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Cladistic Analysis PHYLOGENY AND CHARACTER EVOLUTION IN THE BLAKEEAE (MELASTOMATACEAE) By DARIN S. PENNEYS 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 2007 1 © 2007 Darin S. Penneys 2 To my family 3 ACKNOWLEDGMENTS I acknowledge the assistance of numerous people and organizations that have contributed to the success of this investigation. First and foremost, I thank my advisor and committee chairperson, Walter S. Judd, for his exceptional guidance throughout my graduate career. Frank Almeda has generously shared his wisdom and insights regarding Melastomataceae systematics. Norris H. Williams and W. Mark Whitten provided assistance with DNA sequencing. Doug E. Soltis and Jon Reiskind are acknowledged for their helpful comments. Amongst the people who assisted with fieldwork, or who provided collections, a special gratitude is extended to Diana Férnandez who accompanied me in the field in Ecuador, and later arranged for the liberation from governmental control the entire set of collections from that expeditition. Maria-Eugenia Morales-P. is gratefully acknowledged for sharing collections of Colombian melastomes, and also for her ongoing collaborations. Ricardo Kriebel and Frank Almeda for providing material of Blakea venusta and T. gerardoana; Bill Haber for bringing me to material of T. brenesii; Fabian Michelangeli for B. schlimii; Barry Hammel for his help in finding B. austin-smithii on Cerro Chompipe; J. Richard Abbott for T. calycularis; Chris Baraloto for collections of Bellucia, Henriettea, Loreya, and Votomita; and Judy Chen for Astronia and Pternandra. Mario Blanco assisted with fieldwork in Costa Rica and Panamá. Fabian Michelangeli and the Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies (NYBG) provided laboratory support at an early stage in this study. Matt Gitzendanner assisted with instruction on the use of GARLI. Organizations that provided critical support and collection permits include in Costa Rica, Javier Guevara and the Ministerio del Ambiente y Energiá; the Bosque Eterno de los Niños for permission to collect in their biological stations, San Gerardo and Pocosol; and the Las Cruces Biological Station. In Panamá, the Autoridad Nacional del Ambiente for collecting permits, and 4 Andres Maduro for assisting with permits and generously sharing his home at the Finca Dracula. In Ecuador, the Ministerio del Ambiente, Hugo Navarette, Diana Férnandez, Florian Werner, Nestor León, Jaime Jaramillo, Fundación Jocotoco, Fundación Jatun Sacha, and the San Francisco Biological Station. Funding was generously provided by the National Science Foundation, Doctoral Dissertation Improvement Grant DEB: 0508582, the American Society of Plant Taxonomists, and the Botanical Society of America. The staff of the University of Florida Herbarium (FLAS), especially the careful curatorial work done by Kent Perkins and Trudy Linder, is gratefully acknowledged. The curators and staff at CAS, INBio, LOJA, MO, NY, PMA, QCA, QCNE, STRI, and US are all acknowledged; MO, NY, and US in particular for providing specimens on loan. 5 TABLE OF CONTENTS page ACKNOWLEDGMENTS ...............................................................................................................4 LIST OF TABLES...........................................................................................................................9 LIST OF FIGURES .......................................................................................................................10 ABSTRACT...................................................................................................................................13 CHAPTER 1 INTRODUCTION ..................................................................................................................14 2 MORPHOLOGICAL CLADISTIC ANALYSIS OF THE BLAKEEAE (MELASTOMATACEAE).....................................................................................................20 Introduction.............................................................................................................................20 Materials and Methods ...........................................................................................................20 Taxon Sampling...............................................................................................................20 Plant Materials.................................................................................................................21 Phylogenetic Analysis .....................................................................................................21 Character Selection and Coding ......................................................................................22 Characters........................................................................................................................23 Results.....................................................................................................................................40 Analysis of Qualitative Characters..................................................................................40 Analysis of Quantitative Characters................................................................................41 Analysis of All Morphological Characters......................................................................42 Discussion...............................................................................................................................43 Support for Blakeeae .......................................................................................................43 Chalybea and Huilaea .....................................................................................................44 Monophyly of the Blakea + Topobea Clade....................................................................46 Anther Morphology and Generic Limits of Blakea and Topobea...................................47 Character Evolution: Noteworthy Examples...................................................................50 Growth habit and form .............................................................................................51 Formicaria and ant associations .............................................................................52 Acarodomatia and mite associations ......................................................................54 Stipules....................................................................................................................56 Leaf venation ..........................................................................................................57 Encapsulating floral bracts ......................................................................................57 Fused bracts .............................................................................................................58 Bracts and pubescence .............................................................................................59 Calyx ........................................................................................................................60 Corolla......................................................................................................................61 Androecium..............................................................................................................62 Gynoecium ...............................................................................................................66 6 Noteworthy Clades ..........................................................................................................68 The fused-bract clade .............................................................................................68 Topobea parasitica complex ...................................................................................69 Rodent-pollinated clade ..........................................................................................71 Hexandrous Topobea................................................................................................73 3 MOLECULAR AND COMBINED MOLECULAR AND MORPHOLOGICAL CLADISTIC ANALYSES OF THE BLAKEEAE (MELASTOMATACEAE)..................108 Introduction...........................................................................................................................108 Materials and Methods .........................................................................................................108 Plant Material ................................................................................................................108 Morphological Data.......................................................................................................109 DNA Extraction.............................................................................................................110 DNA Regions and Primers ............................................................................................110 Amplification.................................................................................................................111 Sequencing ....................................................................................................................111 Sequence Editing and Alignment ..................................................................................111 Cladistic Analysis..........................................................................................................112
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