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University of Florida Thesis Or Dissertation THE USE OF MULTIPLE DATA TYPES FOR ELUCIDATING DRIVERS OF SPECIATION IN THE BUTTERFLY GENUS HERMEUPTYCHIA (NYMPHALIDAE: SATYRINAE: EUPTYCHIINA) By DENISE TAN A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2018 © 2018 Denise Tan To my Grandmother and Uncle William ACKNOWLEDGMENTS I am extremely grateful to members of my graduate committee, Dr. Akito Kawahara, Dr. Andrea Lucky, Dr. Colette St. Mary and Dr. Jacqueline Miller for their encouragement and guidance. I would especially like to thank my supervisor, Dr. Keith Willmott for his patience, advice and mentoring throughout my Ph.D. program. I would like to express my gratitude to Dr. Jaret Daniels and Dr. Thomas Emmel, the current and founding directors of the McGuire Center for Lepidoptera and Biodiversity (Florida Museum of Natural History), as well as the Dean of the College of Agricultural and Life Sciences (University of Florida) for allowing me to pursue my Ph.D. degree via a Graduate Research Assistantship and the Grinter Fellowship. I thank also the Office of Graduate Diversity Initiatives for providing tuition assistance during my final semester via the Supplemental Retention Scholarship. I thank the National Science Foundation (Grant No. DEB-1256742 and DEB- 1416127, Richard Glider Graduate School (American Museum of Natural History; Theodore Roosevelt Memorial Fund), Dr. Norm Leppla, the Entomology and Nematology Student Organisation (ENSO Travel Grant) and Dr. Rudolf Meier (National University of Singapore) for funding my research, fieldwork and trips for professional development. I am deeply appreciative of Dr. Nick Grishin (University of Texas Southwestern Medical Center) and members of his lab, Qian Cong, Wenlin Li and Jinhui Shen, as well as Dr. Frank Rheindt (National University of Singapore) and members of his research group, Keren Sadanandan, Elize Ng and Nathaniel Ng, for so graciously hosting me at their institutions and for generously sharing their knowledge and expertise. 4 Additionally, I thank Dr. Andrew Warren for advice on collection sites and techniques. For assistance pertaining to the rearing of Hermeuptychia butterflies, as well as the generous provision of laboratory space, I am grateful to Dr. Jaret Daniels, Dr. Andrei Sourakov and Matthew Standridge. I am also appreciative of Stacey Huber and Jonathan Bremer for their guidance on the usage of the imaging systems found at the McGuire Center for Lepidoptera and Biodiversity. I would also like to acknowledge the incredible contributions of my undergraduate assistants and volunteers, Anamaria Parus, Michelle Dunbar, Mario Abels, Alana Pacheco and Addison Eggert – Thank you for your enthusiasm and hard work! On a more personal note, I would like to express my deepest appreciation to Marianne Espeland, Elena Ortiz, Lei Xiao, Jose Martinez and all my brilliant colleagues at McGuire Center for Lepidoptera and Biodiversity and the Department of Entomology and Nematology. It is unbelievably inspiring to be able to work alongside like-minded individuals who devote themselves so entirely to their vocations. To Qinwen Xia, Chao Chen, Kayla Chen, Mengyi Gu, Chia-Yin Tsai, Yao Xu, Claudia Pagano, Kok Ben Toh, Gaurav Vaidya, Matthew Standridge, Kristin Rossetti and members of SEAEC, you have my heartfelt gratitude for your friendship and for making Gainesville feel like home for the past four and a half years. To Heather Chan and Leonard Chan, thank you for sharing my love for animals (especially insects!) and Disney movies. I look forward to learning, exploring and laughing with you for many years to come. The unwavering support I receive from my friends and family is why I feel empowered to see the world and cultivate my passions. So, to my parents, David Tan 5 and Brenda Ho, Bernice Tan, Nathaniel Ng and Siti Yaakub, I honestly can’t thank you enough for embracing all my eccentricities and being there every step of the way. Lastly, I am proud to dedicate this dissertation to two people whose absence has been deeply felt, my grandmother, Ming Geok Chin and uncle, William Ho. 6 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES .......................................................................................................... 10 LIST OF FIGURES ........................................................................................................ 11 LIST OF OBJECTS ....................................................................................................... 14 LIST OF ABBREVIATIONS ........................................................................................... 15 ABSTRACT ................................................................................................................... 18 CHAPTER 1 INTRODUCTION .................................................................................................... 20 The Genus Hermeuptychia ..................................................................................... 21 Research Aims ....................................................................................................... 25 2 USING COI-BASED SPECIES DELIMITATION METHODS TO ESTIMATE DIVERSITY AND GENERATE PRELIMINARY SPECIES HYPOTHESES ............. 30 Materials and Methods............................................................................................ 33 Sampling .......................................................................................................... 33 DNA Extraction, Amplification and Sequencing ................................................ 33 Inferring Phylogenetic Relationships ................................................................ 34 Species Delineation Based on Genetic Variation ............................................. 36 Results .................................................................................................................... 38 Molecular Phylogenetic Analyses ..................................................................... 38 Defining Putative Species Boundaries ............................................................. 39 Discussion .............................................................................................................. 41 Updated Molecular Phylogeny .......................................................................... 41 Preliminary Species Diversity Estimates .......................................................... 42 3 USING GENOME-WIDE, SINGLE-NUCLEOTIDE POLYMORPHISMS TO RIGOROUSLY INVESTIGATE PHYLOGENETIC RELATIONSHIPS AND SPECIES LIMITS IN ECUADORIAN HERMEUPTYCHIA ...................................... 49 Materials and Methods............................................................................................ 53 Hermeuptychia Genome Assembly .................................................................. 53 Sampling and DNA Extraction .......................................................................... 54 Double-Digest RAD-Seq Library Preparation ................................................... 55 Pipeline for SNP-Based Analyses .................................................................... 55 Quality filtering and SNP calling ................................................................. 55 7 Investigating population substructure ......................................................... 57 Inferring species tree from biallelic markers ............................................... 58 Pipeline Resulting in Supermatrix of ddRAD-Seq Loci ..................................... 59 Results .................................................................................................................... 60 Genetic Structure within Putative Species ........................................................ 60 ‘Atalanta’ group .......................................................................................... 61 ‘Harmonia’ group ........................................................................................ 62 ‘Gisella’ and ‘Clara’ groups ........................................................................ 62 Species 3 group ......................................................................................... 63 ‘Maimoune’ and ‘Hermes’ groups ............................................................... 63 Phylogeny Inferred from Genome-Wide Variation ............................................ 64 Discussion .............................................................................................................. 65 Investigating Species Limits with ddRAD-Seq .................................................. 65 Phylogenomic Relationships across Ecuadorian Hermeuptychia ..................... 68 4 RE-SURVEY OF WING AND MALE GENITALIA MORPHOLOGY IN ECUADORIAN HERMEUPTYCHIA ........................................................................ 95 Methods .................................................................................................................. 97 Ventral Wing Images ........................................................................................ 97 Male Genitalia Images ...................................................................................... 97 Results .................................................................................................................... 98 ‘Atalanta’ Group ...............................................................................................
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