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

Marcheco-Teruel B, Parra EJ, Fuentes-Smith E, Salas A, Buttenschøn HN, Demontis D, Torres-Español M, Marín-Padrón LC, Gómez-Cabezas EJ, Alvarez-Iglesias V, Mosquera-Miguel A, Martínez-Fuentes A, Carracedo A, Børglum AD, Mors O - PLoS Genet. (2014)

Bottom Line: 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.Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.

View Article: PubMed Central - PubMed

Affiliation: National Centre of Medical Genetics, Medical University of Havana, La Habana, Cuba.

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.

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Distribution of ancestral contributions in the total sample and stratified by province as inferred from mtDNA markers.
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pgen-1004488-g005: Distribution of ancestral contributions in the total sample and stratified by province as inferred from mtDNA markers.

Mentions: A total of 943 mtDNA haplotypes could be allocated to a specific branch of the mtDNA phylogeny resolved by the mtSNPs genotyped in the present study (see the mtDNA phylogeny of Figure S5). A detailed list of the haplogroup assignations based on the 18 markers genotyped in this study is presented in Table S5. 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 (Figure 5). The highest maternal Eurasian proportions were found in the provinces of Matanzas (58%), Artemisa (53%), and Pinar del Rio (49%) and the lowest in Santiago de Cuba (6%), Granma (7%) and Holguín (7.5%). The highest maternal African proportions were observed in the provinces of Santiago (57%) and Granma (52%), and the lowest in Las Tunas (21%) and Camagüey (24%). With respect to the maternal Native American proportions, the highest were found in Holguín (59%) and Las Tunas (58%), and the lowest in Matanzas (13%), Cienfuegos (13%) and Pinar del Río (13%). An analysis of contingency tables using exact tests (Table S6) indicates that many of the Western provinces have significantly higher Eurasian proportions than some of the Eastern provinces, in particular Holguín, Granma and Santiago de Cuba. These tests also show that the province of Santiago de Cuba has significantly higher African proportions than other Cuban provinces, and that the provinces of Holguín, Las Tunas and to some extent, Granma, have significantly higher Native American proportions than most of the Western provinces.


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

Marcheco-Teruel B, Parra EJ, Fuentes-Smith E, Salas A, Buttenschøn HN, Demontis D, Torres-Español M, Marín-Padrón LC, Gómez-Cabezas EJ, Alvarez-Iglesias V, Mosquera-Miguel A, Martínez-Fuentes A, Carracedo A, Børglum AD, Mors O - PLoS Genet. (2014)

Distribution of ancestral contributions in the total sample and stratified by province as inferred from mtDNA markers.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4109857&req=5

pgen-1004488-g005: Distribution of ancestral contributions in the total sample and stratified by province as inferred from mtDNA markers.
Mentions: A total of 943 mtDNA haplotypes could be allocated to a specific branch of the mtDNA phylogeny resolved by the mtSNPs genotyped in the present study (see the mtDNA phylogeny of Figure S5). A detailed list of the haplogroup assignations based on the 18 markers genotyped in this study is presented in Table S5. 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 (Figure 5). The highest maternal Eurasian proportions were found in the provinces of Matanzas (58%), Artemisa (53%), and Pinar del Rio (49%) and the lowest in Santiago de Cuba (6%), Granma (7%) and Holguín (7.5%). The highest maternal African proportions were observed in the provinces of Santiago (57%) and Granma (52%), and the lowest in Las Tunas (21%) and Camagüey (24%). With respect to the maternal Native American proportions, the highest were found in Holguín (59%) and Las Tunas (58%), and the lowest in Matanzas (13%), Cienfuegos (13%) and Pinar del Río (13%). An analysis of contingency tables using exact tests (Table S6) indicates that many of the Western provinces have significantly higher Eurasian proportions than some of the Eastern provinces, in particular Holguín, Granma and Santiago de Cuba. These tests also show that the province of Santiago de Cuba has significantly higher African proportions than other Cuban provinces, and that the provinces of Holguín, Las Tunas and to some extent, Granma, have significantly higher Native American proportions than most of the Western provinces.

Bottom Line: 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.Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.

View Article: PubMed Central - PubMed

Affiliation: National Centre of Medical Genetics, Medical University of Havana, La Habana, Cuba.

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.

Show MeSH
Related in: MedlinePlus