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Phylogenetic Systematics of the Ulvophyceae (Chlorophyta) Based on Cladistic Analyses of Ribosomal RNA Genes and Morphology

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Phylogenetic Systematics of the Ulvophyceae (Chlorophyta) Based on Cladistic Analyses of Ribosomal RNA Genes and Morphology Louisiana State University LSU Digital Commons LSU Historical Dissertations and Theses Graduate School 1992 Phylogenetic Systematics of the Ulvophyceae (Chlorophyta) Based on Cladistic Analyses of Ribosomal RNA Genes and Morphology. Frederick William Zechman Louisiana State University and Agricultural & Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_disstheses Recommended Citation Zechman, Frederick William, "Phylogenetic Systematics of the Ulvophyceae (Chlorophyta) Based on Cladistic Analyses of Ribosomal RNA Genes and Morphology." (1992). LSU Historical Dissertations and Theses. 5368. https://digitalcommons.lsu.edu/gradschool_disstheses/5368 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 affect 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 corner 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. University Microtilms International A Ben 4 Howell Information Company 300 North Z eeb Road Ann Arbor. Ml 48106-1346 USA 313 761-4700 800 521-0600 Ord«r Number 9801116 Phylogenetic systematica of the Ulvophyceae (Chlorophyta) based on dadistic analyses of ribosomal UN A genes and m orphology Zechman, Frederick William, Ph.D. The Louisiana State University and Agricultural and Mechanical Col., 1992 UMI 300 N. Zeeb Rd. Ann Arbor, Ml 48106 PHYLOGENETIC SYSTEMATICS OF THE ULVOPHYCEAE (CHLOROPHYTA) BASED ON CLADISTIC ANALYSES OF RIBOSOMAL RNA GENES AND MORPHOLOGY 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 Botany by Frederick W. Zechman B.S., The University of North Carolina at Wilmington, 1979 M.S., The Universily of New Hampshire, 1984 May 1992 ACKNOWLEDGEMENTS This dissertation was developed under the direction of my graduate advisor, Dr. Russell L. Chapman, Chair of the Department of Botany. I am indebted to him for his support and guidance throughout my studies at Louisiana State University. I would also like to thank Dr. Elizabeth A. Zimmer for her support in providing equipment and supplies to initiate the project. Dr. Edward C. Theriot is also thanked for his patient assistance in the theory and practice of phylogenetic inference. For many interesting discussions and their endless friendship and support, I would also like to thank Joey Spatafora, Mark Buchheim, Keith Hamby, Tom Kantz, and Debra Waters. I gratefully acknowledge the assistance of Dr. Meredith Blackwell, Dr. William Platt, and Dr. Robert M. Zink for critical review of the manuscript and insightful suggestions. Dr. Donald F. Kapraun and Steven M. Blair are thanked for help in collection and identification of some field collected specimens. I also thank Dr. M. Dennis Hanisak and Harbor Branch Oceanographic Institution for furnishing valuable ship time for collection of specimens. I also thank Dennis for his encouraging me to return to graduate school for the doctoral degree. I would especially like to thank my parents, Fred and Nancy Zechman, for their love and encouragement during my years as a graduate student. Without them, my education would not have been possible. Most of all, I would like to thank my son, Dylan Hayes Zechman. For the past three and a half years he has been an inspiration to me. With his little ii hands, big heart, and all-seeing eyes he has shown me once again how to seize the day and live life to its fullest. Thank you, little one. ii TABLE OF CONTENTS Page ACKNOWLEDGMENTS............................................................................ ii LIST OF TABLES..................................................................................... vii LIST OF FIGURES................................................................................... viii ABSTRACT................................................................................................. xi CHAPTER 1 INTRODUCTION AND LITERATURE REVIEW 1 GREEN ALGAL SYSTEMATICS........................... 2 History ......................................................... 2 Ultrastructure ............................................. 4 The Ulvophyceae...................................... 8 Ulvophycean O rders .................................. 9 Analysis of D ata ......................................... 11 PHYLOGENETIC SYSTEMATICS...................... 13 Introduction .................................................. 13 Terminology and Concepts ...................... 14 Classification ................................................ 16 Homoplasy .................................................. 16 Polarity of Inferred Relationships 17 Parsimony ..................................................... 18 Alternative Methods of Phylogeny Reconstruction ............................... 20 Ribosomal RNA ....................................................... 25 Introduction .................................................. 25 rRNA Gene Organization ........................... 26 rDNA Sequence Variation ........................ 26 2 CLADISTIC ANALYSIS OF NON-MOLECULAR DATA 29 Introduction .............................................................. 30 Materials and Methods ......................................... 32 Results..................................................................... 35 Discussion .............................................................. 40 3 PHYLOGENY OF THE ULVOPHYCEAE (CHLORO- iv PHYTA): CLADISTIC ANALYSIS OF NUCLEAR* ENCODED rRNA SEQUENCE DATA................. 45 Introduction ............................................................. 46 Materials and Methods ........................................ 48 RNA extraction ................................. 49 Direct sequencing of rRNA ........................ 51 Computer assisted sequence alignment. 52 Phylogenetic inference ............................... 52 Results.................................................................... 53 The cladograms ........................................... 53 Forced tree topologies ............................... 58 Discussion ............................................................. 59 4 RIBOSOMAL RNA GENES AND A PHYLOGENY FOR THE ULVOPHYCEAE: INCREASED TAXON SAMPLING AND FURTHER EXPLORATION OF THE DATA......................................................... 66 Introduction ............................................................. 67 Materials and Methods ........................................... 70 Taxon sampling ........................................... 70 Collection of plant material ........................ 72 DNA extraction ........................................... 73 PCR............................................................. 73 DNA sequencing ........................................ 74 Sequence alignment ................................. 75 Character data........................................... 75 Phylogenetic analysis ............................... 75 Bootstrapping ............................................. 76 Decay Index ............................................... 76 Randomized data ...................................... 77 Testing outgroups ...................................... 77 Four taxon tests ........................................ 78 Results.................................................................... 78 The cladograms ........................................ 81 Outgroup experiments 1 ............................. 84 Testing relative support of relationships. 86 Decay Index ............................................... 69 Randomized data ...................................... 91 Outgroup experiments II .......................... 93 Discussion ............................................................. 98 General Results of Phylogenetic Analyses ...................................................... 98 Pattern and Process of Evolution in Siphonous and Siphonocladous Green Algae: Fossils Rates and Biogeography ................................. 106 V Phylogenetic pattern: congruence with fossil d a ta ..................
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