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Ribosomal RNA and the Early Evolution of Flowering Plants. Robert Keith Hamby Louisiana State University and Agricultural & Mechanical College

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Ribosomal RNA and the Early Evolution of Flowering Plants. Robert Keith Hamby Louisiana State University and Agricultural & Mechanical College Louisiana State University LSU Digital Commons LSU Historical Dissertations and Theses Graduate School 1990 Ribosomal RNA and the Early Evolution of Flowering Plants. Robert Keith Hamby Louisiana State University and Agricultural & Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_disstheses Recommended Citation Hamby, Robert Keith, "Ribosomal RNA and the Early Evolution of Flowering Plants." (1990). LSU Historical Dissertations and Theses. 5053. https://digitalcommons.lsu.edu/gradschool_disstheses/5053 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 Microfilms International A Bell & Howell Information Company 300 North Zeeb Road. Ann Arbor. Ml 48106-1346 USA 313/761-4700 800 521-0600 Order Number 9123196 Ribosomal RNA and the early evolution of flowering plants Hamby, Robert Keith, Ph.D. The Louisiana State University and Agricultural and Mechanical Col., 1990 UMI 300 N. ZeebRd. Ann Arbor, MI 48106 RIBOSOMAL RNA AND THE EARLY EVOLUTION OF FLOWERING PLANTS 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 Biochemistry by Robert Keith Hamby B.S.Ch.E., Auburn University, 1978 .S., Virginia Polytechnic Institute and State University, 1984 December 1990 ACKNOWLEDGEMENTS There are many people to whom I am indebted for their help, encouragement, support and friendship through the many years of graduate school which are now ended. As this was the absolute last thing I added to this dissertation, I almost certainly omitted the names of some people. I ask everyone’s indulgence. I would like to thank Dr. Elizabeth Zimmer, my major professor, for the direction she provided in the completion of this project and her friendship and help in the transition from the world of engineering to the world of molecular biology. Dr. Zimmer has also provided generous support for research and travel over the past five years, and for that I am also grateful. I want to thank the people who have collaborated and conspired with me, especially the past and present members of the Zimmer lab including Joey Spatafora, Eldon Jupe, Lynne Sims, Mike Arnold, Julie Dowd, Kelly Mullen, Gretchen Stein, Laurie Issel, Vishal Sachdev, Bryan Peavy, Jay DeSalvo, Dianne Dennis, Mary Bowen, Monique LeBlanc and all the other people who have worked in our lab. I wish to thank Russ Chapman and the people from his lab, including Debra Waters, Rick Zechman, Tom Kantz and Mark Buchheim, for their encouragement and comraderie. I am indebted to Sue Bartieit and the members of her lab for their generous help with my cloning experiments and to Sue in general for her friendship and support. I want to express my gratitude to the other members of my committee, all of whom have been very helpful: Kathy Morden, Martin Hjortso, Andy Deutsch, Simon Chang and Russ Chapman. I have many frienas outside of LSU to whom I am also grateful for moral support and encouragement and understanding when I had to "go to the lab." This list includes, but is by no means limited to, Rene and Smith Jackson, Wayne Lowther, Charlotte Adcock, Jim Anding, Gary Daniels, David Motes and James and Peggy Denny. I would like to dedicate this dissertation to my parents, Bob and Ann Hamby who gave me life, and to David Walker who taught me about living life. iii TABLE OF CONTENTS Pag© Acknowledgements ii Table of Contents iv List of Tables v List of Figures vi Abstract ix Introduction 1 Literature Review 7 Materials and Methods 59 Results 79 Discussion 107 Summary 159 Conclusions 163 Recommendations Toward Future Work .................................................... 165 References 169 Appendix 1 202 Appendix 2 207 Appendix 3 231 Vita 241 iv LIST OF TABLES Table Page 1 A partial list of investigators who have used ribosomal DNA or RNA for systematics studies. 9 2 Summary of the groupings of taxa key to this study by various authors. 38 3 Taxa sequenced in this study. 60 4 A list of primers used in direct rRNA sequencing. 80 5 Location of gap sites within the 1701 aligned nucleotide sequences, and the corresponding position of this gap score in the last 13 positions of the 1714 entries in the data set. 83 6 Summary of rRNA data over Poaceae and Colocasia. 85 7 Summary of rRNA data over 60 taxa. 97 8 Templeton’s (1983) test comparing alternative topologies with either the Gnetales as sister group to the flowering plants, or the conifer-cycad-G/'n/cgo clade as sister group to the flowering plants. 139 9 Results of a Templeton test comparing the alternative arrangements at the base of the phylogenetic tree of flowering plants. 143 10. A list of primers useful for PCR and sequencing within the chloroplast 16S rDNA. 233 v LIST OF FIGURES Figure Page 1 A typical plant rDNA repeat unit. 14 2 One of Crane’s (1985) trees for seed plants based on cladistic analyses of morphological data. 42 3 One of Donoghue and Doyle’s (1989a) most parsimonious trees for seed plants from a cladistic analysis of morphological data. 43 4 One of Donoghue and Doyle’s (1989a) most parsimonious trees for angiosperms. 45 5 A sample phylogenetic tree. 52 6 An example data set and alternative topologies for four taxa rooted by an outgroup. 55 7 A schematic of the procedure for direct rRNA sequencing. 69 8. A typical autoradiogram. 71 9 Location of the regions sequenced by each primer. 81 10 The most parsimonious tree for Poaceae inferred from rRNA sequences. 87 11 The distribution of trees found in an exhaustive search over the Poaceae rRNA sequence data. 88 12 A comparison of the most parsimonious tree (187 steps) and the next-most parsimonious tree (188 steps) based on the Poaceae rRNA sequence data. 90 vi Figure Page 13 A majority-rule consensus tree after 250 bootstrap replications of the Poaceae rRNA sequence data. 92 14 The distribution of trees found after 100 randomizations of the Poaceae rRNA data set. 94 15 One of two equally parsimonious trees found for 60 taxa based on rRNA sequence data. 101 16 The distribution of trees found after 25 randomizations of the rRNA data set of 30 taxa. 105 17 The most parsimonious arrangement for Poaceae shown as a phylogram. 110 18 The most parsimonious arrangement for 60 taxa shown as a phylogram. 111 19 The most parsimonious tree for Poaceae inferred from rRNA sequence data. 113 20 The majority-rule consensus trees for Poaceae calculated for the indicated range of trees. 115 21 A comparison of an arrangement based on rRNA sequence data and an arrangement based on rbcL sequence data by Doebley et al., 1990. 121 22 One of the two most parsimonious trees for 60 taxa based on rRNA sequence data. 123 vii Figure Page 23 One of the two most parsimonious trees for 60 taxa based on rRNA sequence data. 124 24 Two alternative topologies to test the relationships between gymnosperm lineages and flowering plants. 135 25 An alternative topology for 60 taxa in which the Gnetales are the sister group of the angiosperms. 137 26 The majority-rule consensus of 12 shortest trees with the Magnoliales as the basal angiosperm. 141 27 Three alternative arrangements at the base of the angiosperm radiation. 142 28 The majority-rule consensus of 8 shortest trees with the four- state characters eliminated from the data set. 147 29 The distribution of trees after 25 randomizations of the data set for 30 taxa when the four-state characters were removed from the data set. 148 30 A series of majority-rule consensus trees for 60 taxa. 150 31 Results of a phenetic analysis of rRNA sequences from 60 taxa. 156 32 Results of a phenetic analysis when the distances are calculated with Jukes-Cantor (1965) or Kimura (1980) formulae. 157 viii ABSTRACT Since the end of the last century, the predominant theories of the early radiation of the angiosperms have been that the earliest flowering plants were most similar to the present-day Magnoliidae (sensu Takhtajan, 1969). This position has been adopted by many, though there are some who suggest that the base of angiosperm radiation lies within the monocots (Burger, 1981) or a combination of monocots and dicots (Burger, 1977; Donoghue and Doyle, 1989a, 1989b).
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