Fishery Ecosystem Dynamics

Cover
Fishery Ecosystem Dynamics
Copyright
Preface
	About this Book
	Acknowledgments
	About the Authors
Contents
Chapter 1: Introduction
	1.1 Overview
		1.1.1 Historical perspectives
		1.1.2 Scientific developments
	1.2 Process and pattern in fishery ecosystems
	1.3 Confronting complexity
	1.4 Summary
		Additional reading
Part I: Ecological Models: An Overview
	Chapter 2: Density-Independent Population Growth
		2.1 Introduction
		2.2 Simple population models
			2.2.1 Continuous-time model
			2.2.2 Discrete-time model
		2.3 Age- and stage-structured models
			2.3.1 Age-structured model
				2.3.1.1 Sensitivities and elasticities of matrix models
				2.3.1.2 Stage-structured models
		2.4 Summary
			Additional reading
	Chapter 3: Density-Dependent Population Growth
		3.1 Introduction
		3.2 Compensation in simple population models
			3.2.1 Continuous-time models
				3.2.1.1 The generalized logistic model
			3.2.2 Multiple equilibria
				3.2.2.1 Depensation
				3.2.2.2 Alternative stable states
			3.2.3 Discrete-time models
				3.2.3.1 Complex dynamics
		3.3 Time-delay models
			3.3.1 Continuous-time models
			3.3.2 Discrete-time models
		3.4 Matrix models
			3.4.1 Age-structured models
			3.4.2 Stage-structured models
		3.5 Summary
			Additional reading
	Chapter 4: Interspecific Interactions I: Predation and Parasitism
		4.1 Introduction
		4.2 Predation
			4.2.1 Density-independent models in continuous time
			4.2.2 Density-dependent models in continuous time
			4.2.3 Refugia
				4.2.3.1 The foraging arena
			4.2.4 The functional feeding response
				4.2.4.1 Implications for stability
				4.2.4.2 Environmental effects
			4.2.5 Predator dependence
			4.2.6 Discrete-time models
				4.2.6.1 Density-independent models
				4.2.6.2 Prey density dependence
		4.3 Parasitism and disease
			4.3.1 Models for microparasites
			4.3.2 Models for macroparasites
			4.3.3 Epidemiological models
		4.4 Summary
			Additional reading
	Chapter 5: Interspecific Interactions II: Competition and Mutualism
		5.1 Introduction
		5.2 Competition
			5.2.1 Competition and the niche
				5.2.1.1 Niche metrics
			5.2.2 Experimental evidence for competition
				5.2.2.1 Species removal experiments
				5.2.2.2 Species addition “experiments”
				5.2.2.3 Estimating interaction strength
			5.2.3 Models of competition in continuous time
				5.2.3.1 Non-linear isoclines
			5.2.4 Models of competition in discrete time
			5.2.5 Model-based estimation of competition coefficients
			5.2.6 Altering competitive outcomes
			5.2.7 The competitive production principle
		5.3 Mutualism
			5.3.1 Continuous-time models
			5.3.2 Discrete-time models
		5.4 Summary
			Additional reading
	Chapter 6: Community Dynamics
		6.1 Introduction
		6.2 Some attributes of communities
			6.2.1 Species diversity
			6.2.2 Keystone species and trophic cascades
			6.2.3 Guilds and functional groups
			6.2.4 Community compensation
			6.2.5 Stability and complexity
		6.3 Models of community dynamics
			6.3.1 Continuous-time models
				6.3.1.1 Intraguild predation
				6.3.1.2 Competition-predation
				6.3.1.3 Non-linear predation
			6.3.2 Discrete-time models
				6.3.2.1 Multispecies delay–difference models
		6.4 Complex dynamics
		6.5 Size-spectrum models
		6.6 Qualitative modeling approaches
		6.7 Summary
			Additional reading
	Chapter 7: Spatial Processes
		7.1 Introduction
			7.1.1 Patterns of distribution and abundance
		7.2 Spatial distribution of single populations
			7.2.1 Measures of distribution and dispersion
				7.2.1.1 Area occupied
				7.2.1.2 Lloyd’s index
				7.2.1.3 Lorenz curves
				7.2.1.4 Center of gravity
				7.2.1.5 Geographical spread
				7.2.1.6 Kernel density estimators
			7.2.2 Climate and distribution
		7.3 Models of movement and dispersal
		7.4 Spatial population models
			7.4.1 Models in continuous time and space
				7.4.1.1 The basin model
			7.4.2 Models in continuous time and discrete space
				7.4.2.1 Metapopulation models
				7.4.2.2 Spatially explicit production models
			7.4.3 Models in discrete time and space
				7.4.3.1 Delay–difference model
				7.4.3.2 Full age-structured models
		7.5 Summary
			Additional reading
Part II: Ecological Production
	Chapter 8: Production at the Individual Level
		8.1 Introduction
		8.2 Energy budgets for individual organisms
		8.3 Growth
			8.3.1 Growth in length
			8.3.2 Seasonal growth
			8.3.3 Growth models in discrete time
				8.3.3.1 Discontinuous growth
		8.4 Reproductive processes
			8.4.1 Partitioning somatic and reproductive growth
		8.5 Temperature-dependent growth
			8.5.1 Physiological time units
			8.6 Full bioenergetic models
				8.6.1 Ingestion
				8.6.2 Respiration
				8.6.3 Egestion and excretion
				8.6.4 Energy density of predators and prey
				8.6.5 Yellow perch in Lake Erie
		8.7 Metabolic ecology
		8.8 Summary
			Additional reading
	Chapter 9: Production at the Cohort and Population Levels
		9.1 Introduction
			9.1.1 Compensation and regulation in aquatic populations
		9.2 Cohort production
			9.2.1 Growth
			9.2.2 Mortality
				9.2.2.1 Predation mortality
				9.2.2.2 Parasitism/Disease
				9.2.2.3 Other mortality
			9.2.3 Estimating cohort production
		9.3 Population production
			9.3.1 Deterministic recruitment models
				9.3.1.1 Null model
				9.3.1.2 Intra-cohort competition
				9.3.1.3 Cannibalism by adults
				9.3.1.4 Size-dependent processes
				9.3.1.5 Compensatory reproductive output
			9.3.2 Recruitment variability
				9.3.2.1 Recruitment models with environmental covariates
				9.3.2.2 Stochastic recruitment models
		9.4 Summary
			Additional reading
	Chapter10: Production at the Ecosystem Level
		10.1 Introduction
		10.2 Food webs
		10.3 Energy flow and utilization
		10.4 Linear network models
			10.4.1 Bottom-up calculations
			10.4.2 Top-down calculations
		10.5 Biogeochemical models
			10.5.1 Lower trophic level models
			10.5.2 End-to-end models
		10.6 Biomass spectra
		10.7 Dynamic ecosystem models
		10.8 Summary
			Additional reading
Part III: Harvesting Models and Strategies
	Chapter 11: Harvesting at the Cohort and Population Levels
		11.1 Introduction
			11.1.1 Humans as predators
		11.2 Harvesting at the cohort level
			11.2.1 Yield-per-recruit
				11.2.1.1 Continuous-time model
				11.2.1.2 Discrete-time model
			11.2.2 Egg production and spawning biomass-per-recruit
		11.3 Biomass dynamic models
			11.3.1 Continuous-time models
				11.3.1.1 Linear harvest functions
				11.3.1.2 Non-linear harvesting
				11.3.1.3 Depensatory production
			11.3.2 Discrete-time models
				11.3.2.1 Biomass dynamic models
		11.4 Delay–difference models
			11.4.1 Complex dynamics
		11.5 Full age-structured models
		11.6 Harvesting in randomly varying environments
			11.6.1 Discrete-time models
			11.6.2 Low-frequency variation and climate change
		11.7 Summary
			Additional reading
	Chapter 12: Harvesting at the Community Level
		12.1 Introduction
		12.2 Technical interactions in mixed-species fisheries
			12.2.1 Mixed-species cohort models
			12.2.2 Mixed species biomass dynamic models
			12.2.3 Identifying vulnerable species
				12.2.3.1 Productivity-susceptibility analysis
				12.2.3.2 Eventual threat index
		12.3 Aggregate biomass dynamic models
		12.4 Multispecies biomass dynamic models
			12.4.1 Continuous-time models
				12.4.1.1 Linear interaction terms
				12.4.1.2 Non-linear predation terms
			12.4.2 Discrete-time models
				12.4.2.1 Multispecies production models
				12.4.2.2 Multispecies delay–difference models
				12.4.2.3 Functional group models
		12.5 Complex dynamics
		12.6 Harvesting in random environments
		12.7 Size- and age-structured multispecies models
			12.7.1 Predation module
		12.8 Multispecies assessment models
			12.8.1 Multispecies virtual population analysis
			12.8.2 Multispecies statistical catch-at-age analysis
		12.9 Multispecies process models
		12.10 Multispecies biologicalreference points
		12.11 Summary
			Additional reading
	Chapter 13: Harvesting at the Ecosystem Level
		13.1 Introduction
		13.2 Fishery ecosystem production
			13.2.1 Simple food chain models
		13.3 Network models for exploited ecosystems
			13.3.1 Mass-balance models
			13.3.2 Ecosim
		13.4 Size spectra
		13.5 Habitat impacts andcarrying capacity
			13.5.1 Effects on productivity and yield
			13.5.2 By-catch and impacts on protected species
				13.5.2.1 Protected species
		13.6 Alternative ecosystem states
		13.7 Conceptual and qualitative models
		13.8 Summary
			Additional reading
	Chapter 14: Empirical Dynamic Modeling
		14.1 Introduction
		14.2 Core elements of the approach
			14.2.1 State-space reconstruction
			14.2.2 State-dependence
		14.3 Multivariate analysis
			14.3.1 Causality and convergent cross-mapping
		14.4 Assessing species interaction strength
		14.5 Forecasting
		14.6 Complexity in social-ecological data
		14.7 Summary
			Additional reading
	Chapter 15: Toward Ecosystem-Based Fisheries Management
		15.1 Introduction
		15.2 Place-based management
			15.2.1 Delineating the ecosystem
			15.2.2 Spatial management strategies
				15.2.2.1 Single-species models
				15.2.2.2 Habitat and biodiversity
				15.2.2.3 Interspecific interactions
				15.2.2.4 Priority areas for APAs
		15.3 Maintaining ecosystem structure and function
			15.3.1 Concepts of balance in fishery ecosystems
				15.3.1.1 Trophic balance
				15.3.1.2 Balanced harvest
		15.4 Defining overfishing in an ecosystem context
			15.4.1 Community-level reference points
			15.4.2 Ecosystem-level reference points
			15.4.3 System-level yield
		15.5 Management strategy evaluation
		15.6 Summary
			Additional reading
Bibliography
Index