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University of Florida Thesis Or Dissertation Formatting SYSTEMATICS AND PHYLOGENOMICS OF THE EREBINAE (LEPIDOPTERA: NOCTUOIDEA, EREBIDAE) By NICHOLAS T. HOMZIAK A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2016 © 2016 Nicholas T. Homziak To: Mary, Jurij, Allie, and Maya, and Nichole ACKNOWLEDGMENTS Foremost, I sincerely thank Dr. Kawahara and Dr. Branham for their support throughout this study. Dr. Kawahara provided assistance in developing this project, provided funding for field expeditions to French Guiana and Rwanda, and helped me complete this project, including reviewing countless drafts of this thesis. My sincere thanks also goes to my co-chair, Dr. Marc Branham for providing a research assistantship for my first year of my Masters research, and for his guidance and understanding as I adjusted to life as a graduate student while working in his lab, in addition to his thoughtful and helpful suggestions regarding the scope of this project. This project would not have been possible without the help of Dr. Jesse Breinholt. He spent many hours helping prepare the crucial sequence data so that it could be analyzed. He was always gladly willing to sit down with me to share his knowledge of molecular phylogenetics. I thank him for his patience and time taken to teach me these methods over many days. I was very fortunate to be able to conduct my research at the McGuire Center for Lepidoptera and Biodiversity, where in addition to the facilities, there are many people who make it such a great place to work. I would like to offer my sincere gratitude to Dr. Lei Xiao for teaching me proper lab protocol and extraction techniques, in addition to keeping the molecular lab in great shape to work in. I would also like to thank Dr. Marianne Espeland for answering numerous questions regarding DNA extraction techniques. My sincere gratitude goes to Samm Epstein and the Kawahara lab volunteers for their help in preparing the wing vouchers of molecular specimens that I used in this project. I would not be able to complete a project such as this without their help. I would also like to thank Geena Hill, Peter Houlihan, Chris Johns, Oliver Keller, 4 Jack Kramer, Matt Moore, David Plotkin, Lary Reeves, and the other Kawahara and Branham lab members. Additional McGuire Center students and staff, including Dale Halbritter, Shinichi Nakahara, Elena Ortiz Acevedo, and Matt Standridge, were very helpful and provided enjoyable company. I also thank Dr. Kelly Miller of the University of New Mexico, who introduced me to Dr. Kawahara and Dr. Branham during my undergraduate studies, and for his significant funding contributions to my fieldwork in Kenya in the summer of 2013. This research would not have been possible without the help from many other institutions both here and abroad. Dr. Dino Martins of Nature Kenya for granted me permission to collect samples for this project during that trip, Dr. Nathan Kabanguka helped procure collecting permits in Rwanda, and Philippe Gaucher and Jerome Chave helped to arrange our fieldwork in French Guiana. Dr. Seth Bybee and Dr. Gavin Svenson graciously allowed me to take part in the collecting expedition to Rwanda they organized in the summer of 2014. My sincere thanks go to the library staff at both the University of Florida, and the Florida Department of Plant Industry. I would not have been able to conduct as extensive a literature review without their help. I thank my family Mary, Jurij, Allie, and Maya for their unwavering support of my studies. From paper editing to pep talks, I am sincerely thankful for their love, support and encouragement with this project, and for my life long interest in Lepidoptera. Special thanks to Nichole -- I am grateful for her support and encouragement during the most challenging moments of this project, sharing kind words, inspiration and great 5 company. I could not ask for a better person to be by my side as I worked on this project. I thank the National Science Foundation for their financial support through the Graduate Research Fellowship Program, funding the second year of my Masters research. 6 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 9 LIST OF FIGURES ........................................................................................................ 10 ABSTRACT ................................................................................................................... 11 CHAPTER 1 INTRODUCTION .................................................................................................... 13 2 REVIEW OF EREBINAE CLASSIFICATION .......................................................... 16 Period 1: Early Classifications (1816-1902) ............................................................ 16 Period 2: Hampson's Division (1902-1984) ............................................................. 19 New Character Systems: Genitalia and Tympanum ............................................... 21 Additional Morphological Character Systems ......................................................... 25 Period 3: Cladistics and Erebine Classification (1984 - Present) ............................ 26 Current Status of the Erebinae ............................................................................... 33 Tribes of the Erebinae............................................................................................. 34 Acantholipini ..................................................................................................... 34 Arytrurini ........................................................................................................... 35 Audeini ............................................................................................................. 35 Catephiini ......................................................................................................... 36 Catocalini .......................................................................................................... 37 Cocytiini ............................................................................................................ 37 Ercheiini............................................................................................................ 38 Erebini .............................................................................................................. 38 Euclidiini ........................................................................................................... 38 Hulodini ............................................................................................................ 40 Hypopyrini ........................................................................................................ 40 Melipotini .......................................................................................................... 40 Ommatophorini ................................................................................................. 42 Omopterini ........................................................................................................ 43 Ophiusini .......................................................................................................... 43 Pandesmini ....................................................................................................... 44 Pericymini ......................................................................................................... 44 Poaphilini .......................................................................................................... 45 Sypnini.............................................................................................................. 47 Thermesiini ....................................................................................................... 47 3 ANCHORED PHYLOGENOMICS RECOVERS A ROBUST PHYLOGENY OF EREBINAE .............................................................................................................. 54 7 Methods .................................................................................................................. 56 Taxon and Gene Sampling ............................................................................... 56 DNA Sequencing and Alignment ...................................................................... 57 Phylogenetic Analyses ..................................................................................... 57 Concatenation analyses. ............................................................................ 58 Species-tree methods ................................................................................ 59 Results .................................................................................................................... 60 Sequence Capture ........................................................................................... 60 Rogue Taxa and Maximum Likelihood ............................................................. 60 Parsimony Analysis .......................................................................................... 63 Coalescent-Based Methods ............................................................................. 63 Hypothesis Testing ........................................................................................... 64 Discussion
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