Encyclopedia of Modern Coral Reefs · Structure, Form and Process (Encyclopedia of Earth Sciences Series) by Cabioch, Guy -- Read -- Imperial Library of Trantor

Index

Cover Encyclopedia of Earth Sciences Series Encyclopedia of Modern Coral Reefs ISBN 9789048126385 2011, DOI: 10.1007/978-90-481-2639-2 A

Acanthaster Planci

Bibliography

Accommodation Space

Definition Accommodation space Bibliography

Acropora

Synonyms Definition Introduction Nomenclatural issues The skeleton and polyps Habitats and ecology Sexual and asexual reproduction Genetics and phylogeny Biogeography and evolution Summary Acknowledgments Bibliography

Adaptation

Definition Introduction Coral-zooxanthellae symbiosis as an illustration of adaptation Current investigations, controversies, and gaps in current knowledge

Coral bleaching Long-term change

Bibliography

Aerial Photography of Coral Reefs

Aerial photography of coral reefs Bibliography

Agassiz, Alexander (1835-1910)

Bibliography

Airborne Dust Impacts

Definition Background Processes Effects Asian dust Summary Bibliography

Algae, Blue-Green Boring

Synonyms Definition Bibliography

Algae, Coralline

Synonyms Definition Introduction Systematics Life history Rhodoliths Geology and evolution Distribution patterns and functional significance Pathogens Summary Bibliography

Algae-Macro

Synonyms Definition Introduction Human utilization of macroalgae Ecological significance of macroalgae Major macroalgal groups

Rhodophyta (red algae) Phaeophyceae (brown algae) Chlorophyta (green algae) Cyanobacteria (blue-green ``algae´´)

Summary Bibliography

Algae, Turf

Synonyms Definition Bibliography

Algal Rims

Definition and morphology Relation with sea level Bibliography

Antecedent Platforms

Definition Introduction In the beginning

Antecedence post-1974 - the purdy revolution Growth antecedence Non-karst antecedence

Conclusions Bibliography

Aragonite

Definition Bibliography

Atoll Islands (Motu)

Synonyms Definition

Number, dimensions, and location of atoll islands

Motu Classification of atoll islands

Geomorphic features of atoll islands Sediments, soils, and groundwater Processes of formation and change on atoll islands Stabilization processes Origin and development of atoll islands Future status of atoll islands

Bibliography

Atolls

Definition Introduction Surface morphology

Outer reef Reef rim Lagoon

Geological evolution of atolls Quaternary evolution of atolls

Accretion of the reef rim

Reef islands on atolls

Island sediments Processes of island formation Island soils, vegetation, and ecosystems Atoll hydrology

Human impacts on atolls Summary Bibliography

AUVs (ROVs)

Synonyms Definitions Introduction ROV technology AUV technology Applications to coral reef science Summary Bibliography

Back-Stepping

Synonyms Definition Introduction Reef back-stepping in stable terranes Reef back-stepping in subsiding terranes Cause of reef back-stepping Bibliography Cross-references

Bafflestone

Bibliography Cross-references

Bahamas

Definition Introduction

Reef distribution Reef biota and zonation Reef health

Summary Bibliography

Banks Island: Frasnian (Late Devonian) Reefs In Northwestern Arctic Canada

Bibliography

Banks, Joseph (1743-1820)

Bibliography Cross-references

Barbados

Introduction Pleistocene reef terraces Reef zonation Diagenesis and caliche Submerged reefs Acropora palmata demise and the origin of Cobblers Reef Hydrogeology (Humphrey, 1997) Conclusion Bibliography

Barrier Reef (Ribbon Reef)

Definition and introduction Cross-references Morphology Locations Drilling in barrier reefs Bibliography Cross-references

Bassett Edges

Synonyms Definition Bibliography Cross-references

Beach Rock

Synonyms Definition Description Distribution Grain size and composition Cements Origin of cement

Speed of cementation Age of beach rock and problems of dating Morphodynamics and shoreline change Beach rock as a sea-level indicator Surface features and beach rock erosion

Bibliography Cross-references

Belize Barrier and Atoll Reefs

Definition Geomorphology Organisms and reef zonation Sediments Geology Late Quaternary reef development, sea level, and antecedent topography Summary Bibliography Cross-references

Bermuda

Definition and introduction Major reef types and their communities

Fore-reef slope reefs Main terrace reefs Rim reefs Algal-vermetid cup reefs Lagoonal reefs Inshore reefs

Factors affecting Bermuda´s reefs

Coral bleaching Pollution and ship groundings

Summary Bibliography

Bikini Atoll, Marshall Islands

Definition Introduction Physical environment Scientific surveys at Bikini Atoll Marine biology Vegetation Seabirds and shorebirds Sea turtles Atmospheric nuclear tests at Bikini Early cultural history Recent history The nuclear nomads of Bikini Restoration for resettlement Summary and conclusions Current investigations, controversies, and gaps in current knowledge Bibliography Cross-references

Binding Organisms

Definition and introduction Algal structures Polychaetes Summary and conclusion Bibliography Cross-references

Bindstone

Bibliography Cross-references

Bioerosion

Definition Introduction Microborers

Components and processes Method by which microborers bore

Macroborers

Polychaetes Molluscs Sipunculans Sponges

Succession of macroborer communities Grazers

Echinoids Molluscs Parrotfishes

Predation on live coral Determining rates of bioerosion Habitat creators Environmental factors influencing rates and agents of bioerosion Anthropogenic factors influencing rates and agents of bioerosion

Poor water quality Increasing water temperatures Cumulative impacts

Conclusions Acknowledgments Bibliography Cross-references

Bioherms and Biostromes

Definitions and history Discussion Conclusions Bibliography Cross-references

Bioturbation

Definition and introduction Effects of bioturbation on sediment sorting and texture Depth and rate of bioturbation Time-averaging and preservation potential in reefal environments Geochemical aspects of bioturbation Summary and conclusion Bibliography Cross-references

Blowholes

Definition

Blue Hole

Bibliography Cross-references

Boat Channel

Synonyms Description Bibliography Cross-references

Boulder Beaches

Synonyms Definition Bibliography Cross-references

Boulder Zone/Ramparts

Definition Bibliography Cross-references

Brazil, Coral Reefs

Synonyms Definition Introduction Regional setting Reef-building coral fauna Major reef types Summary Bibliography Cross-references

Bryozoa

Synonyms Definitions Introduction: Bryozoans in modern reefs History of discovery Extension into the fossil record Roles seen among reefal bryozoans Continuing investigations Summary Bibliography Cross-references

Calcite

Definition Bibliography

Calcrete/Caliche

Synonyms Definition Calcrete textures Bibliography

Carbon Fluxes of Coral Reefs

Synonyms Definition Introduction Fluxes of dissolved inorganic carbon Net production of carbon Fluxes of planktonic carbon Fluxes of dissolved organic matter Fluxes of sediment carbon Pore-water carbon Summary Bibliography

Carbonate Budgets and Reef Framework Accumulation

Definition Introduction

Quantifying reef framework production and cycling Variations in carbonate production at the reef system scale Carbonate budgets and long-term rates of reef framework accumulation Using carbonate budgets to monitor changes in reef ``health´´

Summary Bibliography

Carboniferous Reefs

Definition Bibliography

Cay Formation

Definition Formation Summary Bibliography

Chamisso, Adelbert Von (1781-1838)

Bibliography

Classification of Carbonates

Definition and introduction A short history of limestone classifications Application of the recommended carbonate classification schemes Summary Bibliography

Climate Change and Coral Reefs

Definition A rapidly changing climate Climate factors affecting coral reefs

Physical climatic environment of coral reefs: defining the envelope Other weather and climatic factors affecting coral reefs

Impacts of climate change on coral reefs

Warmer waters and coral bleaching Consequences of coral bleaching Warmer water temperatures and coral diseases Warmer water temperatures: other effects Changing ocean chemistry Sea level

Linking the physical environment with biological processes Projected future climates for coral reefs

Predicting future climate Projected global changes

A changing climate for coral reefs: future impacts

Combined disturbances and recovery intervals

Potential actions Summary Bibliography

Climate Change: Impact of Sea Level Rise on Reef Flat Zonation and Productivity

Definitions Introduction Reef flat attributes and sea level rise Reef flat response to sea level rise Reef island responses Other factors influencing reef flat change Summary Bibliography

Climate Change: Impact On Coral Reef Coasts

Definition Introduction Quantification of the problem: a case study Summary Bibliography

Climate Change: Increasing Storm Activity

Synonyms Definition Introduction Evidence Conclusions: consequences for coral reefs Bibliography

Cocos (Keeling) Islands

Definition Introduction History Atoll morphology and physical characteristics Atoll rim and Lagoon Reef islands Summary Bibliography

Cold-Water Coral Reefs

Synonyms Definition Introduction Dimensions and time constraints of cold-water coral reefs Colony, thicket, coppice, reef Coral habitats, some key species and trophic webs Summary Bibliography

Conglomerates

Synonyms Definition Parental features Bibliography

Conservation and Marine Protection Areas

Definitions Introduction Status of coral reefs globally Key threats to marine conservation and especially coral reefs Effective reef conservation Marine protected areas The benefits of MPAs Tools for marine management Key lessons learnt What is the future for reef conservation? Websites Bibliography

Cook, James (1728-1779)

Bibliography

Coral Cay Classification and Evolution

Definition Introduction Cay formation: wave influences Cay sediments Criteria used in classification Classification: island types

Unvegetated cays Vegetated cays Mangrove islands Multiple islands Low wooded islands

Reef-island vegetation Age, evolution, and relationships to Holocene sea level Factors influencing cay stability Coral cay dynamics Future for reef cays

Sea-level rise Reduced carbonate production and ocean acidification

Bibliography

Coral Cays - Geohydrology

Synonyms Definition Introduction The dual aquifer model Lens thickness and freshwater resources Summary Bibliography

Coral Cays, Vegetational Succession

Definition Early colonization Peripheral zone of shrubs Herb meadows Savannah Forests Erosion Marine washover Seabirds Sea turtles Drought Humans Summary Bibliography

Coral Reef, Definition

Definition Introduction Coral community: geological and ecological definitions A tract of corals Massive structure Wave resistant structure Associated sediments Substantially built by successive generations of corals and other reef builders Summary Bibliography

Coral Reefs of India

Definition and introduction Coral reefs: East Coast of India

Gulf of Mannar Andaman and Nicobar Islands West Coast of India Malvan Lakshadweep Islands Gulf of Kachchh

Geology and geomorphology of Indian coral reefs Coral reef associated biodiversity

Scleractinian corals Algae Sea grass Other marine fauna

Threats to coral reefs Coral damage from the Tsunami of 26th December, 2004 Conservation Conclusion Bibliography

Corals: Biology, Skeletal Deposition, and Reef-Building

Definition Introduction Reefs and coral reefs Reef carbonates Reef building

Light Algal symbiosis Water depth, turbidity, and latitude Temperature Low-temperature limits to reef growth High-temperature limits to reef and coral growth Substrate, turbulence, and mechanical effects Water quality

Rates of growth and erosion

Coral growth rates Reef growth rates Rates of reef erosion

Summary Bibliography

Corals: Environmental Controls on Growth

Definitions Introduction Coral: the animal-plant symbiosis Environmental controls on global distribution of corals

Chemistry Solar radiation Temperature

Environmental variability within regions

Hydrodynamics, light, and sediments Nutrients

Microenvironment controls on coral growth Coral growth

From primary polyp to coral colony Modes of nutrition and coral growth forms Depth and light Environmental controls on coral´s presettlement stage

Global climate change: implications for coral growth Summary Bibliography

Core Plugs

Definition

Daly, Reginald Aldworth (1871-1957)

Bibliography

Dana, James Dwight (1813-1895)

Bibliography

Darwin Point

Darwin Point Bibliography

Darwin, Charles (1809-1882)

Introduction Voyage of the Beagle and Darwin´s coral reef theory A deductive theory Second edition of ``Coral Reefs´´ Conclusions Bibliography

David, Tannant Edgeworth (1858-1934)

Bibliography

Davis, William Morris (1850-1934)

Davis and Coral Reefs Bibliography

Density and Porosity: Influence on Reef Accretion Rates

Bibliography

Devonian Reef Complexes of the Canning Basin

Bibliography

Diagenesis

Definition Introduction General approach and technical methods Cementation

Early cements Cementation in reefs

Internal sediments

Marine internal sediments Nonmarine internal sediments

Dissolution

Selective dissolution of skeletal elements Dissolution of early cements Dissolution of dolomite Distribution of dissolution features in reefs Controls of dissolution

Dolomite in reefs

Petrography of dolostones Distribution of dolomite in reefs Dolomitizing fluids

Diagenetic alteration - crystalline modifications

Calcitization of aragonite Transformation of HMC to LMC Dolomitization Skeletal diagenesis

Models of reef diagenesis

Early marine cementation Meteoric cementation Dolomitization

Outlook: What we still do not know about reef diagenesis

Role of organic matter Role of microbial processes in reef diagenesis

Bibliography

Dolomitization

Definition Dolomite, the mineral, and the dolomitization process Dolomite occurrences and hydrological processes Dolomite in reefs, atolls, and guyots Summary Bibliography

Double and Triple Reef Fronts

Definition Bibliography Cross-references

Earthquakes and Emergence or Submergence of Coral Reefs

Synonyms Definition Introduction Mysterious origin of emerged and submerged coral reefs Scientific reports of coseismically displaced coral reefs Scientific significance of coseismically emerged coral reefs Methods to measure coseismic coral reef emergence Recognition of coseismically emerged reefs Determining the ages of vertical displacements recorded by corals Summary/outlook Bibliography

East Indies Triangle of Biodiversity

Synonyms Definition Introduction Tectonic and oceanographic basis Coral triangle conservation initiative Summary Bibliography

Eastern Caribbean Coral Reefs

Synonyms Definition Reef types Oceanography and reef-community structure Holocene reef geology in the southeastern Caribbean

Deep Holocene reefs Shelf-edge reefs Inner-shelf reefs

What have we learned?

The role of ``inimical bank waters´´ St. Croix as a ``Caribbean model´´ The role of sea level A simpler model

Bibliography

Eastern Indian Ocean - Northern Sector

Definition Background Geological history and sea floor topography Oceanography and major physical features Biology of coral reefs of the Andaman Sea Summary Bibliography

Eastern Tropical Pacific Coral Reefs

Introduction

Background

Physical environment

Climate Hydrography

Coral reefs

Geological history Holocene growth history Types of coral reefs

Threats/impacts

El Niño-Southern Oscillation (ENSO) Subaerial exposure Sedimentation Organism extraction Climate change Coral reef resilience

Conclusions Bibliography

Echinodermata

Definition Introduction Conclusion Bibliography

Eco-Morphodynamics

Definition Introduction Morphodynamic origins Eco-morphodynamic framework

Boundary controls Time and space scales of change Feedbacks

Summary Bibliography

Ecomorphology

Definition Introduction Environmental stresses and their effect on corals Variation in coral communities across a section of reef Applications of the model Summary Bibliography

El Niño, La Niña, and ENSO

Synonyms Definition Introduction ENSO effects on corals

SST anomalies and coral mortality Coral bleaching Mitigation by depth and light Coral reproduction and dispersal Secondary biological impacts

Summary Bibliography

Electro Mineral Accretion

Synonyms Definition Bibliography

Electron Spin Resonance Dating (ESR)

Definition Introduction Methodology Case study 1: ESR dating of Pleistocene coral reef terraces Case study 2: ESR dating of Holocene corals Summary Bibliography

Emerged Reefs

Synonyms Definition Introduction Types of emerged morphological structures

Abraded reef flats Coral terraces

Uplift in island arc archipelagos and tectonically active areas

Caribbean: Barbados Pacific: Papua New Guinea Pacific: Vanuatu Pacific: Solomon islands Pacific: Fiji Pacific: Ryukyu Indian Ocean: Indonesia Red Sea

Lithospheric flexure

Isostatic readjustment

Magma chamber inflation Summary Bibliography

Enewetak Atoll, Marshall Islands

Introduction Physical characteristics Cultural history

Recent history The Nuclear Era

Enewetak Marine Biological Laboratory Deep Drilling Program at Enewetak Atoll Biogeography and ecology Summary and Conclusions Bibliography

Engineering on Coral Reefs with Emphasis on Pacific Reefs

Definition Introduction Engineering and coastal construction requirements on coral reefs Adverse ecological consequences of poorly designed engineering activities and structures Summary Bibliography

Eolianite

Synonyms Definition Bibliography

Faroes Reefs

Synonyms Bibliography Cross-references

Floatstone

Bibliography

Florida Keys

Synonyms Definitions Geographic and geomorphic setting Seven coral ecosystems and reef decline Two structural architectures Four coral nuclei Coral spurs and zonations Key Holocene events and effects Other aspects Summary Bibliography Cross-references

FORAM Index

Bibliography Cross-references

Foraminifera

Definition and introduction Conclusions Bibliography Cross-references

Forereef/Reef Front

Synonyms Definition Morphology Factors controlling the morphology Biozonation Biological encrusting zonation Occurrence of micritic crusts Summary Bibliography

Fossil Coralline Algae

Definition Introduction Applications of fossil CCA Summary Bibliography

Framestone

Bibliography Cross-references

Fringing Reef Circulation

Synonyms Definition Introduction Waves and wave generated circulation Wind-generated circulation Topographically controlled circulation Flushing Summary Bibliography Cross-references

Fringing Reefs

Definition Introduction Fringing reefs and terrestrial influence

Fringing reef substrates Influence of terrestrial runoff, sediments and nutrients on fringing reefs

Fringing reef growth and sea level Fringing reef structure and growth models

Vertical accretion and progradation Progradation out from shore over rocky substrate Progradation over terrigenous sediments Pulsed progradation Reef crest and backfill Storm-reworked framework and infill Other models

Fringing reef morphology and processes

High water shingle and debris Terrigenous boulder beach Inner moat Shingle rampart Algal terraces Northern fossil microatolls Amorphous southern reef flat Outer living coral zone and reef slope

Summary Bibliography Cross-references

Funafuti Atoll

Synonyms Definition Introduction The Royal Society Coral Reef Expeditions Holocene reef growth at Funafuti Reef Island formation: higher sea-level or storm impacts? Funafuti and predicted sea-level rise Summary Bibliography

Gardiner, John Stanley (1872-1946)

Definition Bibliography

General Evolution of Carbonate Reefs

Introduction Biological fixation of carbonate

Calcareous metazoans Calcareous algae Microbes

Internal cavity systems Synsedimentary lithification Bioerosion and predation Geologic history of reefs

Skeletal reefs Mixed skeletal-microbial reefs Deep-water skeletal-microbial reefs Microbial reefs Mud mounds Origin of the modern coral reef ecosystem

Response to long-term environmental change

Climate Carbonate saturation Evolving ocean chemistry

The rise of predation and bioerosion

Response to increased biological disturbance

The role of mass extinctions Summary Bibliography

Geomorphic Zonation

Introduction Standard geomorphic reef zonation Lagoon Patches, knolls, and pinnacles Cellular reefs

Formation of lagoonal reefs

Reef flat Algal rims Coralgal flat Sand flat Islands and storm deposits

Formation of reef flats

Reef front

Spur and groove Formation of spur and grooves

Mid-shelf scarp and sand terrace

Formation of terrace-scarp reef-front features

Reef slope Shelf-edge chute and buttress (shelf-edge reefs)

Formation of shelf-edge chutes and buttresses

Lower reef slope

Formation of the reef slope

Summary and conclusions Bibliography

Glacial Control Hypothesis

Synonyms Definition `Glacial control´ of coral reef development

Development of the hypothesis Tests of the hypothesis Alternative explanations for the morphology of modern reef surfaces

Conclusions Bibliography

Glacio-Hydro Isostasy

Synonyms Definition Introduction Models for glacio-hydro isostasy The sea-level response Some examples Conclusion Bibliography

Global Ocean Circulation and Coral Reefs

Synonyms Definition Introduction

Origins of modern circulation patterns Ocean circulation and biogeographic patterns Ocean circulation and reef formation Surface currents and dispersal Ocean circulation and evolution Meso- and microscale circulation and environments

Summary Bibliography

Great Barrier Reef Committee

Bibliography

Great Barrier Reef: Origin, Evolution, and Modern Development

Introduction The architecture of offshore northeast Australia Eastern Fields Plateau Queensland Plateau Marion Plateau The Swains Reef and Bunker Highs The Great Barrier Reef The rift basins Bunker and Swains Highs Causes of architecture

Rifting Subsidence Drift Sea-level variations Collision

Establishment of reefs in northeast Australia Establishment of the Great Barrier Reef

Ribbon Reef No. 5 Ocean drilling program site 820

Relations between Ribbon 5 core and ODP site 820 and implications

Cross-shelf growth of the great barrier reef

The modern reef Holocene reef start-up Growth at sea level Types of reefs Growth - the facies produced Growth models The One Tree Reef Model The Stanley Reef Model The Ribbon 5 model Summary Bibliography

Halimeda

Synonyms Definition Phytochemistry

Photosynthetic pigments Cell wall General

Appearance Taxonomy Distribution Internal structure Growth Calcification Diurnal color change Grazing Reproduction Contribution to carbonate sediments Fossil Halimeda Bibliography

Halimeda Bioherms

Introduction The biology of Halimeda bioherms and adjacent meadows (biostromes) The global distribution of Halimeda bioherms

The Great Barrier Reef The Sahul shelf The Java Sea bioherms The Miskita bank/channel bioherms

Descriptive features of Halimeda bioherms Rates of growth of Halimeda bioherms Relations between bioherms (banks) and meadows (biostromes) and the lagoonal meadows at Enewetak Growth of Halimeda bioherms Significance of Halimeda bioherms Summary Bibliography

Hawaiian Emperor Volcanic Chain and Coral Reef History

Definition Outlook Bibliography

Heavy Metal Accumulation in Scleractinian Corals

Synonyms Definition

Heavy metals in the marine environment This study Scleractinian corals Outcomes

Bibliography

Historical Ecology of Coral Reefs

Definition Introduction The tools of marine historical ecology Historical ecology of coastal ecosystems Key findings on coral reefs Management implications Summary Bibliography

Holocene High Energy Window

Definition Introduction Global and regional scale perspectives Impacts of a high energy ``window´´ at the reef and reef island scale Summary Bibliography

Holocene Reefs: Thickness and Characteristics

Bibliography

Huon Peninsula, P.N.G.

Bibliography

Hydrodynamics of Coral Reef Systems

Synonyms Definition Hydrodynamics of coral reef systems

Water flow in coral reef systems

Friction on reefs Spatial variability of roughness

Rough reef flat Smooth reef flat

Currents around reefs Waves on reefs

Wave processes Wave boundary layer

Tidal influences Turbulent energy Flushing times of reef systems Richardson Plot Porous reef models Summary Bibliography

Impacts of Sediment on Coral Reefs

Introduction A geological perspective Demonstrated effects of sediments on reefs

Decrease in coral growth rates Partial or total mortality Decrease in metabolic rate Changes in coral population structure Changes in coral morphology Reduced species richness and diversity Reduced larval settlement

Mode of action of sediments

Decreasing the available light Metabolic drain Microbially mediated decline

Summary of impacts Status of research Guidelines - how much sedimentation is too much? Sclerochronology: the two-edged sword How to identify if a reef is sediment-stressed Summary Acknowledgments Bibliography

Indian Ocean Reefs

Definition Introduction Madagascar Mayotte Maldives Postglacial development Summary Bibliography

Indonesian Reefs

Definition Introduction Biodiversity Environmental setting Fossil reefs Living reefs Sumatra Java Kalimantan

Sulawesi

Bali and Nusa Tenggara Maluku West Papua Summary Bibiliography

Infrastructure and Reef Islands

Definitions Introduction Infrastructure for reef island communities Flooding and disaster protection Infrastructure for navigation and weather monitoring Conclusion Bibliography

Internal Circulation

Synonyms Definition Introduction Driving mechanisms Experimental studies Summary Bibliography

Intrinsic And Extrinsic Drivers On Coral Reefs

Synonyms Introduction Causal typologies Evolving models of reef dynamics Summary Bibliography

Lagoon Circulation

Synonyms Definition Fringing and barrier reef lagoons Atoll lagoons Summary Bibliography

Lagoons

Bibliography

Last Glacial Interstadials

Definition Bibliography

Last Glacial Lowstand and Shelf Exposure

Definition Bibliography

Last Interglacial and Reef Development

Introduction Reef development in uplifted terrains

Barbados Huon Peninsula, Papua New Guinea Red Sea

Reef development in more stable terrains

Florida Bahamas Grand Cayman Northeast Yucatan Peninsula Western Australia Hawaii

Summary and conclusions Bibliography

Low Wooded Islands

Definition Introduction Geomorphic characteristics

Emergent reef flat Shingle ramparts Moats Platforms or promenades Shingle islands Mangrove swamp Leeward sand cay Boulder zone

Formation of low wooded islands Temporal development and morphological change Summary Bibliography

Lyell, Charles (1797-1875)

MacNeil, F. Stearns (1909-1983)

Bibliography

Makatea

Definition Bibliography

Maldives

Definition Introduction Early exploration Geologic history Reef structure Latitudinal gradients in atoll characteristics and processes Reef ecology and biodiversity Reef islands Summary Bibliography

Mangrove Islands

Definition Bibliography

Mangroves

Synonyms Definition Introduction Uniquely mangrove origins and vulnerability Rich and diverse Structural diversity Factors influencing mangrove distributions Conclusion Bibliography

Mariana Islands, Coral Reef Geology

Definition Holocene coral reefs in the southern Marianas General geology of the southern Marianas - volcanics and limestones Conclusions Bibliography

Mass Extinctions, Anoxic Events and Ocean Acidification

Introduction Mass extinctions, corals, and reef gaps

The end Ordovician mass extinction The late Devonian mass extinction The end Permian mass extinction The end Triassic mass extinction The end Cretaceous mass extinction (K/T)

Causes of mass extinctions

Causes independent of the carbon cycle Links between mass extinctions and the carbon cycle

Conclusions Bibliography

Mayor, Alfred Goldsborough (1868-1922)

Bibliography

Megablocks

Synonyms Definition Introduction Examples Origin and mechanism of transport: Tsunamis or storms? Dating the emplacement of megablocks How fast the current? How high the wave? Summary Bibliography

Meltwater Pulses

Synonyms Definition Introduction Glacial Termination I (MIS-2) Last glaciation (MIS-3) Glacial Termination II (MIS-6) Last Interglacial (MIS-5e) Origin of meltwater pulses Bibliography

Micrite

Synonyms Definition Introduction Conclusion Bibliography

Microatoll

Definition Introduction Microatoll description Microatoll formation Microatolls and sea level Microatoll records of ENSOs, earthquakes, and other environmental conditions Summary Bibliography

Microbes

Definition Microbial association with corals: holobiont Functional role of microbes Microbial role in coral stress Microbial role in altering environmental conditions Bibliography

Mid Holocene

Definition Introduction Equatorial ocean siphoning and continental levering Effects on reef development

Caribbean model Indo-Pacific model

Case study: the Great Barrier Reef Summary/conclusions Bibliography

Midway Atoll (Hawaiian Archipelago)

Introduction Geology Human history Marine species and habitats Terrestrial wildlife and habitats Current investigations Controversies and gaps in current knowledge Summary and conclusions Bibliography

Mining/Quarrying of Coral Reefs

Definition Background Methods of coral extraction Biological effects of coral mining Alternative management options and restoration of mined reefs Summary Bibliography

Moating

Definition Bibliography

Moats

Synonyms Definition Bibliography

Molluscs

Definition Bibliography

Mururoa Atoll

Definition Geological setting Modern reef morphology and zonation

The outer reef rim The lagoon

Lithology and structure of the sedimentary pile

The volcaniclastic series The carbonate cap

Carbonate diagenesis Pleistocene reef growth and sea-level changes Summary Bibliography

New Caledonia

Introduction Climatic conditions Geological setting History of coral reefs and lagoons

Fringing reefs Barrier reefs Lagoon

Climatic and/or oceanographic factors affecting the reef growth and the coral development Summary Bibliography Cross-references

Notch and Visor

Definition Bibliography Cross-references

Nutrient Pollution/Eutrophication

Synonyms Definition Summary What is eutrophication? Effects of nutrient pollution and eutrophication on coral reefs

Effects of the increased availability of nutrients and organic matter Effects of decreasing light availability due to turbidity Effects of altered sediment properties

Factors determining the vulnerability of a specific coral reef to eutrophication Conclusions Acknowledgments Bibliography Cross-references

Ocean Acidification, Effects on Calcification

Synonyms Definition Introduction Chemistry of ocean acidification Effects on formation and dissolution of calcium carbonate Effects on calcification of marine organisms Effects on coral reef structures Other effects of ocean acidification on coral reefs Summary Bibliography

Oceanic Hotspots

Definition Introduction Origin of oceanic hotspots Mantle plumes and hotspot swells Intraplate seamounts produced at oceanic hotspots Summary Bibliography Cross-references

Octocorallia

Synonyms Definition Introduction Classification Evolution and biogeography Biology and ecology

Threats and conservation issues

Summary/Outlook Acknowledgments Bibliography

Oil and Gas Reservoirs and Coral Reefs

Synonyms Definition Reservoir characteristics of coral reef systems Reef reservoirs and climate Neogene reef platform oil and gas reservoirs Summary Bibliography Cross-references

Ooids

Synonyms Definition Ancient marine ooids Origin of ooids Bibliography

Pacific Coral Reefs: An Introduction

Introduction Categories of reefs in the Pacific Ocean Geology Oceanographic and climatic processes affecting Pacific coral reefs Geography and biogeography of the tropical Pacific Ocean Early cultural settlement of the central Pacific Ocean Political history of the Pacific since the European rediscovery Status of and threats to Pacific coral reefs The future of Pacific coral reefs Responses to global climate change Summary and conclusions Appendix A: Gallery of coral reefs at the margins and Equator of the Pacific Ocean Bibliography Cross-references

Packstone

Bibliography Cross-references

Palaeosols

Synonyms Definition Bibliography Cross-references

Paleoclimate from Corals

Synonyms Definition Introduction Reconstructing climate records from corals Coral paleoclimate records Interannual and multi-decadal variability in the tropical Pacific: variations past and present Interannual modes in the Atlantic and Indian Ocean Summary Bibliography Cross-references

Patch Reefs: Lidar Morphometric Analysis

Setting Lidar surveys Morphometric analysis Summary Bibliography Cross-references

Permian Capitan Reef System

Bibliography Cross-references

Persian/Arabian Gulf Coral Reefs

Definition The distribution of coral reefs in the Gulf The coral fauna Types of frameworks Structure of coral assemblages Environmental factors shaping coral assemblages Environmental impacts and changes Conclusions Bibliography Cross-references

Peysonnell, Jean-Andre (1694-1759)

Bibliography

Phosphatic Cay Sandstone

Definition Formation Relationship with Pisonia An alternative model of formation Mineralogy Age and rate of accumulation Phosphatic deposits and eutrophication Utilization of phosphatic cay sandstone and resulting environmental impacts References Cross-references

Plate Tectonics

Synonyms Definition Introduction Plate tectonics The morphology of the ocean floor The ages of seamounts and oceanic islands Studies of absolute plate motions

Motion of the African plate Motion of the Pacific plate

Discussion Summary Bibliography Cross-reference

Platforms (Cemented)

Synonyms Definition Bibliography Cross-references

Poleward Extension of Reefs

Definition Introduction The latitudinal limit to reef growth Daly and marginal seas Holocene changes in range Pleistocene reefs beyond the present latitudinal limit Future global warming and the limit to coral growth Summary Bibliography Cross-references

Porites

Synonyms Definition Introduction Colony formation and skeletal detail Palaeontological and taxonomic history Geographic distribution

Colony shape and size

Ecological requirements

Temperature Salinity Light Sedimentation Water motion Emersion

Population biology

Reproduction Growth and growth rates

Mortality Summary Bibliography Cross-references

Porosity Variability In Limestone Sequences

Synonyms Definition Bibliography Cross-references

Postglacial Trangression

Synonyms Definition Reef growth mode, tectonic and reconstruction of sea-level variations The sea-level curves from the last deglacial rise Episodes of rapid sea-level rise

The 19 ka event The MWP 1A The MW 1B The 7.5 ka event

Prospects Summary Bibliography Cross-references

Quoy, Jean Rene (1790-1869) and Gaimard, Joseph Paul (1796-1858)

Bibliography

Radiocarbon (14C): Dating and Corals

Definition Introduction

Production and decay History of radiocarbon dating Measuring 14C Calibration to time Tree-ring calibration Calibration curves

Radiocarbon in the ocean

``Bomb´´ radiocarbon

Summary Bibliography Cross-references

Recent Sea Level Trends

Synonyms Definitions Introduction Recent sea level trends Understanding the observed sea level rise Changes in extreme sea levels Predictions of future sea level trends Need for ongoing monitoring of sea level Bibliography Cross-references

Red Sea And Gulf Of Aqaba

Definition Red Sea coral reefs - geology and ecology

Setting Reefs - morphology, distribution, and description Geological history of coral reefs at the Red Sea Present conditions Modern fauna

Bibliography Cross-references

Reef Balls

Definition Bibliography Cross-references

Reef Classification by Fairbridge (1950)

Introduction Fringing reefs Barrier reefs Atoll reefs Patch or platform reefs Coral reefs with islands Conclusions Bibliography Cross-references

Reef Classification by Hopley (1982)

Definition Introduction Background to the evolutionary classification The 1982 evolutionary reef classification system (Figures 1 and 2) (Hopley, 1982; Hopley et al., 2007) Rates of reef growth and evolutionary change Conclusions Bibliography Cross-references

Reef Classification by Maxwell (1968)

Definition and Introduction Summary Bibliography Cross-references

Reef Classification, Response To Sea Level Rise

Definition Introduction The classification Summary Bibliography Cross-references

Reef Drilling

Synonyms Definition Background The coring method What we have learned from reef cores

Paleoenvironment Modern reef environments and fossil reef facies Sea level versus reef accretion Environmental proxies How reefs build

Is what you see what you get?

The taphonomic filter Time averaging Why is reef zonation preserved at all?

Potential coring artifacts

Accurate core logging The ``Two-Inch Outcrop´´

Summary Acknowledgments Bibliography Cross-references

Reef Flats

Synonyms Definition Example of reef flats Coral-dominated reef flats Components of the coral-dominated reef flat

Algal flat Rubble band Coral windrows Coral composition of the coral windrows Coral patches Sand flat

Formation of the coral-dominated reef flat Stages of development Rubble-dominated reef flats Formation of the rubble-dominated reef flat Conclusions Bibliography Cross-references

Reef Front Wave Energy

Synonyms Definition Introduction Wave transformations over the reef front Selected effects of reef front wave energy changes Summary Bibliography Cross-references

Reef Interconnectivity/Larval Dispersal

Synonyms Definition Introduction Larval dispersal in coral reef ecosystems Scales of connectivity Description of larval dispersal and reef interconnectivity Influence of hydrodynamic and biological process Reef interconnectivity and habitat Estimating reef interconnectivity

Empirical approaches Numerical modeling approaches

Summary Bibliography Cross-references

Reef Restoration

Synonyms Definitions Introduction Legal mandate for reef restoration in the FKNMS Vessel-grounding injuries to coral reefs in the FKNMS Emergency salvage (triage) of corals in the FKNMS Restoration of small- to medium-size grounding sites in the FKNMS Restoring large-size grounding sites in the FKNMS Lessons learned Conclusions Bibliography Cross-references

Reef Structure

Synonyms Definition Introduction Reef morphology Controls on reef architecture Models for reef architecture Setting, antecedent topography, subsidence and sea level change in reef architecture: a ``three reefs´´ comparison Summary Bibliography Cross-references

Reef Topographic Complexity

Definitions Introduction Reef Surface Rugosity Reef Surface Roughness Summary Bibliography Cross-references

Reef Typology

Definition A variety of reef-related typology Geomorphological typology

Criteria for a reef typology

Examples of existing reef typology Future typologies Bibliography Cross-references

Reefal Microbial Crusts

Introduction Recognition Structure and fabric Origin Living examples Sedimentological role Distribution and controls Eukaryote competition

Fore-slope drowning Older examples

Acknowledgments Bibliography Cross-references

Reefal Sediments

Definition Sediments of the Great Barrier Reef, Australia Sediments of Florida Reefs and Bahamian Reef Sediments of the Belize Reefs Summary Bibliography Cross-references

Reefs at Risk: Map-Based Analyses of Threats to Coral Reefs

Definition Bibliography Cross-references

Remote Sensing

Definition Introduction Electromagnetic and acoustic spectrum Categories of remote sensing systems Spatial, spectral, and temporal resolutions The infrared limit Processing Spectral signatures and the hyperspectral potential Past and current application of optical passive sensors for direct reef remote sensing Past and current application of acoustic and optical active sensors for direct reef remote sensing Past and current application of thermal infrared passive sensors for indirect reef remote sensing Past and current application of ocean color passive sensors for indirect reef remote sensing Conclusions Bibliography Cross-references

Residence Time

Synonyms Definition Bibliography Cross-references

Reticulated Reefs

Definition Introduction Mode of formation of reticulate reefs Summary Bibliography Cross-references

Rhodoliths

Synonyms Definition Bibliography Cross-references

River Plumes and Coral Reefs

Definitions Introduction Formation of River Plumes Materials in River Plumes Summary Bibliography Cross-references

Royal Society of London

Definition Background and roles Support of exploration of the reef seas Summary Bibliography Cross-references

Rudstone

Bibliography Cross-references

Ryukyu Islands

Synonyms Introduction Geological setting Climate conditions Start-up growth of the postglacial reefs Development of Holocene reefs and their zonation Latitudinal gradient in reef geomorphology Summary Bibliography Cross-references

Scleractinia, Evolution and Taxonomy

Definition Fossil record Species variation

Environmental variation Geographic variation Genetic links among populations

Evolutionary mechanisms

Reticulate evolution Competing hypotheses Where reticulate evolution and Darwinian evolution meet

Taxonomy

Traditional concepts of species Classification Taxonomic issues

Summary Acknowledgments Bibliography

Sclerochronology

Synonyms Definition Introduction History Growth measurements from density banding Skeletal basis of density banding Causes of density banding and correlates of coral growth Coral growth and climate change Summary Bibliography

Sea Level Change and Its Effect on Reef Growth

Introduction Pleistocene sea level change and its effects on coral reefs

Pleistocene sealevel change Effect of sea level change on coral reefs

Postglacial sea level change and its effects on coral reefs

Postglacial sea level change Effect of postglacial sea level change on coral reefs

Conclusion Bibliography

Seagrasses

Definitions Introduction Seagrass biology Seagrass research Seagrass taxonomy Seagrass biogeography The geomorphological role of seagrasses The ecological roles of seagrasses Conservation issues affecting seagrasses Summary Bibliography

Sea-level Indicators

Definition Introduction Key attributes of useful sea-level indicators Main sea-level indicators on reefs

Coral reefs and corals Microatolls Oysters and encrusters Beachrock and cemented deposits Mangrove deposits Marine notches Microfossils Other indicators

Summary Bibliography

Sediment Durability

Definition Introduction Determining sediment durability Implications of durability on sedimentary systems Conclusion Bibliography

Sediment Dynamics

Definition Introduction Sediment generation

Calcium carbonate production Carbonate production vs. sediment generation

Characteristics of reefal sediments Hydrodynamic properties of carbonate sediments Controls on sediment entrainment, transport, and deposition Sediment transport studies

Quantitative studies of contemporary sediment dynamics Sedimentological interpretation of sediment dynamics

Dynamics of sedimentary landforms Summary Bibliography

Sediments, Properties

Definition Composition Texture The mud problem Sediment alteration Aspects of reef sediment dynamics Summary Bibliography

Seismic Reflection

Synonyms Definition Introduction to reflection seismology Rock properties, geophysical response, and the challenges of carbonate imaging Reef architecture Reef seismic facies Seismic expression of karst Summary Bibliography

Seismic Refraction

Definition Introduction Method Reef studies using seismic refraction Summary Bibliography

Shingle Ridges

Definition Introduction Formation of coral shingle ridges Sedimentary and stratigraphic characteristics and preservation potential Shingle ridges as records of the frequency and intensity of tropical cyclones Summary Bibliography

Soils of Low Elevation Coral Structures

Definition and introduction Soil forming factors on low elevation coral structures Diversity of low elevation coral soils Physicochemical and mineralogical properties of low elevation coral soils

Physicochemical properties and plant nutrition Mineralogy

Conclusions Bibliography

Solution Processes/Reef Erosion

Definition Solution processes Other erosion processes Biological erosion Zonation Exposure, process, and erosion rates Summary Bibliography

Solution Unconformities

Definition Bibliography

Spiculite

Bibliography

Sponges

Synonyms Definition Sponges of coral reefs and linked ecosystems Filtering the water column Reef-building and rebuilding, carbonate balance, and coral survival Losses of sponges to disease, deteriorated water quality, and physical disturbance Spongivory Interactions with neighbors Symbiotic associations Bibliography

Spurs and Grooves

Definition Morphology Composition Processes Summary Bibliography

Stable Isotopes and Trace Elements

Synonyms Definitions Overview Stable isotopes

Oxygen isotopes Carbon isotopes

Minor and trace elements

Paleothermometry Ocean-atmosphere-land interactions Human impacts on the marine environment

Summary Bibliography

Steers, James Alfred (1899 - 1987)

Bibliography

Stoddart, David Ross (1937-)

Bibliography

Stromatolites

Synonyms Definition Introduction Stromatolites on early Earth

Stromatolite decline

Modern stromatolites Summary Bibliography

Submarine Groundwater Discharge

Synonyms Definition Bibliography

Submarine Lithification

Synonyms Definition Introduction Environmental conditions that promote submarine lithification Composition of submarine cements Textural characteristics of lithified reef frameworks

Lithified micritic crusts Pavement limestones

Origin of submarine lithification in coral reefs Conclusions Bibliography

Submerged Reefs

Synonyms Definition Introduction Tectonic setting and geology Submerged reef morphology Geological significance Modern significance Conclusions Bibliography

Subsidence Hypothesis of Reef Development

Definition Introduction Darwin´s insight into atoll formation Alternative theories Evidence from deep drilling Accommodating the subsidence hypothesis into plate tectonic theory Sea-level fluctuations and the significance of karst erosion processes Summary Bibliography

Swathe Mapping

Synonyms Definition Multibeam sonar Lidar Examples The future Conclusion Bibliography

Symbiosis

Synonyms Definition Bibliography Cross-references

Tahiti/Society Islands

Definition Environmental setting Coral diversity and distribution Stratigraphy, lithology, and growth history of late Pleistocene to Holocene reefs

The last deglacial sequence The older Pleistocene sequence Emerged reefs and related features

Coral paleoclimatology Summary Bibliography

Taphonomy

Definition Introduction Reef coral taphonomy

Taphonomic bias Fidelity Comparisons of life, death, and fossil assemblages Interpretation of depositional environments Applications to modern reef ecology

Conclusion Bibliography

Temperature Change: Bleaching

Definition Introduction Geographical patterns of bleaching Variability in coral sensitivity to thermal stress Summary: Temperature change and coral reef futures Bibliography

Tethys Ocean

Definition and introduction History Tethyan reefs Summary Bibliography

Tidal Effects on Coral Reefs

Introduction Upper limit of coral reefs Coral desiccation and solar insolation Diurnal and semi diurnal tides Atoll lagoon tidal flushing & residence time Tidal distribution of coral eggs/planula Tidal stirring/island wakes Tidal jets Tidal shelf fronts Tidal mixing and coral bleaching Tides in resonance Internal tides & waves Tide data Summary Bibliography

Tidal Jets

Definition Bibliography

Tropical Cyclone/Hurricane

Definition Introduction Cyclone genesis Waves and currents Hindcasting winds, waves, and coral damage Cyclone effects on coral reefs After the cyclone Contrasting perspectives on tropical cyclones Summary Bibliography

Tsunami

Definition Introduction Mechanisms of tsunami generation Characteristics of tsunami waves

Tsunami wave propagation

Interaction of tsunami with coral reefs

Macro-scale influence of reef systems on transoceanic tsunami behavior Reef platform - tsunami interactions Tsunami shoaling and energy dissipation on coral reefs

Impacts of tsunami on coral reef ecology

Earthquake-related impacts Tsunami impacts on corals and reefs Patterns of impact

Geomorphic impacts on reefs and reef associated landforms

Geomorphic impacts on coral reefs Geomorphic impacts on reef-associated sedimentary landforms

Summary Bibliography

Turbid-Zone and Terrigenous Sediment-Influenced Reefs

Definition Introduction Terrigenoclastic sediments and turbidity as a limit to coral reef growth

Sedimentation Turbidity

A framework model for understanding reef development under conditions of terrigenous sediment accumulation and elevated turbid Geomorphic settings and styles of turbid-zone reef development

Example 1: Muddy, coastal embayment site: South Thailand Example 2: Leeward, barrier island setting: Inhaca Island, southern Mozambique Example 3: Open sedimentary coastal setting: Paluma Shoals, inner-shelf, Great Barrier Reef

Reef facies and framework fabrics in turbid-zone and terrigenous sediment-influenced environments Temporal and spatial variations in turbid-zone reef development: a regional perspective based on the Great Barrier Reef Shelf Impacts of increased terrigenous sediment yields Summary Bibliography

Underwater Landscape Mosaics

Synonyms Definition Introduction Background Landscape mosaic technology

Key benefits

Bibliography

Unvegetated Cays

Bibliography

Upwelling and Coral Reefs

Definition Introduction Upwelling systems and coral reefs

Topographic upwelling

Intrusive upwelling Internal waves Ekman upwelling Upwelling and reefal food webs Summary Bibliography

Uranium Series Dating

Synonyms Definition Introduction to uranium series and uranium series dating 238U-234U-230Th disequilibrium dating or U-Th dating: theoretical principle U-Th dating: analytical methods U-Th dating: applications Bibliography Cross-references

Vanuatu

Introduction The modern reefs Neotectonics and sea-level variations Paleoclimatology Radiocarbon calibration and reservoir ages Reef development during the last 24ka of the deglacial sea-level rise Summary Bibliography

Vaughan, Thomas Wayland (1870-1952)

Bibliography

Vegetated Cays

Bibliography

Volcanic Disturbances and Coral Reefs

Definition Introduction Reef growth Modern assemblages Bibliography

Volcanic Loading and Isostasy

Bibliography Cross-references

Wackestone

Bibliography

Walther, Johannes (1860-1937)

Bibliography

Wave Set-Up

Definitions Introduction Wave set-up on beaches Wave set-up on coral reefs Measurements of wave set-up on coral reefs Summary Bibliography

Wave Shoaling and Refraction

Definitions Introduction Shoaling of waves Refraction of waves Refraction of waves by currents Wave refraction around reefs Summary Bibliography

Waves and Wave-Driven Currents

Definitions Introduction Ocean waves and coral reefs Wind-generated ocean waves Wave propagation Wave breaking Irregular waves Wave transformation on reefs Wave-driven currents Modeling wave-driven flow across reefs Wave pumping Summary Bibliography

West Indian Coral Reef Classification

Definition Introduction Composite structure of shallow Caribbean coral reef types Regional and local distribution of reef types Lateral transitions along a single reef tract from one to another reef type Vertical transitions in time from one to another reef type and sea-level history

Horizontal zonation pattern (Type A) Vertical zonation pattern (Type B) Lens-shaped zonation pattern (Type C) Cap-on-cap zonation pattern (Type D)

Occurrence and distribution of reef types in the Pleistocene of the West Indies Bibliography

Western Atlantic/Caribbean, Coral Reefs

Definition and introduction The coral fauna Loss of long-term ecological stability

Types of reefs and frameworks Similarities and differences to Indo-Pacific reefs

Conclusion Bibliography

Western Australian Reefs

Synonyms Definition Introduction Regional oceanography Reef morphology Mid-outer shelf reefs: the Houtman Abrolhos Ningaloo fringing reef Reefs of the Pilbara coast Reefs of the Kimberley coast Reefs and shoals of the Sahul Shelf, Northern Australia Summary Bibliography

Western Indian Ocean

Definition Reef sites Main attributes of reef communities Sediment components and carbonate production Reef growth history during the last deglaciation Emerged reefs and related features Coral paleoclimatolgy Summary Bibliography Cross-references

Yonge, Sir Maurice (1899-1986)

Definition Cross-reference

Zooxanthellae

Synonyms Definition Introduction Diversity and distribution of zooxanthellae Diversity and flexibility in coral-algal symbiosis Summary Bibliography Cross-references

Author Index Subject Index

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