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University of Florida Thesis Or Dissertation Formatting Template EVOLUTION AND BIOGEOGRAPHY OF CAMPANULACEAE: FROM GLOBAL PATTERNS TO SHALLOW, SPECIES-LEVEL PROCESSES IN THE MEDITERRANEAN BASIN By ANDREW ALAN CROWL 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 2016 © 2016 Andrew Alan Crowl To SED, for giving me the confidence to complete this while constantly reminding me to not take it too seriously. “It was the tension between these two poles - a restless idealism on one hand and a sense of impending doom on the other - that kept me going.” HS Thompson ACKNOWLEDGMENTS First, my deepest gratitude to my friend and supervisor, Dr. Nico Cellinese, who taught me everything I know about phylogenetics, biogeography, and “species” – and to always use quotes when talking about them. Her knowledge and supervision made this work possible...and enjoyable. Also many thanks to my committee: Dr. Pam Soltis, Dr. David Reed, and Dr. Matthew Smith. Our many insightful discussions were integral to my successful completion of this dissertation. Thanks to my mom for her green thumb and a childhood introduction to botany, my dad for passing on his science genes, Gregg (DOM) Stull for all the ‘late night discussions’, Heather-Rose Kates and Rebecca Stubbs for the soft discussions – scientific and otherwise, Volta and The Bull for providing a big, wooden table and cold beverages while writing, Benjamin Crowl, Michael Dudley, and Thomas Wondergem for help with the grueling fieldwork, Michael Chester and Clayton Visger for help with chromosome counts and niche modeling, Dr. Walter Judd for his help with morphological work, Dr. Matthew Gitzendanner for always having an answer to the many, many random questions I had throughout the years, my many collaborators and co-authors around the world for their helpful manuscript edits and discussions, and finally, my amazing wife, Susan Dalton, for putting up with me through all of this, listening to me ramble about DNA and bellflowers, following me through the Mediterranean, and believing in me. Financial support for this research was provided by a Doctoral Dissertation Improvement Grant from the National Science Foundation (DEB-1501676), with additional funding from the Botanical Society of America, Society of Systematic Biologists, and American Society of Plant Taxonomists. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 9 LIST OF FIGURES ........................................................................................................ 10 ABSTRACT ................................................................................................................... 11 CHAPTER 1 OVERVIEW OF CAMPANULACEAE AND INTRODUCTORY REMARKS ............. 13 2 A GLOBAL PERSPECTIVE ON CAMPANULACEAE: BIOGEOGRAPHIC, GENOMIC, AND FLORAL EVOLUTION ................................................................. 15 Introduction ............................................................................................................. 15 Phylogenetics ................................................................................................... 16 Biogeography ................................................................................................... 17 Genome Evolution ............................................................................................ 18 Secondary Pollen Presentation ........................................................................ 18 Summary .......................................................................................................... 20 Methods .................................................................................................................. 20 Sampling .......................................................................................................... 20 Phylogenetic Analyses ..................................................................................... 21 Character Reconstruction ................................................................................. 22 Divergence Dating ............................................................................................ 23 Biogeographic Analyses ................................................................................... 24 Genome Evolution ............................................................................................ 25 Results .................................................................................................................... 26 Phylogenetics ................................................................................................... 26 Divergence Dating ............................................................................................ 27 Character Reconstruction ................................................................................. 28 Biogeographic Analyses ................................................................................... 29 Genome Evolution ............................................................................................ 29 Discussion .............................................................................................................. 30 Phylogenetics ................................................................................................... 30 Floral Evolution ................................................................................................. 31 Biogeography ................................................................................................... 32 Genome Evolution ............................................................................................ 36 Conclusion ........................................................................................................ 39 3 PHYLOGENY OF CAMPANULOIDEAE (CAMPANULACEAE) WITH EMPHASIS ON THE UTILITY OF NUCLEAR PENTATRICOPEPTIDE REPEAT (PPR) GENES ........................................................................................................ 46 5 Introduction ............................................................................................................. 46 Methods .................................................................................................................. 50 Taxon Sampling, Amplification, & Sequencing ................................................. 50 Phylogenetic Analyses ..................................................................................... 52 Dating Analyses ............................................................................................... 53 Results And Discussion .......................................................................................... 55 Phylogenetic Resolution ................................................................................... 56 Plastid loci .................................................................................................. 56 Pentatricopeptide repeat (PPR) loci ........................................................... 60 Combined plastid and PPR loci .................................................................. 62 Plastid–Nuclear Incongruence .......................................................................... 65 Final Conclusions ................................................................................................... 68 4 EVOLUTION AND BIOGEOGRAPHY OF THE ENDEMIC ROUCELA COMPLEX (CAMPANULACEAE: CAMPANULA) IN THE EASTERN MEDITERRANEAN ................................................................................................. 76 Introduction ............................................................................................................. 76 Oceanic and Continental Islands ...................................................................... 77 Geologic and Climatic History of the Eastern Mediterranean Basin ................. 77 Roucela Complex ............................................................................................. 79 Summary .......................................................................................................... 80 Materials and Methods............................................................................................ 81 Taxon Sampling and DNA Amplification ........................................................... 81 Phylogenetic Analysis ...................................................................................... 81 Species Tree .................................................................................................... 82 Molecular Dating .............................................................................................. 83 Biogeographic Analysis .................................................................................... 84 Ecological Niche Modeling ............................................................................... 85 Diversification ................................................................................................... 86 Results .................................................................................................................... 88 Phylogenetic Analyses ..................................................................................... 88 Plastid .......................................................................................................
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