The following book was published on 5 August 2010: Marine Mammal Ecology and Conservation: A Handbook of Techniques Edited by Ian L. Boyd, W. Don Bowen and Sara J. Iverson Oxford University Press http://ukcatalogue.oup.com/product/9780199216574.do Contents List of abbreviations xviii List of contributors xxiii Ch 1 Ethics in marine mammal science Nick J. Gales, David Johnston, Charles Littnan, and Ian L. Boyd 1.1 Introduction 1 1.1.1 Ethics: defining the boundaries between right and wrong 3 1.1.2 Financial and professional costs of compliance 4 1.1.3 Keeping the research ethics and conservation ethics apart 5 1.2 Guiding principles 6 1.2.1 Science for the common good 6 1.2.2 Principle 1 6 1.2.3 Principle 2 7 1.2.4 Principle 3 7 1.2.5 Principle 4 7 1.2.6 Principle 5 8 1.3 The role of professional societies in developing and maintaining ethics in marine mammal science 8 1.4 The 3 Rs (refinement, reduction, and replacement) 9 1.5 Type I and Type II errors 11 1.6 Best practice 12 1.6.1 Threatened versus abundant 12 1.6.2 Timing and location 13 1.6.3 Experimental procedures and equipment 13 1.6.4 Training 13 1.6.5 Environmental considerations 13 1.6.6 Cultural consideration 14 1.6.7 Decision analysis frameworks and cost–benefit analyses 14 1.7 Summary 15 Ch2 Marking and capturing Tom Loughlin, Louise Cunningham, Nick J. Gales, Randall Wells, and Ian L. Boyd 2.1 Introduction 16 2.2 Applying marks 17 2.2.1 Flipper tagging pinnipeds 17 2.2.2 Discovery tags 19 2.2.3 PIT tags 19 2.2.4 Hot-iron branding 20 2.2.5 Freeze-branding 21 2.2.6 Fur clipping 23 2.2.7 Dye marking 23 2.2.8 Dorsal fin tags on cetaceans 24 2.3 Photo-identification 25 2.3.1 Strengths and weaknesses 26 2.3.2 Application 26 2.3.3 Pattern recognition methods 26 2.3.4 Assessing errors 28 2.4 Capture and restraint 28 2.4.1 Techniques for restraint in pinnipeds 29 2.4.2 Chemical restraint and immobilization in pinnipeds 33 2.4.3 Techniques for capture–release of cetaceans 35 2.4.4 Techniques for restraint and handling 38 2.4.5 Risks to cetaceans during capture and handling 39 2.5 Risks to researchers during marine mammal capture and handling 40 Ch3 Estimating the abundance of marine mammals Philip S. Hammond 3.1 Introduction 42 3.2 Extrapolation of counts 44 3.3 Mark–recapture methods 45 3.3.1 Assumptions in theory and practice 47 3.3.2 Data collection 49 3.3.3 Analysis 51 3.4 Line transect sampling 53 3.4.1 Assumptions in theory and practice 55 3.4.2 Extensions and variants of conventional line transect sampling 56 3.4.3 Data collection on visual line transect surveys 59 3.4.4 Analysis 63 3.5 Concluding remarks 65 3.6 Acknowledgements 67 Ch4 The spatial analysis of marine mammal abundance Jason Matthiopoulos and Geert Aarts 4.1 Introduction 68 4.2 The importance of life history 69 4.3 Usage data and sampling design 72 4.4 Basic concepts and challenges 75 4.5 Pre-processing 81 x j Contents 4.6 Analysis techniques 82 4.7 The spatial analyst’s software toolbox 91 4.8 Prospects and trends 95 Ch5 Morphometrics, age estimation, and growth W. Don Bowen and Simon Northridge 5.1 Introduction 98 5.2 Standard morphometrics 98 5.2.1 General issues 98 5.2.2 Body condition 100 5.2.3 Standard measurements 101 5.3 Age determination 107 5.3.1 Dental growth layers 108 5.3.2 Other age-structured material 114 5.3.3 Chemical methods 115 5.4 Growth rates 116 5.5 Conclusions 117 Ch6 Vital rates and population dynamics Jason D. Baker, Andrew Westgate, and Tomo Eguchi 6.1 Introduction 119 6.2 Reproductive rate 120 6.2.1 Description of parameters 120 6.2.2 Techniques 123 6.3 Survival rate 126 6.3.1 Cross-sectional age structure analysis 126 6.3.2 Capture–recapture 127 6.3.3 Study design considerations 131 6.3.4 Model selection 132 6.3.5 Multi-state models 134 6.3.6 Recoveries from dead animals 134 6.3.7 Robust design 135 6.4 Population models 135 6.4.1 Exponential and geometric models 136 6.4.2 Matrix models 137 6.4.3 Incorporating uncertainty: deterministic versus stochastic models 138 6.4.4 Density dependence 139 6.4.5 Individual-based models (IBM) 140 6.4.6 Population viability analysis (PVA) 141 6.4.7 Bayesian approach to modelling 142 6.4.8 Model fit and selection 142 Ch7 Epidemiology, disease, and health assessment Ailsa J. Hall, Frances M.D. Gulland, John A. Hammond, and Lori H. Schwacke 7.1 Introduction 144 7.1.1 Exposures and responses 146 7.1.2 Confounding factors 147 7.2 Effects, responses, and diagnostic techniques 148 7.2.1 Measuring disease occurrence 148 7.2.2 Responses, health panels, and disease classification 149 7.2.3 Sample and data collection 152 7.2.4 Disease diagnosis 155 7.3 Epidemiological study designs 158 7.4 Risk assessment 160 Ch8 Measurement of individual and population energetics of marine mammals Sara J. Iverson, Carol E. Sparling, Terrie M. Williams, Shelley L.C. Lang, and W. Don Bowen 8.1 Introduction 165 8.1.1 Definitions 167 8.2 Measurement of metabolism 169 8.2.1 Direct calorimetry 170 8.2.2 Respirometry (measurement of gas exchange) 170 8.2.3 Doubly labelled water (DLW) and isotope dilution 173 8.2.4 Proxies for assessing energy expenditure (EE)—heart rate (fH) and stroking rate (fS) 176 8.2.5 Proxies for assessing energy expenditure (EE)—allometry 178 8.3 Estimating body composition 179 8.3.1 Carcass analysis and the relationship between chemical constituents 179 8.3.2 Total body water (TBW) measurement 180 8.3.3 Ultrasound 181 8.3.4 Bioelectrical impedence analysis (BIA) 182 8.3.5 Novel approaches to estimating body composition 182 8.4 Energy balance analysis 183 8.5 Energetics of lactation 184 8.5.1 Milk composition 185 8.5.2 Milk output and milk energy output 187 8.6 Population energetics 189 Ch9 Diet Dominic J. Tollit, Graham J. Pierce, Keith A. Hobson, W. Don Bowen, and Sara J. Iverson 9.1 Introduction 191 9.2 Collection of gastrointestinal tract contents 194 xii j Contents 9.2.1 Sampling dead animals 194 9.2.2 Lavage 195 9.2.3 Rectal enema and faecal loops 195 9.3 Collection of faeces and regurgitated/discarded prey remains 196 9.4 Sampling bias 197 9.5 Laboratory processing of prey hard structures 198 9.5.1 Prey extraction 198 9.5.2 Prey identification 199 9.5.3 Prey enumeration using minimum number of individuals (MNI) 200 9.5.4 Measurement of prey structures 201 9.6 Quantification of diet composition using GI tract and faecal analyses 203 9.6.1 Accounting for complete digestion of hard part structures 203 9.6.2 Other factors affecting recovery of hard part structures 204 9.6.3 Accounting for partial digestion of hard part structures 204 9.6.4 Prey length and mass reconstruction 205 9.6.5 Quantification methods 206 9.7 Molecular identification of prey remains 208 9.8 Fatty acid (FA) signatures 210 9.8.1 Tissues for analysis 211 9.8.2 Sample storage and chemical analysis 213 9.8.3 Using predator FAs to qualitatively infer diet 214 9.8.4 Using predator and prey FAs to quantitatively estimate diet 214 9.9 Stable isotopes and other markers 216 9.9.1 Tissues for analysis 217 9.9.2 Trophic modelling 218 9.9.3 Source of feeding and marine isoscapes 219 9.9.4 Other elements and compounds 219 9.9.5 Field and laboratory methods and data analysis 219 9.10 Summary 221 Ch 10 Telemetry Bernie McConnell, Mike Fedak, Sascha Hooker, and Toby Patterson 10.1 Introduction 222 10.2 Design considerations 223 10.3 Attachment 224 10.4 Location determination 227 10.5 Sensors 228 10.6 Information relay 230 10.7 Data modelling and compression 234 10.8 Visualization and analysis of individual paths 234 10.8.1 Heuristic approaches to position filtering 236 10.8.2 Statistical approaches to path analysis 237 10.9 Concluding remarks 241 Ch 11 Foraging behaviour Mark A. Hindell, Dan Crocker, Yoshihisa Mori, and Peter Tyack 11.1 Introduction 243 11.2 Observation of foraging 243 11.2.1 Following focal animals 243 11.2.2 Passive acoustic observations 244 11.3 Cameras 245 11.4 Reconstruction of foraging behaviour 246 11.4.1 Time–depth recorders 246 11.4.2 Sampling strategies 249 11.4.3 Interpretation of ‘foraging’ dives 249 11.5 Feeding success 252 11.6 Acoustics and echolocation 254 11.7 Foraging tactics 256 11.7.1 Central place foraging 256 11.7.2 Search tactics and characterizing the prey field 257 11.7.3 Functional response 258 11.8 Foraging models 259 11.8.1 Optimal foraging models 259 11.8.2 Stochastic models 261 Ch12 Studying marine mammal social systems Hal Whitehead and Sofie Van Parijs 12.1 Introduction 263 12.1.1 The definition of social structure 263 12.1.2 How do we study social structure? 263 12.1.3 Styles of studying social structure 265 12.2 Field research 265 12.2.1 Identifying individuals 265 12.2.2 Collecting interaction, association, and group data 266 12.2.3 Collecting social data without observing animals 268 12.3 Relationship measures 269 12.3.1 Interaction rates 269 12.3.2 Association indices 269 12.3.3 Temporal measures 270 12.3.4 Matrices of relationship measures 270 12.4 Describing and modelling social structure 271 12.4.1 Visual displays 271 12.4.2 Testing for preferred/avoided companions 273 12.4.3 Network analyses 274 12.4.4 Lagged association rates 276 12.4.5 Describing mating systems 277 12.4.6 Other methods of social analysis 277 12.4.7 Useful software 278 12.5 Broader issues 278 12.5.1 Evolutionary forces behind marine mammal social structures 278 12.5.2 How can we study culture in marine mammals? 279 12.6 Acknowledgements 280 Ch13 Long-term studies W. Don Bowen, Jason D. Baker, Don Siniff, Ian L. Boyd, Randall Wells, John K.B. Ford, Scott D. Kraus, James A. Estes, and Ian Stirling 13.1 Introduction 283 13.2 Grey seal (Halichoerus grypus) W. Don Bowen 284 13.2.1 Motivation 284 13.2.2 Nesting of short-term objectives within long-term objectives and change in focus through time 285 13.2.3 Standardization of methods and effects of changing technology and techniques 285 13.2.4 Challenges 286 13.3 Hawaiian monk seal (Monachus schauinslandi) Jason D. Baker 286 13.3.1 Motivation 286 13.3.2 Nesting of short-term objectives within long-term objectives and change in focus through time 286 13.3.3 Standardization of methods and effects of changing technology and techniques 287 13.3.4 Challenges 287 13.4 Weddell seal (Leptonychotes weddellii) Don Siniff 288 13.4.1 Motivation 288 13.4.2 Nesting of short-term objectives within long-term objectives and change in focus through time 289 13.4.3 Standardization of methods and effects of changing technology and techniques 290 13.4.4 Challenges 290 13.5 Antarctic fur seals (Arctocephalus gazella) Ian L. Boyd 290 13.5.1 Motivation 290 13.5.2 Nesting of short-term objectives within long-term objectives and change in focus through time 291 13.5.3 Standardization of methods and effects of changing technology and techniques 292 13.6 Bottlenose dolphin (Tursiops truncatus) Randall Wells 292 13.6.1 Motivation 292 13.6.2 Nesting of short-term objectives within long-term objectives and change in focus through time 293 Contents j xv 13.6.3 Standardization of methods and effects of changing technology and techniques 294 13.6.4 Challenges 294 13.7 Killer whale (Orcinus orca) John K.B. Ford 295 13.7.1 Motivation 295 13.7.2 Nesting of short-term objectives within long-term objectives and change in focus through time 295 13.7.3 Standardization of methods and effects of changing technology and techniques 296 13.7.4 Challenges 296 13.8 North Atlantic right whale (Eubalaena glacialis) Scott D. Kraus 297 13.8.1 Motivation 297 13.8.2 Advances in methods and changing objectives through time 298 13.8.3 Challenges 299 13.9 Sea otters (Enhydra lutris) and kelp forests James A. Estes 299 13.9.1 Motivation 299 13.9.2 Approaches 299 13.9.3 Methods 300 13.9.4 Rewards 301 13.9.5 Challenges 301 13.9.6 Serendipity 301 13.10 Polar bears (Ursus maritimus) Ian Stirling 302 13.10.1 Motivation 302 13.10.2 Standardization of methods and sampling 303 13.10.3 Two long-term approaches 303 13.10.4 Challenges 305 13.11 Conclusions 305 Ch14 Identifying units to conserve using genetic data Barbara L. Taylor, Karen Martien, and Phillip Morin 14.1 The biology of structure and the role of genetics 306 14.2 Scale—units to conserve 308 14.2.1 Taxonomy 308 14.2.2 Evolutionary significance 309 14.2.3 Demographically independent populations (DIPs) 309 14.3 Genetic markers 312 14.3.1 Mitochondrial DNA sequencing (mtDNA) 313 14.3.2 Microsatellites 314 14.3.3 Single nucleotide polymorphisms (SNP) 315 14.3.4 Amplified fragment length polymorphisms (AFLP) 315 14.3.5 Nuclear locus sequencing 316 14.4 Analytical methods 317 14.4.1 Choosing methods to match questions 317 14.4.2 Assessing the strength of inference 320 Ch15 Approaches to management John Harwood 15.1 Introduction 325 15.2 Sustainable use and the importance of economic factors 326 15.3 A brief history of marine mammal exploitation 328 15.4 Lessons from whaling and sealing 330 15.4.1 The International Whaling Commission 330 15.4.2 Northern fur seals 332 15.4.3 Harp seals 332 15.5 Ecotourism 333 15.6 Obtaining indirect benefits from the management of marine mammals 334 15.7 Defining and achieving the objectives of management 334 15.8 The future of management 338 Ch16 Conservation biology Andrew J. Read 16.1 Introduction 340 16.2 What is conservation biology? 341 16.3 The road map 342 16.4 Which populations are at risk? 343 16.5 Quantitative assessment of extinction threat 349 16.6 Experimentation 350 16.7 Direct intervention 352 16.8 Fisheries by-catch 353 16.9 Case study: by-catch of harbour porpoises in the Gulf of Maine 355 16.10 Future directions 358 16.11 Conclusions 359 References 360 Index 433 -- Professor Ian L Boyd BSc PhD DSc FRSE Director, Scottish Oceans Institute and NERC Sea Mammal Research Unit University of St Andrews East Sands St Andrews KY16 8LB UK Phone 44-(0)1334-463628 The University of St Andrews is a charity registered in Scotland : No SC013532