Ocean Ecology

J. Emmett Duffy is director of the Smithsonian Institution's Tennenbaum Marine Observatories Network and MarineGEO program. He is the coeditor of Evolutionary Ecology of Social and Sexual Systems: Crustaceans as Model Organisms. Twitter @JEmmettDuffy

• PrefaceChapter 1: IntroductionA Framework for Functional Marine EcologyPlan of the bookSome recurrent themesHumans in marine ecosystemsEcology in PracticeThe central challenges of marine ecologyThe ocean and the shoreThe major patternsChapter 2: Life in the OceanThe Magnitude of BiodiversityDiversity on Land and SeaPhylogenetic Classification of Marine BiodiversityThe tree of lifePhylogenetic relationships and tree thinkingThe web of lifeFunctional Organization of Pelagic and Benthic LifeFunctional groups of pelagic lifeFunctional groups of benthic lifeMarine Life in the AnthropoceneFuture DirectionsSummaryChapter 3: Geography of Marine LifeA Short History of the Oceans and ContinentsClimate and Circulation of the World OceanGeostrophic flow and the central ocean gyresConvergence zones and frontsThermohaline circulation and the origins of deep waterCoasts, shallows, and their consequencesMajor Patterns in the Distribution of Marine LifeA conceptual framework for understanding biodiversityThe spatial organization of diversityThe latitudinal diversity gradientThe longitudinal diversity gradientThe depth diversity gradientThe role of bottom typeThe Origin of SpeciesThe ecology of speciationHabitat area and geographic rangeHabitat ageTemperature, energy, and metabolic rateBody sizeLife history and dispersal abilityEcological specializationEcological opportunity and speciationThe Dispersal of SpeciesThe Theory and Evidence for Island BiogeographyThe End of Species: ExtinctionIntegrative Models of Marine DiversificationBiogeographic Classifications of the OceanThe ecological geography of the seaMarine ecoregions of the worldLarge marine ecosystemsThe Biogeography of Functional TraitsThe Biogeography of Species InteractionsBiogeography of the Anthropocene OceanClimate warming and redistribution of global marine faunaTropicalizationThe Arctic openingThe sixth mass extinction?Future DirectionsSummaryChapter 4: Introduction to the Anthropocene OceanFirst, the Good NewsThe Great AccelerationCoal and climate changeNitrogen: Detonator of the population explosionThe limits to growthThe Natural and Cultural History of Homo SapiensEcology for the AnthropoceneCulture and the evolution of human societyEnergetics and economics of Homo sapiensThe tragedy and triumph of the commonsThe Anthropocene oceanOcean WarmingWarming effects on communitiesSea level riseOcean AcidificationEffects of acidification on organismsEffects of acidification on communitiesHomo Sapiens: Top Predator of the OceanThe history and extent of fishingThe current state of marine fisheriesEcosystem impacts of fishingThe future of fisheriesMarine Biodiversity in the AnthropoceneSpecies decline and extinctionFunctional consequences of declining biodiversityMarine globalizationEvolution in the domesticated oceanNovel ecosystemsFuture DirectionsScience for solutionsPolicy for solutionsReasons for cautious optimismSummaryChapter 5: OrganismsBuilding Blocks of LifeEcological stoichiometryNutrient uptake and useIronPowering LifeAutotrophyHeterotrophyKinetics of LifeDimensions of LifeMechanics of LifeCoding LifeNatural selection and adaptationGenotype and phenotypeFunctional Ecology and the NicheHistorical and modern concepts of the nicheToward a trait-based ecology of marine organismsFunctional Ecology of Marine Primary ProducersFunctional groups of phytoplanktonFunctional groups of benthic macrophytesMacroecologyOrganisms in the AnthropoceneFuture DirectionsSummaryChapter 6: PopulationsDevelopment and Life HistoryThe Problem of Larval DispersalPopulation Growth: A Brief ReviewGrowth of Age- and Stage-Structured Populations: Matrix ApproachesDemographic Models in Conservation and ManagementMaximum sustainable yield in fisheriesStrategic conservation of vulnerable life stagesLife history and the effectiveness of marine reservesOrganismal Fitness and Adaptation to the EnvironmentDispersal, Recruitment, and MetapopulationsTagging and trackingHydrodynamic simulation of larval movementLarval behaviorPopulation genetic markers of dispersal and connectivityGeochemical tagsMacroecology of PopulationsMetabolic scaling and life historyAbundance and the energetic equivalence ruleThe macroecology of range sizeMarine Populations in the AnthropoceneFuture DirectionsSummaryChapter 7: Species InteractionsInteractions among Species: General ConsiderationsInteractions between CompetitorsInteractions between Plants and HerbivoresControls on herbivory: Plant traitsControls on herbivory: Herbivore traitsInteractions between Prey and PredatorsControls on predation: Prey traitsControls on predation: Predator traitsParasitism and diseasePredation and community diversityFacilitation and MutualismEcological NetworksFunctional traits as a lens into community organizationTraits in interaction networksEmergent properties of ecological networksEcological Interactions in the AnthropoceneChanging species interactions in a changing climateFood web decapitation and trophic skewFuture DirectionsSummaryChapter 8: Ecological CommunitiesWhat Is a Community?Community Dynamics: A Conceptual FrameworkEcological selectionDispersal and metacommunitiesEcological driftSynthesis: Diversity in Ecological CommunitiesNeutral models and their assumptionsThe unified neutral theory of biodiversityTesting the neutral theory in natureDisturbance and diversity in communitiesThe role of historyDispersal and species richnessMetabolic theory and species diversitySpace and species diversityLinking Communities to EcosystemsFunctional structure of communitiesPhylogenetic structure of communitiesCommunities in the AnthropoceneClimate change and communitiesMarine defaunation and trophic skewFuture DirectionsSummaryChapter 9: EcosystemsHistory of the Ecosystem ConceptEvolution of the ecosystem conceptEcosystems as complex adaptive systemsPrimary ProductionLight and photosynthesisNutrient uptake and useHerbivoryControl of Biomass Distribution and Productivity in Marine EcosystemsThe green world hypothesisBottom-up control of biomass and productivity by resourcesTop-down control of biomass and productivity by consumersTrophic cascades in the oceanDetritus-consumer interactionsFunctional Structure of Marine EcosystemsOrganismal traits in ecosystemsThe size spectrumThe macroecology of trophic interactionsBiodiversity and the Functioning of EcosystemsBiodiversity and ecosystem functioning: TheoryBiodiversity and ecosystem production: Empirical evidenceBiodiversity and ecosystem stabilityAlternative Stable States and Regime Shifts in Complex Adaptive EcosystemsEmpirical evidence for regime shifts in marine ecosystemsMechanisms of marine regime shiftsApplications of Marine Ecosystem Modeling in Fisheries and ManagementModels of the Global EcosystemMarine Ecosystems in the AnthropoceneEutrophicationDefaunation and trophic skewFuture DirectionsSummaryChapter 10: The Open OceanPhysical Forcing of Pelagic EcosystemsThe global distribution of ocean productivityVertical structure of the pelagic water columnThe spring bloomHigh-nitrogen low-chlorophyll (HNLC) regionsOrganisms and TraitsThe phytoplankton: Major functional typesGrazers: Major functional typesGrazingStructure and Organization of Pelagic CommunitiesSpecialization and resource partitioningNonequilibrium dynamicsChaosFunctioning of Pelagic EcosystemsPelagic food webs: The microbial loopThe biological pump and the global carbon cycleTrophic control in pelagic ecosystemsThe Deep SeaAdaptations to life in the deep seaPelagic-benthic couplingDeep-sea biodiversityChemosynthetic Ecosystems: Vents and SeepsHydrothermal ventsCold seepsMacroecology of the Open OceanControls on biodiversity in the open oceanGlobal controls on microbial diversityMacroecology of open-ocean ecosystem processesDeep-Sea FisheriesThe Open Ocean in the AnthropoceneClimate and the Anthropocene oceanOcean acidificationHigh-seas fisheriesFuture DirectionsSummaryChapter 11: Estuaries and Coastal SeasThe Edge of the SeaInteracting ocean and continentsEstuariesCoastal life and communitiesCoastal ecosystem processesRocky ShoresGeomorphology and environmentOrganisms and traitsCommunity organization and key interactionsEcosystem processes and servicesRocky shores in the AnthropoceneSediment BottomsGeomorphology and environmentOrganisms and traitsCommunity organization and key interactionsEcosystem processes and servicesSediment bottoms in the anthropoceneSeagrass MeadowsGeomorphology and environmentOrganisms and traitsCommunity organization and key interactionsEcosystem processes and servicesSeagrass meadows in the AnthropoceneSalt MarshesGeomorphology and environmentOrganisms and traitsCommunity organization and key interactionsEcosystem processes and servicesSalt marshes in the AnthropoceneMangrove ForestsGeomorphology and environmentOrganisms and traitsCommunity organization and key interactionsEcosystem processes and servicesMangrove forests in the AnthropoceneThe Seascape: Interactions among HabitatsCoastal Ecosystems in the AnthropoceneClimate change and the coastDecline of foundation speciesTrophic skewNonnative and invasive species in coastal ecosystemsCoastal fisheriesEutrophication and hypoxiaMultiple stressors in coastal ecosystemsCoastal anthropogenic biomes: Urbanized estuariesFuture DirectionsSummaryChapter 12: Coral ReefsGeomorphology and Environment of Coral ReefsGeomorphologyAbiotic environmentOrganisms and Traits: Functional Diversity in Reef EcosystemsBiodiversity: Foundation speciesDiversity and functional ecology of primary producersDiversity and functional ecology of consumersCommunity Organization and Key InteractionsOrigin and maintenance of diversity in reef communitiesHerbivory in reef ecosystemsTrophic cascades in reef ecosystemsDisease in reef ecosystemsPhase shifts and alternative stable states on coral reefsRegional variation in coral reef dynamicsEcosystem and Biogeochemical ProcessesCoral reef production and nutrient cyclingCoral reef fisheriesCoral Reefs in the AnthropoceneCoral reefs in a warming oceanOcean acidificationCoral reef fisheriesThe future of coral reefsStrategic coral reef conservation and managementFuture DirectionsSummaryChapter 13: Ocean 2.0The Earth Is a Complex Adaptive SystemBiodiversity Is as Important as ClimateHumans Are Now the Force of NatureApocalypse NotBut What about Nature?Rays of HopeGlossaryLiterature CitedPhoto CreditsIndex