PHYLOGENY RECONSTRUCTION of PERIPLOCOIDEAE (APOCYNACEAE) BASED on MORPHOLOGICAL and MOLECULAR CHARACTERS and a TAXONOMIC REVISION of Decalepis
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PHYLOGENY RECONSTRUCTION OF PERIPLOCOIDEAE (APOCYNACEAE) BASED ON MORPHOLOGICAL AND MOLECULAR CHARACTERS AND A TAXONOMIC REVISION OF Decalepis By GRETCHEN M. IONTA 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 2009 1 © 2009 Gretchen M. Ionta 2 To Kurt 3 ACKNOWLEDGMENTS I thank my advisor, Walter Judd, for his support, encouragement, patience and generosity throughout my PhD program. I also thank my present and past committee members, Norris Williams, Pamela Soltis, and Jonathan Reiskind for their advice and guidance, and Timothy Martin for kindly stepping in as an external committee member at the last minute. Special thanks go to former committee member Mary Endress, who welcomed me into her home and laboratory, introduced me to the community of Apocynaceae researchers, shared her taxonomic expertise and provided essential plant material. Throughout the course of my doctoral degree, W. Mark Whitten provided invaluable support in the molecular lab and insightful advice and guidance. I thank the current and former members and staff of FLAS Herbarium, the U.F. Botany Department, the Soltis Lab, and the Electron Microscopy Core Laboratory for their assistance, friendship and encouragement, in particular Richard Abbott, Barbara Carlsward, Paul Corogin, Barry Davis, Lorena Endara, Marc Frank, Grant Godden, Kim Holloway, Cathleen Kabat, Karen Kelley, Kim Backer-Kelley, Trudy Lindler, Kurt Neubig, Christine Mella, Kent Perkins, and Pamela Williams. This research would not have been possible without the generosity of numerous Apocynaceae researchers who provided expertise, guidance and plant material, including Lucille Allorge, Peter Bruyns, Laure Civeyrel, Sigrid Liede, Tatyana Livshultz, Ulrich Meve, and David Middleton. I would particularly like to thank Johan Venter, Andor Venter, and Lize Joubert for their invaluable assistance and friendship during my visit to South Africa. I thank the curators and staff of A, BRI, K, L, MO, P, US, and Z. Last, but certainly not least, I would like to thank my family and friends for their endless patience, support and encouragement. Funding for this research was provided by grants from the Botanical Society of America (BSA), the American Society of Plant Taxonomists (ASPT) and the Deep Time Research 4 Coordination Network. Norris Williams generously provided access to the supplies and equipment in his molecular laboratory. 5 TABLE OF CONTENTS page ACKNOWLEDGMENTS.................................................................................................................... 4 LIST OF TABLES................................................................................................................................ 9 LIST OF FIGURES ............................................................................................................................ 10 ABSTRACT ........................................................................................................................................ 12 CHAPTER 1 GENERAL INTRODUCTION .................................................................................................. 14 2 PHYLOGENETIC RELATIONSHIPS IN PERIPLOCOIDEAE (APOCYNACEAE S.L.) AND INSIGHTS INTO THE ORIGIN OF POLLINIA ................................................. 18 Introduction ................................................................................................................................. 18 Materials and Methods ................................................................................................................ 21 Taxon Sampling ................................................................................................................... 21 PCR Amplification and DNA Sequencing ......................................................................... 22 Phylogenetic Analyses ........................................................................................................ 23 Results .......................................................................................................................................... 24 ITS ........................................................................................................................................ 24 Plastid Regions..................................................................................................................... 25 Total Evidence ..................................................................................................................... 26 Morphology .......................................................................................................................... 27 Discussion .................................................................................................................................... 28 Phyllanthera – Sister to the Rest of Periplocoideae? ........................................................ 28 A Grooved Translator Clade ............................................................................................... 29 An Asian Pollinial Clade ..................................................................................................... 30 A Malagasy Clade? .............................................................................................................. 32 Monophyly of Genera and the Genus Periploca ............................................................... 32 Omphalogonus calophyllus-Periploca nigrescens ............................................................ 33 A Polyphyletic Finlaysonia................................................................................................. 34 Raphionacme lobulata Renders Raphionacme Non-monophyletic.................................. 35 Evidence for Multiple Origins of Pollinia .......................................................................... 35 General Conclusions ................................................................................................................... 37 3 SYSTEMATICS OF PERIPLOCOIDEAE (APOCYNACEAE) BASED ON MOLECULAR AND MORPHOLOGICAL CHARACTERS ................................................ 45 Introduction ................................................................................................................................. 45 Materials and Methods ................................................................................................................ 49 Taxon Sampling for Molecular Analyses........................................................................... 49 DNA Isolation, Amplification and Sequencing ................................................................. 50 6 Morphological Taxon Sampling and Characters ............................................................... 51 Sequence Alignment and Phylogenetic Analysis .............................................................. 51 Alignment ..................................................................................................................... 51 Data partitions .............................................................................................................. 52 Congruence ................................................................................................................... 52 Parsimony ..................................................................................................................... 53 Maximum likelihood .................................................................................................... 53 Results .......................................................................................................................................... 54 Sequence Characteristics ..................................................................................................... 54 Parsimony Analyses ............................................................................................................ 54 ITS ................................................................................................................................. 54 Plastid regions .............................................................................................................. 55 DNA combined............................................................................................................. 56 Morphology .................................................................................................................. 57 Molecular and morphological data combined ............................................................ 58 Maxiumum Likelihood Analyses ....................................................................................... 60 Discussion .................................................................................................................................... 61 Effect of Missing Data......................................................................................................... 61 Position of Phyllanthera...................................................................................................... 62 Clades of Interest ................................................................................................................. 62 Grooved translator clade .............................................................................................. 62 Asian pollinial clade....................................................................................................