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Spatio-Temporal Dynamics of Atlantic Cod Bycatch in the Maine Lobster Fishery and Its Impacts on Stock Assessment Robert E

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Spatio-Temporal Dynamics of Atlantic Cod Bycatch in the Maine Lobster Fishery and Its Impacts on Stock Assessment Robert E The University of Maine DigitalCommons@UMaine Electronic Theses and Dissertations Fogler Library Spring 5-12-2018 Spatio-Temporal Dynamics of Atlantic Cod Bycatch in the Maine Lobster Fishery and Its Impacts on Stock Assessment Robert E. Boenish University of Maine, [email protected] Follow this and additional works at: https://digitalcommons.library.umaine.edu/etd Part of the Aquaculture and Fisheries Commons, Biostatistics Commons, Longitudinal Data Analysis and Time Series Commons, Marine Biology Commons, Natural Resources and Conservation Commons, Natural Resources Management and Policy Commons, Population Biology Commons, Statistical Methodology Commons, Statistical Models Commons, and the Zoology Commons Recommended Citation Boenish, Robert E., "Spatio-Temporal Dynamics of Atlantic Cod Bycatch in the Maine Lobster Fishery and Its Impacts on Stock Assessment" (2018). Electronic Theses and Dissertations. 2829. https://digitalcommons.library.umaine.edu/etd/2829 This Open-Access Dissertation is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of DigitalCommons@UMaine. For more information, please contact [email protected]. SPATIO-TEMPORAL DYNAMICS OF ATLANTIC COD BYCATCH IN THE MAINE LOBSTER FISHERY AND ITS IMPACTS ON STOCK ASSESSMENT By Robert E. Boenish B.S. Western Washington University, 2013 A DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy (in Marine Biology) The Graduate School The University of Maine May 2018 Advisory Committee: Yong Chen, Professor of Fisheries Population Dynamics, Advisor Robert S. Steneck, Professor of Marine Biology, Oceanography, Marine Policy Kate Beard-Tisdale, Professor of Spatial Information Science Joseph Zydlewski, Professor of Wildlife, Fisheries, and Conservation Biology Burton Shank, Research Fishery Biologist, NOAA © 2018 Robert Boenish All Rights Reserved ii SPATIO-TEMPORAL DYNAMICS OF ATLANTIC COD BYCATCH IN THE MAINE LOBSTER FISHERY AND ITS IMPACTS ON STOCK ASSESSMENT By Robert E. Boenish Dissertation Advisor: Dr. Yong Chen An Abstract of the Dissertation Presented in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy (in Marine Biology) May 2018 Of the most iconic fish species in the world, the Atlantic cod (Gadus morhua, hereafter, cod) has been a mainstay in the North Atlantic for centuries. While many global fish stocks have received increased pressure with the advent of new, more efficient fishing technology in the mid- 20th century, exceptional pressure has been placed on this prized gadoid. Bycatch, or the unintended catch of organisms, is one of the biggest global fisheries issues. Directly resulting from the failed recovery of cod in the GoM, attention has been placed as to possible sources of unaccounted catch. Among the most prominent is that of the GoM American lobster (Homarus americanus) trap fishery. My dissertation research contributes to solving these problems by making progress in five areas: Evaluating cod discard survivability, characterizing lobster effort, estimating cod bycatch, incorporating various bycatch scenarios into the current stock assessment framework, and providing an in-depth policy analysis for management to move forward. This dissertation proceeds as follows: Chapter 1 will briefly introduce regional fishing history, and the study species. Chapter 2 a will provide a preliminary habitat analysis and field project with the object of understanding when and where cod are caught as bycatch, and their subsequent survivability post-release. Chapter 3 develops a quasi-stationary bootstrapped Generalized Additive Model method to estimate Maine’s effective lobster effort spanning 2006- 2013. Chapter 4 builds on the same methodologies to estimate Atlantic cod bycatch rates on the congruent spatiotemporal scale, then incorporates uncertainties from both lobster effort and bycatch rates to estimate spatiotemporal cod bycatch. Chapter 5 uses estimates from the previous chapter alongside available federal cod data to estimate historic age-structure and magnitude of cod bycatch from 1982-2016. Then, multiple scenarios are evaluated in the current assessment framework and I report on updated assessment model diagnostics and a novel approach to retrospective analysis. Chapter 6 will conclude with a detailed policy analysis of the state of fisheries in the GoM, and how cod bycatch from the lobster fishery may be equitably incorporated as to ensure productive fisheries across groundfish and lobster sectors while minimizing conflicts. DEDICATION I have been beyond fortunate in my life to have been afforded the opportunities to spend my time thinking about and solving problems that may positively affect the lives of others. I had a realization in graduate school that, “Wow, I actually get paid to think!” First, I would not be in this position without my supportive family, specifically my mother and father who bought me my first crab trap when we moved to Whidbey Island. Second, I have absolutely been irreversibly molded by my days commercial fishing aboard the FV Lil’ Buddy under captain Mike Schille. Without the endless days fishing in Bristol Bay, I would not have the perspective that has been beyond useful in my study of the oceans and the people who depend on them. Further, I dedicate this body of work to all teachers at all levels that go above and beyond to inspire and captivate their students. I believe everyone who is successful at something achieves in part only because somebody took the time or resources to plant a seed or help one grow. Looking back on my past, I am grateful for the patience and time I have received. For all the amazing teachers I’ve had (there are too many too name), thank you. iii ACKNOWLEDGEMENTS This work would not be possible without the help and advice of many, both on and off the water. I thank Yong for the support and vision over the past four years to see this project through. No graduate students in the country are as lucky as those in the Chen lab. Whenever I needed help, I always had multiple avenues in the Chen lab ‘family’. Specifically, this work would not have run as smoothly without Kisei Tanaka, Bai Li, Jocelyn Runnebaum, Zengguang Li, Max Ritchie, Mike Palmer, Chris Legault, Jintao Wang, Mackenzie Mazur, Rebecca Van Beneden, William Ellis, Sue Thibodeau, Carrie Love, Kevin Staples, Gavin Fay, or Jeff Vieser. I would not have had as much fun if it were not for Cayla Calderwood, Andrew O’Malley, Haley Viehman, Constantin Scherelis, Betsy Barber, Megan Switzer, Melissa May, Mattie Codrigue, Bobby Ingalls, Dustin Delano, Justin Papkee, or the fish and ducks of the Penobscot. To my committee I am greatly indebted. Most forthcoming is my advisor. I cannot thank Yong enough for the opportunity and his tireless efforts working with me. All other committee members have been incredible throughout my time and have provided thought-provoking questions and support. I further thank Bob Steneck for expanding my horizons and taking me to Bonaire. Bob showed me there is more in the ocean than just cod and lobster. I could not be more grateful and feel more privileged to attend the University of Maine. During my time in Orono I have received a world-class education and have been able to surround myself with truly remarkable people. Without any piece of the above cast of characters, my work would not have been possible. Finally, I would like to thank my funding. My original work was supported by the NOAA Salltonsall-Kennedy Program, and since, the Maine Research Reinvestment Fund and Maine Sea Grant kept a roof over my head. iv TABLE OF CONTENTS DEDICATION ............................................................................................................................... iii ACKNOWLEDGEMENTS ........................................................................................................... iv LIST OF TABLES ......................................................................................................................... ix LIST OF FIGURES ....................................................................................................................... xi 1. DYNAMIC TECHNICAL INTERACTIONS OF ATLANTIC COD AND AMERICAN LOBSTER FISHERIES IN A CHANGING GULF OF MAINE............................. 1 2. SURVIVABILITY OF ATLANTIC COD (GADUS MORHUA) BYCATCH IN THE MAINE AMERICAN LOBSTER (HOMARUS AMERICANUS) FISHERY.............................. 7 Chapter Abstract ......................................................................................................................... 7 Introduction ................................................................................................................................. 7 Methods....................................................................................................................................... 9 Study area................................................................................................................................ 9 Bycatch rates ......................................................................................................................... 10 Cod habitat suitability indices (HSIs) ................................................................................... 10 Spatial analysis.....................................................................................................................
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