On The Development Of The Turtle Scute Pattern And The Origins Of Its Variation February 20, 2019 Roland Zimm Institute of Biotechnology Helsinki Institute of Life Science (HiLife) and Department of Biosciences Faculty of Biological and Environmental Sciences Doctoral Programme in Integrative Life Science (ILS) University of Helsinki Academic dissertation To be presented for public examination with the permission of the faculty of Biological and Environmental Science of the University of Helsinki in Sali 1041 (Biokeskus 2, Viikinkaari 5, Helsinki) on 12. March 2019 at 12:00. Supervisor Isaac Salazar-Ciudad, University of Helsinki Thesis advisory committee Jukka Jernvall, University of Helsinki Mikael Fortelius, University of Helsinki Ritva Rice, University of Helsinki Pre-examiners Ann Campbell Burke, Wesleyan University, United States of America Shigeru Kondo, Osaka University, Japan Opponent Marcelo S´anchez-Villagra, University of Z¨urich, Switzerland Custos Liisa Holm, University of Helsinki Copyright c 2019 Roland Zimm ISSN (print) : 2342-3161 ISSN (e-thesis) : 2342-317X ISBN (paperback) : 978-951-51-4953-4 ISBN (e-thesis) : 978-951-51-4954-1 http://ethesis.helsinki.fi Helsinki 2019 Unigrafia Acknowledgements Working on my thesis has been a process of many years, at times joyful, at times strenuous. All this would have hardly been possible without the support of many people and institutions who believed in me and many more people whose contributions are usually rarely mentioned. At first, I want to express my thanks to my supervisor Isaac Salazar-Ciudad who taught me new ways of thinking in the contexts of biology, science and society in general, and my thesis in particular, as well as new ways “cross-country” the wilderness of Finland and Catalonia. In particular, I am grateful for all the honest and detailed feedback I received from him, and it is safe to say that without all our discussions I would be scientifically and personally far from where I stand today. Another important person to whom I owe a lot in context of my thesis is Jacqueline Moustakas-Verho. She has been my closest collaborator on the turtle project and become a great friend to me. Also, I owe to Scott Gilbert, without whose committment the turtles would never have arrived to Finland. I want to thank Jukka Jernvall, who, despite being usually busy with more important matters, was always approachable and extremely helpful, whenever some help and major or minor feedback was needed. Together with him, I want to thank the other members of my thesis committee, Mikael Fortelius and Ritva Rice, who gave equally helpful advice by pointing out risks, finding solutions and offering different views upon my ongoing research, especially by taking all my concerns seriously and telling me when my objectives were too ambitions. My thesis committee meetings have always been very easy-going, motivating, supportive and greatly contributing to the advancement of my research. During my time at Helsinki University, I was financially supported by the Academy of Finland, the Cluster of Excellence in Computational and Developmental Biology, and a GPBM grant that I was lucky to be awarded with during my first years of my studies. I want to acknowlege the support and guidance I got from my grad school(s), GPBM and ILS, who helped making my time at the university enjoyable, as well as guiding me through the duties towards the end of my PhD. As my work was mainly based on heavy computation, I do not want to miss to acknowledge the help by the CSC. The CSC Grand Challenge Grant I received with my collaborators played a crucial role in enabling us to perform computational experiments efficiently. The transition time between the end of my thesis-related research and my defense was sub- stantially facilitated by the opportunity to work at the Konrad Lorenz Institute for Evolution and Cognition Research (KLI) for half a year and essentially write my thesis there. It has also been a very inspiring place where people with very diverse, theoretical questions in Biology come together. In particular, I want to thank Isabella Sarto-Jackson, Eva Lackner and Gerd M¨uller,but also the former director Johannes J¨agerwho convinced me to apply there. Since I meanwhile started working in the lab of Nicolas Goudemand, I want to thank him for his readiness to accept me as “pre-postdoc”. I also do not want to forget to acknowledge the lab in which I completed my Diploma of Biology, the group of theoretical biology at Dresden University of Technology, especially Andreas Deutsch, Lutz Brusch and my former supervisor, Walter DeBack, who had crucial impact in diverting my scientific path towards the mathematical and computational field. Working inside a group in which it is equally natural to collaborate in scientific terms and to share an after-work beer, while discussing about all possible aspects of life, is a great luck which I have been endowed with. So, I am grateful to have been with my colleagues and friends, Irepan, who shared a lot of time with me and introduced me into the vast Mexican “morphospace of spices”, an indispensable asset in resisting the Finnish winter, Miguel, who has been a great companion in exploring the morphospace of unknown places and theories, Miquel, with whom I survived the wild slopes of Barcelona’s hinterland, Pascal, who has become my “scientific brother” in continuing in the projects I have begun, Lisandro and Jhon. I am also grateful for the wider environment at the Helsinki EvoDevo community: Mona, who rescued me whenever I was unable to cope with the Finnish language, Susanna, who facilitated my arrival and helped me coping with all “practical contingencies” in uncountable ways, Richi, Outi, Teemu, Ian, Mia, Yoland, Tuomas A., Tuomas K., Maria, Solja, Alison, Ewelina, Otto, Vinod, Isabel, Ana-Maria, Martin, Julia, Lotta, Fabien, Blanca, Joni, Simone, Filipe, Umair, Irma Thesleff, Marja Mikkola and Nicolas DiPoi, and all the other people whom I may have forgotten to mention here. Although personally disliking the concept of “life-work balance”, my life in Finland would have been severely disbalanced without the different activities and distractions that diversified and en- riched my past six years, such as participating in the Aland˚ bird rallyes with Tuomas K, Kalle and Joni, joyful and creative weekly board game evenings with Maja, Billy, Julia, Barbie, Teemu and Juhani, evenings to break down philosophical frontiers with Matan, Jani and Aura, French cheese challenges with Fabien and Valerio, after-work “Stammtisch” with Julia and Wojciech, bike trips with Irepan, Helene and Ekaterina, international evenings at Caf´eLingua with Julian and Jimena, great social events with Pekko and Anna, and Birgitta Ahlberg, who offered me to stay with my frinds at her M¨okkis,thereby possibly providing the most finnish times ever. Thank you Loic, Joan, Irepan and Erno for being almost perfect flatmates. You all have been great friends and contributed to the experience I have had at Helsinki and will remember. Finally, my biggest thank goes to the people who spent more time, effort, nerves and love on me than anybody else, during most of my scientific journey and much beyond, and, thereby, have shaped what I am: my parents and grandparents, my brother, and Vit´oria,the one person who has accompanied me during the last years through all distances in time and space, understanding me, providing support in so many ways, and bearing all the additional stresses and restrictions that a shared life in academia conveys. Contents 1 Literature review 1 1.1 Novelties . 2 1.2 The origins and diversity of the turtle shell . 4 1.3 Development of turtle scutes . 7 1.4 Development of periodic structures . 10 1.5 Reaction-diffusion systems . 14 1.6 Epidermal appendages and their development . 18 1.7 The origins of variation through development . 22 1.8 Origins of variation in turtle scute patterns . 26 1.9 Models of development . 31 1.10 Towards a unified model of development . 35 2 Aims 38 3 Methods 38 4 Results 42 5 Discussion 43 5.1 Caveats and Limitations . 43 5.1.1 Caveats due to model limitations . 43 5.1.2 Caveats due to limited data . 46 5.2 Classification of the turtle scute pattern development and implications for variation 48 5.3 The carapacial ridge as a developmental organizer . 50 5.4 Comparison between scutes and other ectodermal appendages from a developmental perspective . 52 5.5 Interspecific variation of turtle scutation . 58 5.6 A genetic origin of turtle scute anomalies? . 61 5.7 Origins of intraspecific variation: Hypotheses revised . 62 5.8 Possible mechanisms by which epigenetic factors may interfere with development . 66 5.9 Turtle anomalies and climate change . 70 5.10 Has the role of epigenetic factors in phenotypic variation been underrated? . 70 5.11 Evo-devo and the value of non-model organisms . 71 5.12 A dialogue of experimental and mathematical approaches in evo-devo . 73 6 Concluding remarks 74 7 Bibliography 77 Contributed Publication I . 100 Contributed Publication II . 122 Contributed Publication III . 134 Abstract The turtle carapace has been considered one of the classic examples of an evolutionary novelty. It is diagnostic of the turtle clade and probably largely responsible for its success in evolution. In more detail, it consists of ossified dermal plates overlaying laterally extended ribs, as well as a reg- ular array of epidermal scutes. Interestingly, the unique and complex mosaic pattern formed by the carapacial scutes is highly conserved amongst almost all extant turtle taxa. Since the morphogenesis of this remarkable pattern has not been studied much before, I present, in this dissertation, a novel computational approach to elucidating carapacial scute development.