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Phylogeny of the Polygalaceae and a Revision of Badiera

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Phylogeny of the Polygalaceae and a Revision of Badiera PHYLOGENY OF THE POLYGALACEAE AND A REVISION OF BADIERA By J. RICHARD ABBOTT 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 J. Richard Abbott 2 ACKNOWLEDGMENTS I thank Ralph Thompson (Berea College) for his assistance, support, training, and mentorship as I first fell in love with botany. I thank Walter Judd for picking up where Ralph left off, guiding me through graduate school. Countless other University of Florida faculty, staff, and other students provided assistance over the years, notably: Norris Williams, Mark Whitten, Kent Perkins, Trudy Lindler, Kaoru Kitajima, Jon Reiskind, Kurt Neubig (to whom Figure 4-33D is dedicated), and Mario Blanco. The Electron Microscopy Core Laboratory at the University of Florida (especially Karen L. Kelley and Kim Backer) was essential for scanning electron microscopy work. I am also grateful for the assistance of Dan Skean (Michigan), Teodoro Clase (Dominican Republic), Brigido Peguero (Dominican Republic), Felix Forest (England), Folkert Aleva (The Netherlands), Bruno Wallnöfer (Austria), Peter Raven (Missouri), Eldis Bécquer (Cuba), Luis Roberto (Cuba), Fredy Archila (Guatemala), German Carnevali (Mexico), Y.C. Chan (Malaysia), Tom Yukawa (Japan), Tom Wendt (Texas), and the curators of all the herbaria that loaned specimens for study. Finally, I cherish Barbara Carlsward for putting up with me all these years. 3 TABLE OF CONTENTS page ACKNOWLEDGMENTS.................................................................................................. 3 LIST OF TABLES............................................................................................................ 6 LIST OF FIGURES.......................................................................................................... 7 LIST OF OBJECTS ....................................................................................................... 10 ABSTRACT ................................................................................................................... 11 CHAPTERS 1 INTRODUCTION .................................................................................................... 13 2 BADIERA SUBRHOMBIFOLIA (POLYGALACEAE), A NEW SPECIES FROM HISPANIOLA, WITH A DISCUSSION OF GENERIC CIRCUMSCRIPTION........... 17 Description of New Species .......................................Error! 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Distribution and Habitat........................................................................................... 31 Phenology............................................................................................................... 33 Additional Specimens Examined ............................................................................ 33 Diagnostic Key to Hispaniolan Species of Badiera ................................................. 37 3 PHYLOGENY AND BIOGEOGRAPHY OF NORTH AMERICAN POLYGALACEAE: NOTES ON THE DISINTEGRATION OF POLYGALA, WITH FOUR NEW GENERA FOR THE FLORA OF NORTH AMERICA.......................... 42 Introduction ............................................................................................................. 42 Materials and Methods............................................................................................ 45 Results.................................................................................................................... 49 General Discussion................................................................................................. 59 Taxonomic Conclusions.......................................................................................... 68 North American Groups and Biogeographic Discussion. ........................................ 76 New Combinations and Changes of Status ............................................................ 87 4 TAXONOMIC REVISION OF BADIERA (POLYGALACEAE): A CARIBBEAN CLADE.................................................................................................................. 110 Introduction ........................................................................................................... 110 Taxonomic History ................................................................................................ 112 Materials and Methods.......................................................................................... 114 Morphology ........................................................................................................... 118 Anatomy................................................................................................................ 129 Pollination Biology and Fruit Dispersal.................................................................. 139 4 Species Concepts................................................................................................. 143 Phylogenetic Relationships within Badiera ........................................................... 144 Habitats and Distribution....................................................................................... 146 Taxonomy ............................................................................................................. 149 5 RESULTS AND CONCLUSIONS ......................................................................... 244 APPENDICES A VOUCHER TAXA USED IN THIS STUDY............................................................ 246 B DISCUSSION OF SPECIES CONCEPTS AND DELIMITATION ISSUES............ 257 List of Unresolved, Potentially Problematic Species Complexes in North America ............................................................................................................. 261 Discussion of Historical Infrageneric Classification of Polygala, in Part Provided as a Guide for Taxon Selection for Future Phylogenetic Analyses .................... 264 C CLADOGRAMS NOT INCLUDED IN THE PRIMARY CHAPTER, WITH FOCUS ON NORTH AMERICAN TAXA ............................................................................ 282 LIST OF REFERENCES ............................................................................................. 283 BIOGRAPHICAL SKETCH.......................................................................................... 291 5 LIST OF TABLES Table page 3-1 DNA primers used in this study. ......................................................................... 91 3-2 Numerical results of phylogenetic analyses in this study.................................... 92 3-3 Absolute increases and percent increases in the number of characters and length with increasing number of taxa. ............................................................... 93 3-4 Node support values........................................................................................... 94 3-5 Bootstrap support values for named clades across all analyses. ....................... 95 4-1 List of taxa, vouchers, and provenance for specimens included in DNA-based phylogenetic analyses of Badiera. .................................................................... 206 4-2 DNA primers used in this study. ....................................................................... 208 6 LIST OF FIGURES Figure page 2-1 Badiera subrhombifolia, vegetative features....................................................... 39 2-2 Badiera subrhombifolia, line drawing.................................................................. 40 2-3 Badiera subrhombifolia, distribution map............................................................ 41 3-1 Generic clades supported across bootstrap and strict consensus analyses. Combined chloroplast, ITS, and combined nuclear and plastid results. ............. 97 3-2 Generic clades -- chloroplast details. Plastid trnL-F spacer and trnL intron results................................................................................................................. 98 3-3 Generic clades with support values and known base chromosome numbers. Based on the combined 179 taxa analyses. ....................................................... 99 3-4 Synopsis of ITS 56 taxa analyses..................................................................... 100 3-5 Synopsis of ITS 109 taxa analyses................................................................... 101 3-6 Synopsis of ITS 179 taxa analyses................................................................... 102 3-7 Synopsis of chloroplast (trnL-F and trnL intron) 56 taxa analyses.................... 104 3-8 Synopsis of chloroplast (trnL-F and trnL intron) 109 taxa analyses.................. 105 3-9 Synopsis of combined (ITS, trnL-F, and trnL intron) 56 taxa analyses. ............ 106 3-10 Synopsis of combined 109 (ITS, trnL-F, and trnL intron) taxa analyses. .......... 107 3-11 Synopsis of combined 179 (ITS, trnL-F, and trnL intron) taxa analyses. .......... 108 4-1 Synopsis of phylogenetic analysis of combined nuclear and plastid data for multiple populations of Badiera, with bootstrap values and branch lengths...... 209 4-2 Flowers............................................................................................................. 210 4-3 Close-up of flower parts, all alcoholized. .......................................................... 211 4-4 Floral features (scanning electron micrographs), Badiera oblongata................ 212 4-5 Alcoholized gynoecia (except I, which is dried), lateral view, with most sepals removed for visibility of nectar disk,
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