MACROECOLOGY OF EXPLOITED MARINE SYSTEMS: HUMAN IMPACTS AND THE EFFECTS OF SCALE by Derek Paul Tittensor Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Dalhousie University Halifax, Nova Scotia November 2007 © Copyright by Derek Paul Tittensor, 2007 Library and Bibliotheque et 1*1 Archives Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A0N4 Ottawa ON K1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-39078-8 Our file Notre reference ISBN: 978-0-494-39078-8 NOTICE: AVIS: The author has granted a non­ L'auteur a accorde une licence non exclusive exclusive license allowing Library permettant a la Bibliotheque et Archives and Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par Plntemet, prefer, telecommunication or on the Internet, distribuer et vendre des theses partout dans loan, distribute and sell theses le monde, a des fins commerciales ou autres, worldwide, for commercial or non­ sur support microforme, papier, electronique commercial purposes, in microform, et/ou autres formats. paper, electronic and/or any other formats. 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) This thesis is dedicated to the memory of Ransom A. Myers IV Table of Contents List of Tables x List of Figures xi Abstract xiii List of Abbreviations and Symbols Used xiv Acknowledgements xviii Chapter 1. Introduction 1 1.1 General Introduction 1 1.2 Thesis Structure 2 1.3 Miscellanea 4 Chapter 2. Macroecological Changes in Exploited Marine Systems 6 2.1 Introduction 6 2.2 Changes in Life-History Parameters 10 2.3 Loss of Populations and Species 13 2.3.1 Directed Fisheries 14 2.3.2 Bycatch Effects 15 2.3.3 Range Contraction 16 v 2.3.4 The Allee Effect 17 2.3.5 Loss of Genetic Diversity 19 2.3.6 Historical and Prehistorical Exploration 21 2.4 Changes in Community and Ecosystem Structure, Biodiversity, and Habitat 22 2.4.1 Changes in Community Structure and Ecosystem Dynamics 22 2.4.2 Habitat Modification 33 2.4.3 Emerging Fisheries 34 2.4.4 Destabilisation of Ecosystems 35 2.5 Conclusions 35 2.6 Acknowledgements 38 Chapter 3. Human Impacts on the Species-Area Relationship in Reef Fish Assemblages 39 3.1 Abstract 39 3.2 Introduction 40 3.3 Theory 43 3.4 Materials And Methods 46 3.4.1 Fish Data Collection 46 3.4.2 Habitat Data Collection 49 3.4.3 Calculating Species-Area Relationships 49 3.4.4 Mixed Effects Models 51 3.5 Results 53 3.6 Discussion 62 3.7 Conclusion 67 vi 3.8 Acknowledgements 68 3.9 Appendix 1 - Supplementary Material 69 3.9.1 Testing Functional Forms for the Species-Area Model 69 3.9.2 Tests of Statistical Robustness 72 3.9.3 Mixed-Effects Model Equations 74 3.10 Appendix 2 - Theoretical Model of The Effects of Exploitation on the Power-Law SAR 81 Chapter 4. Predicting Global Habitat Suitability for Stony Corals on Seamounts 91 4.1 Abstract 91 4.1.1 Aim 91 4.1.2 Location 92 4.1.3 Methods 92 4.1.4 Results 92 4.1.5 Main Conclusions 93 4.2 Introduction 93 4.3 Data 97 4.3.1 Coral Data 97 4.3.2 SeamountData 99 4.3.3 Environmental Data 99 4.4. Models 101 4.4.1 Maximum Entropy Modelling 103 4.4.2 Environmental Niche Factor Analysis 105 vii 4.4.3 Model Evaluation 106 4.5 Results 108 4.5.1 Model Evaluation 108 4.5.2 Maxent Results 108 4.5.3 ENFA Results 112 4.5.4 Habitat Suitability for Seamount Summits 112 4.6 Discussion 116 4.7 Conclusions 122 4.8 Acknowledgements 123 Chapter 5. Impact of Anthropogenic Ocean Acidification on Global Cold-Water Stony Coral Habitat 124 5.1 Abstract 124 5.2 Introduction 125 5.3 Methods 127 5.3.1 Coral Database 127 5.3.2 Environmental Layers 129 5.3.3 Habitat Suitability Model 131 5.4 Results 134 5.5 Discussion 141 5.6 Conclusions 144 5.7 Acknowledgements 145 vm Chapter 6. Endemism at Low Sampling Effort: Real or Artefact? 146 6.1 Introduction 146 6.2 Models of Endemism and Sampling 147 6.3 Application of the Method To Data 155 6.3.1 Data 155 6.3.2 The Heuristic Approach 158 6.3.3 Generating Estimates of Confidence 158 6.4 Conclusions and Further Work 162 Chapter 7. Conclusions 164 7.1 Exploitation, Scale and Sampling: Thesis Results 164 7.2 The Macroecological Approach: Strengths and Weaknesses 167 7.3 Management Implications 168 7.4 Where Next? Considerations for Future Marine Macroecological Research 170 References 173 Appendix A: Species List for Species-Area Reef Study 193 Appendix B: Copyright Permissions 202 ix List of Tables Table 3.1: Results for minimal adequate mixed-effects Model (Power Law) 55 Table 3.2 (Part 1): Indices of diversity for protected and exploited sites 59 Table 3.2 (Part 2): Indices of diversity for protected and exploited sites 60 Table 3.3: Mean adjusted r-squared values for the seven least-squares regression models fit to species-area data 71 Table 3.4: Results for minimal adeqaute mixed-effects models (exponential model) 73 Table 3.5: Spatial combinations of transects used to calculate SARs in the Pacific 78 Table 3.6: GPS coordinates for Pacific and Indian sites 79 Table 3.7: Family names for Figure 3.5 80 Table 4.1: Environmental parameters used to predict habitat suitability 100 Table 4.2: AUC Values for all model runs 109 Table 4.3: Correlation between environmental parameters Ill Table 4.4: Variance explained by the first eight ecological factors in the ENFA model 113 Table 5.1: Sources of environmental data used to predict habitat suitability 130 Table 5.2: AUC values for all cross-validation model runs 140 Table Al: Species list for all study locations in the species-area relationship reef study (Chapter 3) 193 x List of Figures Figure 2.1: Trends in community biomass of large predatory fishes in open ocean (a-i) and shelf (j-m) ecosystems 8 Figure 2.2: Proportional changes under exploitation in mean age and length at Maturity for marine fishes from the north-temperate regions of the Atlantic and Pacific Oceans 11 Figure 2.3: Changes in the northern limits of fur seal breeding range in New Zealand 18 Figure 2.4: Temporal changes in New Zealand snapper (Pagrus auratus) populations for two locations 20 Figure 2.5: a) Fish biomass plotted against body mass (circles) for the fish community in the North Sea in 2001 and the fitted size spectrum (steep bold line) 24 Figure 2.6: Linear correlations between cod and shrimp biomass time series from nine North Atlantic locations are suggestive of top-down control 29 Figure 2.7: Changes in species abundance, mean body mass, and community composition in the tropical Pacific between the 1950s and the 1990s 31 Figure 3.1: Conceptual diagram depicting an example of changes in the SAR (a) with (b) a decrease in species richness and (c) an increase in mean species patch occupancy for a set of nested sampling units 45 Figure 3.2: Mean fitted power-law species-area relationships for each region, from minimal adequate mixed-effects models except Atlantic (includes depth) and Mediterranean (includes island) 54 Figure 3.3: The effects of fishing on the species-area slope of the power-law model 56 Figure 3.4: Patterns of rarity under fishing pressure 61 Figure 3.5: Normalised change in family abundance relative to protected areas 77 Figure 4.1: Potential large seamount (greater than 1000 m elevation) locations (-14,000) predicted from an analysis of global digital elevation data generated by Kitchingman & Lai (2004) 95 Figure 4.2: Locations of Scleractinia coral samples from seamounts 98 Figure 4.3: Predicted habitat suitability for seamount Scleractinia, using a maximum entropy model 110 Figure 4.4: ENFA predicted habitat suitability for seamount Scleractinia 114 XI Figure 4.5: Predicted habitat suitability for Scleractinia (on a scale from 0 To 100) on the summits of potential large seamounts 115 Figure 5.1: Locations of scleractinian coral records in our database 128 Figure 5.2: Predicted present-day habitat suitability for scleractinians 136 Figure 5.3: Predicted 2099 habitat suitability for Scleractinians given ocean chemistry changes modelled following the IS92a 'business-as-usual' scenario 137 Figure 5.4: Global and regional changes in cold-water stony coral habitat suitability 138 Figure 6.1: False endemics predicted from sampling two identical communities as described in the text 151 Figure 6.2: Percentage of false endemics for differing scenarios of evenness, species richness, and sampling intensity 153 Figure 6.3: Ranked species abundance pooled from abyssal sites (blue bars) and predicted by the TNBD (red dots) 157 Figure 6.4: Mean estimates of false endemics (top) and number of species sampled (bottom) from two identical simulated communities 159 Figure 6.5: Mean false endemics (black) and margin of error (red) for simulated communities derived from TNBD fitted to abyssal data 161 xn Abstract Macroecology is the study of emergent statistical patterns in ecology.