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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 Y-chromosome markers.
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pgen-1004488-g006: Distribution of ancestral contributions in the total sample and stratified by province as inferred from Y-chromosome markers.

Mentions: Y-chromosome SNPs could be genotyped in 384 males and haplotypes were classified into haplogroups following the phylogeny of Figure S6. A detailed list of the haplogroup assignations based on the 12 Y-SNPs genotyped in this study is presented in Table S7. 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 (0.5%) (Figure 6). The Native American haplotypes belong to two individuals, one from the province of Camagüey and the other from Santiago de Cuba. Regarding Eurasian and African ancestry, the highest Eurasian paternal contributions were found in Matanzas, and Pinar del Río, and the highest African paternal contributions correspond to the province of Santiago de Cuba. Although the size of the Y-chromosome sample was substantially smaller than the mtDNA sample, the contingency table analysis (Table S8) identified significant differences in paternal Eurasian contributions between Matanzas and Villa Clara, Cienfuegos and Santiago, and also between Pinar del Río and Guantánamo and Santiago. The province of Santiago showed a significantly higher African paternal contribution than Pinar del Río, Matanzas and Guantánamo.


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 Y-chromosome markers.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004488-g006: Distribution of ancestral contributions in the total sample and stratified by province as inferred from Y-chromosome markers.
Mentions: Y-chromosome SNPs could be genotyped in 384 males and haplotypes were classified into haplogroups following the phylogeny of Figure S6. A detailed list of the haplogroup assignations based on the 12 Y-SNPs genotyped in this study is presented in Table S7. 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 (0.5%) (Figure 6). The Native American haplotypes belong to two individuals, one from the province of Camagüey and the other from Santiago de Cuba. Regarding Eurasian and African ancestry, the highest Eurasian paternal contributions were found in Matanzas, and Pinar del Río, and the highest African paternal contributions correspond to the province of Santiago de Cuba. Although the size of the Y-chromosome sample was substantially smaller than the mtDNA sample, the contingency table analysis (Table S8) identified significant differences in paternal Eurasian contributions between Matanzas and Villa Clara, Cienfuegos and Santiago, and also between Pinar del Río and Guantánamo and Santiago. The province of Santiago showed a significantly higher African paternal contribution than Pinar del Río, Matanzas and Guantánamo.

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