University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2019 The Formation of Diversity - The Role of Environment and Biogeography in Dung Beetle Species Richness, and the Adequacy of Current Diversification Models Orlando Manuel Schwery University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Schwery, Orlando Manuel, "The Formation of Diversity - The Role of Environment and Biogeography in Dung Beetle Species Richness, and the Adequacy of Current Diversification Models. " PhD diss., University of Tennessee, 2019. https://trace.tennessee.edu/utk_graddiss/5724 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Orlando Manuel Schwery entitled "The Formation of Diversity - The Role of Environment and Biogeography in Dung Beetle Species Richness, and the Adequacy of Current Diversification Models." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Ecology and Evolutionary Biology. Brian C. O'Meara, Major Professor We have read this dissertation and recommend its acceptance: James Fordyce, Kimberly Sheldon, Colin Sumrall Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) The Formation of Diversity - The Role of Environment and Biogeography in Dung Beetle Species Richness, and the Adequacy of Current Diversification Models: A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Orlando Manuel Schwery December 2019 Copyright © 2019 by Orlando Schwery All rights reserved. ii DEDICATION I dedicate my work to my parents, René and Carmen Schwery for their continuous support throughout my life, and the sacrifice it involved from them, even when my path became more and more unrelatable to what they knew. To my childhood mentor, and to my primary school teacher, Paul “Böbi” Weber, and Ernst Giger who sparked my love for nature and books, supported my interest to gain knowledge about the world around me, and supplied me with endless opportunities to do so. And finally, to my high school teacher, Bruno Koch who taught me to have the hold myself to the highest standards, be critical of myself and others and abhor complacence, and to always strive to know and achieve more. iii ACKNOWLEDGEMENTS I owe many thanks to my advisor Brian O’Meara, for his steady support from the first inquiry email on, and throughout the following graduate school years. He always provided a good combination of criticism and encouragement, and went to great lengths to be available for questions and concerns of mine. Apart from sharing his knowledge and expertise to advise on my science, he also readily spent time discussing many other concerns, be it from adjusting to a new culture in the beginning, own and general graduate student concerns, to discussing private, academic, or global issues on my mind. This, together with his determination to advocate on behalf of me while holding me to high standards make him one of the most supportive advisors to have. Furthermore, I want to thank my dissertation committee for their support and their critical thoughts throughout the process. More specifically: Jim Fordyce for his advice on sequencing and statistics; Kimberly Sheldon for inspiring me to pick dung beetles as my empirical study system and for taking me to the field to get acquainted with them; and Colin Sumrall for providing the paleontological perspective on diversification, and support in writing. I thank the various members of the O’Meara lab, first and foremost Jeremy Beaulieu, for various inputs and advice along the way, and particularly for his help in letting me recognize the overarching story that unifies my dissertation. I thank my fellow grad students Sam Borstein, Katie Massana, and Jen Bosco, and Rosana Zenil-Ferguson for their comradery and shared insights along the path to graduation. Further, I thank Luna Sanchez-Reyes for various helpful comments on diversification models, phylogenetics resources, and for being a great conference travel companion; Nick Matzke for his advice on biogeography in general and BioGeoBEARS in particular; Dave Bapst and Michelle Lawing for their advice on paleontological problems; Sergei Tarasov for his help in the lab, and for sharing his knowledge and experience on dung beetle evolution; and finally Sandy Kawano, Nate Jackson, Dominic Evangelista, Tony Jhwueng, Megan Rua, and Jodie Wiggins, for stimulating discussions and support of all kinds. I thank the members of the department of Ecology and Evolutionary Biology at UT for providing an environment that supported my progress, first and foremost all my grad school friends, especially Angela Chuang for her support and help in staying sane during the numerous challenges along the way to graduation. I further particularly thank Veronica Brown, Marisol Sanchez, Todd Pierson, Hailee Korotkin, Claire Winfrey, and Jess Dreyer for all their help and advice with sequencing and other molecular lab issues. I thank Elizabeth Johnson, Joel Corush, and Dan Simberloff their time discussing various ideas; Athmanathan Senthilnathan and Lucas Santana-Souza for helping me understand modified graph Laplacians; Jordan Bush for sharing her polygon code; Maggie Mamantov for being a field-companion and for sharing specimens; and Nina Fefferman for modeling insights and for taking the time to help me better understand academic careers and negotiations in the process of pursuing them. iv For Chapter I, I additionally thank Frederik Matsen IV and two anonymous reviewers for well- considered criticism to improve the associated manuscript, Brian Looney and Sam Borstein for beta testing, and the members of the Tank lab, Arne Mooers, Karen Cranston, Bruce Cochrane and Daniel Gates for great ideas on increasing the usefulness of the MonoPhy R-package. For Chapters II and III, I additionally want to thank Matt Pennell, Dean Anderson, and Emma Goldberg for helpful discussions and comments. Finally, I thank the Society of Systematic Biologists, the Systematics Association, the department of Ecology and Evolutionary Biology at UT, their grad student association GREBE, and the Graduate Student Senate, for their financial support towards my projects and travel. v ABSTRACT Model based approaches to study the driving factors behind diversification have become increasingly popular, but in the recent years, various weaknesses of these models have received increased attention. One way to ensure those issues do not affect one’s inferences, is to test a model’s adequacy as a way to judge its suitability to describe the data in an absolute sense. Here, I implement a simple adequacy test for diversification models in the R package BoskR, using metrics for tree shape. I demonstrate the method’s ability to distinguish trees simulated under different models, and then use it to test the adequacy of a range of birth-death diversification models for a large set of empirical phylogenies. I find that while most models are adequate to describe a majority of the empirical trees, a few trees cannot be described by any of those models. Furthermore, the best fitting of a set of models may not always be adequate, highlighting the practical use of incorporating model adequacy tests in the standard procedures for diversification studies. For the empirical parts of my dissertation, I investigate the diversification and biogeography of dung beetles. It has been hypothesized that their origin and distribution are either the result of Gondwanan vicariance, or out-of-Africa dispersal. Furthermore, dung beetle diversification is thought to have been affected by mammals – particularly large herds of herbivores inhabiting the vast grasslands after the Miocene – and potentially also by non-avian dinosaurs, if dinosaur dung-adapted beetles were affected by the K-Pg extinction of their dung producers. Crucial to answering these questions is to know whether dung beetles are of Mesozoic or Cenozoic origin. Thus, I construct a large dated phylogeny, and use model-based inference to estimate their ancestral area, and the influence of range evolution and diversity of dung producers on their diversification rates. My results suggest that dung beetles originated in Gondwana during the Mesozoic, but it remains unclear to which extent range evolution affected diversification. While adaptation to dinosaur dung and subsequent co-extinction are plausible, the available data cannot support a radiation with the rise of grasslands and herds of herbivores. vi TABLE OF CONTENTS INTRODUCTION ............................................................................................................. 1 References ..................................................................................................................... 3 CHAPTER I MONOPHY: A SIMPLE PACKAGE TO FIND AND VISUALIZE MONOPHYLY ISSUES ...........................................................................................................................