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Development of Representative Species-Level Molecular Markers and Morphological Character Analysis of Leucothoid Amphipods (Crustacea: Amphipoda)

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The University of Southern Mississippi The Aquila Digital Community Dissertations Spring 5-2010 Development of Representative Species-Level Molecular Markers and Morphological Character Analysis of Leucothoid Amphipods (Crustacea: Amphipoda) Kristine Nicolle White University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/dissertations Part of the Biology Commons, Marine Biology Commons, and the Molecular Genetics Commons Recommended Citation White, Kristine Nicolle, "Development of Representative Species-Level Molecular Markers and Morphological Character Analysis of Leucothoid Amphipods (Crustacea: Amphipoda)" (2010). Dissertations. 929. https://aquila.usm.edu/dissertations/929 This Dissertation is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Dissertations by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. The University of Southern Mississippi DEVELOPMENT OF REPRESENTATIVE SPECIES-LEVEL MOLECULAR MARKERS AND MORPHOLOGICAL CHARACTER ANALYSIS OF LEUCOTHOID AMPHIPODS (CRUSTACEA: AMPHIPODA) by Kristine Nicolle White Abstract of a Dissertation Submitted to the Graduate School of The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2010 ABSTRACT DEVELOPMENT OF REPRESENTATIVE SPECIES-LEVEL MOLECULAR MARKERS AND MORPHOLOGICAL CHARACTER ANALYSIS OF LEUCOTHOID AMPHIPODS (CRUSTACEA: AMPHIPODA) by Kristine Nicolle White May 2010 Leucothoid amphipods were investigated using morphology and molecular rDNA gene sequence fragments. The morphological diagnostic characters for traditional taxonomy have been clarified, a molecular marker for representative species has been developed, and one of the current anamorph-leucomorph connections has been confirmed with molecular sequence data. Ultimately this study has combined traditional morphological and modern molecular methods to clarify the taxonomy and to propose a preliminary phylogeny of the Leucothoidae. Analysis of 18S rDNA gene fragments from 13 species in two genera supported the current morphological species designations and the separation of the family into two clades. Combined analysis of 18S rDNA and COI mtDNA gene fragments revealed cryptic speciation in one species occurring in Belize and Florida. For the first time in a single work, diagnostic descriptions were presented for all extant species of the Leucothoidae. Fourteen new species of Leucothoe and one new species of Paranamixis were described from Lizard Island, Australia. Morphological cladistic analysis of 64 species of the “leucothoid clade” and 33 species of the “anamixid clade” supported the collapse of the genus Leucothoella and the classification of the genera Anamixis and Paranamixis as a single genus. The poor resolution of trees in these cladistic analyses suggests that rapid ancient speciation is likely a driving factor in the evolution of this family. ii COPYRIGHT BY KRISTINE NICOLLE WHITE 2010 ACKNOWLEDGEMENTS I thank my committee members, Dr. Richard W. Heard, Dr. Jeffery Lotz, Dr. Robin Overstreet, Dr. Trisha Spears, and Dr. James Darwin Thomas for their help in producing this dissertation. I thank Dr. Richard Heard for his tremendous support of my studies and for his relentless enthusiasm for natural history. I thank Dr. Jeffery Lotz for the use of his molecular laboratory, equipment, and supplies and for his input on my research and writing. I thank Dr. Robin Overstreet for filling in gaps with supplies, for sharing his immense knowledge of taxonomy and systematics, and his critical editing of this dissertation. I thank Dr. Trisha Spears for her incredible patience, big heart, and guidance in the molecular work for this dissertation. I thank my mentor, Dr. James Darwin Thomas, for all of his support, guidance, and friendship over the last 9 years; especially the hundreds of hours of conversation that made this dissertation possible. Special thanks go to my honorary committee member, Sara E. LeCroy. Sara has been a friend, colleague, and advisor to me over the last 4 years. My success here at The Gulf Coast Research Laboratory would not be possible without the support she has provided. I thank all of the people at The Gulf Coast Research Laboratory who have assisted with different aspects of this dissertation, especially the molecular work, and who have encouraged me not to give up when things got frustrating. These people include Allison Walker, David Drumm, Brent Thoma, Jana Thoma, Sarah Ballard, Jerry McClelland, Jana Rocker, Jean Jovonovich, Steve Curran, and Marie Mullen. I thank the Gordon Gunter Library staff for their hard work and assistance. Special thanks go to Cathy Schloss for locating a tremendous amount of ancient literature through interlibrary loans. I thank my family for their ongoing support over the many years I have been pursuing degrees. They have always believed in me and encouraged my quest for knowledge. Special thanks go to my husband, Nathan, who constantly reminds me that there is nothing left to do but smile, smile, smile. iii Funding for this and other related studies was provided by National Science Foundation awards (NSF-DEB) Partnerships for Enhancing Expertise in Taxonomy (PEET) (0529749) and (NSF-DBI) Biological Research Collection (BRC) (0749755); The Crustacean Society Fellowship in Graduate Studies, 2007; The University of Southern Mississippi Dissertation and Thesis Research Grant, 2008; Lerner-Gray Fund for Marine Research Grant, 2009; Lytle Coastal Sciences Scholarship, 2009; and Marine and Estuarine Graduate Student Association Student Travel Award, 2009. iv TABLE OF CONTENTS ACKNOWLEDGEMENTS ............................................................................................... iii LIST OF ILLUSTRATIONS ............................................................................................. vi LIST OF TABLES ............................................................................................................. ix CHAPTER I. INTRODUCTION TO THE LEUCOTHOIDAE ................................................... 1 Objectives .............................................................................................................. 1 Historical Background ........................................................................................... 2 Speciation ............................................................................................................ 13 Statement of Problem ........................................................................................... 14 Importance of Study ............................................................................................. 16 Taxonomic Background ....................................................................................... 17 Distribution .......................................................................................................... 22 II. TAXONOMY AND SYSTEMATICS OF THE LEUCOTHOIDAE .................. 30 Material Studied ................................................................................................... 30 Morphological Laboratory Techniques and Data Management .......................... 30 Systematics of the Leucothoidae ......................................................................... 31 III. MORPHOLOGICAL CHARACTER ANALYSIS AND A PRELIMINARY PHYLOGENY FOR THE LEUCOTHOIDAE ................................................. 295 Material Studied ................................................................................................. 295 Morphological Laboratory Techniques and Data Management ........................ 295 Molecular Laboratory Techniques ..................................................................... 296 Morphological Analyses .................................................................................... 298 Molecular Analyses ........................................................................................... 299 Morphological Results ....................................................................................... 302 Molecular Results .............................................................................................. 306 Discussion of Morphological Cladograms ......................................................... 315 Molecular Discussion ........................................................................................ 357 Conclusions ........................................................................................................ 368 APPENDIXES ................................................................................................................ 374 REFERENCES ............................................................................................................... 409 v LIST OF ILLUSTRATIONS Figure 2.1 Leucothoe adelphe, White and Thomas, 2009, holotype male, 1.6 mm, AM P71436 (QLD 1792), Three Sisters Bommie, Yonge Reef; paratype female, 1.9 mm, AM P71271 (QLD 1767), Horseshoe Reef, Lizard Island, Great Barrier Reef .................................................................................................................... 213 2.2 Leucothoe adelphe, White and Thomas, 2009, holotype male, 1.6 mm, AM P71436 (QLD 1792), Three Sisters Bommie, Yonge Reef; paratype female, 1.9 mm, AM P71271 (QLD 1767), Horseshoe Reef, Lizard Island, Great Barrier Reef ...................................................................................................................
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