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We carried out an admixture analysis of a sample comprising 1, individuals from all the provinces of Cuba. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers.
Finally, we analyzed the association of 16 single nucleotide polymorphisms SNPs with quantitative estimates of skin pigmentation. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces.
We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information.
Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Cuba is the largest island of the Greater Antilles and its most populous country. The post-Columbian history of the Caribbean has been marked by the encounter of people from different continents.