Ecology of Marine Fish

Front Cover
Ecology of Marine Fish
Copyright
Contents
Contributors
About the editors
Preface
Part I: Introduction to the ecology of marine fishes
	Chapter 1: History of the ecology of marine fishes
		1.1. Introduction
		1.2. The origins of ecology
		1.3. Main milestones of the ecology theory
		1.4. Early beginnings of fish ecology across the world
		1.5. Main technical and technological advances for the study of the ecology of marine fishes
		1.6. Perspectives
		References
	Chapter 2: The diversity and life-history patterns of marine fishes
		2.1. Introduction
		2.2. Taxonomical diversity
			2.2.1. The evolution of fish taxonomy
			2.2.2. Agnatha
			2.2.3. Chondrichthyes
			2.2.4. Osteichthyes
		2.3. Morphological diversity
		2.4. Habitats, ecological niches and life-history patterns of marine fishes
		2.5. Main conclusions and future perspectives
		References
Part II: Life-cycle and Fish-Environment interactions
	Chapter 3: The early life stages of marine fishes
		3.1. Introduction
			3.1.1. Nomenclature
		3.2. Reproduction and development: First-year life stages
			3.2.1. Spawning
			3.2.2. Eggs
			3.2.3. Larvae
			3.2.4. Age-0 juveniles
		3.3. Ecological processes and vital rates
			3.3.1. Foundational science in fish early life history: Prerecruitment mortality and the mass culling of individuals
			3.3.2. Transport and dispersal
			3.3.3. Growth and condition
			3.3.4. Habitat dependency
				At larval stage
				At age-0 juvenile stage
				Conceptual integration
			3.3.5. Predation
				Predation, the individual Russian Roulette
				Population effects
				ELH stages as predators
				Climate change effects
		3.4. Concluding remarks and perspectives
		References
	Chapter 4: Fish growth: Patterns and modeling
		4.1. Introduction
		4.2. Overview of fish growth
			4.2.1. What is growth?
			4.2.2. Ecophysiological factors determining growth
				Food conditions
				Oxygen
				Temperature
				Salinity
			4.2.3. Intrinsic factors determining growth
		4.3. Measuring growth
			4.3.1. Measuring size and body mass
			4.3.2. Direct measurement of growth: Lab monitoring and mark-recapture data
			4.3.3. Size-composition data
			4.3.4. Sclerochronology for estimating age and growth
			4.3.5. Biochemical growth proxies
			4.3.6. Epigenetic aging, a future generalized tool for estimating age?
		4.4. Growth patterns and analytical equations
			4.4.1. Growth patterns
			4.4.2. The (Pütter) von Bertalanffy growth function (VBGF)
			4.4.3. S-shaped growth curves
			4.4.4. Biphasic growth models
			4.4.5. Which growth model should you choose?
		4.5. Growth in population and stock assessment models
			4.5.1. From an implicit toward an explicit and integrated modeling of growth
			4.5.2. The effect of selective fishery: From a modification of the length or age pyramid to fisheries-induced evolution
		4.6. Back to a bioenergetics approach to growth
			4.6.1. System definitions
			4.6.2. The basis of bioenergetics
			4.6.3. A matter of coefficients
				Terms of the debate
				VBGF as a bioenergetic approach
				The metabolic theory of ecology
				The gill-oxygen limitation theory
			4.6.4. Toward a more explicit description of metabolic fluxes
				Scope for growth in bioenergetics models
				The dynamic energy budget theory
			4.6.5. When theories meet (and when they dont)
				VBGF as a particular case of DEB theory
				MTE versus DEB theory, a matter of exponents (again)
		4.7. Main conclusions, future perspectives, and knowledge gaps
		References
	Chapter 5: Fish movement
		5.1. Introduction
		5.2. Diel vertical migration
			5.2.1. Case study: Vertical migration of European sardine
			5.2.2. Case study: Short-period movements of adult Pacific halibut
		5.3. Ontogenetic movement
			5.3.1. Case study: Variability in larval dispersal in six flatfish species
			5.3.2. Case study: Variability in nursery origin of gilthead seabream
			5.3.3. Case study: Spawning and feeding migrations of European plaice
			5.3.4. Case study: Migration between spawning, feeding, and overwintering grounds in Atlantic herring
		5.4. Transoceanic movement
			5.4.1. Case study: Overwinter movement patterns of juvenile Atlantic bluefin tuna
			5.4.2. Case study: Transoceanic migration of blue shark
		5.5. Diadromous migration
			5.5.1. Case study: Anadromous migration of sea lamprey
			5.5.2. Case study: Catadromous migration in anguillids
		5.6. Future perspectives
		References
	Chapter 6: Trophic ecology of marine fish
		6.1. Introduction
		6.2. The ``ecomorphology´´ hypothesis, or the relationship between fish shape and feeding ecology
		6.3. Methodologies to investigate marine fish diet
			6.3.1. Stomach content analysis
			6.3.2. Stable isotopes analysis (SIA)
			6.3.3. Lipids and fatty acids as trophic biomarkers
			6.3.4. DNA-based approaches
		6.4. Behavioral adaptations related to marine fish feeding
			6.4.1. Feeding/foraging behavior
			6.4.2. Factors influencing feeding behavior
			6.4.3. Feeding behavior in relation to senses
			6.4.4. Endocrine and metabolic control of feeding
			6.4.5. Feeding rhythms
			6.4.6. Resource polymorphism
			6.4.7. Personality and foraging behavior
		6.5. Trophic guilds
		6.6. Feeding physiology: Focus on acquisition and synthesis pathways of some dietary essential components
			6.6.1. N-3 LC PUFA sources and synthesis in fish
			6.6.2. Limited de novo production of n-3 LC PUFA in marine fish
			6.6.3. Impact of global change on n-3 LC PUFA availability for fish
			6.6.4. Impact of lower n-3 LC PUFA availability on fish performance
		6.7. Conclusion and perspectives
		References
	Chapter 7: Reproduction of marine fishes
		7.1. Introduction
		7.2. Fish reproductive strategies
			7.2.1. Spawning and reproductive behavior
			7.2.2. Fecundity
			7.2.3. Egg size
		7.3. Reproductive ecology
			7.3.1. Reproductive timing (diel, seasonal, annual, lifetime scales)
			7.3.2. Spatial dynamics
				Spawning site selection
				Spawning site selection and annual fecundity estimates
				Sex-specific movements to spawning sites
				Maturation and movement
			7.3.3. Reproductive energetic part
				Energetic trade-offs between life history traits
				Energy storage and allocation within a reproductive cycle
			7.3.4. Maternal effects
		7.4. Highlights in fish reproduction studies: Phenological versus genetic adaptation of reproductive cyclicity
			7.4.1. Phenological regulation: Cues, mechanisms, and relevance for population persistence under climate change
				Daylength as zeitgeber
				The two-step maturity decision function
				Taken together
			7.4.2. Genetic regulation of reproductive seasonality
				Population structure revealed by genomics
				Genetic adaptions to reproductive timing
				Genetic adaptations to salinity gradients
				Taken together
		7.5. Synthesis conclusion and future perspectives
		References
	Chapter 8: Behaviors of marine fishes
		8.1. Introduction
		8.2. Activity
		8.3. Boldness
		8.4. Aggressiveness
		8.5. Sociality and schooling
		8.6. Reproduction and parental care
		8.7. Concluding remarks and perspectives
		References
Part III: Population and community ecology
	Chapter 9: Methods for estimating the occurrence and abundance of marine fishes
		9.1. Introduction
		9.2. Considerations for sampling designs
			9.2.1. Controlling spatio-temporal scales of variability in experimental designs
			9.2.2. Accuracy versus precision of estimations
			9.2.3. The importance of fish identification and taxonomic knowledge
			9.2.4. Considering fish biology variability on sampling designs
			9.2.5. Diurnal and seasonal activity
		9.3. Estimating fish abundance: Gears, methods, and techniques
			9.3.1. From abundance to biomass estimations
			9.3.2. Methods based on traditional fishing and fisheries science: Gears and techniques
				Fishing gears
				Light-traps
				Electrofishing
				Other destructive methods
			9.3.3. Standardization of data and abundance estimations in techniques based on fisheries
			9.3.4. Fish tagging and mark-recapture methods
				Electronic tags
			9.3.5. Direct and quantitative standardized methods
				Ichthyoplankton
				Neritic and benthic fishes
					Underwater visual censuses (UVC)
					Underwater remote video (URV)
				Acoustic methods
			9.3.6. New approaches
				Environmental DNA (eDNA)
				Abundance estimates using eDNA
				Citizen science
				Machine learning models (IA)
		References
	Chapter 10: Spatial and temporal patterns in the distribution of fishes
		10.1. Geographical distribution range
		10.2. Main environmental drivers of species spatial and temporal occurrence patterns
			10.2.1. Temperature
			10.2.2. Depth
			10.2.3. Salinity
			10.2.4. Dissolved oxygen
			10.2.5. Substrate
			10.2.6. Moon phase and tides
			10.2.7. Biotic factors
			10.2.8. Anthropogenic factors
		10.3. Ecological niche and habitat selection
			10.3.1. Ecological niche theory
			10.3.2. Habitat colonization and habitat selection diversity in fish
			10.3.3. Density-independent and density-dependent processes
			10.3.4. Response curves and ecological niches
		10.4. Ontogenetic variation
		10.5. Future perspectives
		References
	Chapter 11: Modeling spatiotemporal distribution of fish species richness and abundance
		11.1. Introduction
		11.2. Data for spatiotemporal representation of fish species distribution, density, and richness
		11.3. Methods, models, and related mapping approaches
			11.3.1. Modeling fish species richness and abundance
				Modeling fish species distribution and abundance
				Modeling fish species richness and biodiversity
				Evaluating habitat suitability models and improving the reliability of their outputs
			11.3.2. Mapping
				Maps from simple representation and interpolation of georeferenced data
				HSM and maps
		11.4. Model and map applications and management issues
			11.4.1. Estimating habitat suitability and spatial patterns
				Drivers of fish species richness and abundance
				Consequences of anthropogenic disturbances
			11.4.2. Estimating and assessing ecological status from models of fish species richness and abundance
			11.4.3. Mapping habitats, species distribution, and species richness, toward spatial management
				Direct use of habitat maps
				From mapping to projection
				Management applications, tools, and spatial planning
		11.5. Main conclusions and research needs
		References
	Chapter 12: Connectivity and genetic structure of marine fish populations
		12.1. Introduction
		12.2. What is a population?
			12.2.1. Genetic diversity
			12.2.2. Census and effective population size
		12.3. What is connectivity?
		12.4. Neutral population structure
		12.5. Adaptation and phenotypic plasticity
		12.6. Cryptic subdivision and local adaptation
		12.7. Hybridization and introgression
		12.8. Seascape genomics
		12.9. Applications
		12.10. Future perspectives
		References
	Chapter 13: The role of fish in marine food webs
		13.1. Introduction
			13.1.1. Characteristics of marine food webs
			13.1.2. Fish specificities in marine food webs
			13.1.3. Assessing the role of fish in marine food webs
		13.2. Modeling fish within marine food webs
			13.2.1. Ecopath as a representative of functional group models
			13.2.2. Trait-based spectrum models
			13.2.3. Fish-focused models
			13.2.4. Model limits and opportunities
		13.3. How much fish is in marine food webs?
		13.4. Role of fish in food web dynamics
			13.4.1. From photosynthesis to fish production
			13.4.2. Top-down and wasp-waist trophic control
			13.4.3. Fish trophic ecology and the stability of food webs
		13.5. Role of fish in the flux of matter
			13.5.1. Horizontal matter exchange between ecosystems
			13.5.2. Bentho-pelagic coupling and biological carbon pump
			13.5.3. Fish as a vector of pathogen distribution
		13.6. Conclusion, perspectives, and knowledge gaps
		References
	Chapter 14: Functional diversity in marine fish assemblages
		14.1. Functional diversity concepts and selection of functional traits
		14.2. Key ecological traits of marine fishes
			14.2.1. Fish trait studies and traits expression
			14.2.2. Trait data availability versus ecological relevance in marine fishes
		14.3. Functional trait patterns-Measurements and approaches
			14.3.1. Functional diversity indices
			14.3.2. Combining different traits-Life-history approaches
			14.3.3. Trait-based community modeling
				Univariate methods
				Ordination methods
				Joint species distribution modeling
		14.4. Functional diversity across scales-Recent trends, approaches, and challenges
			14.4.1. Global-scale patterns and drivers of functional diversity
				Shallow reefs
				Large marine ecosystems
				Estuaries
			14.4.2. Regional-scale patterns and drivers of functional diversity
				European seas
				Gulf of California
				Southeast Brazil
			14.4.3. Local-scale patterns and drivers of functional diversity
			14.4.4. Commonality in patterns and drivers across scales
		14.5. Functional diversity of fishes as indicators of anthropogenic impacts
			14.5.1. Bioindicators and monitoring of anthropogenic impacts
			14.5.2. Assessing changes in the functional structure of marine fish assemblages
			14.5.3. Main known changes in traits and/or diversity induced by climate change and anthropogenic drivers
		14.6. Key points and perspectives
		References
	Chapter 15: Main typologies of marine fish communities
		15.1. Introduction
		15.2. Intertidal areas
		15.3. Coastal rocky reefs
		15.4. Coastal sandy areas
		15.5. Estuarine systems
		15.6. Coral reefs
		15.7. Continental shelf
		15.8. Open ocean
		15.9. Deep-sea
		15.10. Main knowledge gaps and future directions
		References
Part IV: Anthropogenic impacts on marine fish populations and communities
	Chapter 16: Habitat degradation impacts on marine fish
		16.1. Main drivers and trends of marine habitat degradation
			16.1.1. Habitat loss
			16.1.2. Marine pollution
				Trace metals and organometallic compounds
				Hydrocarbons and oil spills
				Persistent organic pollutants
				Nutrient pollution
				Emerging pollutants
				Marine litter
				Underwater noise and light pollution
			16.1.3. Nonindigenous species
		16.2. Effects at various levels of biological organization and related methodologies
			16.2.1. Measuring impacts at an individual level
			16.2.2. Measuring impacts at the population level
			16.2.3. Measuring impacts at the assemblage/community level
		16.3. Effects of habitat degradation on marine fish, global case studies
			16.3.1. Habitat loss in estuarine essential fish habitats-Eastern Channel, France
			16.3.2. Corals reefs, habitat destruction, and soundscapes-Moorea Island, French Polynesia
			16.3.3. Oil spill-Deepwater horizon, Gulf of Mexico, USA
			16.3.4. Marine pollution-Baltic Sea, Europe
			16.3.5. Eutrophication linked to green tide habitat degradation-Knysna Estuary, South Africa
			16.3.6. Invasive species-The case of slipper limpet proliferation in Western Europe
		16.4. Conclusion and future perspectives
		References
	Chapter 17: Fisheries impact on marine fish populations
		17.1. Introduction
		17.2. Demographic effects-Introduction to the dynamics of exploited marine populations
			17.2.1. Less old fish and biomass in the sea
			17.2.2. Impacts on recruitment
			17.2.3. Overfishing and the debate on fisheries management
		17.3. Trend and diagnostic on stocks status and biomass-Where do we stand?
		17.4. Adaptation/selection-Fisheries-induced evolution
			17.4.1. Fishing-induced selection pressures on fish life-history traits
			17.4.2. Evidence of changes in maturation: Demography, plasticity or evolution?
			17.4.3. Which consequences of fishing-induced evolution for fish stock dynamics and fisheries productivity?
			17.4.4. Toward global erosion of genetic diversity and adaptive potential in fish?
		17.5. Ecosystem effects
			17.5.1. Fishing preys and bottom-up effects (supporting habitats, primary production)
			17.5.2. Fishing predators and top-down effects (trophic cascade, instability)
			17.5.3. Minimizing the impact of fishing-Toward an ecosystem approach to fisheries management
		17.6. Concluding remarks and perspectives
		References
	Chapter 18: Climate change impacts on marine fish ecology and fisheries
		18.1. Introduction
		18.2. Understanding fish responses to climate change across levels of organization
			18.2.1. Individuals and ecophysiology
			18.2.2. Populations and species biogeography
			18.2.3. Communities and biotic interactions
			18.2.4. Ecosystem services and socioeconomic impacts
		18.3. Methods for detecting and anticipating climate impacts
		18.4. Fisheries adaptation and mitigation to climate change
		18.5. Future perspectives and knowledge gaps
		References
	Chapter 19: Conservation of marine fish
		19.1. The bases for marine fish conservation
			19.1.1. History of marine conservation
			19.1.2. Marine fish conservation
		19.2. Species-based marine conservation tools
			19.2.1. The IUCN Red List Categories and Criteria
				Forage species (Teleostei: Clupeiformes)
				Parrotfishes (Labridae, Scarinae) and surgeonfishes (Acanthuridae)
				Groupers (Epinephelidae)
				Scombrids (Scombridae) and billfish (Istiophoridae and Xiphiidae)
				Chondrichthyans (sharks, rays, and chimeras)
			19.2.2. Classifications based on resilience and vulnerability
		19.3. Fisheries management measures: From a single-species approach to multispecies and ecosystem approaches
			19.3.1. Fish conservation through fisheries management measures
				Technical measures
				Input controls
				Output controls
			19.3.2. The context of the EU CFP
			19.3.3. Assessment of highly migratory species (tunas, billfishes, sharks)
			19.3.4. Multispecies and ecosystem-based conservation and management
		19.4. Marine protected areas
			19.4.1. Ecological outcomes of MPA
				Ecological effects inside and outside FPA and PPA
			19.4.2. MPA conditions for success
				Age and size
				MPA networks
		19.5. Conclusions and perspectives
		References
	Chapter 20: Restoration of fish habitats, populations, and communities
		20.1. Restoring marine fish: Utopia or real challenge?
		20.2. Fish habitat restoration
			20.2.1. Seagrass habitat restoration
			20.2.2. Bivalve reefs habitat
			20.2.3. Artificial reefs: A lure or an effective solution
		20.3. Restoring fish population: The case of diadromous species
		20.4. Protecting early stage to restore population
			20.4.1. Early life history stage (ELHS)
			20.4.2. Example of operational ecological marine restoration solutions
				Biohut
				BioRestore, a tool for coastal fisheries enhancement
		20.5. Thinking wide for community effect
		20.6. The need to go further
		References
Part V: Future perspectives
	Chapter 21: Perspectives on marine fish ecology research
Index
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