Note: Intro -- Contents -- Contributors -- 1: Introduction and Background -- 1.1 International Workshops -- 1.2 IOC/WESTPAC Summer Training Courses Were Organised -- 1.3 This Monograph Is an Output from These Activities! -- References -- 2: Anthropogenic Environmental Impacts on Coral Reefs in the Western and South-Western Pacific Ocean -- 2.1 Introduction -- 2.1.1 The Western and South-Western Pacific Region and the Coral Reefs -- 2.1.2 Population Change and Migration of People to Coastal Areas -- 2.1.3 Subsistence Living and Impacts of the Global Economic Situation on Reef Resources -- 2.1.4 Pollution from Small-Scale Developments -- 2.1.5 Shipping Impacts -- 2.1.6 Coastal City Expansion -- 2.1.7 Large Industry Impacts -- 2.1.7.1 Agriculture and Forestry -- 2.1.8 Tourism -- 2.1.9 Commercial Fishing Including Marine and Coastal Mariculture -- 2.1.10 Mining -- 2.1.11 Military Activities and Atomic Bomb Testing -- 2.1.12 Dredging and Dumping of Dredge Materials (Spoils) -- 2.2 Hydrodynamic Impacts of Anthropogenic Activities on Coral Reefs -- 2.3 Climate Change -- 2.4 Conclusions -- Appendix:Tribute to Dr. William G. L. (Bill) AALBERSBERG (1949-2018) -- References -- 3: Advances in Coral Biology -- 3.1 Introduction -- 3.2 Coral Biology -- 3.2.1 Reproduction, Development, and Recruitment of Larvae -- 3.2.1.1 Coral Spawning -- 3.2.1.2 Fertilization -- 3.2.1.3 Hybridization -- 3.2.1.4 Embryonic Development -- 3.2.1.5 Recruitment -- 3.2.2 Coral Taxonomy and Species Identification -- 3.2.2.1 Molecular Taxonomy and Systematics -- 3.2.2.2 Population Genetics -- 3.3 Current Threats on the Health of Reef Corals -- 3.3.1 Coral Bleaching -- 3.3.1.1 Spatial and Temporal Variation -- 3.3.1.2 Causes, Mechanisms, and Consequences -- 3.3.2 Coral Diseases -- 3.3.2.1 Identification and Prevalence -- 3.3.2.2 Disease Transmission -- 3.3.2.3 Prevention and Therapy. , 3.4 Management Consideration Based on Coral Biology -- References -- 4: Reef Ecology in the Western Pacific for Adaptation to Global Change -- 4.1 Introduction -- 4.2 Coral Reef Biodiversity Decline and Extinction Risk -- 4.2.1 Coral Reef Biodiversity Loss -- 4.2.2 Extinction Risk of Corals -- 4.3 Coral Reef Recovery After Disturbances -- 4.3.1 Disturbance Types and Impacts -- 4.3.2 Coral Reef Recovery -- 4.4 Coral Reef Resilience -- 4.4.1 Ecological Resilience -- 4.4.2 Coral Reef Resilience Indicators -- 4.4.3 Coral Reef Resilience Assessment -- 4.4.4 Coral Reef Resilience-Based Management -- 4.5 Coral Reef Connectivity -- 4.5.1 Concepts of Marine Population Connectivity -- 4.5.2 Ocean Circulation Drives Population Connectivity -- 4.5.3 Population Connectivity Among Corals and Reef Fishes -- 4.5.4 Applied Population Connectivity -- 4.6 Coral Reef Bioerosion -- 4.6.1 The Role of Bioerosion in Reef Development -- 4.6.2 Endolithic Bioerosion -- 4.6.3 External Bioerosion -- 4.6.4 Environmental Impacts on Bioerosion -- 4.7 Coral Reef Refugia Under Global Change -- 4.7.1 Coral Reef Refugia Concepts -- 4.7.2 Coral Reef Refugia from Thermal Stress -- 4.7.3 Coral Reef Refugia from Ocean Acidification -- 4.8 Marine Protected Area Networks (MPA Networks) -- 4.8.1 MPA Network Design Principles -- 4.8.2 Spatial Variations in MPA Networks -- 4.8.3 Fisheries in MPA Networks -- 4.8.4 Assessment and Conservation in MPA Networks -- 4.9 Passive and Active Restoration of Degraded Coral Reefs -- 4.9.1 Passive Coral Restoration -- 4.9.2 Direct Coral Transplantation -- 4.9.3 Coral Gardening -- 4.9.4 Substratum Addition (Artificial Reefs) -- 4.9.5 Substratum Stabilization and Enhancement -- 4.9.6 Coral Larval Enhancement -- References -- 5: Biogeochemical Dynamics of Coral Reef Systems -- 5.1 Introduction -- 5.2 External Driving Forces of Coral Reefs. , 5.2.1 Solar Radiation -- 5.2.2 Tide and Waves -- 5.2.3 Winds and Monsoon -- 5.2.4 Water Circulation and Currents -- 5.2.5 Land-Sourced Influxes -- 5.3 Sources of Chemical Elements in Coral Reef Systems -- 5.3.1 Terrestrial Material Inputs -- 5.3.2 Atmospheric Depositions -- 5.3.3 Coastal Upwelling -- 5.3.4 Recycling Within the System -- 5.4 Major Pathways of Biogeochemical Cycles -- 5.4.1 Autotrophic Production and Symbiosis -- 5.4.2 Heterotrophic Processes -- 5.4.3 Coupling Between Pelagic and Benthic Sub-systems -- 5.4.4 Food Web Dynamics -- 5.5 Interactions Between Biogeochemistry and Coral Reef Ecosystems -- 5.5.1 Impact of Nutrients on the Coral Ecosystems -- 5.5.2 Carbon Chemistry and Calcification -- 5.5.3 Mass Flow and Relationship with Energy Budgets -- 5.5.4 Discussion -- 5.6 Prospect of Climate Change and Anthropogenic Perturbations -- 5.6.1 Global Warming and Ocean Acidification -- 5.6.2 Impacts of Sea Level Rise -- 5.6.3 Roles of Human Society from Land- and Marine-Based Activities -- 5.6.4 Feedbacks to the Earth System -- 5.7 Modeling Approach to the Biogeochemistry of Coral Reefs -- 5.7.1 Quantitative Description of the Coral Symbiosis -- 5.7.2 Reef-Scale Model for Coral Ecosystems -- 5.7.3 Examples of Numerical Simulations in Coral System -- 5.7.4 Future Perspectives -- 5.8 Summary and Way Forward -- References -- 6: Environmental and Climate Proxies Embedded in Coral Skeletons -- 6.1 Introduction -- 6.1.1 Anatomy of Coral Skeleton -- 6.1.2 Basic Chemical Reactions Leading to Aragonite Formation in Coral -- 6.1.3 Solubility of CaCO3 and Water Temperature -- 6.1.4 Biomineralization Process for Aragonite Precipitation in Coral -- 6.1.5 Organic Matter in Coral Skeleton -- 6.2 Coral Core Sampling and Handling for Further Chemical and Isotopic Measurements -- 6.2.1 Retrieval of Coral Core and Slab Cutting -- 6.2.2 Slab Cleaning. , 6.2.3 Micro-Sampling -- 6.2.4 Subsample Cleaning for Chemical and Isotope Analysis -- 6.3 Intra- and Inter-skeletal and Colony Variability in the Chemical and Isotope Compositions -- 6.3.1 Intra-skeletal Variations -- 6.3.2 Inter-colony and Gender Variability -- 6.3.3 Calcite Formation Within the Aragonite Lattice -- 6.4 Age Model -- 6.4.1 Annual Growth Band -- 6.4.2 14C Dating (t1/2 = 5730 Years) (Valid for < -- 5 x t1/2 Years Old Coral) -- 6.4.3 230Th Dating (Valid < -- 123,000 Years Old Coral) -- 6.4.4 210Pb Dating (Valid < -- 100 Years Old Coral) -- 6.4.5 228Th Dating (Valid < -- 30 Years Old Coral) -- 6.4.6 90Sr Dating (Valid Since the 1950s) -- 6.4.7 Amino Acid Racemization (Valid Up to 40,000 Years Old Coral) -- 6.5 Principles of Application of Proxies/Tracers to the Past Climate and Environment -- 6.6 Chemical Elements and Isotopes Proxies -- 6.6.1 Lithium (Li) and Lithium Isotopes -- 6.6.2 Boron (B) and Boron Isotopes -- 6.6.3 Carbon (C) Isotopes -- 6.6.4 Nitrogen (N) Isotopes -- 6.6.5 Oxygen (O) Isotopes and Carbonate Clumped Isotopes -- 6.6.6 Fluorine (F) -- 6.6.7 Sodium (Na) -- 6.6.8 Magnesium (Mg) and Magnesium Isotopes -- 6.6.9 Phosphorus (P) -- 6.6.10 Sulfur (S) and Sulfur Isotopes -- 6.6.11 Calcium (Ca) Isotopes -- 6.6.12 Vanadium (V), Chromium (Cr), Manganese (Mn), Iron (Fe), Nickel (Ni), Copper (Cu), and Zinc (Zn) -- 6.6.13 Strontium (Sr) and Sr Isotopes -- 6.6.14 Yttrium -- 6.6.15 Molybdenum (Mo) Isotopes -- 6.6.16 Cadmium (Cd) -- 6.6.17 Iodine (I) and Iodine Isotopes -- 6.6.18 Barium (Ba) and Barium Isotopes -- 6.6.19 Rare Earth Elements (REEs) -- 6.6.20 Neodymium (Nd) -- 6.6.21 Lead (Pb) and Lead Isotopes -- 6.6.22 Uranium (U) -- 6.6.23 Plutonium (Pu) Isotopes -- 6.7 Discussion and Summary -- References -- 7: Synthesis and Future Perspectives on the Coral Reefs in the Western Pacific Region -- 7.1 Introduction. , 7.2 Function of Coral Reefs in a Sustainable Anthropocene -- 7.3 Coral Reefs in the Western Pacific Region and Comparison to Other Areas -- 7.4 External Forcings and Systems Response Threats to Coral Reefs in the Indo-Western Pacific Region -- 7.5 Summary and Main Conclusions of This Study -- 7.5.1 Anthropogenic Impacts Become Dominant Issues for the Sustainable Development of Coral Reef Systems -- 7.5.2 Coral Biology Is Critical in Our Knowledge of Tropical and Subtropical Environments -- 7.5.3 Coral Reef Ecology Bridges System Functions and Adaptive Management Towards a Sustainable Development -- 7.5.4 Biogeochemical Processes of Coral Reefs Play a Key Role in Understanding the Element Cycles and Connectivity Between Dif... -- 7.5.5 Proxies Embedded in Coral Skeletons Are Powerful Tool to Track the Impact of Environmental and Climate Variabilities -- 7.6 Challenges for the Ecosystem-Based Management (EbM) -- 7.7 Future Scientific Research Priorities on Coral Reefs -- References -- Postscript.