Cuba: exploring the history of admixture and the genetic basis of pigmentation using autosomal and uniparental markers

PLoS Genet. 2014 Jul 24;10(7):e1004488. doi: 10.1371/journal.pgen.1004488. eCollection 2014 Jul.


We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs) to estimate the admixture proportions. 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. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40%) and Santiago de Cuba (39%), and the highest proportion of Native American ancestry in Granma (15%), Holguín (12%) and Las Tunas (12%). 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. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • African Continental Ancestry Group / genetics
  • Chromosomes, Human, Y / genetics
  • Cuba
  • DNA, Mitochondrial / genetics
  • European Continental Ancestry Group / genetics
  • Gene Flow / genetics*
  • Genetics, Population*
  • Haplotypes / genetics*
  • Hispanic Americans / genetics
  • Humans
  • Indians, North American / genetics
  • Pigmentation / genetics*
  • Polymorphism, Single Nucleotide / genetics


  • DNA, Mitochondrial

Grant support

This project was supported by the Ministry of Public Health, Cuba, The Villum Kann Rasmussen Foundation, Denmark, and Aarhus University, Denmark. This work was also partially supported by the Natural Science and Engineering Research Council (NSERC) Discovery grant, Canada and FIS Intrasalud PS09/02368, Spain. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.