Note: Intro -- Coral Reefs: An Ecosystemin Transition -- Preface -- Contents -- Part I:History and Perspective -- Coral Research: Past Efforts and Future Horizons -- 1 Introduction -- 2 Early Coral Reef Research -- 3 Present Areas of Research and Future Directions -- 4 Future Horizons -- References -- Part II:Geology and Evolution -- The Paleoecology of Coral Reefs -- 1 Introduction -- 1.1 What Is Paleoecology? -- 1.2 A Brief History of Reefs -- 1.3 The Past, The Present, and The Future -- 2 Constraints and Influences over Coral Reef Development -- 2.1 Local Controls -- 2.2 Regional and Global: Secular -- 2.3 Latitudinal Range Limits -- 2.4 Biotic Factors -- 2.5 Autecology of Reef Organisms -- 3 Reef Paleoproductivity -- 4 Biotic Interactions -- 5 Paleo Community Ecology -- 6 Global Change: Environmental Influences on Species Distribution Patterns -- 6.1 Reef Growth and Global Change -- 6.2 Range Expansions/Contractions -- 7 Diversity Through Time: Evolutionary Ecology and Biotic Turnover -- 7.1 Cenozoic Patterns -- 7.2 Deep Time -- 8 The History of Modern Biogeographic Patterns -- 9 Reef Paleoecology, Historical Ecology, and Conservation Biology -- 10 Proxies for Environmental Change -- 11 Summary -- References -- Remote Sensing of Coral Reef Processes -- 1 Introduction -- 2 Brief History of Coral Reef Remote Sensing -- 3 Remote Sensing Basics -- 4 Coral Reef Remote Sensing Considerations -- 5 Remote Sensing of Optically Shallow Waters -- 6 Coral Reef Remote Sensing Applications -- 7 Conclusion -- References -- Coral Taxonomy and Evolution -- 1 Taxonomy -- 1.1 Traditional Concepts of Species -- 1.2 Classification -- 1.2.1 Syngameons -- 2 Variation in Species -- 2.1 Environmental Variation -- 2.2 Geographic Variation -- 2.3 Genetic Links Among Populations -- 3 Taxonomic Issues -- 3.1 Taxonomic Certainty and Geographic Range. , 3.2 Arbitrary Decisions -- 3.3 Geographic Variation in Synonymies -- 4 Natural Organization -- 5 Evolutionary Mechanisms -- 5.1 Reticulate Evolution -- 5.2 Ocean Currents and Reticulate Patterns -- 5.3 Competing Hypotheses -- 5.3.1 Darwin's Centers of Origin -- 5.3.2 Croizat's Panbiogeography -- 5.3.3 Vicariance Biogeography -- 5.3.4 Dispersion and the Founder Principle -- 5.3.5 Equilibrium Theory -- 5.3.6 Competing Hypotheses in Summary -- 5.4 Where Reticulate Evolution and Darwinian Evolution Meet -- Acknowledgments -- References -- The Coral Triangle -- 1 Introduction -- 2 Delineating the Coral Triangle -- 3 Hotspots of Biodiversity and Endemism -- 4 Characteristics of the Coral Triangle -- 5 Reasons for Existence of the Coral Triangle -- 5.1 Geological History -- 5.2 Dispersion -- 5.3 Biogeographic Patterns -- 5.4 Evolution -- 6 Future Impacts in the Coral Triangle -- References -- Part III:oral Biology: Symbiosis, Photosynthesisand Calcification -- Sexual Reproduction of Scleractinian Corals -- 1 Introduction -- 2 Coral Life Cycle and Reproduction -- 2.1 Asexual Budding and Reproduction -- 3 Historical Perspectives on Coral Reproduction -- 4 Recent Advances in Coral Reproduction Research -- 4.1 Biogeographical Patterns of Coral Reproduction -- 4.2 Environmental Influences on Coral Reproduction -- 4.3 Molecular Perspectives on Coral Reproduction -- 5 Patterns of Sexual Reproduction -- 6 Sexual Patterns -- 6.1 Systematic Trends in Sexual Patterns -- 7 Mode of Development -- 8 Summary and Conclusions -- References -- Zooxanthellae: The Yellow Symbionts Inside Animals -- 1 Introduction -- 2 Geological History -- 3 Cellular Anatomy and the Symbiosome -- 4 Division and Reproduction -- 5 Taxonomy from Morphology to Molecular Biology, Genus to Genotype -- 6 Inter- and Intrahost Transmission -- 7 Host Specificity. , 8 The Host Factor and the Nature of Translocated Compounds -- 9 Population Dynamics and Controls -- 10 Distribution Within Colony and Polyp -- 11 Photosynthesis -- 12 Ecology: Geography, Temperature, and Host Effects -- References -- Light as a Source of Information and Energy in Zooxanthellate Corals -- 1 Introduction -- 2 The Underwater Light Field to Which Corals are Exposed -- 3 Light as an Informational Signal in Corals -- 4 Fluorescent Proteins -- 5 Light as an Energy Source -- 6 The Zooxanthellae-Coral Association -- 7 Photoacclimation of the Zooxanthellae -- 8 Energy and Nutrient Fluxes -- 9 Colony Architecture -- 10 Conclusions -- References -- Coral Calcification, Cells to Reefs -- 1 Introduction -- 2 The Different Types of Biomineralization and the Coral Calcification -- 3 The Site of Coral Calcification: The Subcalicoblastic Extracellular Calcifying Medium -- 3.1 The Skeletogenic Tissue: The Calicoblastic Epithelium -- 3.2 The Subcalicoblastic Extracellular Calcifying Medium -- 3.3 ECM: Open or Closed Compartment? -- 3.4 Physicochemical Characteristics of the Subcalicoblastic Extracellular Calcifying Medium -- 3.5 Site of the Initial Mineral Deposition -- 4 Physiology of Coral Calcification -- 4.1 Coral Calcification: A Chemical Reaction with Four Molecules -- 4.2 Measurement of Coral Calcification -- 4.3 Ion Supply or Removal for Calcification: Paracellular and Passive or Transcellular and Active? -- 4.3.1 Ion Delivery to the Site of Mineralization: Three Possibilities -- 4.3.2 Energetic Dependence of Ion Transport -- 4.3.3 Calcium Transport -- 4.3.4 Dissolved Inorganic Carbon (DIC) -- 4.3.5 Removal of H+ -- 4.3.6 What About Other Mineralizing Organisms? -- 4.4 The First Mineral: Amorphous or Crystalline? -- 4.5 Carbonic Anhydrase: A Key Enzyme -- 4.6 The Key Role of Organic Matrix -- 4.6.1 Content in OM -- 4.6.2 Synthesis of OM. , 4.6.3 Biochemical Characterization of OM -- 4.6.4 Role of OM in Calcification -- 4.6.5 Interaction of OM and Calcium Carbonate -- 4.6.6 Comparison with OM from Other Invertebrates -- 4.6.7 Conclusions -- 4.7 The Cost of Calcification -- 5 Environmental Control of Calcification -- 5.1 Light -- 5.1.1 Background History of LEC -- 5.1.2 LEC During a Daily Cycle -- 5.1.3 Controversy on LEC -- 5.1.4 Hypothesis for LEC -- LEC and Inorganic Chemistry -- LEC and Inorganic Carbon -- LEC and Supply of Ions -- LEC and Removal of Phosphates -- LEC and Organic Chemistry -- LEC and Supply of Precursors for Organic Matrix Synthesis -- LEC and Oxygen -- LEC and Supply of ATP -- LEC and Nitrogen -- 5.1.5 Paradox of LEC -- 5.1.6 Conclusion on LEC -- 5.2 Temperature -- 6 Unity and Diversity of Coral Skeletons -- 6.1 The Basic Mechanism: Fibers and Centers of Mineralization -- 6.2 Concentric Layers: Annual, Diel Patterns -- 6.3 Nanograins as Units of Mineralization? -- 7 Conclusions -- References -- Coral Calcification Under Ocean Acidification and Global Change -- 1 Introduction -- 1.1 The Ecological Importance of Coral Calcification -- 1.2 Global and Local Environmental Changes and Their Effects on Coral Reef Calcification -- 1.2.1 Global Warming and Bleaching -- 1.2.2 Eutrophication -- 1.2.3 Coral Breakage by Tourism, Boating, and Fishing -- 1.2.4 Ocean Acidification -- 2 Basics of Coral Calcification Relevant to Ocean Acidification -- 2.1 Light and Dark Calcification, the Effect of the Symbiotic Algae, and the Classical Calcification Hypothesis of Goreau -- 2.2 Direct Supply of Seawater to the Biomineralization Site -- 2.3 Information from Shell Chemistry and Isotopes -- 3 Sensitivity of Corals and Coral Reefs to Changes in the Carbonate Chemistry of the Water -- 3.1 Carbonate Chemistry of Seawater and the Use of Variable Experimental Techniques. , 3.2 The Effects of Ocean Acidification on Individual Corals and the Connection to Cell- and Tissue-Level Processes -- 3.2.1 Direct Effects on Coral Calcification -- 3.2.2 Potential Effect on Symbiotic Algae -- 3.2.3 Direct Effect of CO2 -- 3.2.4 pH-Mediated Effects -- 3.2.5 Change in the Buffering Capacity -- 3.2.6 Conclusion: Origins of the Sensitivity of Corals to Ocean Acidification -- 3.3 Ocean Acidification and Coral Reefs at the Community Level -- 3.3.1 Community Calcification as a Function of Warag -- 3.3.2 CaCO3 Dissolution in Coral Reefs -- 3.4 Implications for the Future Existence of Coral Reefs -- 4 General Conclusions -- References -- Simulating and Quantifying the Environmental Influence on Coral Colony Growth and Form -- 1 Introduction -- 2 Three-Dimensional Images of Coral Colonies Obtained Using Computer Tomography Scanning -- 3 Morphometrics of Three-Dimensional Complex-Shaped Branching Colonies -- 4 The Accretive Growth Model -- 5 Comparison Between Coral Colony Morphologies and Simulated Forms -- References -- Physiological Adaptation to Symbiosis in Cnidarians -- 1 The Coral/Zooxanthella Holobiont: A Chimera? -- 2 First Adaptation: A Marine Microalgae Living in an Intracellular Medium -- 3 Second Adaptation: The Need of a Permanent Supply of CO2 for Symbiont Photosynthesis -- 4 Third Adaptation: Withstand Hyperoxia -- 4.1 High Diversity of Enzymatic Antioxidative Defense is a Consequence of Symbiosis -- 4.2 Nonenzymatic Antioxidative Mechanisms -- 5 Fourth Adaptation: Withstand Solar Radiations -- 5.1 Ultraviolet Screens -- 5.2 Host and Symbiont Pigments -- 6 Conclusion -- References -- Part IV:The Coral Reef Ecosystem: Bacteria, Zooplankton,Algae, Invertebrates, Fishes and Model -- Biogeochemistry of Nutrients -- 1 Introduction -- 2 Summary of Reviews -- 3 Nutrient Pool Sizes -- 4 Productivity -- 5 Mass Transfer. , 6 Implications of Mass Transfer and Questions Revisited.