USING VESSEL MONITORING SYSTEM DATA TO UNDERSTAND THE SPATIAL AND TEMPORAL DYNAMICS OF THE COMMERCIAL VERTICAL LINE FISHERY FOR REEF FISH IN THE GULF OF MEXICO By NICHOLAS DAVID DUCHARME-BARTH A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2018 © 2018 Nicholas David Ducharme-Barth To Meghan Sarah for being the reason I follow my dreams ACKNOWLEDGMENTS There are a number of individuals who are responsible for getting me through (and furthering my research) these last five years at the University of Florida. First and foremost, I would like to thank my two funding sources the NOAA Fisheries - Sea Grant Population and Ecosystem Dynamics Fellowship (grant # NA15OAR4170182) and the NOAA Fisheries – RTR program (grant # NA11NMF4550121) as well as the following current and former NOAA- Fisheries scientists: Liz Scott-Denton, Neil Baertlein, and Carlos Rivero for making this research possible. Additionally, I would like to thank Andre Punt (University of Washington), Tom Carruthers (University of British Columbia) and several anonymous reviewers for their thoughtful commentary which greatly improved the quality of Chapters 2 and 3 as well as Sarah Glaser (One Earth Future Foundation) and Hao Ye (University of Florida) for their help thinking through the EDM analysis in Chapter 4. My supervisory committee played a large role in my development as a scientist and I thank them for helping me grow intellectually over the last 5 years specifically Kai Lorenzen for making me realize that you can only learn so much from analyzing data at a computer and that it is often much simpler to get your answer if you just talk to people; Sherry Larkin for teaching me that research questions with well-defined, testable hypotheses are a lot easier to answer; Bill Lindberg for instilling in me the importance of having a solid theoretical understanding of the processes being studied before jumping into the modeling and the analysis; and Kyle Shertzer for taking the time to help me develop interesting questions relevant to the needs of NOAA Fisheries and for going above and beyond as a mentor to help me achieve my career goals after graduation. I would also like to thank my major advisor Rob Ahrens for taking a chance on someone straight out of undergrad that, in retrospect, had no idea how to be a scientist. I thank Rob for being patient, for being willing to talk to me at (mostly) all hours of the day, and for giving me 4 the guidance I needed even if I didn’t always like hearing it. I thank Rob for giving me the freedom to work through my challenges and create opportunities for myself because in doing so you allowed me to gain belief in myself. I know I still have a long way to go and a lot to learn, but I feel confident in my own abilities moving forward having learned from Rob these last five years. Most importantly, I would like to thank those that provided me the social support and inspiration needed on a project of this scale. I thank all of those in the greater Gainesville area and the University of Florida community; friends, family, and lab mates, that have made these last five years so enjoyable. I thank the Crockett family for welcoming me to Florida and teaching me how to be a proper Gator. I thank my parents for all the opportunities that they provided me over the years (including many visits to aquariums worldwide) that allowed me to develop intellectually and that prepared me for this challenge. I thank my sister for being an inspiration to me and someone that I look up to because no matter life’s challenges she always finds a way to rise to the occasion while looking out for others at the same time. Lastly, I would like to thank my wife Meghan. Without her none of this would have been possible. Meghan is the reason I went to grad school and the reason I’m still smiling five years later. 5 TABLE OF CONTENTS page ACKNOWLEDGMENTS ...............................................................................................................4 LIST OF TABLES ...........................................................................................................................8 LIST OF FIGURES .........................................................................................................................9 LIST OF ABBREVIATIONS ........................................................................................................11 ABSTRACT ...................................................................................................................................13 CHAPTER 1 OVERVIEW ...........................................................................................................................15 2 CLASSIFICATION AND ANALYSIS OF VMS DATA IN VERTICAL LINE FISHERIES: INCORPORATING UNCERTAINTY INTO SPATIAL DISTRIBUTIONS ..................................................................................................................21 2.1 Introduction .......................................................................................................................21 2.2 Methods ............................................................................................................................26 2.2.1 Data .........................................................................................................................26 2.2.2 Classification ..........................................................................................................29 2.2.3 Uncertainty in Spatial Predictions ..........................................................................31 2.2.4 Analysis ..................................................................................................................33 2.3 Results...............................................................................................................................37 2.4 Discussion .........................................................................................................................41 3 INDICES OF ABUNDANCE IN THE GULF OF MEXICO REEF FISH COMPLEX: A COMPARATIVE APPROACH USING SPATIAL DATA FROM VESSEL MONITORING SYSTEMS....................................................................................................61 3.1 Introduction .......................................................................................................................61 3.2 Material and Methods .......................................................................................................65 3.2.1 Study Frame ............................................................................................................66 3.2.2 Data .........................................................................................................................67 3.2.3 Abundance Indices .................................................................................................68 3.2.3.1 VMS .............................................................................................................68 3.2.3.2 Delta-GLM (status-quo) ...............................................................................69 3.2.4 Abundance Index Agreement .................................................................................70 3.2.5 Simulation ...............................................................................................................73 3.2.5.1 Base simulation ............................................................................................73 3.2.5.2 Scenarios ......................................................................................................75 3.2.5.3 Abundance indices .......................................................................................76 3.2.5.4 Multivariate analysis ....................................................................................78 6 3.2.5.5 Sequential depletion simulation ...................................................................78 3.3 Results...............................................................................................................................79 3.4 Discussion .........................................................................................................................83 4 SPATIAL CHARACTERIZATION OF THE COMMERCIAL VERTICAL LINE FISHERY FOR REEF FISH IN THE GULF OF MEXICO ................................................100 4.1 Introduction .....................................................................................................................100 4.2 Methods ..........................................................................................................................104 4.2.1 Study Frame ..........................................................................................................104 4.2.2 Data .......................................................................................................................104 4.2.3 Métier Identification .............................................................................................106 4.2.4 Spatially-Explicit Characterization of Species Dynamics ....................................107 4.3 Results.............................................................................................................................110 4.3.1 Métier Identification .............................................................................................110 4.3.2 Characterization of