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The Distribution of Copepods in the Shubenacadie River Estuary Relative to the Diet of Larval Striped Bass (Morone Saxatilis)

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The Distribution of Copepods in the Shubenacadie River Estuary Relative to the Diet of Larval Striped Bass (Morone Saxatilis) THE DISTRIBUTION OF COPEPODS IN THE SHUBENACADIE RIVER ESTUARY RELATIVE TO THE DIET OF LARVAL STRIPED BASS (MORONE SAXATILIS) by Kamryn Rose Findlay Submitted in partial fulfilment of the requirements for the degree of Master of Science at Dalhousie University Halifax, Nova Scotia April 2019 © Copyright by Kamryn Rose Findlay, 2019 DEDICATION I dedicate this thesis to my Dad, Ronald Findlay, expert bass and salmon angler. Thank you for inspiring me to continue my studies in the field of aquatic sciences and fisheries. Thank you for instilling your love of fish upon me and teaching me to appreciate life under water. ii TABLE OF CONTENTS LIST OF TABLES ........................................................................................................................ vii LIST OF FIGURES ....................................................................................................................... ix ABSTRACT ................................................................................................................................. xiv LIST OF ABBREVIATIONS USED ........................................................................................... xv ACKNOWLEDGEMENTS ......................................................................................................... xvi CHAPTER 1: INTRODUCTION ................................................................................................... 1 CHAPTER 2: STATE OF KNOWLEDGE AND RESEARCH RATIONALE ............................. 4 2.1 PHYSICAL CHARACTERISTICS OF THE STEWIACKE-SHUBENACADIE RIVER ESTUARY ............ 4 2.2 STRIPED BASS (MORONE SAXATILIS) TAXONOMY AND GEOGRAPHIC DISTRIBUTION ............... 9 2.3 STRIPED BASS LIFE HISTORY ............................................................................................... 10 2.4 PREDATOR-PREY RELATIONSHIPS: STRIPED BASS LARVAE AND PREY................................. 14 2.4.1 Copepod Biology and the Match-Mismatch Hypothesis .............................................. 14 2.4.2 Plankton of the Inner Bay of Fundy and Shubenacadie River ..................................... 17 2.5 SUMMARY OF THESIS OBJECTIVES ....................................................................................... 26 CHAPTER 3: MATERIALS AND METHODS .......................................................................... 27 3.1 STUDY AREA: TEMPERATURE AND SALINITY OF THE SHUBENACADIE RIVER ESTUARY ....... 27 3.2 PLANKTON NET SAMPLING: DISTRIBUTION RELATIVE TO TIME OF YEAR AND SALINITY ..... 32 3.3 SAMPLE SORTING AND ENUMERATION ................................................................................. 34 3.4 COPEPOD DNA EXTRACTION, PCR, AND SEQUENCING ........................................................ 35 iii 3.4.1 PCR Amplification ....................................................................................................... 35 3.4.2 Gel Electrophoresis and Clean-Up ............................................................................... 36 3.4.3 DNA Sequencing .......................................................................................................... 38 3.5 GUT CONTENT ANALYSIS ..................................................................................................... 39 3.6 COPEPOD IMAGE ANALYSIS .................................................................................................. 39 3.7 STATISTICAL METHODS ........................................................................................................ 40 3.7.1 Copepod Abundance Relative to Salinity and Time of Year (2013 to 2017) ............... 40 3.7.2 2016 and 2017 Striped Bass Egg and Larvae Abundance Relative to Salinity and Time of Year ................................................................................................................................... 42 CHAPTER 4: COPEPOD DIVERSITY, ABUNDANCE AND DISTRIBUTION RELATIVE TO TIME OF YEAR AND SALINITY .............................................................................................. 44 4.1 INTRODUCTION ..................................................................................................................... 44 4.2 METHODS SUMMARY ........................................................................................................... 45 4.3 RESULTS: COPEPOD DIVERSITY ............................................................................................ 46 4.3.1 Chronology of Copepod Identification ......................................................................... 46 4.3.2 Copepod Body Size ...................................................................................................... 47 4.3.3 Ectinosomatidae Copepod Morphology ....................................................................... 48 4.3.4 Scanning Electron Microscopy (SEM) Images of the Ectinosomatidae Copepod ....... 52 4.4 RESULTS: COPEPOD DISTRIBUTIONS RELATIVE TO TIME OF YEAR ....................................... 59 4.5 RESULTS: COPEPOD DISTRIBUTIONS RELATIVE TO SALINITY ............................................... 64 4.6 DISCUSSION .......................................................................................................................... 69 iv 4.6.1 Copepod Diversity: Identification Methods ................................................................. 69 4.6.2 Copepod Body Length .................................................................................................. 70 4.6.3 Ectinosomatidae DNA Sequencing and Identification ................................................. 71 4.6.4 Copepod Distributions Relative to Time of Year ......................................................... 75 4.6.5 Copepod Distributions Relative to Salinity .................................................................. 78 4.7 CONCLUSION ........................................................................................................................ 82 CHAPTER 5: STRIPED BASS SPAWNING, LARVAE ABUNDANCE, DISTRIBUTION, AND GUT CONTENTS ........................................................................................................................ 83 5.1 INTRODUCTION ..................................................................................................................... 83 5.2 METHODS SUMMARY ........................................................................................................... 83 5.3 RESULTS: STRIPED BASS SPAWNING .................................................................................... 84 5.4 RESULTS: DISTRIBUTION OF STRIPED BASS LARVAE RELATIVE TO TIME OF YEAR .............. 86 5.5 RESULTS: DISTRIBUTION OF STRIPED BASS LARVAE RELATIVE TO SALINITY ...................... 88 5.6 RESULTS: TRANSITION FROM ENDOGENOUS TO EXOGENOUS NUTRITION RELATIVE TO GAPE AND BODY LENGTH .................................................................................................................... 91 5.7 RESULTS: GUT CONTENTS OF FIRST FEEDING STRIPED BASS LARVAE ................................. 92 5.8 DISCUSSION: STRIPED BASS SPAWNING ............................................................................. 101 5.9 DISCUSSION: DISTRIBUTION OF STRIPED BASS LARVAE ..................................................... 102 5.10 DISCUSSION: IDENTIFICATION OF POTENTIAL ZOOPLANKTON PREY ITEM SPECIES AND GUT CONTENTS OF LARVAE ............................................................................................................. 106 5.10.1 The Transition of Striped Bass Larvae from Endogenous to Exogenous Nutrition . 106 5.10.2 Striped Bass Larval Gape Limitation ....................................................................... 108 v 5.10.3 Relative Abundance of Copepods in the Gut Contents Versus Water Column ....... 109 5.10.4 Relationship Between the Ectinosomatidae Harpacticoid Copepod and Striped Bass Larvae .................................................................................................................................. 110 5.10.5 Match-Mismatch of Copepods and First Feeding Striped Bass Larvae ................... 113 5.11 CONCLUSION .................................................................................................................... 116 CHAPTER 6: CONCLUSION ................................................................................................... 117 BIBLIOGRAPHY ....................................................................................................................... 119 APPENDIX A: RAW DATA ..................................................................................................... 132 APPENDIX B: PHYLOGENETIC ANALYSIS ........................................................................ 139 APPENDIX C: 150µM RAW DATA ......................................................................................... 140 vi LIST OF TABLES Table 1. Striped bass early life stage synonymized nomenclature with Hardy (1978) as standard description. Shubenacadie River Estuary stock descriptions in comparison to Hardy (1978). ........................................................................................................................ 13 Table 2. Taxonomic classification of copepod species captured in the Shubenacadie River Estuary from 2013-2017, not including the previously undescribed harpacticoid species. Kingdom Animalia, Phylum Arthropoda, Class Maxillopoda, and Sub-Class Copepoda (Dole-Olivier et al., 2000; Walter and Boxshall, 2018; Webref 1, 2018). 18 Table
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