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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 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 MOLECULAR GENETIC ANALYSIS OF THE PHYLOGENETIC RELATIONSHIPS OF LAKE VICTORIA CICHLID FISH DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Gregory Charles Bonner Booton, B. S. The Ohio State University 199 5 Dissertation Committee: Approved by Paul A. Fuerst C. W. Birky P. Parker R. Skavaril \ Advisor J. Downhower Department of Molecular Genetics UMI Number: 9525995 UMI Microform 9525995 Copyright 1995, 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 To my family, thank you ii ACKNOWLEDGEMENTS I would like to sincerely thank my adviser, Dr. Paul A. Fuerst for his support and encouragement from the beginning of this project. Without him as my advisor, I am sure my project would have never come to fruition. My thanks also go the other members of my committee for their helpful suggestions. My thanks also go to the staff of The Johnson Aquatic Complex and The Columbus Zoo for their support, both personally and financially. In addition, the financial support of The Ohio State University and The National Science Foundation has been critical to the completion of this project, and I greatly appreciate that assistance. I would also like to thank Drs. Les Kaufman and Mark Chandler for their support and insight into the Lake Victoria cichlid problem. Also, without the support of the fellow members of my laboratory, none of this work would have been possible. Finally, I would like to deeply thank my family, without their support, understanding, and faith, this achievement would certainly have never been possible. VITA November 7, 1958 .......................................................Bom- Columbus, Ohio 1988 .................................................................................B.S., The Ohio State University, Columbus, Ohio 1988-1993 .....................................................................Graduate Assistant, The Ohio State University, Columbus, Ohio 1993-1995 .....................................................................Research Assistant, The Ohio State University, Columbus, Ohio PUBLICATIONS Booton, Gregory C., Doug Warmolts, Sandy Andromeda, and Paul A. Fuerst. 1991. Analysis of Mitochondrial Sequence Variation in Endangered Species of Lake Victoria cichlid fish. Ohio Journal of Science, 92: 2. FIELDS OF STUDY Major Field: Molecular Evolution Studies in Phylogenetic Reconstruction, Molecular Genetic Analysis of Taxonomic Relationships, Dr. Paul A. Fuerst TABLE OF CONTENTS DEDICATION................................................................................................................. ii ACKNOWLEDGEMENTS.......................................................................................... iii VITA................................................................................................................................. iv LIST OF TABLES........................................................................................................viii LIST OF FIGURES..........................................................................................................x CHAPTERS I. INTRODUCTION ...........................................................................1 A. The Cichlidae Taxa of The Great Lakes of Africa 1 B. The Family Cichlidae.......................................................................8 C. Taxonomic History of The Lake Victoria Cichlid Species Flock ...................................................................................11 D. Historical and Current Challenges to the Lake Victoria Cichlid Fauna, and Conservation Efforts 18 E. Phylogenetic Reconstruction and its Importance to Conservation Efforts Regarding Lake Victoria Cichlids............................................................................................23 II. TAXONOMIC SYNONOMIES AND PHYLOGENETIC RECONSTRUCTION METHODS...........................................................29 A. Taxa ................................................................................................29 B. Phylogenetic Reconstruction Methodology ....................... 37 III. PHYLOGENETIC RELATIONSHIPS OF A LAKE VICTORIA SPECIES DERIVED FROM 18S RIBOSOMAL DNA ................... 42 A. Introduction ...................................................................................... 42 B. Materials and Methods ................................................................. 43 C. Results................................................................................................56 D. Discussion .........................................................................................70 IV. AN ANALYSIS OF PHYLOGENETIC RELATIONSHIPS OF LAKE VICTORIA CICHLID SPECIES USING INTERNAL TRANSCRIBED SPACER ONE (ITS 1) OF THE RIBOSOMAL GENE OPERON.........................................72 A. Background......................................................................................72 B. Methods and Materials ................................................................ 76 C. Results..............................................................................................84 D. Discussion ...............................................................................91 V. COMPARISON OF A RANDOMLY AMPLIFIED POLYMORPHIC DNA (RAPD) PHYLOGENY OF LAKE VICTORIA CICHLID SPECIES WITH A PHYLOGENY PRODUCED FROM MORPHOLOGICAL DATA...................................................................................................... 95 A. Background......................................................................................95 B. Methodology ............................................................................101 a. Experimental Design ............................................................. 101 b. Collections ...............................................................................101 c. Experimental Conditions .................................................... 102 C. Results........................................................................................... 112 D. Discussion .................................................................................... 142 SUMMARY................................................................................................ 145 APPENDICES............................................................................................147 Appendix A: Data relevent to Chapter III ........................ 148 Appendix B: Data relevent to Chapter V ............................157 Appendix C.Animal Use Protocol LIST OF REFERENCES........................... LIST OF TABLES T a b le s Page 1. Taxonomic synonomy of 18S rDNA analysis species ........................30 2. Taxonomic synonomy of taxa analyzed for Internal Transcribed Spacer One (ITS 1) .................................................................... 32 3. Taxonomic synonomy of taxa examined by RAPD analyis ...........34 4. 18S Ribosomal DNA Primers usen in Amplification and Sequencing ..................... 51 5. Distance matrix of the five species in the first 18S rRNA primary sequence alignment ...........................................................................61 6. Corrected Genetic Distances of 18S rRNA Sequences ........................65 7. Species examined for ribosomal ITS 1 study .........................................77 8. Internal Transcribed Spacer One Amplification and Sequencing Primers ............................................................................................. 82 9. Distance Matrix and Sequence Dissimilarity of Internal Transcribed Spacer One (ITS 1) .................................................................... 89 10. Primers used for RAPD Analysis .................................................................109 11. Taxonomic Designation of Species Analyzed in RAPD study.....................................................................................................................117

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