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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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Related in: MedlinePlus

Distribution of melanin index stratified by census categories.
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pgen-1004488-g002: Distribution of melanin index stratified by census categories.

Mentions: Age did not have a significant effect on melanin levels (M), measured quantitatively with the reflectometer (melanin index) [20], but there were significant differences in melanin index by sex (males M = 40.68±10.7; females M = 39.17±9.45; P = 0.015). The average melanin index of the total sample was 39.8, but there was a broad distribution of values, from 23.4 to 85.9. In individuals who self-reported to be “blanco”, the average melanin index was 34.06±3.70 (mean ± SD), in those who self-reported to be “mestizo” 41.69±6.29 and in those who self-reported to be “negro” 60.59±8.87 (Figure 2). The differences in melanin levels between census groups were significant (ANOVA with sex as a covariate: F = 4.30, P<0.001).


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 melanin index stratified by census categories.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004488-g002: Distribution of melanin index stratified by census categories.
Mentions: Age did not have a significant effect on melanin levels (M), measured quantitatively with the reflectometer (melanin index) [20], but there were significant differences in melanin index by sex (males M = 40.68±10.7; females M = 39.17±9.45; P = 0.015). The average melanin index of the total sample was 39.8, but there was a broad distribution of values, from 23.4 to 85.9. In individuals who self-reported to be “blanco”, the average melanin index was 34.06±3.70 (mean ± SD), in those who self-reported to be “mestizo” 41.69±6.29 and in those who self-reported to be “negro” 60.59±8.87 (Figure 2). The differences in melanin levels between census groups were significant (ANOVA with sex as a covariate: F = 4.30, P<0.001).

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