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Ancestry, Admixture and Fitness in Colombian Genomes

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Ancestry, Admixture and Fitness in Colombian Genomes Guarda 1 Página 1 de 65 Genómica de Poblaciones Colombianas: Ancestralidad y Adaptación. Augusto Elías Valderrama Aguirre Universidad del Valle Escuela de Ciencias Básicas Médicas Doctorado en Ciencias Biomédicas Cali, 2016 Página 2 de 65 Genómica de Poblaciones Colombianas: Ancestralidad y Adaptación. Tesis para optar el título de Doctor en Ciencias Biomédicas Director: I. King Jordan, PhD Augusto Elías Valderrama Aguirre Universidad del Valle Escuela de Ciencias Básicas Médicas Doctorado en Ciencias Biomédicas - 9695 Cali, 2016 Página 3 de 65 Página de aceptación Jurado 1 ____________________________________ _________________________ Nombre Firma Jurado 2 ____________________________________ _________________________ Nombre Firma Jurado 3 ____________________________________ _________________________ Nombre Firma Cali, ________________________________. Página 4 de 65 Dedicatoria A mis hijos David e Isabella… A mi madre Hortensia y mis hermanos Lina y Hernando… A King, amigo y verdadero consejero… A ese sol que siempre está a mi lado, ella sabe quién es… Página 5 de 65 Contenido Contenido .......................................................................................................................... 6 Listado de Figuras ............................................................................................................. 8 Listado de Tablas ............................................................................................................... 9 Resumen .......................................................................................................................... 10 Capítulo 1 ........................................................................................................................ 12 Introgresión adaptativa en poblaciones humanas ................................................................... 12 Resumen ............................................................................................................................................ 12 Problema de Investigación .................................................................................................................. 12 Pregunta de investigación................................................................................................................... 14 Presentación de la Hipótesis ............................................................................................................... 14 Prueba de la Hipótesis y Justificación .................................................................................................. 17 Referencias capítulo 1 ........................................................................................................................ 19 Capítulo 2 ........................................................................................................................ 21 Ancestralidad y Mestizaje Genómico en Colombianos. ........................................................... 21 Resumen ............................................................................................................................................ 21 Introducción ....................................................................................................................................... 21 Metodología....................................................................................................................................... 22 Resultados ......................................................................................................................................... 25 Discusión ............................................................................................................................................ 28 Referencias Capítulo 2 ........................................................................................................................ 31 Capítulo 3 ........................................................................................................................ 33 Adaptación Genómica y Salud en Colombianos. ...................................................................... 33 Resumen ............................................................................................................................................ 33 Introducción ....................................................................................................................................... 33 Metodología....................................................................................................................................... 34 Resultados ......................................................................................................................................... 35 Discusión ............................................................................................................................................ 44 Referencias capítulo 3 ........................................................................................................................ 48 Capítulo 4 ........................................................................................................................ 51 El Chocó Colombia: un hotspot de biodiversidad humana ....................................................... 51 Resumen ............................................................................................................................................ 51 Introducción ....................................................................................................................................... 51 Metodología....................................................................................................................................... 53 Resultados ......................................................................................................................................... 55 Discusión ............................................................................................................................................ 61 Página 6 de 65 Referencias capítulo 4 ........................................................................................................................ 61 Conclusiones .................................................................................................................... 63 Recomendaciones............................................................................................................ 64 Anexos ............................................................................................................................. 65 Anexo 1: Manuscrito publicado en Nature Scientific Reviews. Anexo 2: Manuscrito publicado en Revista de Biodiversidad Neotropical Anexo 3: Acta de sustentación de tesis doctoral Página 7 de 65 Listado de Figuras Capítulo 1 ........................................................................................................................ 12 Introgresión adaptativa en poblaciones humanas ................................................................... 12 Figura 1.1: El intercambio colombino.….. ........................................................................................ 13 Figura 1.2: Modelo para la fijación de alelos adaptativos… .............................................................. 16 Figura 1.3: Análisis de enriquecimiento ancestral para los eventos de introgresión…....................... 17 Capítulo 2 ........................................................................................................................ 21 Ancestralidad y Mestizaje Genómico en Colombianos. ........................................................... 21 Figura 2.1: Descripción de los orígenes geográficos mundiales de los genomas genotipificados y secuenciados alrededor del mundo………... ..................................................................................... 23 Figura 2.2: PCA de distancias compartidas de alelos apareados entre genomas colombianos de Medellín comparados con poblaciones ancestrales putativas de África, América, Asia y Europa. ..... 26 Figura 2.3: Gráfico de mestizaje genómico que muestra las tres poblaciones ancestrales y la población colombiana mestizada.. .................................................................................................. 27 Figura 2.4: Distribución de las proporciones de mestizaje ancestral y promedios para la población de Colombia........................................................................................................................................ 27 Figura 2.5: Contribuciones específicas de sexo al mestizaje genómico triple en varios países de Latinoamérica….. ... ........................................................................................................................ 28 Capítulo 3 ........................................................................................................................ 33 Adaptación Genómica y Salud en Colombianos. ...................................................................... 33 Figura 3.1: Regiones (locus) y el mestizaje genético ancestral en genomas de Colombia.. ................ 36 Figura 3.2: Distribución de los tamaños de los segmentos cromosómicos con ancestralidad específica usados para el análisis de enriquecimiento. .................................................................................... 36 Figura 3.3: Análisis de enriquecimiento ancestral poblacional.. ....................................................... 37 Figura 3.4: Gráfico de Manhattan mostrando
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