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.
Highlights
Populations of the Americas were founded by early migrants from Asia, and some have experienced recent genetic admixture
The analysis of mitochondrial DNA (mtDNA) hypervariable segments (HVS) I and II showed that all Bolivian and Totonac samples belong to haplogroups A2, B2, C1 and D1, consistent with pre-Columbian New World maternal ancestry
Our analysis indicates that some admixed Bolivians have Native American mtDNA and Y-chromosomes but harbor up to 30% European autosomal ancestry, demonstrating the need for autosomal markers to assess ancestry in admixed populations
Summary
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 Ychromosome STRs from 24 Mesoamerican Totonacs and 23 South American Bolivians. A number of New World populations have remained isolated, while many others have experienced admixture from one or more Old World populations. A few studies of indigenous American populations have been performed using large numbers of autosomal markers. Additional detailed studies of native and admixed populations using high-density autosomal markers are needed to resolve the effects of population history and to further characterize the genetic architecture of New World groups
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