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Coevolutionary Analysis of the Transposon Galileo in the Genus Drosophila

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Coevolutionary Analysis of the Transposon Galileo in the Genus Drosophila Coevolutionary analysis of the transposon Galileo in the genus Drosophila Andrea E. Acurio Armas Departament de Genètica i de Microbiologia Universitat Autònoma de Barcelona Advisor: Dr. Alfredo Ruiz 0 Coevolutionary analysis of the transposon Galileo in the genus Drosophila Análisis coevolutivo del transposon Galileo en el género Drosophila ─TESIS DOCTORAL─ Andrea E. Acurio Armas Bellaterra, Diciembre del 2014 Facultat de Biociències Memoria presentada para optar al grado de doctor por la Universidad Autónoma de Barcelona, Programa de Doctorado en Genética. El Doc tor Alfredo R uiz, C atedràtic del De partament de Ge nètica i de Mi crobiologia de la Facultat de Biociències de la Universitat Autònoma de Barcelona, CERTIFICA: que Andrea E. Acurio Armas ha d ut a terme sota la se va dirección el treball de recerca realizat a l De partament de Genètica i de Microbiologia de l a F acultat de B iociències d e la Universitat Autònoma de Barcelona que h a po rtat a l’elaboració d’aquesta Tesi Doctoral, titulada “Coevolutionary analysis of the transposon Galileo in the genus Drosophila”. I per què consti als efectes oportuns, signa el present certificat a Bellaterra, 1 de de sembre Noviembre de l 2014. Dr. Alfredo Ruiz. DEDICATORIA Esta disertación está dedicada a: Mi familia por que su apoyo y cariño me acompañan siempre. Los amigos que se han convertido en mi segunda familia. Gloria Luo R.I.P ACKNOWLEGMENTS This dissertation encompasses several fields in Evolutionary Biology ranging from Alpha-Taxonomy to Cophylogenetics. I feel very lucky because I have had the advice and support from several specialist and institutions. Here, I am including some of the wonderful people that helped me during the last years. I would like to express my very great appreciation to my advisor Dr. Alfredo Ruiz. I thank him for his guidance through the development of this work. Many thanks to the committee members for generously offering their time to review this dissertation. My sincere appreciation is extended to Dr. Alexis Matamoro-Vidal for the encouragement, advices and inspiring discussions. My special thanks to Dr. Patrick O`Grady for his invaluable help and for receive me as visitor student in his lab at UC, Berkeley. I am also grateful with Dr. Violeta Rafael for her suggestions and the facilities provided to perform the field trips in Ecuador. I would like to offer my special thanks to: Dr. Deodoro Oliveira, Dr. Mar Marzo and Dr. Alejandra Delprat, for their guidance at the beginning of this project; to Dr. Carlos Vilela Sensei for his help in taxonomic identifications; to Dr. Kari Goodman, for her help in the Biogeographical analysis; to Dr. David Houle for his helpful comments and kind hospitality at FSU; to Dr. Amir Yassin for his comments to the D. machalilla manuscript; to Dr. Michael Lang, for his comments to the inca manuscript; to Dr. Virginie Orgogozo for inspiring me to continue working with Drosophila; to Dr. Kasey Creasey for giving me the opportunity to attend the CSHL meeting and Dr. Tandy Warnow for making possible my trip to Washington DC. I am also grateful to the administrative personnel of the Department de Genètica I de Microbiologia de la UAB: Maite Navarro, Elena García, and Maria Josep Mas. The technical assistance provided by Montse Sales and Raquel Ferraz, was greatly appreciated through this research. Many thanks to the people from the Drosophila, Bioinformatics and Evolution Group and my labmates: Nuria Rius, and Yolanda Guillen. Special thanks to Charles J. Simmons for his corrections on English writing. I would like to thank the following institutions: Agència de Gestió d´Ajuts Universitaris i de Recerca (AGAUR), and the European Commission - European Social Found (EC-ESF) by the Pre-Doctorate Grant (FI-DGR 2011). Secretary of Education, Science and Technology from Ecuador (SENESCYT), by the Master Grant (Talento Humano 2009). Many thanks to the Ministry of Environment from Ecuador for the scientific research permissions to collect in Ecuador. I am also very grateful to: the Willi Henning Society (WHS) by the Mary Stopes Travel Award 2013; University of Texas, at Arlington and Smithsonian Museum by the Travel Grant Frontiers in Phylogenetics 2012. Finally, many thanks to Cold Spring Harbor Laboratory (CSHL) by the help on registration at the Mobile Genetic Elements Meeting 2013. CONTENTS I. INTRODUCTION ......................................................................................................... 1 I.1 The genus Drosophila I.1.1 Phylogenetic taxonomy ...................................................................... 2 I.1.2 Evolutionary relationships .................................................................. 3 I.1.3 The Drosophila repleta species group............................................... 7 I.2 Transposable elements I.2.1 Abundance and impact on host genomes ........................................... 8 I.2.2 Classification ...................................................................................... 9 I.2.3 DNA transposons .............................................................................. 11 I.2.4 Dynamics of DNA transposons ........................................................ 11 I.2.5 The transposon Galileo ..................................................................... 13 I.3 Reconstructing the history of Galileo-Drosophila association I.3.1 Coevolution, Codivergence and Cospeciation .................................. 16 II. OBJECTIVES ............................................................................................................ 19 II.1. Chapter 1 .................................................................................................. ...20 II.2. Chapter 2 .................................................................................................. ...20 II.3. Chapter 3 .................................................................................................. ...21 III. MATERIAL AND METHODS ................................................................................ 22 III.1. Drosophilid collections .............................................................................. 23 III.2. Molecular techniques .............................................................................. ...23 III.3. Sequence analysis.................................................................................... ...23 III.4. Dataset analysis ....................................................................................... ...24 III.5. Phylogenetic analysis ................................................................................. 24 III.6. Biogeographical analysis ........................................................................ ...24 III.7. Cophylogenetic analysis.......................................................................... ...24 IV. RESULTS AND DISCUSION ................................................................................. 25 Chapter 1.-Description of a New Spotted-Thorax Drosophila (Diptera: Drosophilidae) Species and Its Evolutionary Relationships Inferred by a Cladistic Analysis of Morphological Traits ........................................................ 26 Chapter 2.-Evidence of a South American origin for the Drosophila repleta lineage. ............................................................................................................. ...38 CONTENTS CONTENTS .............................................................................................. 40 Chapter 3.-Long-term evolutionary dynamic of a DNA transposon, the case of Galileo in Drosophilidae ..................................................................................... 67 CONTENTS ......................................................................................... ...70 V. CONCLUSIONS ...................................................................................................... 166 VI. APPENDICES ........................................................................................................ 170 Appendix 1. .................................................................................................... ...171 Appendix 2. .................................................................................................... ...177 Appendix 3. .................................................................................................... ...188 Appendix 4. .................................................................................................... ...189 Appendix 5. .................................................................................................... ...191 Appendix 6. .................................................................................................... ...193 VII.REFERENCES ....................................................................................................... 196 LIST OF TABLES Table I-1. Examples of the hierarchical classification for TEs ....................................... 10 LIST OF FIGURES Figure I-1. Taxonomic ranks used in the nomenclature of Drosophilidae. ...................... 3 Figure I-2. Latest phylogenetic hypotheses inferred for Drosophilidae.. ....................... 66 Figure I-3. Tree embedded in its host phylogenetic tree ................................................ 18 ABBREVIATIONS aa amino acid AIC Akaike Information Criterion BI Bayesian Inference bp base pairs COI Cytochrome oxidase subunit I gene COII Cytochrome oxidase subunit II gene CPT Cherry-picking test DNA Deoxyribonucleic
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