Insights into mammalian adaptive evolution through genomics data José Luis Villanueva-Cañas TESI DOCTORAL UPF / 2015 DIRECTORA DE LA TESI Dra. Maria del Mar Albà Soler Evolutionary Genomics Group Research Programme on Biomedical Informatics (GRIB) FIMIM (Fundació Hospital del Mar Medical Research Institute) Universitat Pompeu Fabra DEPARTMENT OF EXPERIMENTAL AND HEALTH SCIENCES AUG III A mis abuelos V All men by nature desire to know. Aristotle Try to learn something about everything and everything about something. Thomas Huxley Acknowledgements Uno no llega hasta aquí solo. En realidad nunca nadie llega a ningún lado sin la ayuda y soporte de los demás. Estas líneas que siguen son mi muestra de agradecimiento para todas aquellas personas que aportaron su granito de arena en el desarrollo de este trabajo. A tu Mar, per proporcionar-me l’oportunitat de fer una mica de ciència. També per donar-me la llibertat per a cometre errors, tan necessaris per aprendre. Però sobretot per la teva integritat, com a científica i com a ciutadana. A en Patrick Aloy, Javier de la Cruz i Lourdes Fañanas per mostrar- me el mapa i ajudar-me a triar camins. Als membres del grup d’EG i en especial als doctorands (molts ja doctors): Steve, Alice, Macarena, Núria, Will (thanks also for the oxford comma) i en Jorge. A l’Alfons i Miguel, aka “the IT Crowd”, ja que sense la seva expertesa i diligència en qüestions binaries res d’això hagués estat possible. Anne, thanks for providing me with the great opportunity to make a short internship in your group. Sheena, thanks for being an VII awesome collaborator and introducing me into the lemur world. Also to all the people of the Yoder lab that took good care of me while I was overseas, especially to Erin, Peter and Jason. To Emma and all her irish crowd (Nicole, David, Stephen, Zixia, Una, Graham and George (albeit adopted)), for giving me a human (or a bat) perspective of science and showing me what ‘the craic’ was. To Jens and Salla, for letting me explore their area52. To Sergio and his wonderful wife Marcia, for treating me like a family during my dublinese adventure. To all my MSc classmates, especially to Magda and Yorgos, whom I now call friends. Gràcies a en David, Albert, Pau, Maria, Inés, Armand, Iván i Cinta per compartir les penes i les alegries de la professió. També per les paelles. A tots els meus companys de despatx, passats i presents, que van compartir el dia a dia amb mi, fent la rutina més agradable: Max, Adriano, Salva, Núria, Sergi, Pau, Héctor, Babita, Juan Luis, Juan Ramón, Michael, Eneritz, Nico, Imma, Emma, Abel, Amadís… i tots els que la memòria no em retorna ara mateix. A un trozo de madera, que unas manos artesanas convirtieron en arco, y contribuyó, en gran medida, a despejar mi mente en días tristes o turbios, allá por los bosques de Dosrius. A todos y cada uno de mis compañeros de armas de l’Associació Catalana d’Esgrima Antiga (ACEA), en especial a los instructores Oriol y Diego, que han tenido la paciencia de enseñarme la poca esgrima que sé. A Israel y David por los viajes, las risas y alguna que otra locura. VIII A mis viejos amigos, en especial a Aaron, Marga, Cristina, Elena, Ruth, Borja y Jaume. A Sara, por un gran año y por el futuro. A mis abuelos y abuela, que no llegaron a ver este día. A mi iaia Carmen, que resiste el envite del tiempo. Todos ellos miembros de una dura y noble generación que lo dieron todo, sin pedir nada a cambio. A mi familia y muy especialmente a mis padres (papá y mamá o J. Antonio y María Jesús), mi hermano Javier y mi tía Ana. Por su apoyo, siempre incondicional en cualquier proyecto (o locura) que yo haya decidido emprender. A todo aquel que se atreva a leer más allá de estos agradecimientos. IX Abstract Although the genome sequencing revolution is still in its infancy, we must acknowledge it as the major driver of biology since the beginning of the 21st century. The availability of a large collection of complete mammalian genomes due to high-throughput sequencing technologies allows us to begin the exploration of how the evolutionary diversification of gene content reflects the ecological adaptations of different taxa. Novelty arises in evolution through the transformation or combination of existing systems and, as shown recently, also from scratch. This thesis is centered around these different mechanisms of evolutionary innovation. It includes a common methodological part in which we propose a simple method to optimize multiple alignments and examine its effect in positive selection analyses, the exploration of the origin and evolution of mammalian-specific genes, and the study of gene regulation in mammalian adaptations (e.g. hibernation) using high-throughput technologies. XI Resum Tot i que la denominada era de la genòmica es troba encara a la seva infància, ha estat un dels principals impulsors de la biologia des del començament del segle 21. L’accés a una creixent col·lecció de genomes complets de mamífers, gràcies a les tècniques de seqüenciació massiva, ens permet explorar com la diversificació evolutiva dels gens es tradueix en les diferents adaptacions ecològiques dels diferents tàxons. La innovació apareix a l’evolució a través de la transformació o la combinació de sistemes preexistents, fins i tot, nous gens poden aparèixer a partir de regions prèviament no codificants, com s’ha demostrat recentment. Aquesta tesi s’articula al voltant d’aquests mecanismes d’innovació evolutiva. Inclou una part metodològica comuna on es proposa un mètode simple per optimitzar alineaments múltiples i avaluar-ne l’efecte en anàlisis de selecció positiva, l’exploració de l’origen i evolució de gens específics de mamífers i l’estudi de la regulació gènica en una adaptació pròpia dels mamífers (hibernació) mitjançant tècniques de seqüenciació massiva. XIII “A curious aspect of the theory of evolution is that everybody thinks he understands it.” Jacques Monod Preface - Prolegomena I was, and still am, overwhelmed by the diversity and complexity of the life that surrounds us. My fascination began very early, like every other child, asking questions about everything I could lay my eyes on. I was moved by a power-source that only kids have intact: true curiosity. Mine became mature when I first heard about Darwin’s (and Wallace) theory of evolution. Evolution planted in my head the seed of diversity, of change. I was amazed of how they were able to put together many different pieces of facts and converted them into new knowledge. One that would revolutionize humanity and would have a profound effect in the way we think and perceive the world. After several years scratching the surface of evolution and genomics, and while trying to deliver a small contribution to science, I made a precious discovery: A personal one. I committed plenty of mistakes in my daily work and spent countless hours fixing subtleties, but most importantly, I was able to learn from those mistakes (and solved some problems along the way). I found out that the only possible path to true knowledge is through humility and hard work. XV Everything you know (or you think you know) can change when new evidence appears or a new way to look at it comes into play; that is indeed the beauty of science. To me science is a vision of the world. A true human endeavor, which guides the irrational creature we all have inside through the path of knowledge. José Luis Villanueva-Cañas Barcelona, August 2015 XVI Table of Contents Acknowledgements ........................................................................................... VII Abstract .............................................................................................................. XI Resum .............................................................................................................. XIII Preface - Prolegomena ..................................................................................... XV Table of Contents ........................................................................................... XVII 1. Mammals ..................................................................................................... 1 1.1. Distribution ............................................................................................. 3 1.2. Origin ...................................................................................................... 5 Extant groups ..................................................................................................... 8 1.3. Characteristics and Adaptations ......................................................... 16 2. Genomics ................................................................................................... 25 2.1. Sequence Alignments ........................................................................... 30 3. Molecular Innovation ............................................................................... 32 3.1. Sequence change and positive selection .............................................. 34 3.2. Shifts in gene expression regulation.................................................... 39 3.2.1. Hibernation ........................................................................................... 41 3.3. Origin of New Genes ............................................................................ 47 3.3.1. TRGs and de Novo Genes .................................................................... 50 History and Nomenclature ............................................................................... 50 How do orphan