The Atlantic Salmon: Genetics, Conservation and Management

The Atlantic Salmon Genetics, Conservation and Management......Page 2
Contents......Page 8
Foreword......Page 16
Preface......Page 17
Acknowledgements......Page 19
Contributors......Page 20
1 Introduction......Page 24
1.1 Background......Page 25
1.2 Genetics,management and conservation......Page 29
1.3 Purpose of this book......Page 31
1.4 Organisation of this book......Page 32
1.5 Summary and conclusions......Page 35
Part I Background......Page 38
2 The Atlantic Salmon......Page 40
2.1 Introduction......Page 41
2.2 Taxonomy and geographic range......Page 44
2.3 Life-history variation......Page 45
2.4.1 Distribution and life in fresh water......Page 48
2.4.2 Reproduction......Page 51
2.4.3 Egg size,development and survival......Page 53
2.4.4 Emergence and dispersal of fry......Page 55
2.4.5 Free-swimming juvenile life and production......Page 56
2.4.6 Sexual maturation of parr......Page 57
2.4.7 Movements of parr......Page 58
2.4.9 Marine life and distribution......Page 59
2.4.10 Homing and return marine migration......Page 61
2.5 Biology of non-anadromous populations......Page 63
2.5.1 Geographic distribution......Page 64
2.5.2 Life history and behaviour......Page 65
2.5.3 Maturation and reproduction......Page 66
2.6 Summary and conclusions......Page 68
3 The Atlantic Salmon Genome......Page 80
3.1 DNA......Page 81
3.2.2 Replication,cell division and growth......Page 83
3.2.3 Number and ploidy level......Page 86
3.3.2 Number and molecular distribution......Page 89
3.3.3 Extragenic DNA......Page 91
3.4.1 Genotypes,alleles and loci......Page 92
3.4.3 Gene expression......Page 93
3.5.1 Origin......Page 94
3.5.2 Scope......Page 95
3.5.3 Detection......Page 97
3.6 Summary and conclusions......Page 106
4 Investigating the Genetics of Populations......Page 109
4.1 Overview......Page 110
4.2.1 Basic concepts......Page 112
4.2.2 Models of population structure......Page 113
4.2.3 Population differentiation......Page 115
4.3.1 How it differs from population genetics......Page 116
4.3.2 Quantitative genetic variation......Page 117
4.4 The genetic characterisation of wild populations......Page 118
4.4.1 Allozyme electrophoresis......Page 119
4.4.2 Mitochondrial DNA......Page 121
4.4.3 Microsatellite DNA......Page 122
4.4.4 Other types of molecular marker......Page 124
4.5.1 Types of study and their limitations......Page 125
4.5.2 Mixed-stock analysis and assignment tests......Page 126
4.5.4 Parentage assignment......Page 127
4.5.5 Relatedness estimation......Page 129
4.6 Future perspectives:going beyond quantifying genetic differentiation and understanding local adaptation......Page 130
4.7 Summary and conclusions......Page 132
Part II Population Genetics......Page 138
5 Biodiversity and Population Structure......Page 140
5.1 Introduction......Page 141
5.2 Evolutionary relatedness to other salmonids......Page 143
5.3 Phylogeographic diversity......Page 144
5.3.1 Range-wide......Page 146
5.3.2 Eastern Atlantic......Page 154
5.3.3 Western Atlantic......Page 160
5.3.4 Resident (non-anadromous)salmon......Page 166
5.3.5 Historical origins......Page 170
5.4 Regional and local population structure......Page 176
5.4.1 Spatial scale and boundaries......Page 177
5.4.2 Metapopulation structure and gene €ow......Page 179
5.5 Overview......Page 181
5.6 Summary and conclusions......Page 182
5.7 Management recommendations......Page 183
6 Mating System and Social Structure......Page 190
6.1.1 Definitions,approach and organisation......Page 191
6.1.2 Genetic markers in the analysis of mating system and social structure......Page 192
6.2.1 Effective population size......Page 193
6.2.2 Factors affecting the variance in reproductive success of male alternative reproductive tactics......Page 194
6.2.3 Reproductive success estimates and mate choice under natural conditions......Page 200
6.2.4 Hybridisation......Page 203
6.3 Social structure......Page 207
6.3.2 Patterns of relatedness in nature and €tness......Page 208
6.4 Summary and conclusions......Page 209
6.5 Management recommendations......Page 210
7 Local Adaptation......Page 218
7.1 Introduction......Page 219
7.1.1 Phenotypic diversity and €tness in a changing world......Page 220
7.2 Scope for local adaptations in Atlantic salmon......Page 221
7.2.1 Genetic variation in €tness-related traits......Page 222
7.2.2 Environmental variation and differential selective pressures......Page 224
7.2.3 Reproductive isolation......Page 226
7.3.1 Indirect,circumstantial evidence for local adaptations......Page 227
7.3.2 Direct evidence for local adaptations......Page 233
7.3.3 Challenges to the local adaptation hypothesis......Page 234
7.4 Summary and conclusions......Page 241
7.5 Management recommendations......Page 242
Part III Management Issues......Page 260
8 Population Size Reductions......Page 262
8.2.1 Importance of genetic diversity in natural populations......Page 263
8.2.2 Measuring loss of genetic variation in small populations: heterozygosity and allelic diversity......Page 265
8.3 Effective population size......Page 266
8.3.1 Minimum effective population size......Page 268
8.3.3 Factors in €uencing genetically effective population size in Atlantic salmon......Page 270
8.3.4 Calculating effective population size......Page 272
8.4 The effects of genetic drift and selection in small populations......Page 274
8.5 The effects of inbreeding in small populations:inbreeding depression......Page 279
8.6 Population reductions,gene €ow and local adaptation......Page 282
8.6.1 Small populations of Atlantic salmon and the metapopulation models......Page 286
8.8 Management recommendations......Page 287
9 Genetic Identi €cation of Individuals and Populations......Page 293
9.1 Introduction......Page 294
9.2 Assignment of individuals......Page 296
9.2.1 Application to Atlantic salmon......Page 297
9.2.2 Background to methodology......Page 300
9.3.1 Application to Paci €c salmon €sheries......Page 303
9.3.2 Application to Atlantic salmon €sheries......Page 305
9.3.3 Background to mixed-stock analysis......Page 307
9.4 Resolving power of different markers......Page 312
9.5 Summary and conclusions......Page 314
9.6 Management recommendations......Page 315
10 Fisheries Exploitation......Page 322
10.1 Introduction......Page 323
10.2 A historical perspective on €sheries exploitation......Page 324
10.2.1 Catch statistics......Page 326
10.2.3 Potential for selection......Page 327
10.3.1 Undirected genetic erosion......Page 332
10.3.2 Directed genetic change......Page 335
10.4 Fishing and effective population size:the evidence......Page 336
10.5 Phenotypic and evolutionary changes in exploited populations......Page 337
10.6 Future management of salmon €sheries......Page 340
10.8 Management recommendations......Page 341
11 Stocking and Ranching......Page 348
11.3 Nature of strains reared for stocking and ranching......Page 350
11.4 Approach based on numbers of salmon present......Page 351
11.5 Scenario 1:Where salmon are extinct in a river (reintroduction)......Page 353
11.6 Scenario 2:Where small to near optimal numbers of the local population(s)remain (rehabilitation)......Page 362
11.7 Scenario 3:Attempting to achieve productivity in excess of naturally constrained production (enhancement)......Page 366
11.8 Scenario 4:Mitigation programmes and conservation hatcheries to counter irreversible loss of natural production (mitigation)......Page 368
11.10 Management recommendations......Page 375
12 Farm Escapes......Page 380
12.1 Introduction......Page 381
12.2.1 Identifying escaped farm salmon......Page 383
12.2.2 Escapes from sea cages......Page 384
12.3.1 Founder effects......Page 385
12.3.2 Differences due to domestication......Page 386
12.3.3 Genetic marker differences between wild and farm salmon......Page 387
12.3.4 Phenotypic differences between wild and farm salmon......Page 388
12.4.1 Fate of adult escapees......Page 391
12.4.3 Indirect genetic effects of farm escapes......Page 392
12.4.4 Direct genetic effects of farm escapes......Page 394
12.5.1 Evidence for breeding of escaped farm salmon in the wild......Page 395
12.5.2 Differences in breeding behaviour of farm and wild salmon......Page 396
12.5.3 Increased hybridisation with brown trout as a result of farm escapes......Page 397
12.6.1 Imsa experiment......Page 398
12.6.2 Burrishoole experiment......Page 400
12.7 Discussion of genetic implications of farm escapes......Page 405
12.8 How can the genetic impact of farm escapes be reduced?......Page 408
12.9 Summary and conclusions......Page 410
12.10 Management recommendations......Page 411
13 Genetics and Habitat Management......Page 422
13.1 Introduction......Page 423
13.2 Genetic issues......Page 427
13.2.1 Habitat reduction......Page 430
13.2.2 Habitat fragmentation......Page 431
13.2.3 Habitat expansion......Page 432
13.2.4 Habitat degradation......Page 433
13.2.5 Loss of biodiversity......Page 434
13.2.6 Global climate change......Page 435
13.3 Summary and conclusions......Page 441
13.4 Management recommendations......Page 442
14 Live Gene Banking of Endangered Populations of Atlantic Salmon......Page 448
14.1.1 Genetic concerns associated with the long-term captive rearing of salmonids......Page 449
14.1.2 Impact of long-term genetic changes on captive populations......Page 454
14.2 Live gene banking of inner Bay of Fundy Atlantic salmon: a case study......Page 455
14.2.1 Collection of founder broodstock......Page 457
14.2.2 Captive rearing of broodstock......Page 458
14.2.3 Spawning......Page 460
14.2.4 Captive rearing and river release of offspring......Page 466
14.2.5 Ongoing founder broodstock collection and recovery of wild-exposed live gene bank salmon......Page 468
14.3.1 Prioritising rivers for conservation measures......Page 469
14.3.2 Should very small populations be combined or managed separately?......Page 470
14.4.1 Methods for the cryopreservation of milt......Page 474
14.4.2 Use of cryopreserved milt in the restoration of wild salmon populations......Page 475
14.4.4 Minimising genetic change between founder and subsequent generations of live gene bank populations......Page 480
14.5.1 Monitoring the loss of genetic variation and accumulation of inbreeding......Page 481
14.5.2 Identi €cation of individuals,and evaluation of the relative ef €cacy of alternate management strategies......Page 482
14.7 Management recommendations......Page 486
15 Atlantic Salmon Genetics: Past,Present and What \'s in the Future?......Page 493
15.1 Past......Page 494
15.2 Present......Page 495
15.3 Future......Page 496
Glossary of Terms......Page 504
Index......Page 513