A Molecular Phylogeny of the Sparidae (Perciformes: Percoidei)
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W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2000 A molecular phylogeny of the Sparidae (Perciformes: Percoidei) Thomas M. Orrell College of William and Mary - Virginia Institute of Marine Science Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Genetics Commons, and the Zoology Commons Recommended Citation Orrell, Thomas M., "A molecular phylogeny of the Sparidae (Perciformes: Percoidei)" (2000). Dissertations, Theses, and Masters Projects. Paper 1539616799. https://dx.doi.org/doi:10.25773/v5-x8gj-1114 This Dissertation is brought to you for free and open access by the Theses, Dissertations, & Master Projects at W&M ScholarWorks. It has been accepted for inclusion in Dissertations, Theses, and Masters Projects by an authorized administrator of W&M ScholarWorks. For more information, please contact [email protected]. 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Reproduced with with permission permission of the of copyright the copyright owner. owner.Further reproductionFurther reproduction prohibited without prohibited permission. without permission. A MOLECULAR PHYLOGENY OF THE SPARIDAE (PERCIFORMES: PERCOIDEI) A Dissertation Presented to The Faculty of the School of Marine Science The College of William and Mary in Virginia In Partial Fulfillment Of the Requirements for the Degree of Doctor of Philosophy by Thomas Martin Orrell 2000 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. UMI Number 9989346 UMI* UMI Microform9989346 Copyright 2001 by Bell & Howell Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. Bell & Howell Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, Ml 48106-1346 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. APPROVAL SHEET This dissertation is submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy Thomas M. Orrell Approved 9 November 2000 John A. Musick, Ph.D. Committee Co-Chairman/Advisor Jopn E. Graves, Ph.D. Committee Co-Chairman/Ad visor Kimberly S. Reece, Ph.D. „ . Peter A- Van Veld, Ph.D. Kent E. C inter, Ph.D Department of Biology Old Dominion University, Norfolk, VA njSl G. David Johnson, Pn.D Division of Fishes, National Museum of Natural History Smithsonian Institution, Washington, D.C. Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. DEDICATION I am dedicating this dissertation to the memory of Emo. J. Benvenuti, my grandfather, who died on 13 March 1998. He was a quiet teacher who had all the patience in the world. Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. TABLE OF CONTENTS Page ACKNOWLEDGMENTS....................................................................................................... v LIST OF TA BLES............................................................................................................... vii LIST OF FIG U RES.................................................................................................................ix ABSTRACT........................................................................................................................... xiii GENERAL INTRODUCTION ...............................................................................................2 CHAPTER ONE. A MOLECULAR PHYLOGENY OF THE FAMILY SPARIDAE (PERCOIDEI: PERCIFORMES) INFERRED FROM THE MITOCHONDRIAL CYTOCHROME B GENE ............................................................... 14 INTRODUCTION......................................................................................................15 MATERIALS AND METHODS..............................................................................19 RESULTS ..................................................................................................................26 DISCUSSION ............................................................................................................35 CHAPTER TWO. A MOLECULAR PHYLOGENY OF THE FAMILY SPARIDAE (PERCOIDEI: PERCIFORMES) INFERRED FROM THE MITOCHONDRIAL 16S RIBOSOMAL RNA GEN E .....................................................126 INTRODUCTION................................................................................................... 127 MATERIALS AND METHODS............................................................................130 RESULTS ................................................................................................................ 134 DISCUSSION ..........................................................................................................141 CHAPTER THREE. COMBINED ANALYSIS OF CYTOCHROME B AND 16S MITOCHONDRIAL SEQUENCES ............................. 195 iii Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. INTRODUCTION.....................................................................................................196 MATERIALS AND METHODS............................................................................ 201 RESULTS .................................................................................................................204 DISCUSSION ...........................................................................................................211 CHAPTER FOUR. RECONSTRUCTING SPARID RELATIONSHIPS WITH A SINGLE-COPY NUCLEAR DNA .....................................................................................230 INTRODUCTION....................................................................................................231 MATERIALS AND METHODS............................................................................ 233 RESULTS .................................................................................................................236 DISCUSSION .......................................................................................................... 239 CONCLUSIONS ...................................................................................................................258 LITERATURE CITED ........................................................................................................ 262 VITA ....................................................................................................................................277 iv Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. ACKNOWLEDGMENTS I would like to thank my dissertation committee for their constant support throughout the duration of this study. I am especially indebted to my co-major advisors Drs. Jack Musick and John Graves for giving me encouragement, advice, guidance and funding during my time at VIMS. Dr. Kimberly Reece provided invaluable advice in the laboratory and was an unending source of molecular knowledge. I am very grateful to my outside committee members. Dr. Kent Carpenter inspired this study by suggesting that we work together on a phytogeny of the Sparidae. He generously collected the majority of the samples used in this study and afforded me numerous opportunities to collect samples as well. He graciously provided hours of advice for the completion of this project and his critical review of this dissertation contributed countless suggestions for improvement Dr. G. David Johnson furnished the framework of many of the relationships surveyed in this study. His encouragement and critical eye kept me honest.