Association between Y haplogroups and autosomal AIMs reveals intra-population substructure in Bolivian populations

Abstract

For the correct evaluation of the weight of genetic evidence in a forensic context, databases must reflect the structure of the population, with all possible groups being represented. Countries with a recent history of admixture between strongly differentiated populations are usually highly heterogeneous and sub-structured. Bolivia is one of these countries, with a high diversity of ethnic groups and different levels of admixture (among Native Americans, Europeans and Africans) across the territory. For a better characterization of the male lineages in Bolivia, 17 Y-STR and 42 Y-SNP loci were genotyped in samples from La Paz and Chuquisaca. Only European and Native American Y-haplogroups were detected, and no sub-Saharan African chromosomes were found. Significant differences were observed between the two samples, with a higher frequency of European lineages in Chuquisaca than in La Paz. A sample belonging to haplogroup Q1a3a1a1-M19 was detected in La Paz, in a haplotype background different from those previously found in Argentina. This result supports an old M19 North-south dispersion in South America, possibly via two routes. When comparing the ancestry of each individual assessed through his Y chromosome with the one estimated using autosomal AIMs, (a) increased European ancestry in individuals with European Y chromosomes and (b) higher Native American ancestry in the carriers of Native American Y-haplogroups were observed, revealing an association between autosomal and Y-chromosomal markers. The results of this study demonstrate that a sub-structure does exist in Bolivia at both inter- and intrapopulation levels, a fact which must be taken into account in the evaluation of forensic genetic evidence.

Increased prevalence of human herpesvirus type 8 (HHV‐8) genome among blood donors from North‐Western Argentina

“…In admixed populations, it is essential to analyze matri and patrilineage as well as bi‐parentally transmitted markers of the genome because both can reveal different geographic ancestry components [Kayser et al, , ]. In the results presented herein, the genetic ancestry backgrounds of the Argentines and Bolivians analyzed in this study were similar to those previously described; for the reason that the European ancestry component prevailed in metropolitan Argentina whereas the Native American component was the most prevalent in the North‐western region and Bolivia [Corach et al, ; Avena et al, ; Vullo et al, ] (Supplementary Fig. S2).…”

Genetic admixture patterns in Argentinian Patagonia

“…Using data from the 46 AIM-Indels, pairwise F ST genetic distances were calculated between the five Patagonian populations from this study, and samples from six Argentinian provinces [15], six South American populations from Brazil [23], Bolivia [24] and Colombia [25,26], as well as the European, African and Native American HGDP-CEPH reference populations [22] (S5 Table).…”

“…Dye-labeled amplified fragments were separated and detected using an ABI3130 Genetic Analyzer (Life Technologies), and automated allele calls were obtained with GeneMapper v.3.2 (Life Technologies). This panel showed to be highly informative to analyze genetic admixture in different Latin-American populations, including Argentina [15], Brazil [23], Bolivia [24] and Colombia [25,26].…”

“…Allele frequency estimations, Hardy-Weinberg exact tests, and population differentiation tests were performed using the Arlequin software v.3.5.2 [27]. Population genetic analyses were carried out comparing our five populations with others six Argentinian populations [15] and six South American populations from Brazil [23], Bolivia [24] and Colombia [25,26]. Genetic distances ( F ST ) between populations across 46 AIM-Indel markers were visualized in a multi-dimensional scaling (MDS) plot performed with the R v3.1.1 FactoMineR [28] statistical package.…”

Hepatitis C virus pharmacogenomics in Latin American populations: implications in the era of direct-acting antivirals

“…In general, urban towns of Argentina, Mexico, Chile, Colombia, Uruguay, and South of Brazil showed that >55% of the global ancestry belongs to European contribution followed by Native American and <10% of African contribution 55,60,61. Instead, rural Mexico and urban populations in Peru and Bolivia showed the major contribution of Native American ancestry in part due to the high population density of aboriginal in the region at the moment of the conquest 60–63…”