[MARMAM] Marine Mammal Ecology and Conservation: A Handbook of Techniques

Ian Boyd ilb at st-andrews.ac.uk
Tue Aug 10 00:05:51 PDT 2010


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




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