title: Cuba: exploring the history of admixture and the genetic basis of pigmentation using autosomal and uniparental markers.
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.
authors: National Centre of Medical Genetics, Medical University of Havana, La Habana, Cuba.
authors: Beatriz
authors: B
authors: Marcheco-Teruel
authors: Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada.
authors: Esteban J
authors: EJ
authors: Parra
authors: National Centre of Medical Genetics, Medical University of Havana, La Habana, Cuba.
authors: Evelyn
authors: E
authors: Fuentes-Smith
authors: Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.
authors: Antonio
authors: A
authors: Salas
authors: Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark.
authors: Henriette N
authors: HN
authors: Buttenschøn
authors: Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark; Department of Biomedicine, Aarhus University, Aarhus, Denmark.
authors: Ditte
authors: D
authors: Demontis
authors: Centro Nacional de Genotipado (ISCIII), Nodo Santiago de Compostela, Santiago de Compostela, Spain.
authors: María
authors: M
authors: Torres-Español
authors: National Centre of Medical Genetics, Medical University of Havana, La Habana, Cuba.
authors: Lilia C
authors: LC
authors: Marín-Padrón
authors: Centro de Investigaciones Psicológicas y Sociológicas, La Habana, Cuba.
authors: Enrique J
authors: EJ
authors: Gómez-Cabezas
authors: Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.
authors: Vanesa
authors: V
authors: Alvarez-Iglesias
authors: Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.
authors: Ana
authors: A
authors: Mosquera-Miguel
authors: Departamento de Antropología, Facultad de Biología, Universidad de La Habana, La Habana, Cuba.
authors: Antonio
authors: A
authors: Martínez-Fuentes
authors: Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain; Centro Nacional de Genotipado (ISCIII), Nodo Santiago de Compostela, Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
authors: Angel
authors: A
authors: Carracedo
authors: Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark; Department of Biomedicine, Aarhus University, Aarhus, Denmark; Psychiatric Department, Aarhus University Hospital, Aarhus, Denmark.
authors: Anders D
authors: AD
authors: Børglum
authors: National Centre of Medical Genetics, Medical University of Havana, La Habana, Cuba; Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark; Psychiatric Department, Aarhus University Hospital, Aarhus, Denmark.
authors: Ole
authors: O
authors: Mors
mesh_terms: D044383:Black People / Q000235:genetics; D041322:Chromosomes, Human, Y / Q000235:genetics; D003462:Cuba; D004272:DNA, Mitochondrial / Q000235:genetics; D051456:Gene Flow / Q000235:genetics*; D005828:Genetics, Population; D006239:Haplotypes / Q000235:genetics*; D006630:Hispanic or Latino / Q000235:genetics; D006801:Humans; D007198:Indians, North American / Q000235:genetics; D010858:Pigmentation / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D044465:White People / Q000235:genetics
chemical_list: D004272:DNA, Mitochondrial