Population- and Community-Level Consequences of the Exploitation of Large Predatory Marine Fishes by Julia K. Baum Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Dalhousie University Halifax, Nova Scotia September 2007 © Copyright by Julia K. 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The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in et des droits moraux qui protege cette these. this thesis. Neither the thesis Ni la these ni des extraits substantiels de nor substantial extracts from it celle-ci ne doivent etre imprimes ou autrement may be printed or otherwise reproduits sans son autorisation. reproduced without the author's permission. In compliance with the Canadian Conformement a la loi canadienne Privacy Act some supporting sur la protection de la vie privee, forms may have been removed quelques formulaires secondaires from this thesis. ont ete enleves de cette these. While these forms may be included Bien que ces formulaires in the document page count, aient inclus dans la pagination, their removal does not represent il n'y aura aucun contenu manquant. any loss of content from the thesis. Canada DALHOUSIE UNIVERSITY To comply with the Canadian Privacy Act the National Library of Canada has requested that the following pages be removed from this copy of the thesis: Preliminary Pages Examiners Signature Page (pii) Dalhousie Library Copyright Agreement (piii) Appendices Copyright Releases (if applicable) For RAM IV Table of Contents List of Tables viii List of Figures xi Abstract xiv List of Abbreviations and Symbols Used xv Acknowledgements xvii CHAPTER 1 Introduction 1 CHAPTER 2 Shifting Baselines and the Decline of Pelagic Sharks in the Gulf of Mexico 11 ABSTRACT 12 INTRODUCTION 12 METHODS 14 Data 14 Shark Species 16 Modelling Change in Abundance 17 Estimating Change in Size 21 RESULTS 22 Unstandardized Catch Rates 22 Relative Abundance and Size Estimates 26 DISCUSSION 27 SUPPLEMENTARY MATERIAL 32 v Effect of Soak Time and Depth on Model Estimates 32 Model Robustness 33 Effects of Other Operational Factors 34 ACKNOWLEDGEMENTS 35 CHAPTER 3 Estimating Trends in Abundance from Fishery-Dependent Data: Recent Changes in Northwest Atlantic Pelagic Shark Populations 36 ABSTRACT 37 INTRODUCTION 37 METHODS 41 Data and Shark Species 41 Shark Catch Rates in U.S. Pelagic Longline Observer and Logbook Data 47 Observer Data Models 47 RESULTS 54 Shark Catch Rates in U.S. Pelagic Longline Observer and Logbook Data 54 Model Estimates of Recent Changes in Shark Abundance 63 DISCUSSION 70 Shark Catch Rates in U.S. Pelagic Longline Observer and Logbook Data 70 Estimates of Recent Changes in Shark Abundance 71 CHAPTER 4 Cascading Effects of the Loss of Apex Predatory Sharks from a Coastal Ocean 77 ABSTRACT 78 MAIN TEXT 78 SUPPLEMENTARY MATERIAL 94 Materials and Methods 94 Results and Discussion Ill ACKNOWLEDGEMENTS 115 CHAPTER 5 Top-Down Control in the Ocean: Methods, Evidence, Inferred Mechanisms, and Management Implications 116 ABSTRACT 117 1 INTRODUCTION 118 2 INSIGHTS FROM ECOLOGICAL THEORY AND EXPERIMENTS 121 vi 3 OVERCOMING METHODOLOGICAL & DATA LIMITATIONS 125 Improving Methods for Ecosystem-Scale Analyses 127 4 PREDATOR DEPLETIONS REVEAL TOP-DOWN CONTROL 134 Cascading Effects of a Massive Fisheries Collapse 134 Restructuring Oceanic Ecosystems: Mechanisms and Effects 139 5 MANAGEMENT & CONSERVATION IMPLICATIONS 148 6 SYNTHESIS & CONCLUSIONS 150 CHAPTER 6 Conclusions , 153 REFERENCES.. 159 APPENDIX 1 Models of 1992-2005 Observer Data 191 APPENDIX 2 Copyright Permissions 200 Vll List of Tables Table 1.1. Shark species included in thesis analyses {/ at genus level indicates species within the genus were grouped for analysis) and their life history characteristics (age at maturity (for females), fecundity, size at maturity (for females) and maximum size (FL=fork length, TL=total length)) 8 Table 2.1. Comparison of 1950s and 1990s pelagic longline fishing data from the Gulf of Mexico used in analysis. Mean values ± 1 standard deviation 15 Table 2.2. Recorded oceanic and coastal shark species and sample sizes in 1950s and 1990s datasets, listed within each category in declining order of abundance in the 1950s 17 Table 2.3. Modelled species, coefficients for soak time (Ss) and depth (ysl, ys2, ys3) used to calculate the offset, and efficiency of hooks in the 1990s relative to the 1950s for the mean change in soak time and depth respectively 20 Table 2.4. Modelled species weights in kilograms ±1 standard deviation (sample size). 27 Table 2.5. Estimated declines (± 95% CI) between the 1950s and 1990s of oceanic whitetip, silky and dusky sharks in the Gulf of Mexico from the main model, from models examining the effect of the soak time offset and of the depth offset, and from robustness models 33 Table 3.1. Total of each elasmobranch species recorded in the U.S. Atlantic pelagic longline observer program between 1992 and 2005 43 Table 3.2. Total number of each oceanic and large coastal shark species (group) caught, and the total number of fishing sets monitored, each year between 1992 and 2005 as recorded in the U.S. Atlantic pelagic longline observer program (after data checks and removing shark targeted sets) 44 Table 3.3. Total number of each oceanic and large coastal shark species (group) caught, by fishing area, as recorded in the U.S. Atlantic pelagic longline viii observer program from 1992 to 2005 (after data checks and removing shark targeted sets) 45 Table 3.4. Characteristics of observed sets in the U.S. pelagic longline fishery between 1992 and 2005 51 Table 3.5. Total number of monitored sets directed towards each target species between 1992 and 2005 in the US Atlantic pelagic longline observer program . 51 Table 3.6. Number of fishing sets monitored in the U.S. Atlantic pelagic longline fishery observer program between 1992 and 2005, in the full data set, in the data set with trips with only one fishing set removed (used in the GLMM-t models) and with vessels with only one trip also removed (used in the GLMM-vt models), in the data set with sets without hook type removed, with trips with only one fishing set also removed, and with vessels with only one trip also removed 52 Table 3.7. Final models (generalized estimating equations with trip marginal (GEE), generalized linear mixed models with trip random (GLMM-t), and with vessel random, trip residual (GLMM-vt)) for each species showing covariates included in the final model (shaded) and statistical significance level of each: * = <0.1; **=<0.01; ***=<0.001; ****=<0.0001, otherwise non-significant.... 69 Table 4.1. Data sources 81 Table 4.2. Survey, fisheries and landings data set descriptions, including area, gear type, season and years sampled, and total sample size 82 Table 4.3. Model results for each species of great shark from each of the research survey and fisheries data sources used in the meta-analysis shown in Figure 4.4, including the first and last year of capture in the data set, the number of years caught, the total number of the species caught, the model estimate (± 95% confidence intervals (CI)) of the instantaneous rate of change, for all years of data (All) and for only those years onwards from the baseline of 1970 (1970-).... 85 Table 4.4. Model results for each elasmobranch mesopredator species from each of the research surveys used in the meta-analysis shown in Figure 4.4, including the first and last year of capture in the data set, the number of years caught, the total number of the species caught, the model estimate (± 95% confidence intervals (CI)) of the instantaneous rate of change, for all years of data (All) and for only those years onwards from the baseline of 1970 (1970-) 89 Table 4.5. Taxa of elasmobranchs (sharks, skates, rays) consumed by the apex (or nearly apex) shark species included in the large shark group 96 Table 4.6. Summary of generalized linear models used to estimate trends in abundance for large sharks and elasmobranch mesopredators 105 IX Table 5.1. Studies identifying top-down control in oceanic ecosystems 128 Table Al. 1. Parameter estimates (including standard error and p-value) for fixed effects in final GLMM-vt model of 1992-2005 observer data for blue shark ... 192 Table A1.2. Parameter estimates (including standard error and p-value) for fixed effects in final GLMM-vt model of 1992-2005 observer data for mako sharks .193 Table A 1.3. Parameter estimates (including standard error and p-value) for fixed effects in final GLMM-vt model of 1992-2005 observer data for thresher sharks 194 Table A1.4. Parameter estimates (including standard error and p-value) for fixed effects in final GLMM-vt model of 1992-2005 observer data for oceanic whitetip shark 195 Table A 1.5.