The Atlantic Salmon: Genetics, Conservation and Management

Foreword.

Preface.

Acknowledgements.

1 Introduction.

E. Verspoor.

1.1 Background.

1.2 Genetics, management and conservation.

1.2 Purpose of this book.

1.3 Organisation of this book.

1.4 Summary and conclusions.

Part I Background.

2 The Atlantic Salmon.

J. Webb, E. Verspoor, N. Aubin-Horth, A. Romakkaniemi and P.Amiro.

2.1 Introduction.

2.2 Taxonomy and geographic range.

2.3 Life history variation.

2.4 Biology of anadromous populations.

2.4.1 Distribution and life in fresh water.

2.4.2 Reproduction.

2.4.3 Egg size, development and survival.

2.4.4 Emergence and dispersal of fry.

2.4.5 Free-swimming juvenile life and production.

2.4.6 Sexual maturation of parr.

2.4.7 Movements of parr.

2.4.8 Smolt migration.

2.4.9 Marine life and distribution.

2.4.10 Homing and return marine migration.

2.5 Biology of non-anadromous populations.

2.5.1 Geographic distribution.

2.5.2 Life history and behaviour.

2.5.3 Maturation and reproduction.

2.6 Summary and conclusions.

3 The Atlantic Salmon Genome.

P. Moran, E. Verspoor and W. S. Davidson.

3.1 DNA.

3.2 Chromatin and chromosomes.

3.2.1 Nature and structure.

3.2.2 Replication, cell division and growth.

3.2.3 Number and ploidy level.

3.3 Genes and genome organisation.

3.3.1 Molecular nature and structure.

3.3.2 Number and molecular distribution.

3.3.3 Extragenic DNA.

3.4 Genes and development.

3.4.1 Genotypes, alleles and loci.

3.4.2 Genes and traits.

3.4.3 Gene expression.

3.5 Variation among individuals.

3.5.1 Origin.

3.5.2 Scope.

3.5.3 Detection.

3.6 Summary and conclusions.

4 Investigating the Genetics of Populations.

M. M. Hansen, B. Villanueva, E. E. Nielsen and D. Bekkevold.

4.1 Overview.

4.2 Population genetics.

4.2.1 Basic concepts.

4.2.2 Models of population structure.

4.2.3 Population differentiation.

4.3 Quantitative genetics.

4.3.1 How does it differ from population genetics.

4.3.2 Quantitative genetic variation.

4.3.3 Genotype by environment interaction.

4.3.4 Integration of molecular and quantitative genetics.

4.4 The genetic characterisation of wild populations.

4.4.1 Allozyme electrophoresis.

4.4.2 Mitochondrial DNA.

4.4.3 Microsatellite DNA.

4.4.4 Other types of molecular markers.

4.5 Studying populations: issues and limitations.

4.5.1 Types of studies and their limitations.

4.5.2 Mixed-stock analysis and assignment tests.

4.5.3 Estimating effective population size and detecting population declines.

4.5.4 Parentage assignment.

4.5.5 Relatedness estimation.

4.6 Future perspectives: going beyond quantifying genetic differentiation and understanding local adaptation.

4.7 Summary and conclusions.

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Part II Population Genetics.

5 Biodiversity and Population Structure.

T. L. King, E. Verspoor, A. P. Spidle, R. Gross, R. B. Phillips, M.-L. Koljonen, J. A. Sanchez and C. L. Morrison.

5.1 Introduction.

5.2 Evolutionary relatedness to other salmonids.

5.3 Phylogeographic diversity.

5.3.1 Range-wide.

5.3.2 Eastern Atlantic.

5.3.3 Western Atlantic.

5.3.4 Resident (non-anadromous) salmon.

5.3.5 Historical Origins.

5.4 Regional and local population structure.

5.4.1 Spatial scale and boundaries.

5.4.2 Metapopulation structure and gene flow.

5.5 Overview.

5.6 Summary and conclusions.

5.7 Management recommendations.

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6 Mating System and Social Structure.

W. C. Jordan, I. A. Fleming and D. Garant.

6.1 Introduction.

6.1.1 Definitions, approach and organisation.

6.1.2 Genetic markers in the analysis of mating system and social structure.

6.2 Mating system.

6.2.1 Effective population size.

6.2.2 Factors affecting the variance in reproductive success of male alternative reproductive tactics.

6.2.3 Reproductive success estimates and mate choice under natural conditions.

6.2.4 Hybridisation.

6.3 Social structure.

6.3.1 Kin recognition and kin-biased behaviour.

6.3.2 Patterns of relatedness in nature and fitness.

6.4 Summary and conclusions.

6.5 Management recommendations.

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7 Local Adaptation.

C. García de Leániz, I. A. Fleming, S. Einum, E. Verspoor, W. C. Jordan, S. Consuegra, N. Aubin-Horth, D. L. Lajus, B. Villanueva, A. Ferguson, A. F. Youngson, T. P. Quinn.

7.1 Introduction.

7.1.1 Phenotypic diversity and fitness in a changing world.

7.2 Scope for local adaptations in Atlantic salmon.

7.2.1 Genetic variation in fitness-related traits.

7.2.2 Environmental variation and differential selective pressures.

7.2.3 Reproductive isolation.

7.3 Evidence for the existence of local adaptations in Atlantic salmon.

7.3.1 Indirect, circumstantial evidence for local adaptations.

7.3.2 Direct evidence for local adaptations.

7.3.3 Challenges to the local adaptation hypothesis.

7.4 Summary and conclusions.

7.5 Management recommendations.

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Part III Management Issues.

8 Population Size Reductions.

S. Consuegra and E.E. Nielsen.

8.1 Introduction.

8.2 Loss of genetic variabilition in small populations.

8.2.1 Importance of the genetic diversity in natural populations.

8.2.2 Measuring loss of genetic variation in small populations: heterozygosity and allelic diversity.

8.3 Effective population size.

8.3.1 Minimum effective population size.

8.3.2 Relationship between census and effective population sizes (Ne/Nc).

8.3.3 Factors influencing genetically effective population size in Atlantic salmon.

8.3.4 Calculating effective population size.

8.4 The effects of genetic drift and selection in small populations.

8.5 The effects of inbreeding in small populations: inbreeding depression.

8.6 Population reductions, gene flow and local adaptation.

8.6.1 Small populations of Atlantic salmon and the metapopulation models.

8.7 Summary and conclusion.

8.8 Management recommendations.

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9 Genetic Identification of Individuals and Populations.

M.-L. Koljonen, T. L. King and E. E. Nielsen.

9.1 Introduction.

9.2 Assignment of individuals.

9.2.1 Application to Atlantic salmon.

9.2.2 Background to Methodology.

9.3 Identification of population contributions.

9.3.1 Application to Pacific salmon fisheries.

9.3.2 Application to Atlantic salmon fisheries.

9.3.3 Background to Methodology.

9.4 Resolving power of different markers.

9.5 Summary and conclusions.

9.6 Management recommendations.

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10 Fisheries Exploitation.

K. Hindar, C. García de Leániz, M.-L. Koljonen, J. Tufto and A. F. Youngson.

10.1 Introduction.

10.2 A historical perspective on fisheries exploitation.

10.2.1 Catch statistics.

10.2.2 Exploitation rates.

10.2.3 Potential for selection.

10.3 Fisheries exploitation as an ecological and evolutionary force.

10.3.1 Undirected genetic erosion.

10.3.2 Directed genetic change.

10.4 Fishing and effective population size: the evidence.

10.5 Phenotypic and evolutionary changes in exploited populations.

10.6 Future management of salmon fisheries.

10.7 Summary and conclusions.

10.8 Management recommendations.

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11 Stocking and Ranching.

T. F. Cross, P. McGinnity, J. Coughlan, E. Dillane, A. Ferguson, M.-L. Koljonen, N. Milner, P. O’Reilly and A. Vasemagi.

11.1 Introduction.

11.2 Genetic characteristics of wild salmon populations.

11.3 Nature of strains reared for stocking and ranching.

11.4 Approach based on numbers of salmon present.

11.5 Scenario 1 - Where salmon are extinct in a river (re-introduction).

11.6 Scenario 2 - Where small to near optimal numbers of local population(s) remain (rehabilitation).

11.7 Scenario 3 - Attempting to achieve productivity in excess of naturally-constrained production (enhancement).

11.8 Scenario 4 - Mitigation programmes and conservation hatcheries to counter irreversible loss of natural production (mitigation).

11.8.1 Example 1 – Mitigation programme started simultaneously with the introduction of the constraint to salmon production.

11.8.2 Example 2 – Genetic considerations when the ranching programme begins some years after the construction of the dam and when a large proportion or all of the upstream genetic legacy has been extirpated.

11.9 Summary and conclusions.

11.10 Management recommendations.

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12 Farm Escapes.

A. Ferguson, I. Fleming, K. Hindar, Ø. Skaala, P. McGinnity, T. Cross and P. Prodøhl.

12.1 Introduction.

12.2 Magnitude of farm salmon escapes.

12.2.1 Identifying escaped farm salmon.

12.2.2 Escapes from sea cages.

12.2.3 Juvenile escapes.

12.3 Genetic differences between wild and farm salmon.

12.3.1 Founder effects.

12.3.2 Differences due to domestication.

12.3.3 Genetic marker differences between wild and farm salmon.

12.3.4 Phenotypic differences between wild and farm salmon.

12.4 Potential impact of farm escapes on wild populations.

12.4.1 Fate of adult escapes.

12.4.2 Juvenile escapes.

12.4.3 Indirect genetic effects of farm escapes.

12.4.4 Direct genetic effects of farm escapes.

12.5 Breeding of escaped farm salmon in the wild.

12.5.1 Evidence for breeding of escaped farm fish in the wild.

12.5.2 Differences in breeding behaviour of farm and wild salmon.

12.5.3 Increased hybridization with brown trout as a result of farm.

escapes.

12.6 Experimental studies of the impact of farm escapes.

12.6.1 Imsa experiment.

12.6.2 Burrishoole experiment.

12.7 Discussion of genetic implications of farm escapes.

12.8 How can the genetic impact of farm escapes be reduced?.

12.9 Summary and conclusions.

12.10 Management recommendations.

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13 Habitat Management.

E. Verspoor, C. García de Leániz and P. McGinnity.

13.1 Introduction.

13.2 Genetic issues.

13.3.1 Habitat reduction.

13.3.2 Habitat fragmentation.

13.3.3 Habitat expansion.

13.3.4 Habitat degradation.

13.3.5 Loss of biodiversity.

13.3.6 Global climate change.

13.4 Summary and conclusions.

13.5 Management recommendations.

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14 Live Gene Banking of Endangered Populations.

P. O’Reilly and R. Doyle.

14.1 Introduction.

14.1.1 Genetic concerns associated with the long-term captive rearing of salmonids.

14.1.2 Impact of long-term genetic changes on captive populations.

14.2 Live gene banking of inner Bay of Fundy Atlantic salmon: a case study.

14.2.1 Collection of founder broodstock.

14.2.2 Captive rearing of broodstock.

14.2.3 Spawning.

14.2.4 Captive rearing and river release of offspring.

14.2.5 Ongoing founder broodstock collection and.

recovery of wild-exposed live gene bank salmon.

14.3 Conservation and management of small remnant populations of Atlantic salmon.

14.3.1 Prioritising rivers for conservation measures.

14.3.2 Should very small populations be combined or managed separately?.

14.4 Use of cryopreserved sperm in the conservation of Atlantic salmon.

14.4.1 Methods for the cryopreservation of milt.

14.4.2 Use of cryopreserved milt in the restoration of wild salmon populations.

14.4.3 Addition of genetic variation to impoverished future populations.

14.4.4 Minimising genetic change between founder and subsequent generations of live gene bank populations.

14.5 Research.

14.5.1 Monitoring the loss of genetic variation and accumulation of inbreeding.

14.5.2 Identification of individuals, and evaluation of the relative efficacy of alternate management strategies.

14.6 Summary and conclusions.

14.7 Management recommendations.

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15 Atlantic Salmon Genetics: Past, Present and what’s in the Future?.

J. L. Nielsen.

15.1 Past.

15.2 Present.

15.3 Future.

Glossary of terms.

Index