Advances in Quantitative Methods in Dinosaur Palaeobiology: A Case Study in Horned Dinosaur Evolution by Caleb Marshall Brown A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Graduate Department of Ecology and Evolutionary Biology University of Toronto © Copyright by Caleb Marshall Brown 2013 Advances in Quantitative Methods in Dinosaur Palaeobiology: A Case Study in Horned Dinosaur Evolution Caleb Marshall Brown Doctor of Philosophy Graduate Department of Ecology and Evolutionary Biology University of Toronto 2013 Abstract Discerning modes and rates of biological evolution and speciation are some of the primary objectives of evolutionary biology. Much palaeobiological work has focused on developing robust methods for testing and fitting evolutionary models to samples of fossils across a stratigraphic or temporal axis, with most analyses centering on marine invertebrates. Recent extensive sampling of dinosaur deposits now allows for testing of evolutionary modes in this clade, a first for large-bodied terrestrial vertebrates. Within dinosaur palaeobiology, the relative roles of anagenesis and cladogenesis in diversification, particularly for horned dinosaurs, are hotly debated. Due to their large sample sizes, well-documented stratigraphic positions, highly diagnostic ornamentation, and monodominant bonebeds (representing populations), centrosaurine dinosaurs from the Belly River Group of Alberta make an ideal model system for testing the predictions of these two divergent evolutionary modes. Despite this unparalleled fossil record, it (as well as most fossil records) is limited by missing data, small sample size, taphonomic biases, and stratigraphic error. In this thesis, I ii present case studies that attempt to quantify and better understand these limitations, and inform best practices for overcoming them. The first four chapters, utilizing data sets for crocodilians (extant archosaurs) and a model geological system (upper Belly River Group), allow for a better- constrained quantitative evolutionary analysis of the Belly River Group centrosaurines in chapter five. Correlations and time-series analyses of morphology and stratigraphic position of Centrosaurus apertus and Styracosaurus albertensis are used to test for directional trends and evolutionary model fitting. Evolutionary results are robust to multiple simulations of stratigraphic uncertainty, and overlap between the taxa depends on a single locality. Results find no support for anagenesis, and rather are consistent with taxonomic turnover due to punctuated evolutionary events or, more likely, ecological replacement due to habitat tracking. iii Acknowledgments Firstly I would like to thank my supervisors David Evans and Robert Reisz. David provided a research lab full of like-minded researchers always ready to collaborate on projects, work on developing new ideas or challenge existing ones. He constantly pushed the idea of hypothesis testing in palaeobiology, a powerful tool that has greatly shaped my research program. Robert provided the needed experience and ability to see the big picture in seemingly trivial details. Both supervisors also gave me enough freedom to pursue productive side projects along with my thesis research. Michael Ryan has been a longtime mentor and served on both the thesis and appraisal committee. His extensive experience with all things Centrosaurus was of great asset to the development of the ideas in the thesis. The other members of my thesis and appraisal committee, Peter Dodson, Don Jackson, Deborah McLennan, Mary Silcox, and Denis Walsh, provided encouragement and support, and poignantly illustrated gaps in my knowledge when necessary. David Eberth provided more than one crash course in sedimentology, was the most qualified ‘field assistant’ I will ever have, and was always willing to challenge my ideas as devils advocate. The research and technical crew at the Royal Ontario Museum, both staff and students, provided an amazing environment to grow as a scientist and person. Kevin Seymour was the man responsible for making sure things kept running and took care of numerous administrative hoops, many of which I am sure I am still unaware of. Ian Morrison, Brian Iwama, Shino Sugimoto, Peter Fenton, Janet Waddington, and Jean-Bernard Caron provided a positive research and social environment at the museum. David’s lab (Nicolás Campione, Collin VanBuren, Chris McGarrity, iv Derek Larson, Kirstin Brink, Kentaro Chiba, Ryan Schott, Jessica Hawthorn, and Matt Vavrek), were great collaborators, editors, debaters, and friends. Together they provided an immense amount of feedback and proofreading of my thesis and papers. Jessica Arbour, Nicolás Campione, and Matt Vavrek provided assistance with coding in R. Research discussions with Don Brinkman, Phil Currie, Don Henderson, Jordan Mallon, Tony Russell, Darren Tanke, François Terrien, and Jessica Theodor proved fruitful and greatly benefited the thesis. The specimens utilized for this thesis are housed a numerous institutions across North America and Europe, and access to these specimens is acknowledged in the respective chapters of the thesis. The staff of the Royal Tyrrell Museum and Royal Ontario Museum deserve special mention for their long history of openness and assistance with my research, and both feel like my academic homes. None of this research could have been possible without the collection and research of generations of scientists who have come before me. I am grateful for the financial support that I have been fortunate to receive including: NSERC CGS D - Alexander Graham Bell Canada Graduate Scholarship, Ontario Graduate Scholarship, numerous EEB and University of Toronto fellowships, and funding from the Dinosaur Research Institute and Jurassic Foundation. Finally I would like to family and friends, for their constant support during my thesis. My parents Jim and Deborah Brown encouraged my interest in science and natural history, and without their support I would not have pursued research. Most of all, I thank my partner, Lorna O’Brien, for her tireless support and encouragement. She has proofread and formatted countless manuscripts, listened patiently to all my crazy ideas, and put up with the stress of finishing not only one, but two theses. v Table of Contents ABSTRACT........................................................................................................................ ii ACKNOWLEDGMENTS ................................................................................................. iv TABLE OF CONTENTS................................................................................................... vi LIST OF TABLES........................................................................................................... xvi LIST OF FIGURES ......................................................................................................... xix LIST OF APPENDICES................................................................................................ xxvi GENERAL INTRODUCTION.................................................................................... xxviii Thesis Design and Overview..................................................................................xxx Chapter One............................................................................................................xxx Chapter Two ........................................................................................................ xxxii Chapter Three ..................................................................................................... xxxiii Chapter Four.........................................................................................................xxxv Chapter Five ....................................................................................................... xxxvi Contributions to Co-authored Chapters............................................................. xxxvii References ......................................................................................................... xxxvii CHAPTER 1: Testing of the Effect of Missing Data Estimation and Distribution in Morphometric Multivariate Data Analyses .........................................................................1 Abstract.......................................................................................................................2 Introduction ................................................................................................................3 Institutional Abbreviations .............................................................................6 vi Materials .....................................................................................................................6 Variables.........................................................................................................7 Methods ......................................................................................................................8 Missing Data Input .........................................................................................8 Random .................................................................................................9 Anatomic Bias.......................................................................................9 Taxonomic Bias...................................................................................12 Missing Data Analysis..................................................................................13