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A Molecular Phylogeny of the Echeneoidea (Perciformes: Carangoidei) and an Investigation of Population Structuring Within the Echeneidae

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A Molecular Phylogeny of the Echeneoidea (Perciformes: Carangoidei) and an Investigation of Population Structuring Within the Echeneidae W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2005 A Molecular Phylogeny of the Echeneoidea (Perciformes: Carangoidei) and an Investigation of Population Structuring Within the Echeneidae Kurtis N. Gray College of William and Mary - Virginia Institute of Marine Science Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Marine Biology Commons, Oceanography Commons, and the Systems Biology Commons Recommended Citation Gray, Kurtis N., "A Molecular Phylogeny of the Echeneoidea (Perciformes: Carangoidei) and an Investigation of Population Structuring Within the Echeneidae" (2005). Dissertations, Theses, and Masters Projects. Paper 1539617836. https://dx.doi.org/doi:10.25773/v5-kget-zf43 This Thesis 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]. A MOLECULAR PHYLOGENY OF THE ECHENEOIDEA (PERCIFORMES: CARANGOIDEI) AND AN INVESTIGATION OF POPULATION STRUCTURING WITHIN THE ECHENEIDAE A Thesis Presented to The Faculty of the School of Marine Science The College of William and Mary In Partial Fulfillment Of the Requirements for the Degree of Master of Science by Kurtis N. Gray 2005 APPROVAL SHEET This thesis is submitted in partial fulfillment of the requirements for the degree of Master of Science Kurtis N. Gray Approved December 12, 2005 Graves, Ph.D. Committee Chairman/Advisor McDowell, Ph.D. .-John M. Brubaker, Ph.D. Bruce B. Collette, Ph.D. National Marine Fisheries Service Systematics Laboratory National Museum of Natural History Smithsonian Institution, Washington, D.C. TABLE OF CONTENTS ACKNOWLEDGMENTS................... v LIST OF TABLES........................................................................................................... vii LIST OF FIGURES.......................................................................................................... ix LIST OF APPENDICES.............................................. xii ABSTRACT....................................................................................................................xiv GENERAL INTRODUCTION........................................................................................ 2 Definitions ............................. 2 An Introduction to the Echeneoidea ......................................................................4 Objectives................................................................................................................6 CHAPTER ONE. A MOLECULAR PHYLOGENY OF THE SUPERFAMILY ECHENEOIDEA (PERCIFORMES: CARANGOIDEI) INFERRED FROM MITOCHONDRIAL 12S rRNA, 16S rRNA, ND2, AND NUCLEAR ITS-1 GENE REGION SEQUENCE ANALYSES.................................................................... 8 INTRODUCTION.................................................................................................8 Taxonomic Classification .........................................................................9 Utility of Molecular M arkers..................................................................12 Genome Comparisons ............................................................................. 13 Molecular Marker Selection ...................................................................15 Objectives................................................................................................ 16 MATERIALS AND METHODS........................................................................17 Sample Collection .. ............................................................ 17 DNA Extraction and PCR Amplification ............................................. 18 DNA Sequencing and Sequence Analyses ............................................21 Data Set Partitioning. ........................................................................23 Phylogenetic Analyses. .........................................................................24 RESULTS............................................. 26 Sequence Variation .................................................................................26 Partition Homogeneity Analyses ...........................................................30 Phylogenetic Relationships - Combined .............................................. 30 Phylogenetic Relationships - Individual Gene Regions ........................32 DISCUSSION...................................................................................................... 35 Echeneoid Phylogenetics. ................................................................35 Unresolved Relationships ................... 37 Discrepancies within Echeneis...............................................................38 Importance of Multiple Genes ................................................................40 CHAPTER TWO. AN INVESTIGATION OF POPULATION STRUCTURING WITHIN THE FAMILY ECHENEIDAE (PERCIFORMES: CARANGOIDEI) INFERRED FROM MITOCHONDRIAL CONTROL REGION DNA SEQUENCE ANALYSES................................................................................................63 INTRODUCTION......................................................................................... .63 Host-Symbiont Behavior .........................................................................64 Utility of Molecular Markers .................................................................67 Objectives.................................................................................................69 MATERIALS AND METHODS........................................................................ 71 Sample Collection ...................................................................................71 DNA Extraction and PCR Amplification .............................................72 DNA Sequencing and Sequence Analyses ...........................................73 Population Genetic Analyses ..................................................................74 RESULTS..................................................................................................... 77 Sequence Variation ..................................................................................77 Genetic Diversity ................................................................................... .78 Clade Distribution ...................................................................................78 Phylogeography and Population Structuring .........................................80 Neutrality and Population Demography ............................................... 81 Cladogenesis and Putative Recolonization ............................................82 DISCUSSION 83 Sequence Variation .................................................................................83 Genetic Diversity .............................................................................. 84 Clade Distribution .................................................................................... 85 Phylogeography and Population Structuring .........................................88 Cladogenesis and Putative Recolonization ............................................92 Neutrality and Population Demography ................................................ 93 Host-symbiont Phylogeography ..............................................................94 Sampling Concerns ............................................................................ .98 CONCLUSIONS............................................................................................................101 APPENDICES................................................................................................................ 123 LITERATURE CITED.................................................................................................. 161 VITA................................................................................................................................ 176 iv ACKNOWLEDGMENTS I would like to express my gratitude to everyone who was involved in making this project a success. First and foremost, I would like to thank my advisor, Dr. John Graves, for guidance and support throughout my tenure at VIMS. Thank you for always having an open door, and for providing advice when I needed it most. I am indebted to Dr. Bruce Collette, who provided both the inspiration for this project, and the support to make it a reality. Thank you for your advice, encouragement and unending enthusiasm. I would like to thank Dr. Jan McDowell for her unwavering support, patience, and positive outlook on just about everything. Thank you for being there when I ran into roadblocks, and for taking the time to ensure those obstacles were overcome with relative ease. Special thanks also go to Dr. John Brubaker for the numerous insightful questions and recommendations offered as this study progressed. Thank you for devoting time and effort in a subject area far from the discipline in which you were classically trained. I would like to express my thanks to the following individuals who aided in the collection of specimens, without whose help this project would not have been possible: Dr. John Graves, Dr. Bruce Collette, Dr. Julian Pepperell, Dr. Dave Kerstetter, Melissa Paine, Dave Portnoy, Dr. Erin Burge, John Walter, Whit Davis, Hiroaki Okamoto, Lisa Natanson, and Maki Ohwada. I would also like to acknowledge Dr. Jim Franks
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