The Molecular and Morphological Systematics of Subfamily Epidendroideae (Orchidaceae)
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Louisiana State University LSU Digital Commons LSU Historical Dissertations and Theses Graduate School 1995 The olecM ular and Morphological Systematics of Subfamily Epidendroideae (Orchidaceae). Malcolm Ray Neyland Louisiana State University and Agricultural & Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_disstheses Recommended Citation Neyland, Malcolm Ray, "The oM lecular and Morphological Systematics of Subfamily Epidendroideae (Orchidaceae)." (1995). LSU Historical Dissertations and Theses. 6040. https://digitalcommons.lsu.edu/gradschool_disstheses/6040 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Historical Dissertations and Theses by an authorized administrator of LSU Digital Commons. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely afreet reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back of the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6" x 9" black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. A Bell & Howell Information Company 300 North Zeeb Road. Ann Arbor. Ml 48106-1346 USA 313/761-4700 800/521-0600 THE MOLECULAR AND MORPHOLOGICAL SYSTEMATICS OF SUBFAMILY EPIDENDROIDEAE (ORCHIDACEAE) A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Plant Biology by Malcolm Ray Neyland B.A., University of W est Florida, 1980 August, 1995 UMI Number: 9609114 UMI Microform 9609114 Copyright 1996, by UMI Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. UMI 300 North Zeeb Road Ann Arbor, MI 48103 ACKNOWLEDGEMENTS As an individual with a business background, I am thankful to the Department of Plant Biology for accepting me as a student and giving me the opportunity to pursue a career in botany. I am most grateful for the encouragement and guidance offered by my committee members: Meredith Blackwell, Russell Chapman, Shirley Tucker, Lowell Urbatsch, and Thomas Wendt. Special thanks are extended to my major professor, Lowell E. Urbatsch, who has provided me with unwavering support during my graduate career. I also thank Kevin Jones, William Rootes, and Cindy Henk for technical assistance. Plant specimens generously supplied by Missouri Botanical Garden, Royal Botanic Gardens, Kew, University of Connecticut, Selby Gardens, F.L. Stevenson, Sue Grace, and Margaret Oard were vital to this project. The National Science Foundation (LEGSF RD-A-13) and NSF/LaSER (LASER/EPSCoR 92-96-ADP-02) provided the monetary support necessary to pursue this dissertation project. TABLE OF CONTENTS ACKNOWLEDGEMENTS......................................................................................................... ii LIST OF TABLES....................................................................................................................... iv LIST OF FIGURES.................... v ABSTRACT.............................................................................................. ix CHAPTER 1 INTRODUCTION .............................................................................................. 1 2 PHYLOGENY OF SUBFAMILY EPIDENDROIDEAE (ORCHIDACEAE) INFERRED FROM CHLOROPLAST ndhF GENE SEQUENCES AND MORPHOLOGICAL CHARACTERS BASED ON PARSIMONY ANALYSIS............................................................ 32 3 PHYLOGENY OF SUBFAMILY EPIDENDROIDEAE (ORCHIDACEAE) INFERRED FROM CHLOROPLAST ndhF GENE SEQUENCES BASED ON A MAXIMUM LIKELIHOOD ANALYSIS................................... 112 4 EVOLUTION IN THE NUMBER AND POSITION OF FERTILE ANTHERS IN ORCHIDACEAE INFERRED FROM ndhF CHLOROPLAST GENE SEQUENCES................................................................. 154 5 A TERRESTRIAL ORIGIN FOR THE ORCHIDACEAE INFERRED FROM ndhF CHLOROPLAST GENE SEQUENCES......................................... 169 6 A PHYLOGENETIC ANALYSIS OF SUBTRIBE PLEUROTHALLIDINAE (ORCHIDACEAE)............................................................................ 180 7 SUMMARY AND CONCLUSIONS ...................................................................... 210 APPENDIXES................................... 219 VITA 232 LIST OF TABLES Table 1.1 Recent classification systems of subtribes Epidendroideae and Vandoideae ....................................................................................... 10 Table 2.1 List of taxa included in this study. Orchidaceae members are arranged according to the taxonomy of Dressier (1993)....................................................................................... 37 Table 2.2 Sources of plant material and voucher information for taxa sequenced in this study. Acronyms of herbaria or persons that donated specimens are listed. GenBank accession numbers for ndh? gene sequences are given ............................................................................................................ 40 Table 2.3 Table of informative INDEL characters for the taxa sequenced in this study ....................................................................... 51 Table 2.4 Morphological characters and recognized character states for orchid taxa presented in Table 2.2 ................................ 53 Table 2.5 Morphological character states for the orchid taxa listed in Table 2 .2 ................................................................................... 55 Table 3.1 Log likelihood values and tree topology designations resulting from maximum likelihood searches using the given transversion weighing parameters, with jumble seed (137) parameter in effect versus not in effect .................... 119 Table 3.2 Log likelihood values and designated tree topologies resulting from maximum likelihood searches using the jumble seeds indicated. All tests were performed using the transversion weighing parameter 1.1 .............................. 125 Table 6.1 Classification scheme of Pleurothallidinae from Pridgeon (1982b) ................................................................................... 184 Table 6.2 Outgroup members examined for characters listed in Table 6.3 ............ 186 Table 6.3 Character states for Pleurothallidinae and outgroup members. Characters and character states are identified in Appendix A. Missing data are indicated by question marks........................................................................................................... 188 iv LIST OF FIGURES Figure 2.1 Primer sequences used in this study and their approximate positions on the ndhF gene ...................................... 47 Figure 2.2 Character state changes graph across the entire ndhF gene from single representatives from angiosperm families: Poaceae, Orchidaceae, Caprifoliaceae, and Solanaceae. Each bar represents the number of site changes averaged over 20 base positions ...................................... 48 Figure 2.3 Rate of change graph by codon position from the taxa used in this study (Table 2.2). Graph restricted to ndhF sequence positions 1072-2304 ........................................ 57 Figure 2.4 Strict consensus tree of 570 trees discovered from 100 random addition searches using weighted ndhF sequences. Bootstrap values are indicated below each branch ................................................................................... 59 Figure 2.5 Strict consensus tree of 25,100 trees discovered from a single parsimony analysis of amino acid data converted from ndhF DNA sequences.................................... 60 Figure 2.6 Strict consensus tree of 531 trees discovered from 100 random addition parsimony searches using ndhF sequences ................ 61 Figure 2.7 Strict consensus tree of 90 most-parsimonious trees discovered from 100 random-addition searches using ndhF sequences and binary-coded INDELS............................................................................................ 62 Figure 2.8 Strict consensus tree of 7 most-parsimonious trees discovered from 100 random-addition parsimony searches using a data matrix consisting of 13 morphological characters. Bootstrap values are indicated below each branch ............................. 63 Figure 2.9 Single parsimony tree discovered