Evaluating the X Chromosome-Specific Diversity of Colombian Populations Using Insertion/Deletion Polymorphisms

Adriana Ibarra,Mauricio Camacho,Karen Álvarez,António Amorim,Zuleyma Suarez,Winston Rojas,Leonor Gusmão,Rui Pereira,Tomás Restrepo,Adriana Castillo,Henry Ostos,Beatriz Martínez,German Burgos,Francesc Calafell

doi:10.1371/journal.pone.0087202

Abstract

The European and African contribution to the pre-existing Native American background has influenced the complex genetic pool of Colombia. Because colonisation was not homogeneous in this country, current populations are, therefore, expected to have different proportions of Native American, European and African ancestral contributions. The aim of this work was to examine 11 urban admixed populations and a Native American group, called Pastos, for 32 X chromosome indel markers to expand the current knowledge concerning the genetic background of Colombia. The results revealed a highly diverse genetic background comprising all admixed populations, harbouring important X chromosome contributions from all continental source populations. In addition, Colombia is genetically sub-structured, with different proportions of European and African influxes depending on the regions. The samples from the North Pacific and Caribbean coasts have a high African ancestry, showing the highest levels of diversity. The sample from the South Andean region showed the lowest diversity and significantly higher proportion of Native American ancestry than the other samples from the North Pacific and Caribbean coasts, Central-West and Central-East Andean regions, and the Orinoquian region. The results of admixture analysis using X-chromosomal markers suggest that the high proportion of African ancestry in the North Pacific coast was primarily male driven. These men have joined to females with higher Native American and European ancestry (likely resulting from a classic colonial asymmetric mating type: European male x Amerindian female). This high proportion of male-mediated African contributions is atypical of colonial settings, suggesting that the admixture occurred during a period when African people were no longer enslaved. In the remaining regions, the African contribution was primarily female-mediated, whereas the European counterpart was primarily male driven and the Native American ancestry contribution was not gender biased.

Highlights

The study of the genetic diversity of human populations is important to reveal different aspects associated with the history of these individuals, which, in turn, is highly significant in many applied fields, namely clinical and forensic genetics
It is important to know the genetic composition of the concerned populations, as the results of association studies are sensitive to population substructures that can induce spurious associations between alleles at different loci [4,5]
To improve the visualisation of the results, the pairwise genetic distances were represented in a two-dimensional multidimensional scaling (MDS) plot (Figure 2)

Summary

Introduction

The study of the genetic diversity of human populations is important to reveal different aspects associated with the history of these individuals, which, in turn, is highly significant in many applied fields, namely clinical and forensic genetics. Genetic research studies are designed to identify associations between some alleles and/or genotypes and diseases in different areas [1,2,3]. The history of the Native American groups in the North, Central and South American subcontinents has been the focus of many genetic studies [10,11,13,14]. These studies have faced important challenges because much of the ancient genetic diversity has been eradicated from the extant populations. During the last five centuries, most American populations have been exposed to admixture events involving pre-existing Native groups and European and African people

Objectives

Methods

Results

Conclusion