Limits...
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.

Show MeSH

Related in: MedlinePlus

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

License
getmorefigures.php?uid=PMC4109857&req=5

pgen-1004488-g001: Distribution of ancestral contributions in the total sample and stratified by province as inferred from autosomal AIMs.

Mentions: Estimates of admixture proportions were obtained with the program ADMIXMAP, using data from 128 AIMs. In the total sample, the average European, African and Native American contributions were 72% (range 4.3% to 98.2%), 20% (range 0.8% to 95.2%) and 8% (range 0.4% to 34%), respectively (Figure 1). By province, 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 Spíritus to 40% in Guantánamo, and the average proportion of Native American ancestry from 4% in Matanzas to 15% in Granma (Figure 1). There are significant differences in admixture proportions between provinces (ANOVA: Africans F = 11.54, P<0.001; Native American F = 13.06, P<0.001). Post-hoc tests indicate that, in terms of African proportions, the differences are driven by the higher African proportions in the provinces of Santiago de Cuba (39%) and Guantánamo (40%), with respect to the other provinces (11% to 24%). With respect to the Native American contributions, a clear pattern is also present, with higher average contributions in the Eastern provinces, particularly Granma (15%), Las Tunas (12%) and Holguín (12%) than in 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 autosomal AIMs.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004488-g001: Distribution of ancestral contributions in the total sample and stratified by province as inferred from autosomal AIMs.
Mentions: Estimates of admixture proportions were obtained with the program ADMIXMAP, using data from 128 AIMs. In the total sample, the average European, African and Native American contributions were 72% (range 4.3% to 98.2%), 20% (range 0.8% to 95.2%) and 8% (range 0.4% to 34%), respectively (Figure 1). By province, 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 Spíritus to 40% in Guantánamo, and the average proportion of Native American ancestry from 4% in Matanzas to 15% in Granma (Figure 1). There are significant differences in admixture proportions between provinces (ANOVA: Africans F = 11.54, P<0.001; Native American F = 13.06, P<0.001). Post-hoc tests indicate that, in terms of African proportions, the differences are driven by the higher African proportions in the provinces of Santiago de Cuba (39%) and Guantánamo (40%), with respect to the other provinces (11% to 24%). With respect to the Native American contributions, a clear pattern is also present, with higher average contributions in the Eastern provinces, particularly Granma (15%), Las Tunas (12%) and Holguín (12%) than in 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