About this book
Atlantic Salmon is a cultural icon throughout its North Atlantic range; it is the focus of probably the World's highest profile recreational fishery and is the basis for one of the World's largest aquaculture industries. Despite this, many wild stocks of salmon are in decline and underpinning this is a dearth of information on the nature and extent of population structuring and adaptive population differentiation, and its implications for species conservation.
This important new book will go a long way to rectify this situation by providing a thorough review of the genetics of Atlantic salmon. Sponsored by the European Union and the Atlantic Salmon Trust, this book comprises the work of an international team of scientists, carefully integrated and edited to provide a landmark book of vital interest to all those working with Atlantic salmon.
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 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 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 7 Local Adaptation C. Garcia de Leaniz, 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 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 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 10 Fisheries Exploitation K. Hindar, C. Garcia de Leaniz, 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 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 12 Farm Escapes A. Ferguson, I. Fleming, K. Hindar, O. Skaala, P. McGinnity, T. Cross and P. Prodohl 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 13 Habitat Management E. Verspoor, C. Garcia de Leaniz 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 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 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
Eric Verspoor, FRS Marine Laboratory, Aberdeen, UK Lee Stradmeyer, FRS Marine Laboratory, Aberdeen, UK