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Identification and Incorporation of Quantitative Indicators of Ecosystem

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Identification and Incorporation of Quantitative Indicators of Ecosystem Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2012 Identification and incorporation of quantitative indicators of ecosystem function into single-species fishery stock assessment models and the associated biological reference points Melissa Hedges Monk Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Oceanography and Atmospheric Sciences and Meteorology Commons Recommended Citation Monk, Melissa Hedges, "Identification and incorporation of quantitative indicators of ecosystem function into single-species fishery stock assessment models and the associated biological reference points" (2012). LSU Doctoral Dissertations. 476. https://digitalcommons.lsu.edu/gradschool_dissertations/476 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. IDENTIFICATION AND INCORPORATION OF QUANTITATIVE INDICATORS OF ECOSYSTEM FUNCTION INTO SINGLE-SPECIES FISHERY STOCK ASSESSMENT MODELS AND THE ASSOCIATED BIOLOGICAL REFERENCE POINTS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Oceanography and Coastal Sciences by Melissa Monk B.S., Virginia Tech, 2004 M.S., Virginia Tech, 2007 August 2012 DEDICATION To my husband Dr. Joshua Monk, for his support during my pursuit of a doctoral degree. ii ACKNOWLEDGMENTS First, I would like to thank my major advisor, Dr. Joseph Powers for all of his valuable insight, support, advice, and for challenging me as a student and scientist over the past four years. I also want to thank Dr. Powers for the opportunities he provided for me to attend conferences, symposiums and meetings and exposing me to the world of fisheries management. I am also grateful for Dr. Powers for answering my unending questions and always keeping his door open. I also owe a great amount of my gratitude to my committee members Dr. Jim Cowan, Dr. Chris D’Elia, Dr. Brian Marx, Dr. Kenny Rose, and my dean’s representative Dr. Fern Galvez. All of my committee members have been a wonderful source of knowledge in fisheries, statistics, and modeling. I want to thank all of my committee members for the time and effort they have given to my dissertation. I want to thank Dr. Liz Brooks at the National Marine Fisheries Center for being my mentor through the NMFS/ Sea Grant Fellowship program. Thank you Dr. Brooks for encouraging me to learn R and taking the time to host meet for a week at the Northeast Fisheries Science Center. Dr. Brooks also provided valuable insight during the development process of my dissertation and provided feedback on my chapters. I am especially grateful to Kirsten Simonsen and Dr. Michelle Zapp Sluis for taking me into the field to see real fish, deciding to pursue their “PhDs in Friendship” and for making this process so much more enjoyable. I am also grateful to Lauren Land, Dr. Melissa Baustian and Courtney Saari for making the EnvironMentors program such a huge success. Finally, I would like to thank my husband, parents, grandparents, and in-laws for all of their love and support throughout my dissertation studies. I could not have done this without them. iii This project was funded by the National Marine Fisheries Service / Sea Grant PhD Fellowship for Marine Population Dynamics as well as the Louisiana Department of Wildlife and Fisheries. iv TABLE OF CONTENTS DEDICATION ................................................................................................................................ ii ACKNOWLEDGMENTS ............................................................................................................. iii ABSTRACT .................................................................................................................................. vii GENERAL INTRODUCTION ....................................................................................................... 1 Literature Cited ........................................................................................................................... 5 CHAPTER 1 : SPATIAL AND TEMPORAL PATTERNS IN THE DEMERSAL FISH COMMUNITY ASSOCIATED WITH THE NORTHWESTERN GULF OF MEXICO SHRIMP TRAWL FISHERY ......................................................................................................................... 7 Introduction ................................................................................................................................. 7 Methods..................................................................................................................................... 13 Results ....................................................................................................................................... 22 Discussion ................................................................................................................................. 46 Literature Cited ......................................................................................................................... 59 CHAPTER 2 : UTILIZATION OF A MULTISPECIES LOTKA-VOLTERRA MODEL TO EXPLORE BIOLOGICAL REFERENCE POINTS FROM A SINGLE-SPECIES SURPLUS PRODUCTION MODEL.............................................................................................................. 64 Introduction ............................................................................................................................... 64 Methods..................................................................................................................................... 68 Results ....................................................................................................................................... 78 Discussion ................................................................................................................................. 99 Literature Cited ....................................................................................................................... 103 CHAPTER 3 : EFFECT OF CONNECTANCE ON BIOLOGICAL REFERENCE POINTS FROM MULTISPECIES AND SINGLE SPECIES MODELS ................................................. 108 Introduction ............................................................................................................................. 108 Methods................................................................................................................................... 110 Results ..................................................................................................................................... 111 Discussion ............................................................................................................................... 131 Literature Cited ....................................................................................................................... 135 CHAPTER 4 : SINGLE-SPECIES BIOLOGICAL REFERENCES POINT IN A MULTISPECIES FISHERY ....................................................................................................... 137 v Introduction ............................................................................................................................. 137 Methods................................................................................................................................... 138 Results ..................................................................................................................................... 139 Discussion ............................................................................................................................... 147 Literature Cited ....................................................................................................................... 153 GENERAL SUMMARY AND CONCLUSIONS...................................................................... 155 APPENDIX A : CHAPTER 1 SUPPLEMENTARY MATERIAL ............................................ 158 APPENDIX B : CHAPTER 2 SUPPLEMENTARY MATERIAL ............................................ 175 APPENDIX C : CHAPTER 3 SUPPLEMENTARY MATERIAL ............................................ 176 APPENDIX D : CHAPTER 4 SUPPLEMENTARY MATERIAL ............................................ 188 APPENDIX E : COMPUTER CODE FOR THE LOTKA-VOLTERRA SIMULATIONS ...... 189 VITA ........................................................................................................................................... 196 vi ABSTRACT The move towards an ecosystem approach to fisheries management requires baseline information on the biotic communities and an understanding of the interactions among species. The two objectives of this study were to describe the demersal fish community (DFC) associated with the northwestern Gulf shrimp trawl fishery, and to utilize a multispecies Lotka-Volterra model to examine possible community level effects of fishing. Community level effects include predator-prey interactions and the responses of fish in the same community to fishing pressure. The summer and fall Southeast Area Monitoring and Assessment Program (SEAMAP) bottomfish
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