Abstract
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.
Highlights
The post-Columbian history of the Caribbean has been marked by the encounter of people from different continents
Similar geographic patterns were observed in the analyses of the uniparental markers
The average proportion of European ancestry ranged from 51% in Santiago de Cuba to 84% in Mayabeque, the average proportion of African ancestry ranged from 11% in Mayabeque and Sancti Spıritus to 40% in Guantanamo, and the average proportion of Native American ancestry from 4% in Matanzas to 15% in Granma (Figure 1)
Summary
The post-Columbian history of the Caribbean has been marked by the encounter of people from different continents. This is reflected in the gene pool of the present inhabitants of the Caribbean archipelago, as shown in recent studies using autosomal, mtDNA and Y-chromosome markers [1,2,3,4,5,6,7]. The Guanahatabey were huntergatherers living in western Cuba. They comprised approximately 10% of the indigenous Cuban population, spoke a non-Arawak language and have been considered to be the descendants of the earliest settlers of the island.
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