There and Back Again: Exploring the Roles of Models and Natural History in Macroevolution by Michael C. Grundler A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Ecology and Evolutionary Biology) in The University of Michigan 2020 Doctoral Committee: Associate Professor Daniel L. Rabosky, Chair Assistant Professor Alison R. Davis Rabosky Professor Edward L. Ionides Associate Professor Stephen A. Smith i Michael C. Grundler [email protected] ORCID iD: 0000-0003-0729-6687 © Michael C. Grundler 2020 ii Acknowledgements I thank Bilbo Baggins for use of his evocative phrase there and back again, which is meant to connote the long journey and many helping hands it has taken to see this thesis over the finish line. I thank my advisor, Dr. Dan Rabosky, for his advice and encouragement over many years. Thank you for so patiently helping me along, I learned a lot! I thank my dissertation committee members whose scientific expertise I regrettably did not take advantage of the way I should have but who encouraged and supported me nonetheless: Dr. Stephen Smith, Dr. Alison Davis Rabosky, and Dr. Edward Ionides. They are not responsible for the many shortcomings in this work! My time as a graduate student was immeasurably enriched by many happy hours spent in the field with Dan and Alison and members of their respective labs. To all those who participated in these trips (you know who you are!): thank you, thank you, thank you! When not in the field or in front of a computer terminal, I was privileged to work with the Museum of Zoology’s world-class herpetology collection, and I thank collection manager Greg Schneider for making this possible. And finally, to my family, and to Iris Holmes. I wouldn’t have made it here without you! ii Table of Contents Acknowledgements ............................................................................................................................ ii List of Figures ................................................................................................................................... vii Abstract .............................................................................................................................................. ix Chapter 1 Hello, world ....................................................................................................................... 1 Introduction................................................................................................................................................... 1 Chapter summaries ...................................................................................................................................... 4 Appendix ........................................................................................................................................................ 8 Chapter 2 Macroevolutionary Analysis of Discrete Traits with Rate Heterogeneity ............14 Abstract ........................................................................................................................................................ 14 Introduction................................................................................................................................................. 15 Materials & Methods ................................................................................................................................. 17 Rate-shift model for a binary state character .................................................................................................19 Implementation ............................................................................................................................................20 Simulation study ..........................................................................................................................................21 BAMM analysis...........................................................................................................................................23 Performance assessment ...............................................................................................................................23 iii Results .......................................................................................................................................................... 25 Discussion..................................................................................................................................................... 27 Appendix ...................................................................................................................................................... 31 Chapter 3 Parsimony-based Transition Rate Estimates Outperform Maximum Average Likelihood Estimates for a Two-state Character .........................................................................38 Abstract ........................................................................................................................................................ 38 Introduction................................................................................................................................................. 39 Materials & Methods ................................................................................................................................. 40 General theoretical background ....................................................................................................................40 Simulations ..................................................................................................................................................43 Variation in tempo and mode .......................................................................................................................44 Results .......................................................................................................................................................... 45 Discussion..................................................................................................................................................... 46 Chapter 4 Complex Ecological Phenotypes on Phylogenetic Trees: A Markov Process Model for Comparative Analysis of Multivariate Count Data ..................................................54 Abstract ........................................................................................................................................................ 54 Introduction................................................................................................................................................. 55 Materials & Methods ................................................................................................................................. 59 General overview .........................................................................................................................................59 Model description ........................................................................................................................................60 Interpretation of hyperparameters .................................................................................................................62 Posterior inference .......................................................................................................................................63 Influence of K ..............................................................................................................................................63 iv Implementation ............................................................................................................................................64 Simulation study ..........................................................................................................................................64 Results .......................................................................................................................................................... 67 Discussion..................................................................................................................................................... 68 Summary ...................................................................................................................................................... 71 Appendix ...................................................................................................................................................... 72 Chapter 5 SquamataBase: A Natural History Database and R Package for Comparative Biology of Snake Feeding Habits ....................................................................................................84 Abstract ........................................................................................................................................................ 84 Introduction................................................................................................................................................. 85 Installation ................................................................................................................................................... 87 Data Model .................................................................................................................................................. 88 Filtering Records .......................................................................................................................................