EVOLUTION, SPECIATION, AND GENOMICS OF THE ANDEAN HUMMINGBIRDS Coeligena bonapartei AND Coeligena helianthea Catalina Palacios Laboratorio de Biología Evolutiva de Vertebrados Departamento de Ciencias Biológicas Universidad de los Andes Advisor Carlos Daniel Cadena PhD Dissertation committee Sangeet Lamichhaney PhD Juan Armando Sánchez PhD Dissertation submitted in partial fulfillment of the requirements for obtaining the title of Doctor of Philosophy in Biological Sciences Bogotá, Colombia 2020 To Tim Minchin and Trevor Noah To Martina, Emilia, Zoe, Lucia, Antonia, Eva, Gia and Maya Little bits of light of a better future “Emilia aprendió a no despreciar nada. Menos que nada el lenguaje de los hechos, el que mira en cada peripecia algo único, aunque derive su conocimiento de doctrinas generales” Ángeles Mastretta. Mal de Amores. 1996 Continuidad Las hojas caen en el oscuro silencio Desde lo alto de los árboles del bosque Sobre las aguas plateadas de los ríos corrientes Hasta el latir profundo de las sombras Al suelo húmedo donde aguardan los hongos. Mientras tanto, Los corazones rojos y húmedos laten desbocados Al paso de las alas que se agitan Las lenguas se pronuncian desde el techo de la cabeza Viajan hacia las corolas El azúcar a raudales entra a sus sistemas Atraviesa como hilos los intestinos Se deslíe y en segundos es sangre Viaja entre balsas cargadas de oxígeno Se atropella contra las paredes oscuras Atraviesa las membranas Entra al ciclo, uno, dos, tres ATPs son casi 30 Se hace energía, se va en el aire Retumban los cuerpos a cada impulso Alas adelante, alas atrás, van al vuelo Un milisegundo quietos, vuelven al vuelo Prisioneros de su historia buscan continuarse Una generación, va otra Las lenguas desde el cráneo Los insectos, el néctar, los nidos, los huevos La humedad Al interior del bosque Al borde del bosque Va otra generación y sin anuncio no son los mismos Las envolturas de unas plumas que se rompen La luz que le da paso a los colores se refleja Uno dorado, el otro rosa No son los mismos, aunque estén cerca En el laberinto de sus genes algo ha cambiado ¿Qué los diferencia? Mientras tanto, Al húmedo suelo donde los hongos aguardan Hasta el latir oscuro de las sombras Sobre las corrientes plateadas de las aguas del río Desde los árboles altos de los bosques En el profundo silencio Caen las hojas. Index Acknowledgments ................................................................................................................. 5 Abstract ................................................................................................................................. 7 Resumen .............................................................................................................................. 8 Introduction ........................................................................................................................... 9 “We’re one but we are not the same”1 – Shallow genetic divergence and distinct phenotypic differences between two Andean hummingbirds: Speciation with gene flow? – Chapter 1 ............................................................................................................................ 14 How much is too little? – Complete mitochondrial genomes do not distinguish phenotypically distinct lineages of Andean Coeligena hummingbirds – Chapter 2 ............ 48 Seeking gold and roses – Genomic differentiation and evolution of lineages of Andean Coeligena Hummingbirds – Chapter 3 ................................................................................ 76 Conclusions ...................................................................................................................... 108 Acknowledgments I am very grateful to all institutions and people who contributed to this work. I thank the Universidad de los Andes, the Vicerrectoría de Investigación, and the Facultad de Ciencias for funding through research grants and the teaching assistantship program. I thank Colciencias for funding through a PhD scholarship and to Colfuturo for managing it. I thank the Fundación para la promoción de la investigación y la tecnología from the Banco de la República for funding. I thank the Moore Laboratory of Zoology at the Occidental College, especially John McCormack, Eugenia Zarza, and Whitney Tsai. I thank the Lovette Lab at the Cornell Lab of Ornithology, especially Irby Lovette, Leonardo Campagna, and Bronwyn Butcher. I thank Christopher Witt at the University of New Mexico. I thank the Jarvis Lab and the Vertebrate Genome Lab at Rockefeller University, especially Erich Jarvis and Sadye Paez. I thank the Museo de Historia Natural at the Universidad de los Andes, the Instituto de Ciencias Naturales at the Universidad Nacional de Colombia, and the Instituto de Investigación de Recursos Biológicos Alexander Von Humboldt. I am deeply grateful to my advisor Daniel Cadena; you supported my ideas no matter how unusual they were, from games to genomes, you helped me find the resources, the people, and the way to achieve our work with the best possible quality. In our discussions and lab meetings your recurrent come-back to theory and to the scientific method helped me think not only about a singular problem but about the broad picture of questions and hypotheses; having you as my advisor was a fortunate privilege. I thank all my coauthors; collaborating with you was a pleasure and your contributions to this work were essential. I am very grateful to Leonardo Campagna; I had a great time working with you, I learned a lot, and I enjoyed our conversations; It was a pleasure to find a peer to talk about genes, genomes, lab work, and so many other varied topics. I am extremely grateful to the members of my advisory committee, my qualifying exam, and my candidacy exam, Silvia Restrepo, Andrew Crawford, and Reto Burri; during each occasion I found in you the knowledge and the encouragement to continue. I thank Gary Stiles whom I owe all my love for hummingbirds. I thank the Good Will Runners with whom I ran so many kilometers. I thank my D&D fellows with whom I lived so many adventures. I thank Pedro Andrés Oróstegui, who knows how to look beyond, and whose views helped me find the way back countless times. I thank my mother, my father, my sister, and my brother, always by my side and in my heart. With all my brain and all my heart, I owe my gratitude to my Friends. Life and discussions, scientific or not, are always more lovely and interesting with you. To Tania Pérez, Manuel Franco, María José Contreras, Camila Gómez, Nick Bayly, Andrés Quiñones, Paola Montoya, María Alejandra Meneses, Laura Céspedes, Mateo Dávila, Melanie Ramírez, Natalia Gutiérrez, Valentina Gómez, Ghislaine Cárdenas, Laura Mahecha, Santiago Herrera, Lina Gutiérrez, Luisa Dueñas, Mileidy Betancourth, Jorge Avendaño, Paulo Pulgarín, Oscar Laverde, David Ocampo, Lucas Barrientos, Ana Aldana, Vicky Flechas, Andrew Crawford, Leonardo Campagna, Erich Jarvis, Andrés Cuervo, Carlos Guarnizo, Juan Luis Parra, Catalina Cruz, Iván Páez, Fabian Salgado, Andrea Paz, Gerriet Janssen, Will Vargas, Sauk Naranjo, Alfa, Milo, and Logan Luminus Veroandi. Without your constant support and love none of this work would have ever been possible. I thank you, for reading this document! Abstract The evolutionary mechanisms driving lineage differentiation in a system and the genetic basis of phenotypic differentiation remain central issues in evolutionary biology. In the Colombian Andes, two hummingbird species, Coeligena bonapartei and C. helianthea, show striking phenotypic differences in coloration but low genetic differentiation in a phylogeny of the Coeligena genus. These species comprise five allopatric and sympatric subspecies. In this thesis I studied the evolution of the lineages in C. bonapartei and C. helianthea to identify the evolutionary mechanisms driving their divergence and the genetic basis of their phenotypic differences. I sequenced for the first time the genomes of a population sample of hummingbirds and I used tools from population genetics, comparative genomics, niche modeling, and comparative morphology to clarify the evolutionary relationships among lineages of Coeligena; to test the hypothesis that they diverged in the presence of gene flow; and to identify candidate genes related to their phenotypic differences. I found that C. bonapartei and C. helianthea comprise at least four evolutionary lineages. The evolution of the lineages C. b. eos and C. b. consita was likely driven by genetic drift in the absence of gene flow, whereas C. b. bonapartei and C. helianthea diverged in the presence of gene flow driven by natural selection, sexual selection, or both. The low genetic differentiation among the mitochondrial genomes of these hummingbirds supports their recent divergence and the occurrence of introgression. The landscape of genomic differentiation among these lineages shows many peaks containing genes possibly related to their phenotypic differences. These genes support the idea that structural coloration in hummingbirds is a polygenic trait closely linked to feather development. My work contributes to understanding of comparative genomics in hummingbirds and how species are formed in megadiverse mountain systems in the tropics. Resumen El efecto de los mecanismos evolutivos en la divergencia de un sistema dado, y las bases genéticas de las diferencias fenotípicas son aún temas centrales en evolución. En la cordillera Oriental de los Andes colombianos, habitan las especies de colibríes Coeligena bonapartei