UNIVERSITY OF CALIFORNIA RIVERSIDE AND SAN DIEGO STATE UNIVERSITY Skull Growth and Prenatal Development in Baleen Whales: Teeth to Baleen Transition in Ontogeny and Phylogeny A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Evolutionary Biology by Agnese Lanzetti September 2019 Dissertation Committee: Dr. Annalisa Berta, Co-Chairperson Dr. Mark Springer, Co-Chairperson Dr. John Gatesy Dr. Kevin Burns Dr. Thomas Deméré Copyright by Agnese Lanzetti 2019 The Dissertation of Agnese Lanzetti is approved: Committee Co-Chairperson Committee Co-Chairperson University of California, Riverside San Diego State University Acknowledgments I thank my advisor Annalisa Berta, who believed that I could succeed in a biology program despite my geology background. I also thank my UCR advisor John Gatesy, who patiently taught me many useful skills, and my other committee members Mark Springer, Kevin Burns and Tom Deméré. For Chapter One, I thank John Gatesy and Michael McGowen for their help in the beaked whale phylogeny project. I thank John Gatesy and Mark Springer who designed the sequencing study process of gene C4orf26 that I contributed to. I also thank my co-authors for the review paper on mysticete evolution Annalisa Berta, Eric Ekdale and Tom Deméré. For Chapter Two, I thank my co-authors on the humpback whale development paper Annalisa Berta and Eric Ekdale, and Tim Smith (editor) and two anonymous reviewers for insightful comments on earlier drafts of the manuscript. Also for the humpback whale project, I thank for help handling specimens and the iodine staining Mike Van Patten and John Hansen at San Diego State University, and Daniel Klingberg of the Natural History Museum of Denmark. I thank the curators at the institutions that loaned specimens, in particular Jim Dines LACM, Brian O’Toole AMNH, Chris J. Conroy MVZ, and Morten Tange Olsen ZMUC. Special thanks to Phil Unitt SDNHM who agreed to let me test for the first time the new iodine-enhancement protocol. I also thank the institutions and personnel that performed the CT scanning: Matthew Costa at the Horton Hospital in San Diego, CA, Matt Colbert and Jessie Maisano at UTCT in Austin, TX, and Chiara Villa at the Laboratory of Biological Anthropology of the University of Copenhagen, Denmark. For the minke whale paper, I thank Annalisa Berta and Eric Ekdale and two anonymous reviewers for their thoughtful comments that significantly improved the manuscript. For data collection, a special thanks goes to Yuko Tajima, Tadasu Yamada, Naoki Kohno, Kumiko Matsui, and all the graduate students at the National Museum of Science in Tsukuba, iv Japan (NSMT) that granted access to the specimens, and greatly helped me during my visit to the museum. I am also grateful to Daisuke Hasegawa and the rest of the staff at Nippon Veterinary and Life Science University in Tokyo, Japan that worked after hours to allow me to obtain the CT scans of the fetal specimens from NSMT. For access to the specimens at the Natural History Museum of Denmark in Copenhagen (ZMCU), I thank M. T. Olsen and D. Klingberg. I would also like to thank C. Villa at the Laboratory of Forensic Anthropology of the University of Copenhagen, Denmark for the CT scans of the ZMCU specimens. I thank Emily Buchholtz for sharing the CT images of the Smithsonian Institution (USNM) neonate minke, as well as Giacomo Franci for his dissertation work collecting 3D models of postnatal minke whale skull. I also thank Doug Boyer for his help uploading and organizing the data on the MorphoSource database. For Chapter Three, I thank Annalisa Berta, Eric Ekdale and Tom Deméré for the insightful discussions and help they provided by allowing me to use the scan of Aetiocetus† in this project. I also thank Jonathan Geisler and Rachel Racicot for sharing the scan of Coronodon† with me. Other specimens were kindly provided by E. Buchholtz, G. Franci and E. Ekdale. For access to the fossil specimens in Japan, I would like to thank N. Kohno and K. Matsui, and the director and staff at the Port of Nagoya Public Aquarium. I also thank again the curators at the various institution that lent me fetal specimens, and the staff at the many CT scan facilities I visited. This dissertation was supported by iDigBio, the Lerner-Gray Grant for Marine Research awarded by the American Museum of Natural History, the SDSU Graduate Student Travel Fund, the University of California, Riverside Newell Award, Sigma Xi Grants-in-Aid of Research, the American Society of Mammalogists Grants-in-Aid of Research, the Gretchen L. Blechschmidt Award from the Geological Society of America and by the Mid-American Paleontology Society v (MAPS) Outstanding Student Research Award from The Paleontological Society. I also thank the Fulbright Commission of Italy for awarding me the IIE scholarship that allowed me to apply to this JDP and conduct my research in the United States. Last but not least, I thank my past labmates Giacomo Franci, Reagan Furbish, Meghan Smallcomb Corrie, and Bridget Borce, and all the graduate students in the EB program at SDSU and EEOB at UCR that helped me in many ways throughout my Ph.D.. I also thank the “marine mammal” community for the insightful annual discussions at SVP. Finally, I thank my friends, both the ones I made in these last 5 years and the ones that have always been there, for bearing with me through the good and the bad, and my parents and family for their unconditional love and support. vi Dedication A Speranza, piccola donna dalla grande forza. vii ABSTRACT OF THE DISSERTATION Skull Growth and Prenatal Development in Baleen Whales: Teeth to Baleen Transition in Ontogeny and Phylogeny by Agnese Lanzetti Doctor of Philosophy, Graduate Program in Evolutionary Biology University of California, Riverside and San Diego State University, September 2019 Dr. Annalisa Berta and Dr. John Gatesy, Co-Chairpersons In my dissertation, I aim to add a new ontogenetic perspective to the study of baleen whale’s (Mysticeti, Cetacea) skull evolution. In Chapter One, I analyze changes in dentition in closely-related toothed whales (Odontoceti, Cetacea), focusing on beaked whales, and trace the evolution of inactivating mutations in tooth-related genes in Mysticeti. While there is high variability in tooth counts in odontocetes, with many instances of convergent evolution among living and fossil taxa, all modern clades retain the ability to produce full adult dentition. Mysticetes instead present a variety of inactivating mutations in at least eight tooth- and enamel- related genes. Analyzing the complex inactivation patterns of these genes, I hypothesize that loss of function preceded the complete loss of adult teeth in baleen whales. In Chapter Two, I investigate the anatomical changes that occur in the skull of baleen whales in ontogeny, focusing on the teeth-to-baleen transition. The internal anatomy of 15 specimens of minke and humpback whales was analyzed using CT scanning. I provide qualitative descriptions of the specimens and study skull shape changes using 3D geometric morphometrics (GM) methods. Tooth germs resorb completely just before eruption of the of the baleen from the gums, and they are still present for a brief period along with baleen rudiments. GM analyses show that the rostrum viii progressively grows in length relative to the braincase, with the two parts of the skull showing different patterns of shape and size development. In Chapter Three, I combine developmental data with fossil evidence to directly analyze the connection between ontogeny and evolution of baleen whales using 3D GM methods. I also investigate possible differences in timing of ossification of skull bones between Cetacea and terrestrial artiodactyls. A general acceleration of skull development is likely responsible for modern mysticetes anatomy. The rostrum was the first part of the skull to increase its growth rate, allowing for the evolution of larger buccal cavity needed for bulk filter feeding. These changes in shape were not accompanied by shifts in the ossification sequence, as they appear mostly conserved among all taxa examined and not connected to their feeding adaptations. ix Table of Contents Introduction of the Dissertation p. 1 Chapter One: Evolution of Dentition and Genetic Mechanisms of Tooth Loss in Cetacea p. 5 Introduction p. 5 Materials and methods p. 26 Results p. 30 Discussion p. 43 Conclusions p. 55 Literature Cited p. 58 Chapter Two: Prenatal Development of Skull, Teeth and Baleen in Modern Mysticeti p. 72 Introduction p. 72 Materials and methods p. 83 Results p. 101 Discussion p. 146 Conclusions p. 165 Literature Cited p. 169 Chapter Three: Developmental Basis for the Evolution of Skull Shape and Tooth Loss in Mysticeti p.179 Introduction p. 179 Materials and methods p. 198 Results p. 216 Discussion p. 246 Conclusions p. 263 Literature Cited p. 266 Conclusions of the Dissertation p. 280 Appendices Appendix A: Supplementary Methods/Results for Chapter One p. 285 Appendix B: Supplementary Tables/Figures for Chapter One p. 292 Appendix C: Supplementary Methods/Results for Chapter Two p. 305 Appendix D: Supplementary Tables/Figures for Chapter Two p. 362 Appendix E: Supplementary Methods/Results for Chapter Three p. 375 Appendix F: Supplementary Tables/Figures for Chapter Three p. 394 x List of Figures Chapter One: Figure 1.1 – Convergent loss of enamel and teeth in Mammalia p. 13 Figure 1.2 – Phylogenetic relationships among modern cetacean families p. 16 Figure 1.3 – Phylogeny of living species of mysticetes and their feeding adaptations p. 22 Figure 1.4 – Composite tree of of modern Cetacea with mapped tooth counts p. 31 Figure 1.5 – Dentition evolution in Ziphiidae p. 36 Figure 1.6 – Tooth- and enamel-related gene inactivation in modern Mysticeti p.