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The Evolution of the Mitochondrial Genomes of Calcareous Sponges and Cnidarians Ehsan Kayal Iowa State University

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The Evolution of the Mitochondrial Genomes of Calcareous Sponges and Cnidarians Ehsan Kayal Iowa State University Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2012 The evolution of the mitochondrial genomes of calcareous sponges and cnidarians Ehsan Kayal Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Evolution Commons, and the Molecular Biology Commons Recommended Citation Kayal, Ehsan, "The ve olution of the mitochondrial genomes of calcareous sponges and cnidarians" (2012). Graduate Theses and Dissertations. 12621. https://lib.dr.iastate.edu/etd/12621 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. The evolution of the mitochondrial genomes of calcareous sponges and cnidarians by Ehsan Kayal A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Ecology and Evolutionary Biology Program of Study Committee Dennis V. Lavrov, Major Professor Anne Bronikowski John Downing Eric Henderson Stephan Q. Schneider Jeanne M. Serb Iowa State University Ames, Iowa 2012 Copyright 2012, Ehsan Kayal ii TABLE OF CONTENTS ABSTRACT ........................................................................................................................................... V CHAPTER 1. GENERAL INTRODUCTION.............................................................................. 1 Introduction .......................................................................................................................................................1 Thesis Organization ...........................................................................................................................................5 References ..........................................................................................................................................................6 CHAPTER 2. CALCAREOUS SPONGES REDEFINE THE LIMITS OF MTDNA EVOLUTION IN THE ANIMAL KINGDOM...........................................................................11 Abstract............................................................................................................................................................11 Introduction .....................................................................................................................................................12 Materials and methods.....................................................................................................................................15 Results ..............................................................................................................................................................18 Discussion.........................................................................................................................................................26 Conclusion........................................................................................................................................................32 Acknowledgements...........................................................................................................................................32 CHAPTER 3. EVOLUTION OF LINEAR MITOCHONDRIAL GENOMES IN MEDUSOZOAN CNIDARIANS....................................................................................................51 Abstract............................................................................................................................................................51 Introduction .....................................................................................................................................................52 Materials and methods.....................................................................................................................................55 Results ..............................................................................................................................................................58 Discussion.........................................................................................................................................................66 Acknowledgements...........................................................................................................................................73 References ........................................................................................................................................................80 iii CHAPTER 4. CNIDARIAN PHYLOGENETIC RELATIONSHIPS AS REVEALED BY MITOGENOMICS............................................................................................84 Abstract............................................................................................................................................................84 Background......................................................................................................................................................85 Results ..............................................................................................................................................................89 Discussion.........................................................................................................................................................93 Conclusions ......................................................................................................................................................99 Methods..........................................................................................................................................................100 Acknowledgements.........................................................................................................................................104 CHAPTER 5. THE ERATIC EVOLUTION OF ANIMAL MITOCHONDRIAL DNA............................................................................................................ 118 Abstract..........................................................................................................................................................118 Introduction ...................................................................................................................................................119 Mitochondrial genome structure and organization.......................................................................................121 The size of animal mitochondrial genome is not uniform .............................................................................123 A wide array of mitochondrial genetic content .............................................................................................125 mtDNA-encoded RNAs are prone to a high level of variation in animals ....................................................127 Changing the code is not limited to bilaterian animals .................................................................................129 Concluding remarks.......................................................................................................................................131 References ......................................................................................................................................................133 CHAPTER 6. GENERAL CONCLUSIONS............................................................................ 146 Conclusions ....................................................................................................................................................146 Broader perspectives and future directions...................................................................................................147 References ......................................................................................................................................................149 APPENDIX A. SUPPLEMENTARY MATERIALS FOR CHAPTER 2 ......................... 152 APPENDIX B. SUPPLEMENTARY MATERIALS FOR CHAPTER 3 ......................... 161 iv APPENDIX B. SUPPLEMENTARY MATERIALS FOR CHAPTER 4 ......................... 163 v ABSTRACT The mitochondrial DNA (mtDNA) in animals (Metazoa) is a favorite molecule for phylogenetic studies given its relative uniformity in both size and organization. Yet, as the depth coverage of representative animal groups increases sharply thanks to recent advances in sequencing technology, some clades remain stubbornly under sampled, if even represented at all. Difficulties associated with data collection from problematic taxa can arise from highly derived sequences, fragmented genomes, unusual structure, or any combination of these. Particularly illustrative examples are found in non-bilaterian animals (placozoans, sponges, cnidarians, comb jellies) where the mtDNA is more variable in size and structure. The present dissertation provides several case studies of what is considered “unusual” mtDNA for animals. First, we describe some unusual characteristics of the mitochondrial genomes found in calcareous sponges (Calcarea, Porifera), where one, potentially two, novel genetic codes are inferred, transfer RNAs (tRNAs) are edited, and ribosomal RNA (rRNA) genes are in pieces. We also hypothesize
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