whole genome sequences ( n = 264) and genotypes characterized using SNP microarrays ( n = 257) from a number of sources 25 26 27 69 were analyzed for putative ancestral populations in Africa, the Americas, Asia and Europe. Genotypes ( i.e.…”