Evolutionary processes in mayflies (Ephemeroptera): genomics approaches to the study of ancient origins and recent diversification Inaugural-Dissertation to obtain the academic degree Doctor rerum naturalium (Dr. rer. nat.) submitted to the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin by SEREINA RUTSCHMANN from Winterthur, Switzerland Berlin, 2015 The PhD research presented here was conducted from 01.07.2011 to 31.12.2014 as part of the FREDIE project (www.fredie.eu) at the Leibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin (IGB) and the Berlin Center for Genomics in Biodiversity Research (BeGenDiv). The work was partly financed by the SAW/PAKT program of the Leibniz Association (WGL) and by the IGB. Dr. Michael T. Monaghan supervised the work. 1st Reviewer: Dr. Michael T. Monaghan 2nd Reviewer: Prof. Dr. Klement Tockner Date of Defense: 16.02.2015 I ACKNOWLEDGEMENTS I am extremely thankful for the last three and a half years. I learned a lot doing exciting research, and I met great people within and besides research. First of all, I am deeply thankful to Michael T. Monaghan for being a fantastic supervisor. I appreciated very much all the fruitful discussions that gave me input for my work, and for all the helpful advises he gave me in order to make my scientific life easier. I am very glad that you not only offered me this PhD position but also and moreover gave me a lot of support and freedom to develop my own research interests. Furthermore, I am very thankful for the generous funding to spend three months at the AMNH, to attend scientific conferences and workshops, and to perform all the sequencing needed fot this PhD research. I thank Klement Tockner, director of the IGB and second examiner of my thesis, for his always very positive attitude, the support at the Freie Universität Berlin, and for reviewing this work. I am very thankful to Rob DeSalle and Sabrina Simon for hosting me at the AMNH and their help with the marker design. I really enjoyed my time working together with Sabrina, for discovering together the museum and the city. I very warmly thank Jean-Luc Gattolliat and Michel Sartori for sharing their knowledge with me and greatly supporting my work, sending me many mayfly specimens, providing me with detailed information, and their expertise. I benefited much from the weekly Tuesday/Thursday meetings on Evolutionary Biology at the IGB and want to thank all present and past members. I got a lot of helpful comments on my own work and learned a lot. In particular I want to thank Maribet Gamboa, Christian Wurzbacher, Thomas Mehner, Maria Alp, Ignacio Lucas-Lledo, Elizabeth Bourne, and Paul Schmidt Yáñez for many enlightening and also critical discussions on phylogenetics, population genetics, aquatic insects, species tree reconstruction, specific software, and their help during the sampling trips to Spain and Norway. The great laboratory support from Katrin Preuß, Lydia Wächter, Susan Mbedi, and Berta Ortiz Crespo was substantial for this work. I thank you all for your patience with me in ACKNOWLEDGEMENTS II the laboratory, the moral support during the preparation of the high-throughput sequencing libraries, and your excellent work. The BeGenDiv was a stimulating environment for me to work in the field of genomics/bioinformatics. I am particularly thankful to Camila Mazzoni, Harald Detering, and Felix Heeger for the bioinformatics support. Many thanks go to all members of the FREDIE project. In particular, I am thankful to Matthias Geiger for discussion on BEAST analyses and collecting specimens, Katharina Kurzrock, and Jörg Freyhof for their help in the field, and to Fabian Herder as head of the project. I want to thank Peter Manko for teaching me how to catch most efficiently mayflies and two wonderful field trips to the Carpathians. I am thankful to Marcos Báez for his help to retrieve the sample collecting permits on the Canary Islands and the wonderful day we had in the Barranco del Río. Thanks to Kirsten Pohlman for coordinating the IGB doctoral program that helped me to structure my PhD and to Martin Allgaier and Christian Wurzbacher for co-supervising this PhD research. I especially appreciated the attendance of the scientific writing course held by Thomas Mehner. I am grateful to ‘my PhD fellows’ and all members of the Kinderzimmer, in particular to Marlen Heinz, Francesca Pilotto, Magdalena Czarnecka, and Ann-Christin Honnen for sharing their experiences, for always having an open ear, and the fun moments in our spare time. I am very thankful to my dear “Berlin buddies” and all my friends for all the great moments we had during the Thursday’s mystery movies, the funny evenings in the Belgium beer bar, the beer festival, the carnivals of cultures, “short walks”, delicious Pizza & Indian food…and so much more. More overall, I am deeply indebted to my parents, my brothers, my grandparents, and the wonderful person who came into my life recently. Their incredible support gave me the strength to pursue my interest in science. I am very thankful that you always encouraged me and believed in me especially when I had doubts. Harry, Mum & Paps, Benji & Janine, Andri, Nani & Grospi, Grosmami & Grospapi thank you so much for always being there for me. III PREFACE This thesis is a cumulative work and consists of three manuscripts within a general context. Thus this work contains four sections: Introduction, Objectives, Manuscripts, and Conclusions. The first three sections are structured into the two thematic subsections RECENT DIVERSIFICATION and ANCIENT ORIGINS. At the beginning of my thesis, I start by providing an INTRODUCTION to the study of evolutionary histories and diversification of mayflies, and a section outlining the OBJECTIVES of the thesis. The MANUSCRIPTS section is organized into CHAPTERS 1, 2 & 3. Each of the chapters is an independent manuscript that is either already published (CHAPTER 1), or that will be submitted to peer-reviewed journals (CHAPTERS 2 & 3). Each chapter forms a stand-alone unit, with its own introduction, methods, results and discussion, and can therefore be read independently from the other chapters. In the CONCLUSIONS section, I combine and summarize the main findings of my thesis and highlight future perspectives for research. As result of this structure, the content of the sections overlap to some extent with the different chapters. The layout of the published manuscript has been reformatted to fit the consistent layout throughout this thesis. References are provided separately for each section. The genomic data I generated during my PhD research have been deposited to the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov/), and can be downloaded with the accession numbers given in the chapters. Data included in manuscripts that have not been published yet are listed in this thesis as XXXXXXXX. The bioinformatics program DISCOMARK, which I created to facilitate the development of new genetic markers, can be downloaded from https://github.com/hdetering/discomark. All Python scripts that were written for the automation of bioinformatics processes are available from https://github.com/srutschmann/python_scripts. IV CONTENTS ACKNOWLEDGEMENTS PREFACE SUMMARY ............................................................................................................................ 1 ZUSAMMENFASSUNG ............................................................................................................ 3 1 INTRODUCTION .............................................................................................................. 9 THE STUDY SYSTEM - MAYFLIES (EPHEMEROPTERA) ........................................................ 9 1.1 RECENT DIVERSIFICATION ..................................................................................... 12 1.2 ANCIENT ORIGINS .................................................................................................. 13 2 OBJECTIVES ................................................................................................................. 22 2.1 RECENT DIVERSIFICATION ..................................................................................... 22 2.2 ANCIENT ORIGINS .................................................................................................. 24 3 MANUSCRIPTS ............................................................................................................. 27 3.1 RECENT DIVERSIFICATION ..................................................................................... 27 CHAPTER 1: Rutschmann S, Gattolliat J-L, Hughes SJ, Báez M, Sartori M, Monaghan MT (2014) Evolution and island endemism of morphologically cryptic Baetis and Cloeon species (Ephemeroptera, Baetidae) on the Canary Islands and Madeira. Freshwater Biology. 59, 2516-2527. doi: 10.1111/fwb.12450 ..................................................... 27 CHAPTER 2: Rutschmann S, Simon S, Detering H, DeSalle R, Funk DH, Gattolliat J-L, Raposeiro PM, Sartori M, Monaghan MT (in preparation) Colonization of Macaronesian Freshwaters: Phylogenetics using 59 Nuclear Markers derived from a Whole Genome Draft. ................................................................................................ 57 3.2 ANCIENT ORIGINS ................................................................................................ 107 CHAPTER 3: Rutschmann S, Ping C, Zhou C, Monaghan MT (in preparation) Using mitochondrial mayfly (Ephemeroptera) genomes to resolve