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

<div><p>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.</p></div

Multidimensional scaling plot of the pairwise <i>F</i>_ST genetic distances calculated between samples from Africa, Europe, and different Colombian populations, including a sample from Native Americans (Pastos) (Stress = 0.0556).

<p>The circle in the centre of the plot is grouping the samples with no significant population differentiation <i>p-values</i> detected (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087202#pone.0087202.s003" target="_blank">Table S2</a>).</p

Map showing the departments of Colombia and the location of the samples included in the present study.

<p>The sample sizes (n = total number of chromosomes) are indicated for each population.</p

The interethnic admixture proportions using autosomal and X-chromosomal specific markers, considering three main ancestral contributors to the different regions of Colombia studied.

<p>The interethnic admixture proportions using autosomal and X-chromosomal specific markers, considering three main ancestral contributors to the different regions of Colombia studied.</p

Exact test <i>p-</i>values of linkage disequilibrium for the polymorphic loci not separated more than 1 Mb.

<p>The results are sorted according to the distance between the two loci in the pair.</p>*<p>Significant p-values of gametic association; **low p-values not considered significant after applying Bonferroni’s correction for multiple tests; ***No test was performed because one of the two loci was monomorphic in the sample. Note: the p-values were obtained for 100,172 Markov steps.</p

Schematic representation of the global population (A) and individual (B) admixture estimates (IAEs) in 11 Colombian admixed populations, using STRUCTURE v2.3.3 software (K = 3; parameter set details in Material and Methods), for African, European and Native American ancestry proportions.

<p>Schematic representation of the global population (A) and individual (B) admixture estimates (IAEs) in 11 Colombian admixed populations, using STRUCTURE v2.3.3 software (K = 3; parameter set details in Material and Methods), for African, European and Native American ancestry proportions.</p

Average gene diversity values among the 32 X-indel loci in the samples obtained from the Native American group (Pastos) and the six Colombian regions: South-West Andean Region (Nariño); Central-West Andean Region (Antioquia); Central-East Andean Region (Boyacá-Cundinamarca, Huila and Santander); Orinoquian Region (Arauca, Meta and Casanare); North Colombian Pacific Coast (Chocó); and the Caribbean Region (Cartagena).

<p>Average gene diversity values among the 32 X-indel loci in the samples obtained from the Native American group (Pastos) and the six Colombian regions: South-West Andean Region (Nariño); Central-West Andean Region (Antioquia); Central-East Andean Region (Boyacá-Cundinamarca, Huila and Santander); Orinoquian Region (Arauca, Meta and Casanare); North Colombian Pacific Coast (Chocó); and the Caribbean Region (Cartagena).</p