Evolution, Development and Ecology of Anemonefishes Model Organisms for Marine Science

Cover
Half Title
Title Page
Copyright Page
Dedication
Table of Contents
Preface
Acknowledgements
Editors
Contributors
Part I Evolution, Biogeography, and Genetics
Chapter 1 A Phylogenetic Context: The Diversification of Damselfishes (Pomacentridae)
1.1 Introduction
1.2 Farmers and Clownfishes: Uniqueness of Damselfishes among Ray-Finned Fishes
1.3 Phylogenetic Position of Damselfishes within Ray-Finned Fishes (Actinopterygii)
1.4 Systematics of Damselfishes
1.5 Ecological Radiation of Damselfishes
Acknowledgements
References
Chapter 2 Anemonefish Genomics
2.1 Introduction
2.2 Anemonefish Phylogenomics
2.3 Anemonefish Transcriptomics
2.4 Anemonefish Proteomics
2.5 Conclusions
Acknowledgements
References
Chapter 3 Biogeography and Genetic Barriers in Amphiprion Anemonefishes
3.1 Introduction
3.2 Biogeography and Gene Flow
3.3 Micro- to Macro-Evolutionary Processes That Boost or Potentially Constrain Speciation
3.4 Conclusions and Future Directions
Acknowledgements
References
Appendix and Supplemental Materials
Chapter 4 Genomic Evidence of Hybridization during the Evolution of Anemonefishes
4.1 Introduction
4.2 Whole-Genomic Data for All Anemonefish Species and the Detection of Hybridization Events
4.3 Incongruence in Phylogenomic Inference
4.4 Gene Tree Incongruence across the Genome
4.5 Estimating Past Introgression in Anemonefishes
4.6 Discussion and Perspectives
Acknowledgements
References
Chapter 5 The Use of Modern Genetic Tools in Anemonefishes
5.1 Introduction
5.2 Insights from Comparative Transcriptomics and Genomics
5.3 The Potential for Forward Genetic Studies of Anemonefish Biology
5.4 Reverse Genetic Studies of Anemonefish Biology
5.4.1 General Protocol for Gene Knockout in Fishes
5.4.1.1 Step 1: Design and Preparation of CRISPR-gRNAs
5.4.1.2 Step 2: Preparation of Cas
5.4.1.3 Step 3: Microinjection
5.4.1.4 Step 4: Detection of Induced Mutation by Heteroduplex Mobility Assay
5.4.2 Application and Tips for Genome Editing in Anemonefishes
5.4.2.1 Step 1: Preparation of Fertilized Eggs
5.4.2.2 Step 2: Microinjection of Anemonefish Eggs
5.4.2.3 Step 3: Tips for Anemonefish Microinjection
5.4.3 Examples of Gene KO in Anemonefishes
5.5 Conclusion
References
Part II Life History and Development
Chapter 6 The Post-Embryonic Period of Anemonefishes
6.1 Introduction
6.2 The Post-Embryonic Development of Anemonefish
6.3 Interplay between Environmental Cues and Life History Transitions
6.4 TH and Anemonefish Metamorphosis
6.5 Conclusion
References
Chapter 7 Color Patterns in Anemonefish: Development, Role, and Diversity
7.1 Introduction
7.2 Pigment Cells
7.3 Color Pattern Ontogenesis
7.3.1 Pigmentation during Embryonic Development
7.3.2 Development of Pigmentation during Metamorphosis
7.3.3 Maturation of Pigmentation Patterns in Juveniles
7.4 Functional Aspect of Anemonefish Skin Color and Pattern
7.4.1 Predator Avoidance
7.4.2 Social Function
7.5 Color Pattern Polymorphism
7.6 Color Pattern Variants and Pet Shop Mutants
7.6.1 Imbalance of Chromatophores
7.6.2 Irregular Patterning Mechanisms
7.7 Conclusion
References
Chapter 8 Age and Longevity
8.1 Introduction
8.1.1 Senescence in Teleosts
8.1.2 Theories Concerning the Evolution of Senescence
8.1.3 Searching for a New Long-Lived Model Organism
8.2 Anemonefishes: Ideal Models of Longevity?
8.2.1 Anemonefish: The Answer to the Search for a New Marine Model
8.2.2 Anemonefish Peculiarities
8.2.3 Anemonefish and Predation
8.3 Lifespan Data
8.4 Transcriptomic Analysis of Anemonefish for Longevity Studies
8.4.1 Amphiprioninae vs Chrominae: Positively Selected Genes
8.4.2 Ageing and Anti-Parallel Evolution
8.5 Conclusion
References
Chapter 9 The Visual Ecology of Anemonefishes
9.1 Introduction
9.2 The Light Environment of Anemonefishes
9.3 The Morphological Basis for Vision in Anemonefishes
9.4 The Molecular Basis for Vision in Anemonefishes
9.5 Anemonefish Visual Behavior and Where to Go from Here
Acknowledgements
References
Chapter 10 Sound Communication
10.1 Introduction
10.2 Production of Different Types of Sounds
10.3 Relationships between Sounds and Behaviors
10.4 Mechanism
References
Chapter 11 Neuroendocrinology of Life History and Stress in Anemonefishes
11.1 Introduction
11.2 The Neuroendocrine System in Fish: How to Live in a Fluctuating Environment
11.3 Anemonefishes and Their Environment
11.4 Neuroendocrine Control of Metamorphosis
11.5 Neural Regulation of the Stress Response and Sexual Development
11.5.1 Neuroendocrinology of Plasticity in Teleost Fishes
11.5.2 Social Control of Sex Change – a Superb Example of Sexual Plasticity
11.6 Anemonefish as a Model to Understand Marine Fish Stress in a Changing World
11.7 Future Directions
References
Part III Reproduction and Social Behavior
Chapter 12 Sex Change from Male to Female: Active Feminization of the Brain, Behavior, and Gonads in Anemonefish
12.1 Introduction
12.1.1 Who, When, and Why?
12.1.2 The Particular Case of Anemonefishes
12.2 Active Feminization of the Brain and Behavior
12.2.1 Initiation of Sex Change
12.2.2 POA Sex Change
12.2.3 Behavioral Sex Change
12.2.3.1 Sex Change in Aggression
12.2.3.2 Sex Change in Parental Care
12.2.3.3 Neural Mechanisms of Behavioral Sex Change
12.3 Gonadal Sex Change
12.3.1 Histological Changes across Sex Change in Amphiprion
12.3.2 Endocrine Regulation of Sex Change: Sex Steroids
12.3.3 Molecular Pathways Underlying Gonadal Sex Change
12.4 Conclusion
References
Chapter 13 Anemonefish Behavior and Reproduction
13.1 Introduction
13.2 Who Reproduces?
13.2.1 Group Structure and Hormonal Profiles
13.2.2 Protandrous Sequential Hermaphroditism
13.3 How Does Reproduction Occur?
13.3.1 Spermatogenesis
13.3.2 Oogenesis
13.3.3 Behavior Prior to Spawning
13.3.4 Egg Development and Hatching
13.4 Where Does Reproduction Occur?
13.4.1 Geographically
13.4.2 Oviposition Site
13.5 When Does Reproduction Occur?
13.5.1 Daily (Light–Dark) and Tidal Spawning Rhythms
13.5.2 Lunar Spawning Rhythms
13.5.3 Seasonal Spawning Rhythms
13.5.4 Yearly Spawning Rhythms
13.6 How Many Eggs?
13.6.1 Fecundity
13.6.2 Annual Fecundity
13.6.3 Lifetime Estimates of Reproductive Success
13.7 Why Does Reproduction Vary?
13.7.1 Natural Environmental and Individual Factors
13.7.2 Environmental Stressors
13.7.2.1 Climate Change
13.7.2.2 Motorboat Noise
13.7.2.3 Artificial Light a Night
13.8 Final Remarks
References
Chapter 14 Social Evolution in Anemonefishes: Formation, Maintenance, and Transformation of Social Groups
14.1 Introduction
14.2 Social Group Formation
14.2.1 Why Do Non-Breeders Forgo Their Own Reproduction?
14.2.1.1 Direct Genetic Benefits: Current Reproduction
14.2.1.2 Indirect Genetic Benefits: Kin Selection
14.2.1.3 Future Genetic Benefits: Territory Inheritance
14.2.1.4 Poor Outside Options: Ecological Constraints
14.2.1.5 Poor Inside Options: Social Constraints
14.2.2 Why Do Breeders Tolerate Non-Breeders?
14.2.2.1 Poor Outside Options: Eviction Constraints
14.2.2.2 Direct Genetic Benefits: Current Reproduction
14.2.2.3 Indirect Genetic Benefits: Kin Selection
14.2.2.4 Future Genetic Benefits I: Mate-Replacement Benefits
14.2.2.5 Future Genetic Benefits II: Mutualist-Mediated Benefits
14.3 Social Group Maintenance
14.3.1 How Are Conflicts of Interest among Group Members Resolved?
14.3.2 Non-Lethal Resolution of Conflict in Stable Groups
14.3.3 Non-Lethal Resolution of Conflict at the Initiation of Groups
14.3.4 Adaptive Size Modification on Acquisition of Breeding Status
14.4 Social Group Transformation
14.4.1 How Do Small, Simple Groups Become Large, Complex Groups?
14.4.2 The Size-Complexity Hypothesis
14.5 Interspecific Variation in Anemonefish Societies
14.5.1 What Causes Interspecific Variation in Anemonefish Societies?
14.5.2 Variation in Strength of Indirect Genetic Benefits and Ecological Constraints
14.5.3 Variation in Strength of Future Genetic Benefits and Social Constraints
14.6 Concluding Comments and Future Directions
References
Chapter 15 Parental Care: Patterns, Proximate and Ultimate Causes, and Consequences
15.1 Introduction
15.2 Plasticity and Personality of Parental Care
15.2.1 Plasticity and Personality of Parental Care in Response to Changes in Resources
15.2.2 Plasticity and Personality of Parental Care in Response to Sex Change
15.3 Negotiations over Care
15.4 Step-Fathering and Alloparental Care
15.5 Mechanisms Underlying Parental Care
15.6 Conclusions and Prospects
References
Part IV Ecology
Chapter 16 Habitat Selection of Anemonefish
16.1 Introduction
16.2 Overview of Research on Host Selection
16.2.1 Ecological Requirements
16.2.2 Competition among Anemonefish
16.3 Host Selectivity of Anemonefish in the Ryukyu Archipelago
16.3.1 Plasticity of Host Selection
16.3.2 Human-Induced Environmental Degradation
16.4 Summary and Future Tasks
References
Chapter 17 3D Analysis of Coral Reef Informs Anemonefish Habitat
17.1 Introduction
17.2 Geomorphic Zone and Mapping Anemone on Aerial Image
17.3 Distribution of Anemone and Anemonefishes on a 3D Reef Structure
17.3.1 Distribution of Heteractis Crispa on a Small Fringing Reef
17.3.2 Distribution of Stichodactyla Gigantea on a Large Fringing Reef
17.3.3 Distribution of Entacmaea Quadricolor on a Large Fringing Reef
17.4 Geomorphic Zone and Strategy of Habitat Use
Acknowledgements
References
Chapter 18 Cohabitation and Competition in Anemonefishes: Patterns and Consequences
18.1 Introduction
18.2 Intraspecific Cohabitation
18.3 Intraspecific Competition
18.4 Interspecific Cohabitation
18.5 Interspecific Competition
18.6 Conclusions
Acknowledgements
References
Chapter 19 No Place Like Home: Can Omics Uncover the Secret behind the Sea Anemone and Anemonefish Symbiotic Relationship?
19.1 Introduction
19.2 Influences on Anemonefish Host Selection
19.2.1 Anemone Morphology
19.2.2 Anemone Toxicity
19.2.3 Interspecific Competition amongst Anemonefish Species
19.3 Current Hypotheses and Omics Applications to Uncover the Mechanism behind the Anemone and Anemonefish Symbiosis
19.3.1 Hypothesis 1: Anemonefish Are Innately Protected from Anemone Venom
19.3.2 Hypothesis 2: Anemonefish Have a Thicker Mucus Layer Than Other Fish
19.3.3 Hypothesis 3: Anemonefish Mucus Molecularly Mimics the Composition of Anemone Mucus
19.3.3.1 Omics Application: Metagenomics
19.3.4 Hypothesis 4: Anemonefish Mucus Lacks the Trigger for Firing the Anemone’s Nematocysts
19.3.4.1 Omics Application: Genomics
19.3.5 Hypotheses for Future Research
19.4 Lessons from Other Model Systems
19.5 Future Use of Omics
19.6 Conclusion
References
Chapter 20 Larval Dispersal in Anemonefish Populations: Self-Recruitment, Connectivity, and Metapopulation Dynamics
20.1 Introduction
20.2 Measuring Dispersal
20.3 Emerging Patterns
20.3.1 Increasing Spatial and Temporal Scales
20.3.2 Levels of Self-Recruitment, Dispersal Distances, and the Shape of the Dispersal Kernel
20.3.3 Population Persistence and Metapopulation Dynamics
20.3.4 Reproductive Success and Local Adaptation
20.4 Conclusions and Future Directions
Acknowledgements
References
Part V Human Impact and Conservation
Chapter 21 The Impact of Popular Film on the Conservation of Iconic Species: Anemonefishes in the Aquarium Trade
21.1 Introduction
21.2 The Aquarium Trade
21.2.1 Global Trade
21.2.1.1 What Are the Main Countries Involved in Exporting and Importing Marine Aquarium Species?
21.2.1.2 How Many Fish Species Are Involved in the Aquarium Trade?
21.2.1.3 How Many Individual Fish Are Traded Annually?
21.2.1.4 What Is the Economic Value of the Aquarium Trade?
21.2.1.5 What Is the Value of Anemonefishes in the Marine Aquarium Trade?
21.2.2 Fisheries and Impact on Natural Populations
21.2.2.1 Anemonefish Fisheries
21.2.2.2 Giant Sea Anemone Fisheries
21.2.3 Conservation Aquaculture
21.3 The Condition of the Aquarium Trade
21.3.1 Cyanide Fishing
21.3.2 Mortality Data and the Impact of Mortality
21.3.3 New and Rare Variants: A Saviour or a Risk Factor?
21.4 The Need to Improve Consumer Awareness
21.4.1 The Effect of a Movie
21.4.2 Public Perceptions and Awareness
21.4.3 Citizen Science Initiatives and Relationships with Local Actors to Protect Anemonefish
21.5 Conclusion: The Flag Fish Species Conundrum
References
Chapter 22 Anemonefish Husbandry
22.1 Introduction
22.2 Anemonefish Rearing System at Laboratory Scale
22.2.1 Broodstock System
22.2.2 Broodstock Maintenance
22.2.3 Classic Larval Rearing Systems
22.2.4 Larval Food
22.3 Methods Dedicated for Experimental Purposes
22.3.1 Low Volume Rearing Method
22.3.2 Rearing and Hatching Method without Parental Care
22.4 Conclusion
References
Chapter 23 Resilience and Adaptation to Local and Global Environmental Change
23.1 Introduction
23.2 Global Stressors
23.3 Local Stressors
23.4 Sensitivity to Environmental Change in Anemonefishes
23.4.1 Larval Development
23.4.2 Juvenile Development
23.4.3 Adults, Reproduction, and Embryogenesis
23.4.4 Symbiosis and Indirect Effects
23.5 Resilience and Adaptive Potential to Future Environmental Change
Acknowledgements
References
Chapter 24 Anemonefishes as Models in Ecotoxicology
24.1 Introduction
24.2 The Emergence of Anemonefishes as Model Organisms in Ecotoxicology
24.3 Current Knowledge of Anemonefishes’ Ecotoxicology
24.3.1 Data Survey
24.3.2 Nitrogen Compounds
24.3.3 Petroleum Products
24.3.4 Trace Metals
24.3.5 UV Filters
24.3.6 Cyanide
24.4 How Anemonefish May Fuel Advancements in Ecotoxicology
24.4.1 Full Life-Cycle Fish Tests
24.4.2 Single vs. Multi-Stressor Experiments in Laboratory
24.4.3 Laboratory and In Situ Models
24.4.4 Availability of Genetic and Transcriptomic Data
24.5 Remaining Challenges and Future Perspectives
24.5.1 The Need for Standardized Husbandry
24.5.2 From Individual to Population-Level Responses
24.6 Conclusion
References
Chapter 25 Saving Nemo: Extinction Risk, Conservation Status, and Effective Management Strategies for Anemonefishes
25.1 Introduction
25.2 Threatening Processes
25.2.1 Anemone Bleaching
25.2.2 Ocean Warming
25.2.3 Ocean Acidification
25.2.4 Aquarium Trade
25.2.5 Coastal Development
25.3 Risk Factors: Life History and Ecological Traits
25.3.1 Habitat Specialization
25.3.2 Mutual Dependence
25.3.3 Low Density
25.3.4 Low Connectivity
25.3.5 Small Geographic Range
25.3.6 Depth Range
25.4 Rarity Traits: Double and Triple Jeopardy
25.5 Conservation Status
25.6 Effective Management Strategies
25.6.1 Marine Reserves
25.6.2 Catch Regulations
25.6.3 Protecting Anemones
25.6.4 Captive Breeding
25.7 Conclusions
Acknowledgements
References
Conclusion: Anemonefish Revisited – Future Questions for a Model System
Index