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Information to Users 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 Nortn Z eeb Road. Ann Arbor. Ml 48106-1346 USA 313/761-4700 800/521-0600 EVOLUTIONARY CONSEQUENCES OF THE LOSS OF PHOTOSYNTHESIS IN THE NONPHOTOSYNTHETIC CHLOROPHYTE ALGA POLYTOMA. DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Dawne Vernon, B.S. ★ ★ ★ iHr ★ The Ohio State University 1996 Dissertation Committee: Approved by C. William Birky, Jr. Caroline A. Breitenberger Q Advisor / Thomas J . Byers Department of Mglecular Genetics Daniel J. Crawford UMI Number: 9620082 Copyright 1996 by Vernon, Dawne All rights reserved. UMI Microform 9620082 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 Copyright by Dawne Vernon 1996 To my parents, ii ACKNOWLEDGMENTS Thanks are inadequate relative to the benefits I received from having Dr. C. W. Birky, Jr. as a mentor, both in terms of knowledge gained and thinking skills acquired. I learned from many fine teachers throughout my life, but Dr. Birky and the late Dr. Elton Paddock reminded me how to think (and how to observe), at two times in my adult life when I thought I already knew how to think fairly well. Both professors kept my logic sharp and my perspective broad. I thank Carl Kipp for similar input; no sloppy logic around him. In addition, the positive environment in Dr. Birky's laboratory contributes to the psychological well-being of all the students who pass through it. Thanks to Dr. Tom Byers and Dr. Dan Crawford for advice on phylogeny and for time spent reviewing this manuscript. Thanks to Dr. Caroline Breitenberger for her reviewing time, and for her great assistance in analyzing a hypervariable region in the EF-Tu protein. Thanks to Pam Katko and Cal Griffith for helping me start this project. Thanks for technical help and friendship from Heather Deiderick, Lori Humphrey, and Robin McBride, and especially from Suzanne Nixon. Thanks to Dr. Steve Kuhl, Bob Rumpf and Pam Mackowski for brainstorming. And thanks, again, to Bob Rumpf for more unselfish help with software than I can ever repay. Finally, thanks to my supportive and understanding parents. I have had the rare opportunity to work professionally with both of my parents, so they have been parents, mentors, colleagues and friends to me. I couldn't have finished this project without them. The work reported in Chapters IV and V will be submitted for publication. The joint project reported in Chapter III has already been accepted for publication in the Journal of Phyoology. VITA October 23,1948 .... Born - Akron, Ohio 1971 ................. B.S., The Ohio State University, Columbus, Ohio 1968 - 1972 ......... Mathematician, E.S. Preston & Associates, Civil Engineers Columbus, Ohio 1972 - 1984......... Mathematician, Technical Manager and Business Manager, Right-of-Way Consultants & Associates, Professional Surveyors Marietta, Ohio 1984 - present ..... University Fellow, Graduate Teaching Associate, Graduate Research Associate, or Graduate Student Department of Molecular Genetics The Ohio State University Columbus, Ohio PUBLICATIONS Vernon-Kipp, D., Kuhl, S.A. & Birky, C.W.'Jr. 1989. Molecular evolution of Polytoma, a non-green chlorophyte. In: Boyer, Charles T., Shannon, Jack C., & Hardison, Ross C. [Eds.] Physiology. Biochemistry, and Genetics of Nonareen PLastids. American Society of Plant Physiologists, Rockville, Maryland, pp. 284-6. v Gordon, J., Rumpf, R., Shank, S.L., Vernon, D. & Birky, C.W. Jr. 1995. Sequences of the R m l 8 genes of Chlamydomonas humicola and C. dysosmos are identical, in agreement with their combination in the species C. applanata (Chlorophyta). In: J. Phycol. 31:312-3. Rumpf, R., Vernon, D., Schreiber, D. & Birky, C.W. Jr. 1996. Evolutionary consequences of the loss of photosynthesis in Chlamydomonadaceae: Phylogenetic analysis of Rrnl8 (18S rDNA) in 13 Polytoma strains (Chlorophyta) . (in press, Feb, 1996, Journal of Phycology) . Technical Editor of textbook: Vernon, R.C. 1996. Professional Surveyor's Manual. (in press, Sept., 1996, McGraw-Hill Publishing co.) FIELD OF STUDY Major Field: Molecular Genetics Molecular Genetics and Evolution of Organelles Professor: C. William Birky, Jr. vi TABLE OF CONTENTS ACKNOWLEDGMENTS...................................... iii VITA ................................................ V LIST OF T A B L E S ...................................... ix LIST OF FIGURES ...................................... x CHAPTER PAGE I. INTRODUCTION................................ 1 Introduction ............................... 1 Hypotheses .................................. 6 Project Goals .............................. 7 II. ISOLATION AND CHARACTERIZATION OF PLASTID DNA FROM POLYTOMA UVELLA 964 .................... 15 Introduction ................................ 15 Materials and Methods ...................... 16 R e s u l t s .................................... 39 D i scussion.................................. 47 III. MOLECULAR PHYLOGENETIC ANALYSIS IN POLYTOMA . 59 General Background .......................... 59 Accepted Paper: EVOLUTIONARY CONSEQUENCES OF THE LOSS OF PHOTOSYNTHESIS IN CHLAMYDOMONADACEAE: PHYLOGENETIC ANALYSIS OF RRN18 (18S RDNA) IN 13 POLYTOMA SPECIES (CHLOROPHYTA) .............................. 66 Introduction ................................ 66 Materials and M ethods ...................... 70 Results and Discussion ...................... 79 Conclusions................................ 90 vii Additional Information from Phylogenetic Analysis .............................. 94 IV. EVIDENCE OF FUNCTIONALITY IN TWO POLYTOMA LEUCOPLAST GENES ............................ 105 General Background .......................... 105 Submittable Paper: EVIDENCE THAT PLASTID RRN16 AND TUFA GENES ARE FUNCTIONAL IN THREE NON-GREEN CHLOROPHYTE ALGAE IN THE GENUS POLYTOMA.............................. 114 Introduction ................................ 114 Materials and Met h o d s ...................... 120 R e s u l t s .................................... 127 Discussion.................................. 136 V. ACCELERATED EVOLUTIONARY RATES FOUND IN TWO POLYTOMA LECUOPLAST GENES .................. 151 General Background .......................... 151 Submittable Paper: ANALYSIS OF EVOLUTIONARY RATES IN TWO PLASTID GENES IN THE NONPHOTOSYNTHETIC ALGA POLYTOMA ............ 158 Introduction ................................ 158 Materials and Methods ...................... 163 R e s u l t s .................................... 182 Discussion.................................. 185 VI. S U M M A R Y .................................... 198 LIST OF REFERENCES .................................. 204 viii LIST OF TABLES TABLE PAGE 1. Variations in Gillham & Boynton lysis p r o t o c o l ................................ 18 2. Primers used for Rrnl8, rrnlS, tufA, rrn.23, rbcL . 37 3. Amplification conditions used for Rrnl8, rrnl6, tufA, rrn23, rbcL . 38 4. List of Polytoma s t o c k s ................ 71 5. List of complete Rrnl8 sequences and their sources .......................... 72 6. Numbers of substitution and indel differences between complete sequences of Rrnl8 g e n e s .......................... 73 7. Single-base substitution rate changes in non-green plastid genes .............. 154 8. Relative rate tests for r r n l 6 .......... 175 9. Relative rate tests for t u f A ............ 176 10. Base composition (as % G + C) in chlamydomonad rrnlS and tufA genes .... 177 11. Codon usage in chlamydomonad tufA plastid genes .......................... 178 12. Increase in substitution rates (relative to green species) at synonymous versus non-synonymous sites in Epifagus and P. o b t u s u m ........ 179 ix LIST OF FIGURES FIGURE PAGE 1. Polytoma lpDNA yield from various lysis p r o t o c o l s ............................ 17 2. Buoyant densities in CsCl gradients. 24 3. CsCl + bis gradient for P.u. 964 .... 26 4. P.u.964 DNA digested with Hind III ... 27 5. P. uvella 964 nuclear ribosomal RNA gene(s) identified .................... 29 6. P. uvella 964
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