One of the most interesting aspects of human genomics over the past 10 years or so to me is that it has uncovered that in the Caribbean the Amerindian population was not totally exterminated, but rather its genetic legacy has persisted via females. The most sophisticated paper in this area is probably Reconstructing the Population Genetic History of the Caribbean. But there are other papers, and today PLOS Genetics came out with Cuba: Exploring the History of Admixture and the Genetic Basis of Pigmentation Using Autosomal and Uniparental Markers. The downside of this paper is that they use “Ancestrally Informative Markers,” rather than dense SNPs. This limits what you can do (though the authors do look at specific SNPs of functional significance). More specifically 128 AIMs. But the upside of this paper is its massive sample size. 1,019 individuals from all provinces of Cuba.
There are many results in the paper, but I would like to highlight one aspect: the 55% of sample respondents that identified as “white” almost all had non-European ancestry. This goes back to a discussion I had with readers years back about admixture among white Cubans, who are the dominant community in the United States. Like most Latin American “whites,” and unlike American “whites,” the non-European ancestry in Cubans does seem non-trivial from what I’ve seen. These results would seem to confirm that. The main questions that come to mind in regards to skepticism would be how much of this is due to admixture in Europe (e.g., Spain and the Canaries), and, how precise are these AIMs? I’d have liked to see the AIMs on a European population. Look at the fraction of African and Amerindian ancestry I suspect that these results are valid, but I’m not sure how noisy the inferences are.
The mtDNA and Y results are harder to quibble with, and they’re striking. “The analysis of mtSNPs indicates that 34.5% of the mtDNA haplotypes have Native American ancestry, 38.8% African ancestry, and 26.7% Eurasian ancestry.” And for the Y: “Most of the haplotypes are of Eurasian ancestry (81.8%), while 17.7% have African ancestry and only two haplotypes are of Native American ancestry.” This is in line with what you see in the rest of Latin America, but the disjunction is still sobering.
Citation: Marcheco-Teruel B, Parra EJ, Fuentes-Smith E, Salas A, Buttenschøn HN, et al. (2014) Cuba: Exploring the History of Admixture and the Genetic Basis of Pigmentation Using Autosomal and Uniparental Markers. PLoS Genet 10(7): e1004488. doi:10.1371/journal.pgen.1004488