W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2002 Genetic stock structure of the sailfish, Istiophorus platypterus, based on nuclear and mitochondrial DNA Jan Renee McDowell College of William and Mary - Virginia Institute of Marine Science Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Fresh Water Studies Commons, Genetics Commons, Molecular Biology Commons, and the Oceanography Commons Recommended Citation McDowell, Jan Renee, "Genetic stock structure of the sailfish, Istiophorus platypterus, based on nuclear and mitochondrial DNA" (2002). Dissertations, Theses, and Masters Projects. Paper 1539616769. https://dx.doi.org/doi:10.25773/v5-2wv9-6970 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]. Reproduced with with permission permission of of the the copyright copyright owner.owner. FurtherFurther reproduction reproduction prohibited prohibited without without permission. permission. GENETIC STOCK STRUCTURE OF THE SAILFISH. ISTIOPHORUS PLATY'PTERUS, BASED ON NUCLEAR AND MITOCHONDRIAL DNA. A Dissertation Presented to The Faculty of the School of Marine Science The College of William and Mary in Virginia In Partial Fulfilment Of the Requirements for the Degree of Doctor of Philospophy by Jan Renee McDowell 2002 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. This dissertation is submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Jan Ri McDowell Approved November, 2002 ( a A (Job* E. Graves, Ph.D. Committee Chair/Advisor ft t< Eugene M. Burreson, Ph.D. Bruce B. Collette, Ph.D. f j l . Emmett Duffy, Ph.D^> J7 David /I ilian Pepperell, Ph.D. KimberlydfS.t S. Reece, Pn.D ii Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. TABLE OF CONTENTS Page LIST OF TABLES................................................................................................................ iv LIST OF FIGURES...............................................................................................................viii ABSTRACT............................................................................................................................x GENERAL INTRODUCTION...........................................................................................2 CHAPTER 1. REVIEW OF SAILFISH BIOLOGY.....................................................6 LITERATURE CITED.........................................................................................................21 CHAPTER 2. MODERN AND HISTORICAL POPULATION STRUCTURE OF THE SAILFISH, ISTIOPHRUSPLATYPTERUS, INFERRED FROM ANALYSIS OF MITOCHONDRIAL DNA...........................33 INTRODUCTION..................................................................................................................34 MATERIALS AND METHODS........................................................................................ 41 RESULTS.................................................................................................................................47 DISCUSSION......................................................................................................................... 58 LITERATURE CITED..........................................................................................................68 APPENDIX 1...........................................................................................................................106 CHAPTER 3. GENETIC STOCK STRUCTURE OF THE SAILFISH, ISTIOPHORUSPLATYPTERUS, BASED ON MICROSATELLITE DNA MARKERS.............................................. 149 INTRODUCTION..................................................................................................................150 MATERIALS AND METHODS.........................................................................................154 RESULTS.................................................................................................................................157 iii Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. DISCUSSION.......................................................................................................................... 163 LITERATURE CITED.......................................................................................................... 169 CHAPTER 4. NUCLEAR AND MITOCHONDRIAL DNA MARKERS FOR SPECIFIC IDENTIFICATION OF ISTIOPHORID AND XIPHIID BILLFISHES...................................................................195 INTRODUCTION...................................................................................................................196 MATERIALS AND METHODS....................................................................................... 199 RESULTS.................................................................................................................................202 DISCUSSION..........................................................................................................................205 LITERATURE CITED..........................................................................................................209 VITA..........................................................................................................................................231 iv Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. LIST OF TABLES Table Page 1. Distribution of composite haplotypes based on RFLP analysis of the mitochondrial control region ....................................................................................... 77 2. Haplotypic diversity (/z) and nucleotide diversity (^) within samples of sailfish ............................................................................................................................ 79 3. Analysis of geographic heterogeneity in frequency distributions using a Monte Carlo Simulation with 10,000 replicates ...........................................80 4. Probability of significance for exact tests using pairwise comparisons based on mtDNA RFLP analysis ................................................................................. 81 5. Hierarchical analysis of molecular variance (AMOVA) of sailfish mtDNA RFLP data......................................................................................................... 82 6. Frequency distribution of major clades identified by RFLP analysis ...................83 7. Diversity of within and between major clades based on mtDNA RFLP data...........................................................................................................................84 V Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. 8. Nucleotide sequence diversity estimates based on sequencing of 1636 base pairs of sailfish mitochondrial DNA including the control region ..............85 9. Divergence estimates based on DNA sequence analysis of 1636 base pairs of sailfish mitochondrial DNA including the control region ........................86 10. Average nucleotide usage for the six amplified mitochondrial regions ..............87 11. Position in sequence, state in respective clade (A,G,C,or T), type of change (Tr for transition. Tv for transversion), for the 19 fixed differences between Atlantic and ubiquitous clade sequences ................... 88 12. Diversity within and Divergence between Atlantic and Ubiquitous sailfish clades and White (Atlantic) and Striped (Pacific) marlin based on control region sequences ...................................................................................... 89 13. Haplotype frequencies across all collections .............................................................90 14. Descriptive statistics for microsatellite data ............................................................ 175 15. Hardy Weinburg Equilibrium-test of association at the locus level using the methods of Guo and Thompson (1993) ............................................................ 176 16. Tests of Hardy-Weinburg equillibrium at the level of genotype .........................178 vi Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. 17. Hierarchical analysis of molecular variance (AMOVA) of sailfish microsatellite data based on sum of squared size difference (RST) .................... 179 18. Hierarchical analysis of molecular variance (AMOVA) of sailfish microsatellite data based on number of alleles (FST) ............................................ 181 19. Locus by locus AMOVA of sailfish microsatellite data based on number of different alleles (FST) ................................................................................ 183 20. Population pairwise FST and RST values calculated for the MN01 locus .................................................................................................................................... 187 21. Population pairwise FST and RST values calculated for the MN08 locus ....................................................................................................................................188