Identification of the molecular changes underlying head morphology variation in closely related Drosophila species Dissertation For the award of the degree Doctor rerum naturalium (Dr. rer. nat.) Division of Mathematics and Natural Sciences of the Georg-August-Universität Göttingen within the doctoral program Genes and Development of the Georg-August University School of Science (GAUSS) submitted by Montserrat Torres Oliva from Barcelona (Spain) Göttingen, March 2016 Thesis Committee: Dr. Nico Posnien (1st Reviewer, advisor) Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Georg-August-University Göttingen Prof. Dr. Martin Göpfert (2nd Reviewer) Department of Cellular Neurobiology, Schwann-Schleiden Research Centre, Georg- August-University Göttingen Prof. Dr. Tim Beiβbarth Department of Medical Statistics, University Medical Center Göttingen Further members of the Examination Board: Prof. Dr. Gregor Bucher Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach- Institute of Zoology and Anthropology, Georg-August-University Göttingen Prof. Dr. Daniel Jackson Courant Research Centre Geobiology, Georg-August-University of Göttingen PD Dr. Halyna Shcherbata Research Group Gene Expression and Signaling, Max Planck Institute for Biophysical Chemistry Date of oral examination: 23rd May 2016 ii Declaration Herewith I declare, that I prepared the Dissertation “Identification of the molecular changes underlying head morphology variation in closely related Drosophila species” on my own and with no other sources and aids than quoted. __________________________ Göttingen, 31.03.2016 Montserrat Torres Oliva iii iv I want to dedicate this work to my friend Orla Lawlor v Acknowledgements I would like to take this chance to thank all the people who, in some way or another, I feel have contributed and helped me complete this thesis. First and foremost, I want to thank my supervisor Dr. Nico Posnien. Thank you for your constant support, encouragement and guidance; for so many interesting and productive discussions, and for always listening and valuing my opinions. Thank you for all what you have taught me and for always finding time to answer my questions. I am very happy I could be the first of the many Ph.D. students that will follow. Vielen, vielen Dank! I also want to thank the other members of my Thesis Committee, Prof. Dr. Martin Göpfert and Prof. Dr. Tim Beiβbarth, for the useful comments and directions for my project during the Thesis Committee Meetings. I am also thankful to Prof. Dr. Gregor Bucher, Prof. Dr. Daniel Jackson and PD. Dr Halyna Shcherbata for accepting to be part of my extended Committee. I am grateful to Prof. Dr. Ernst Wimmer for letting me be part of the Department of Developmental Biology. I also want to thank him and Prof. Dr. Gregor Bucher, Prof. Dr. Sigrid Hoyer-Fender, Dr. Nikola-Michael Prpic-Schäper and Dr. Gerd Vorbrüggen for the interesting discussions and constructive input during my Progress Reports. I want to thank especially Dr. Marita Büscher for all her help and advice. I have been lucky to be able to supervise great students that have also contributed to this work. I want to thank Gordon Wiegleb, Julia Schneider and Felix Kaufholz for their work on the Hunchback project and Elisa Buchberger and Melissa Jüds for the endless hours dissecting discs. I also want to thank all the members of Lab2 for creating such a nice working environment. Thanks to Natascha for our long scientific (and not so scientific) conversations and for always seeing through my seriousness. I am also very thankful to Christoph, Felix, Elisa, Yan Li, Natalia and Kefei for all their help and friendship. Thanks also to Reya for her visits that always cheered me up. I would like to thank all the many people that I have met in the Department of Developmental Biology during the last years, including all students, technicians and secretaries. I want to thank especially Ingrid, Sabrina, Alice, Georg, Kolja, Beni, Stefan, Elke and Beate for their help in the lab and for the time we spent together. I also want to thank my friend Anna Stief for introducing me to this Department. A big Thank You goes to everybody in the group of Dr. Alistair P. McGregor in Oxford for the great work together. Especial thanks to Dr. Isabel Almudi for all you have taught me and for always answering my many questions in record time. I also want to thank my former supervisors Prof. Julio Rozas and Prof. Michael Akam for all they taught me and for their trust and encouragement at the very start of my career. vi I want to thank Gabriela Salinas and everybody at the Transcriptome and Genome Analysis Laboratory (TAL) for the useful discussions and for generating all the sequencing data for this project. I also want to acknowledge the people at the GWDG for the great resources they provide. Somehow, I would also like to thank the very many flies that have unwillingly participated in this work. I thank them also for (almost) always laying eggs when I needed them. This would have been impossible without them. I am extremely thankful to Fundació Obra Social La Caixa and the Deutscher Akademischer Austauschdienst (DAAD) for granting me the scholarship that allowed me to carry out this work. I was very fortunate as well to receive funding from the Graduate School for Neurosciences, Biophysics and Molecular Biosciences (GGNB), which allowed me to extend my work for three months. I am also thankful to everybody in the GGNB for all their assistance during my thesis. In my three and a half years in Göttingen I have met some great people and they all made my time here better. I want to especially thank Madlen, Irene and Hans for being the best housemates one could ever wish for. El que m’ha donat més forces els últims anys han sigut les meves escapades a casa. Vull donar les gràcies a l’Angela, la Clara, la Joana, la Mònica, la Gemma, el Pablo i la Irene perquè en cada una de les meves visites heu trobat temps per veure’ns. Gràcies per fer-me sentir sempre com si ens haguéssim vist ahir. Als meus pares els hi vull agrair tot. Gràcies per haver-me permès i ajudat a estudiar i per haver-me ensenyat la importància de la ciència i la cultura. Gràcies també pels valors que sempre heu demostrat i que, espero, ara també són els meus. A vosaltres i a la meva germana Irene, gràcies per fer-me riure, per les vostres visites, per les sobretaules i per tot el que hem fet junts. Gràcies també als meus tiets, tietes i cosins per tot el suport i per les millors festes de Cap d’Any. Danke auch an die Familie Hattendorff, dass sie mich so gut aufgenohmen haben und für die schönen Tage an der Ostseeküste. Der gröβte Dank ist für mein Freund Tobi. Thank you for your love and support and for always making me be the best version of myself. Sense tu, ich hätte es nicht geschaft. vii viii Table of Contents List of Figures xii List of Tables xv 1 Summary 1 2 Introduction 3 2.1 General introduction ........................................................................................................... 3 2.1.1 Evo-Devo and the study of morphological evolution ........................................................... 3 2.1.2 Gene expression divergence and transcriptomics ................................................................... 4 2.1.3 Morphological diversity in insects ............................................................................................. 5 2.1.4 The model species Drosophila melanogaster ................................................................................. 5 2.1.5 Drosophila head structures develop from eye-antennal imaginal discs .................................. 6 2.1.6 Thesis overview and organization ............................................................................................. 7 2.2 New regulatory interactions governing Drosophila head development ....................... 10 2.2.1 Drosophila head and eye development...................................................................................... 10 2.2.2 Discovery of new GRN interactions by developmental transcriptomics ......................... 12 2.3 A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species ........... 14 2.4 Gene expression divergence in closely related Drosophila species ............................... 16 2.4.1 Gene expression divergence, GRN evolution and micro-evo-devo .................................. 17 2.4.2 Allele-specific expression studies ............................................................................................. 18 2.4.3 Regulatory divergence in developing tissues of three closely related Drosophila species . 20 2.5 Eye size variation in two closely related Drosophila species .......................................... 22 2.5.1 Eye size variation between D. mauritiana and D. simulans .................................................... 22 2.5.2 Differences in ommatidia structure ......................................................................................... 23 2.5.3 A quantitative trait locus (QTL) correlates with eye size variation .................................... 25 3 Materials and Methods 27 3.1 Fly strains, culture and crosses ......................................................................................... 27 3.2 Immunohistochemistry ....................................................................................................