Luis Bermudez MMI Online glossary dowloaded 2005-08-01 2005-08-02T07:11:14 CORIS - Coral Reef Information System of NOAA The glossary contains terms concerned with ecology, biogeography, evolution, taxonomy, morphology, physiology, cell and molecular biology, genetics, mapping, development, fisheries, oceanography, geosciences, conservation programs, remote-sensing, physics, chemistry, and data and information management. More information: http://coris.noaa.gov/glossary/welcome.htmlhttp://coris.noaa.gov/glossary/welcome.html Mark Costello Term term definition a receptor organ that senses changes in an electrical current in the surrounding water, for example, the ampullae of Lorenzini in sharks electroreceptor electroreceptor tergum the back of an animal tergum a museum collection of specimens that are stored in ethanol, isopropanol, formalin or other liquid preservatives wet collection wet collection pedicellarium pedicellarium a forceps-like organ which occurs in large numbers on starfishes and sea urchins. Pedicellariae, in general, are multifunctional appendages involved in defense, feeding, and cleaning. They are mainly used to keep small organisms from settling on the aboral surface, to capture small prey, and to discourage predators from feeding on soft tissue. The basic structure of pedicellariae consists of a head, neck, and stalk. The head usually has three jaws and, in some pedicellariae, contains poison glands instinct an unlearned, genetically coded behavior pattern that is internally motivated and characteristic of the species; the innate capacity of an animal to respond to a given stimulus in a relatively fixed way instinct Southern Oscillation Southern Oscillation a large-scale atmospheric and hydrospheric fluctuation centered in the equatorial Pacific Ocean. It exhibits a nearly annual pressure anomaly, alternatively high over the Indian Ocean and high over the South Pacific. Its period is slightly variable, averaging 2.33 years. The variation in pressure is accompanied by variations in wind strengths, ocean currents, sea-surface temperatures, and precipitation in the surrounding areas. El Nino occurrences are associated with the phenomenon phase of the ebb tidal current at the time of maximum speed; also, the speed at this time ebb strength ebb strength the smallest unit of living matter. All organisms are composed of cells and cell products (Cell Theory). Organisms exist either as single cells (unicellular) or as multicellular units cell cell a-naked freshwater or marine protozoan protist that forms temporary pseudopodia for food and water capture, and locomotion - amoeba amoeba Plantae Plantae the kingdom of immobile multicellular eukaryotes that obtain energy through photosynthesis, and have cells encased in cell walls composed of cellulose a male or female that is the result of sex change. A secondary male would be derived from a protogynous female, while a secondary female would be derived from a protandrous male secondary male or female secondary male or female radionuclide any radioactive isotope radionuclide Pliocene epoch an interval of the late Neogene period, from 5.3 to 1.8 million years before present Pliocene epoch vacuole vacuole a membrane-bounded vesicle in eukaryotic cells that has a secretory, endocytotic, phagocytotic or storage function no take zone a marine protected area that is completely (or seasonally) free of all extractive or non-extractive human uses that contribute impact (some exceptions may be permitted for scientific activities); also called "marine reserve" or "fully protected area" no take zone bottom trawler a fishing vessel that uses an open-mouthed fishing net drawn along the sea bottom. This type of fishing is destructive to shallow water and deep sea coral reef communities bottom trawler terpenoid terpenoid a class of organic compound produced by soft corals for defense and for aggressive colonization of new substrates DNA hybridization DNA hybridization the process of joining two complementary strands of DNA, or one each of DNA and RNA, to form a double-stranded molecule; a technique in which single stranded nucleic acids are allowed to interact so that complexes or hybrids are formed by molecules with sufficiently similar, complementary sequences. By this means the degree of sequence identity can be assessed and specific sequences detected excretion a physiological process, originating in cells, that removes waste materials produced by the body excretion gonopodium gonopodium a term given to the anal fin (or the anterior portion of it) of a male fish when it is modified to function as a copulatory organ, e.g., in guppies compound a material made up of two or more elements combined in a fixed ratio compound haploid a haploid cell contains a nucleus with a single complete set of chromosomes. The haploid condition is often abbreviated as n. Most fungi, protists, and algae are haploid, as are some insects, bryophytes, and the gametes of all organisms haploid validated name validated name in taxonomy, a formerly invalid or unavailable name that has been made valid or available by the International Code of Zoological Nomenclature, e.g. by annulment or suppression of senior homonyms or synonyms a system of very small tubules that links the polyps of calcareous colonial hydrozoans cyclosystem cyclosystem in sponges, a surface lined with apopinacocytes apopinacoderm apopinacoderm heavy metal a metal having a specific gravity of 5.0 or greater. Heavy metals are generally toxic to organisms in relatively low concentrations, and tend to accumulate in the food web. Examples include arsenic, cadmium, chromium, lead, and mercury heavy metal megalops larva megalops larva the larval stage in brachyuran crabs that follows the zoea larval stage exteroreceptor a neurological receptor that receives information from the environment external to the organism exteroreceptor carinate shaped liked a keel or ridge carinate ontogeny the development, growth, and maturation of an individual ontogeny Landsat satellite U.S. satellite used to acquire high-resolution (500-800m) remotely sensed multi-spectral images of the earth's land surface and surrounding coastal regions Landsat satellite two nitrogenous bases which form a "rung of the DNA ladder." A DNA nucleotide is made of a molecule of sugar, a molecule of phosphoric acid, and a base molecule. The bases are the "letters" that spell out the genetic code. In DNA, the code letters are A, T, G, and C, which stand for the chemicals adenine, thymine, guanine, and cytosine, respectively. In base pairing, adenine always pairs with thymine, and guanine always pairs with cytosine. In RNA, thymine is replaced by uracil base pair base pair a segmental mass of mesoderm in the vertebrate embryo, occurring in pairs along the notochord, and developing into skeletal muscles and vertebrae; in some invertebrates, the term "somite" refers to a metamere somite somite cells or organisms having more than twice the haploid number of chromosomes polyploid polyploid animations from HotSpot imagery denoting coral reef bleaching events over time HotSpot animation HotSpot animation lophocyte a mobile cell in sponges that produces collagen lophocyte astaxanthin astaxanthin a carotenoid pigment found in crustaceans. Astaxanthins may give a green color to the musculature of fishes which feed on crustaceans bladder any sac or cavity used to store liquids or gases bladder NEPA (National Environmental Policy Act) passed in 1969, the purposes of NEPA are: to declare a national policy which will encourage productive and enjoyable harmony between man and his environment; to promote efforts which will prevent or eliminate damage to the environment and biosphere and stimulate the health and welfare of man; to enrich the understanding of the ecological systems and natural resources important to the Nation; and to establish a Council on Environmental Quality NEPA (National Environmental Policy Act) curvilinear relationship a situation that is best represented by something other than a straight line curvilinear relationship rRNA (ribosomal RNA) rRNA (ribosomal RNA) any one of several large RNA molecules that are structural and functional components of ribosomes inhalant system in sponges, part of the aquiferous system between the ostia and prosopyle inhalant system a chromosomal re-arrangement that reverses the order of a linear array of genes on the chromosome inversion inversion a cavity ("little lake") in a matrix-like substance. For example, cartilage cells (chondrocytes) are located in lacunae in the cartilagenous matrix; bone cells (osteocytes) are located in lacunae in bone matrix lacuna lacuna collecting, processing, and analyzing a representative portion of the resident aquatic community to determine its structural and/or functional characteristics biological survey biological survey heterozooid a specialized non-feeding bryozoan zooid. Heterozooids include forms specialized for producing and brooding eggs, or, more rarely, spermatozoa. Others are specialized to protect the colony, or have a cleaning function, or strengthen and support the colony heterozooid prostomium the anteriormost, presegmental region of the body of an annelid worm, sometimes bearing eyes and antennae; the portion of the head in annelids that is situated anterior to the mouth prostomium of uncertain taxonomic position or affinities (incertae sedis) inc. sed. inc. sed. sand coarse sediment typically found in areas exposed to currents and wave energy sand column column the cylindrical body of an anthozoan polyp an enzyme that hydrolyzes proteins, cleaving the peptide bonds that link amino acids in protein molecules protease protease millipore filter a thin membrane composed of cellulose fibers that is used, for example, as a filter in the bacteriological examination of water millipore filter parturition the process of giving birth parturition a hazardous condition that scuba divers may experience at depths usually in excess of 80 ft (24.38 m). It occurs when nitrogen builds up in the body tissues and replaces some of the oxygen required by the brain. The longer a diver with conventional scuba stays at a deep depth, the more nitrogen accumulates. As the brain is deprived of oxygen, the ability to think and function clearly diminishes. It may progress from a slightly confused feeling to an almost intoxicated state, where thinking and judgement is severely impaired. If the diver does not ascend to a shallower depth and off-gas nitrogen, nitrogen narcossis may eventually cause death. Although this can happen at any depth, it is especially a problem with dives in excess of 80 feet. Nitrogen narcossis is also called 'rapture of the deep' nitrogen narcosis nitrogen narcosis saw-like; notched serrate serrate obtuse obtuse blunt or rounded at the end abatement reducing the degree or intensity of, or eliminating abatement significance level (level of significance) in statistics, the probability of a false rejection of the null hypothesis in a statistical test significance level (level of significance) library library in genomics, an unordered collection of clones (i.e., cloned DNA from a particular organism) whose relationship to each other can be established by physical mapping intertidal zone intertidal zone the region between the highest water line and the mean low tide level the inner germ layer of diploblastic and triploblastic embryos that gives rise to internal tissues such as the gut and gut derivatives, e.g., air bladder, lungs, and the lining of the digestive tract endoderm endoderm mass spectrometer mass spectrometer a laboratory instrument that measures the mass-to-charge ratio of individual molecules that have been converted into ions. This information is then used to determine the masses of the molecules anchialine cave anchialine cave a coastal cave formed in limestone or volcanic rock that is flooded with seawater. These marine or brackish water bodies lack surface connections to the sea. They include the longest submerged caves on Earth trimix a breathing gas mixture of helium, oxygen, and nitrogen. By using trimix, it is possible for divers to descend to hundreds of feet without suffering from toxic partial pressures of oxygen (which increases with depth), and also reduces the effect of nitrogen narcosis trimix a listing of the number, type, label and sequence of all the genes identified within the genome of a given organism gene index gene index albedo albedo the ratio of the amount of light reflected by an object and the amount light falling on it (incident light); a measure of the reflectivity or intrinsic brightness of an object (a white, perfectly reflecting surface would have an albedo of 1.0; a black perfectly absorbing surface would have an albedo of 0.0) the widespread outbreak of a disease, or a large number of cases of a disease in a single community or relatively small area epidemic epidemic pertaining to a zooid, as for example, a zooidal form zooidal zooidal Periodic Table Periodic Table a chart of the known chemical elements, arranged according to their atomic numbers. Elements with similar physical and chemical properties and similar electron arrangements are in the same column thermohaline circulation the density-driven convective circulation system of the world's oceans. Warm Atlantic water moves northward along the axis of the Gulf Stream, and evaporation increases water density while releasing heat to the colder atmosphere in the North Atlantic. Once significantly dense, the water sinks into the deep ocean, forming a downward limb of a giant conveyor-like circulation that extends around the world's oceans thermohaline circulation the relative proportion of individuals in each age group in a population age structure age structure commercially harvested sea cucumbers (Class Holothuroidea). In Asia, it is considered to be a delicacy beche-de-Mer beche-de-Mer an injury that results from rapid or extreme changes in pressure. Scuba divers may experience ear barotrauma, a condition of discomfort in the ear caused by pressure differences between the inside and the outside of the eardrum barotrauma barotrauma a partly land-locked arm of the sea firth firth colony colony a group of the same kind of animals, plants, or one-celled organisms living or growing together lagoon slope lagoon slope the back reef on a barrier or atoll reef booties booties short "boots" usually made of neoprene, worn inside open-heeled fins. they protect a scuba diver's feet from rubbing against the fins while swimming, as well as protecting the entire foot while walking to and from a dive site. Booties also provide warmth AVTAS (AIMS Video Transect Analysis System) AVTAS (AIMS Video Transect Analysis System) video transects are systematically sampled by identifying the benthos occurring at fixed points along the transect to the highest taxonomic level possible. The AVTAS software is used to analyse the video transects. During analysis the data are saved into a Microsoft Access database. In order to eliminate confounding in data analyses due to observer biases, transects from each site are analysed by two observers. The observer who actually surveyed the reef in the field analyses transect one from site one and then every alternate transect. A second observer analyses the remaining transects hemocoel hemocoel the extensive spaces of an arthropod's body through which the hemolymph (blood) circulates contour contour on a map or chart, a line connecting points of equal surface value xylem tissue in vascular plants that carries water and nutrients from the roots to the shoot and leaves. The xylem contains tracheids, vessels, fiber cells and parenchyma. It also provides structural support xylem polypeptide a long chain of amino acids joined by peptide bonds polypeptide one of the segments of a tapeworm, containing both male and female reproductive organs proglottid proglottid autotomy the voluntary shedding of an appendage by snapping it off the base; in corals, some, reproduce asexually by autotomy (fragmentation), for example, Fungia sp autotomy having side branches pinnate pinnate photomosaic photomosaic an assemblage of photographs, each of which shows part of a region, and put together in such a way that each point in the region appears once and only once in the assemblage, and scale variation is minimized NGO (Non-governmental Organization ) NGO (Non-governmental Organization ) a non-profit group or association organized outside of institutionalized political structures to obtain particular social objectives (such as environmental protection) or serve particular constituencies dendriform having a structure that resembles a tree or shrub dendriform supernatant supernatant the soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids side scan sonar side scan sonar sonar designed to look sideways and at a downward angle from both sides of a towed unit, called a towfish. The bottom and any objects in the water above the bottom reflect sound waves back to the towed array. An image is produced fom this information apopinacocyte in sponges, an endopinacocyte lining the excurrent canal apopinacocyte restriction fragment length polymorphism (RFLP) variation in DNA sequence between individuals that is detectable by variation in the length of DNA fragments generated by digestion with restriction endonucleases restriction fragment length polymorphism (RFLP) interface interface the common boundary between two substances such as a water and a solid, water and a gas, or two liquids, such as water and oil an electromagnetic wave or photon emitted from the nucleus gamma ray gamma ray belt transect belt transect a linear or circular transect with the observation area being a specified distance on either side of the transect line to mark substances in a way that they can easily be identified. In an organism, substances may be labeled using stable isotopes or harmless radioactive components so that they can be traced, analyzed or measured labeled labeled tubules of Cuvier eversible toxic or sticky tubules associated with the bases of the respiratory trees of some sea cucumbers (Holothuroidea-Echinodermata) tubules of Cuvier ribbon reef ribbon reef a large offshore linear reef, seaward of a fringing reef, which is linear but does not form a barrier to the land. A synonym of shelf-edge reef and sill reef a membranous vesicle ampulla ampulla organisms with swimming abilities that allow them to move actively through the water column and to move against currents nekton nekton the main body of a mollusk, which contains most of the organs, including a complete digestive and excretory tract as well as the reproductive organs. The visceral hump also includes the mantle, which consists of two external flaps of tissue that secretes the material that forms the shell on some species, and it protects the mantle cavity. The mantle cavity contains the gills, which excrete waste and circulate oxygen. Most mollusks have a shell, which sits on the visceral hump and a protects the main body from predators visceral hump visceral hump buffer zone the region near the border of a protected area; a transition zone between areas managed for different objectives buffer zone an organism whose diet consists of a wide variety of foodstuffs, including plants and animals omnivore omnivore any current flowing away from shore offshore current offshore current a line used to survey the distribution of organisms or substrate across a given area. Sample plots or points are established along the transect for collecting data transect transect intermediate host intermediate host in a parasite's life cycle, it is a host organism in which a parasite undergoes a stage of asexual development an assemblage of diverse organisms inhabiting a common biotope biocoenose biocoenose a symbiotic organism; either of two organisms participating in a symbiotic relationship symbiont symbiont loss of zooxanthellae with resultant bleaching caused by a specific bacterial infection, as opposed to environmental stress. The bacteria (Vibrio sp.) produce a toxin which cause lysis of the zooxanthellae. For additional information and illustrations, see: http://www.coral.noaa.gov/coral_disease/bacterial_bleaching.shtml bacterial bleaching bacterial bleaching hydrogen bond a relatively weak chemical bond consisting of a hydrogen atom between two electronegative atoms (e.g., oxygen or nitrogen), with one side being a covalent bond and the other being an ionic bond hydrogen bond antihelmintic a chemical agent used to combat parasitic worms, such as roundworms and tape worms antihelmintic a substance that increases the hydrogen ion concentration in a solution acid acid the unicellular external surface of a sponge (ectosome composed of pinacocytes) exopinacoderm exopinacoderm cation a particle that carries a positive electrical charge. The cation gets this positive charge from losing negatively charged electrons cation a whip-like appendage used for locomotion in sperm cells and some bacteria, fungi, and protists flagellum flagellum barbel a slender elongate sensory structure protruding from the lips or jaws of certain fishes, such as catfishes, goatfishes, drums, cods, and many deep-sea fishes. Barbels may appear singly or in groups. They are primarily tactile in function but may also bear tastebuds, allowing the fish to taste its environment barbel pertains to systematic differences between males and females. The two sexes are markedly dissimilar in appearance sexual dimorphism sexual dimorphism coral bleaching the process in which a coral polyp, under environmental stress, expels its symbiotic zooxanthellae from its body. The affected coral colony appears whitened coral bleaching seine seine a fish net that hangs vertically, with floats at the top and weights at the bottom archetype the plan or fundamental structure on which a group of organisms, or their systems of organs, are assumed to have been constructed; as, for example, the vertebrate archetype archetype sabellid worm a marine polychaete worm in the family Sabellidae which lives in flexible tubes constructed of sand grains embedded in mucus sabellid worm polygenic trait a phenotype controlled by many genes of small effect (polygenes) polygenic trait lipopolysaccharide lipopolysaccharide a compound containing a lipid bound to a polysaccharide vermivore an animal which feeds upon worms and worm-like animals vermivore net photosynthetic rate net photosynthetic rate the total rate of photosynthetic CO2 fixation minus the rate of loss of CO2 during respiration solute the chemical substances dissolved in a solution, such as salts in seawater solute National Biological Information Infrastructure (NBII) National Biological Information Infrastructure (NBII) a broad, collaborative program to provide increased access to data and information on the nation's biological resources. The NBII links diverse, high-quality biological databases, information products, and analytical toolsmaintained by NBII partners and other contributors in government agencies, academic institutions, non-government organizations, and private industry carnivore an organism that feeds upon animals carnivore metanephros metanephros the final excretory organ that develops in a vertebrate embryo. In birds, reptiles, and mammals it replaces the mesonephros as the functional excretory organ, and develops into the adult kidney a receptor that is stimulated by the presence of certain chemical substances chemoreceptor chemoreceptor aerobic aerobic deriving energy from a process requiring free oxygen the marine iguana (Amblyrhynchus cristatus) inhabits the Galapagos Island, an archipelago on the Equator, 800 kilometers west of the Ecuadorian coast. It differs from the mainland iguanas by the shape of the snout and other morphological features. The species probably rafted to the islands many millions of years ago, and developed a new ecological niche.They feed almost exclusively on marine algae and seaweed in the intertidal zone, and some make shallow dives past the breaker zone marine iguana marine iguana the specific place on a chromosome where a gene is located gene locus gene locus ancestral polyp an anthozoan polyp which develops from a sexually produced larva and gives rise to a colony by asexual budding ancestral polyp U.S. Coral Reef Task Force (USCRTF) U.S. Coral Reef Task Force (USCRTF) established by President Clinton in June, 1998, through Executive Order 13089 on Coral Reef Protection, to lead the U.S. response to this growing global environmental crisis. Chaired by the Secretary of the Interior and the Secretary of Commerce, the USCRTF is composed of the heads of 11 federal agencies and the Governors of 7 states, territories or commonwealths with responsibilities for coral reefs. The USCRTF is responsible for overseeing implementation of the Executive Order, and developing and implementing coordinated efforts to: map and monitor U.S. coral reefs; research the causes and solutions to coral reef degradation; reduce and mitigate coral reef degradation from pollution, overfishing and other causes; and implement strategies to promote conservation and sustainable use of coral reefs internationally a NOAA program that uses satellite and in situ monitoring stations to monitor high sea surface temperature events and to analyze conditions that may lead to coral bleaching Coral Bleaching HotSpot monitoring program Coral Bleaching HotSpot monitoring program the process of depositing eggs oviposition oviposition antinutrient a compounds that inhibits the normal uptake of nutrients antinutrient relating to or coming from the south; of the south temperate region, between the antarctic and tropical regions austral austral a particular form of amensalism found in plants. In this interaction, one species produces and releases chemical substances that inhibit the growth of another species allelopathy allelopathy adaptive behavior adaptive behavior any behavior that enables an organism to adjust to a particular situation or environment mitochondrial genome mitochondrial genome the genetic material of the mitochondria. It is similar in structure to that of the prokaryotic genetic material, formed of a single circular DNA molecule. The mitochondria of sexually-reproducing animals usually comes only from the maternal side, and is essentially the same as that of the mother. Sometimes mitochondria from spermatozoa are also passed on to offspring. Mitochondrial DNA has been studied to trace lineage far back in time restoration ecology restoration ecology activities undertaken by humans to repair ecological damage, such as establishing vegetation on degraded habitat, increasing the populations of endangered species, and decreasing the threatened area of an ecosystem evolutionary tree evolutionary tree a lineage designed to show the evolutionary history of relationships among groups of organisms phytotoxin phytotoxin a substance similar in its properties to an extracellular bacterial toxin in fishes, one of several bones or cartilage with which the base of the rays of the median fins articulate pterygiophore pterygiophore based on experience or observations, as opposed to theory or conjecture empirical empirical the White Water to Blue Water (WW2BW) Initiative was formulated in 2002 during the World Summit on Sustainable Development. WW2BW responds to the World Summit's "Oceans" agenda with an integrated approach to sustainable use of water resources. In an effort to address water pollution and scarcity, United States government agencies, including the State Department, NOAA, USAID, as well as the United Nations, governments of the Wider Caribbean Region, and a number of non-governmental organizations have come together to plan and implement programs which will lead to the conservation and sustainable management of both freshwater and coastal marine resources in the Caribbean. WW2BW stimulates partnerships to promote integrated watershed and marine-based ecosystems management in support of sustainable development. Four thematic areas are supported: integrated watershed management, marine ecosystem-based management, sustainable tourism, and environmentally sound marine transportation. The outcome of the WW2BW partnership in the Wider Caribbean may serve as the blueprint for future programs on watershed and marine ecosystem-based management in Africa and the South Pacific WW2BW (White Water to Blue Water Initiative) WW2BW (White Water to Blue Water Initiative) the lack of any interaction between two organisms or species in a shared habitat. Neither has any effect on the other neutralism neutralism interradial canal one of four branched ciliated canals in scyphozoan medusae that originates from the gastric pouches and move materials from the ring canal back toward the stomach and gastric pouches interradial canal the total of organic waste and waste water generated by residential and commercial establishments sewage sewage describes coral colonies with horizontal interlocking branches and short upright branches corymbose corymbose greenhouse effect the heating that occurs when gases such as carbon dioxide trap heat escaping from the Earth and radiate it back to the surface greenhouse effect the middle of the three germ layers of a triploblastic embryo that gives rise to the skeletal and support, muscular, blood vascular, urogenital and reproductive systems, and contributions to some glands mesoderm mesoderm acoelomate an animal that does not have a true coelom or body cavity, i.e., a body cavity between the outer wall and the gut and lined with mesoderm. Acoelomate phyla include the flatworms (Platyhelminthes), ribbonworms (Nemertea), and jaw worms (Gnathostomulida) acoelomate a polyp in hydrozoans and other colonial cnidarians which is specialized for feeding gastrozooid gastrozooid in cnidarians, the circular raised area of a hydrozoan polyp that lies between the tentacles and the mouth. The term is also used to describe mouthparts in other phyla hypostome hypostome coenosteum pit the point of insertion or commencement of septa in some corals coenosteum pit primer in genomics, a short pre-existing single-stranded polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase. It anneals to a nucleic acid template and promotes copying of the template starting from the primer site; a single-stranded nucleic acid that can "prime" replication of a template primer telolecithal an egg cell in which the yolk is not evenly distibuted throughout the cytoplasm, but is concentrated in one location, and cleavage is incomplete, e.g., a bird egg telolecithal ecosystem ecosystem an ecological community considered together with the non-living factors of its environment as a unit an antigen that provokes an immune response allergen allergen one of several curved bony or cartilaginous structures located on either side of the pharynx that support the gills of fishes and amphibians. Each gill arch is made up of an upper and a lower limb that are joined posteriorly. The gill filaments and gill rakers are attached to the gill arches gill arch gill arch a species which make up a large proportion of a community in terms of its biomass or numbers of individuals dominant species dominant species pyrosome pyrosome a large barrel-shaped colony of colonial pelagic tunicates belonging to the genus Pyrosoma. The colony propels itself through the water by means of cilia that pump water through the individual tunicates. It responds to mechanical, chemical, and light stimuli by moving and by spectacular blue-green bioluminescent displays zoanthid zoanthid an anemone of the family Zoanthidae, usually found in intertidal areas and coral reefs . In some species the polyps separate from each other almost completely after budding, while in other species, the polyps are all interconnected by a common mat of tissue ceras ceras one of many multifunctional horn or lobe-shaped or leaf-like process on the back or side of a nudibranch mollusk (sea slug). It has a major function as a respiratory organ (a gill), and with a branch of the digestive gland, it also serves as an organ for the exchange of gases and other molecules with the blood. The ceras also stores stinging nematocysts in a structure called the cnidosac, from the cnidarians upon which they feed, which gives it a defensive function. Its ability to change color also gives it a protective camouflage function pair bond the temporary or permanent association formed between a female and male animal during courtship and mating. Pair bonding is characteristic of monogamous species pair bond stony, soft, gorgonian, black, and horny corals that inhabit the colder deep waters of continental shelves and offshore canyons, ranging from 50 -1000m+ depths. They lack zooxanthellae and may build reef-like structures or occur solitarily deep-sea corals deep-sea corals DNA-containing bodies in the cell but external to the nucleus cytoplasmic genes cytoplasmic genes a disease which infects coralline algae CLOD (Coralline Lethal Orange Disease) CLOD (Coralline Lethal Orange Disease) heterotrophic eukaryotic unicellular organisms that belong to the kingdom Protista Protozoa Protozoa resident a permanent, non-migratory inhabitant resident encrustation encrustation a crustlike deposit or growth over a substratum pyriform pear-shaped pyriform ecto- a prefix meaning 'outside' ecto- yolk-sac larva a fish larva which has already hatched from the egg but has not yet started feeding and still absorbs the yolk in the ventrally-attached yolk sac yolk-sac larva a genetically continuous line of evolutionary descent lineage lineage disruptive coloration disruptive coloration a color pattern that breaks up the outline of an organism a moderately telolecithal egg, typical of amphibians mesolecithal mesolecithal having pores or openings that permit liquids or gasses to pass through permeable permeable ovoid egg-shaped ovoid bank reef large reef growths, generally having irregular shape, which develop over submerged highs of tectonic or other origin and are surrounded by deeper waters bank reef dredge dredge a metal collar with an attached collecting bag that is dragged along the bottom to obtain samples of rock, sediment, or benthic organisms a dark, fine-grained igneous rock composed of minerals rich in ferromagnesian silicates basalt basalt a logarithmic scale used to denote the intensity (loudness), of a sound relative to the threshold of human hearing. A step of 10 dB is a 10-fold increase in intensity or sound energy decibel decibel colloid a stable suspension of particles that, though larger than in a true solution, do not settle out colloid MMM (Maximum Monthly Mean SST climatology) the highest expected (climatological) monthly SST expected at all ocean locations based on 15 years of monthly mean SST data (serves as the input threshold for the Coral Bleaching HotSpot charts) MMM (Maximum Monthly Mean SST climatology) a change that occurs in an organism to allow it to tolerate a new environment acclimation (acclimatization) acclimation (acclimatization) a band formed yearly on coral by the secretion of CaCO3; one yearly growth band contains two smaller bands representing winter growth and summer growth growth band growth band logarithmic phase logarithmic phase the steepest slope of the growth curve of a culture; the phase of vigorous growth during which cell number doubles every 20-30 minutes; also called 'log or exponential growth phase' meroblastic cleavage meroblastic cleavage incomplete cleavage of the zygote, restricted to the blastodisc, the non-yolky cytoplasm at one end of the egg; typical of teloblastic eggs axoneme axoneme a bundle of microtubules and other proteins forming the core of each cilium or flagellum culture medium culture medium a substance which contains nutrients and a favorable environment for the in vitro growth of microorganisms and cells the principle that when the populations of two species compete for resources, one will use the resources more efficiently, therefore outcompete and eventually eliminate the other population competitive exclusion competitive exclusion Coastal Zone Management Act passed in 1972, the CZMA provides for management of shoreline areas that may include coral reefs Coastal Zone Management Act a projecting structure on the reef margin or reef front wherein the upper surface flares outward, giving the surface a greater diameter then the basal section knob knob a substance that accelerates a chemical reaction, but is not consumed or changed in the process catalyst catalyst author author in taxonomy, the person(s) to whom a work, a scientific name, or a nomenclatural act is attributed Annelida an animal phylum that comprises the segmented worms, and includes earthworms, leeches, and a number of marine and freshwater species Annelida blade a leaf-like structure blade in diving, the degree to which a gas is dissolved in the blood or other tissues. Full saturation occurs when the pressure of gas dissolved in the blood or tissues is the same as the ambient pressure of that gas saturation saturation thigmotactic responding to touch or outer surface contact thigmotactic monofilament a single large filament or threadlike structure of a synthetic fiber, such as a monofilament fishing line monofilament dredging dredging a method for deepening streams, swamps or coastal waters by scraping and removing solids from the bottom. The resulting mud is usually deposited in marshes in a process called filling. Dredging and filling can disturb natural ecological cycles. For example, dredging can destroy coral reefs and other aquatic life; filling can destroy the feeding and breeding grounds for many fish and invertebrate species a species that is particularly at risk because of low or declining numbers, a small range, or for some other reason, but is not threatened or endangered vulnerable species vulnerable species the red lionfish (Pterois volitans) is a venemous coral reef fish belonging to the scorpion fish family (Scorpaenidae). Native to the Indian and western Pacific oceans, lionfish are now an invasive species found in the western Atlantic Ocean from southern Florida to New York and Bermuda. They appear to be a reproducing along the southeastern U.S. coast; Other common names are turkeyfish, dragonfish, and firefish lionfish lionfish solar radiation solar radiation the amount of radiation or energy received from the sun at any given point an area in the littoral zone that retains sea water at a low tide because of a depression or arrangement of rocky substrate tidal pool tidal pool a wind blowing seaward from the land in the coastal area. offshore wind offshore wind triaxon triaxon in sponges, a spicule with three rays the point in the orbit of the Moon or man-made satellite nearest to the Earth; the point in the orbit of a satellite nearest to its companion body perigee perigee a pterygiophore and its associated fin ray actinophore actinophore instead of solely replacing defective genes, gene-based medicine is the application of nucleic acids (DNA, RNA) containing genetic information as therapeutic reagents in general. Nucleic acids are used to add a therapeutically beneficial function to cells, delete pathological functions from cells, or utilize cells for the production of therapeutic proteins. This can be either a transient or a permanent effect gene-based medicine gene-based medicine a small bryozoan heterozooid that strengthens and supports the colony, as well as fill spaces; long, branching, tubular, transparent stolons which extend above the substratum and to which the feeding individuals (autozooids) are attached kenozooid kenozooid correlate to show a relationship between entities correlate bottom dwelling; living on or under the sediments or other substrate benthic benthic biochemical cycle biochemical cycle the flow of an element through the living tissue and physical environment of an ecosystem, e.g., the carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus cycles a molting hormone of arthropods. It stimulates growth and ecdysis (molting) ecdysone ecdysone any eukaryotic DNA sequence that initiates and supports chromosomal replication; also called autonomous(ly) replicating segment ARS (autonomous replicating sequence) ARS (autonomous replicating sequence) a trait shared by a group of organisms as a result of descent from a common ancestor ancestral trait ancestral trait cDNA (complementary DNA) a strong, cloned DNA copy of otherwise fragile mRNA, made using reverse transcriptase. A cDNA is so-called because its sequence is the complement of the original mRNA sequence. However, when double-stranded cDNA is synthesized, it contains both the original sequence and its complement cDNA (complementary DNA) blastopore blastopore the opening into the archenteron (primitive gut) of a gastrula. In some animals it develops into the mouth and, in others, into the anus biogenic rock biogenic rock an organic rock produced by the physiological activities of plants or animals calcite skeleton a skeleton composed of the calcite form of calcium carbonate calcite skeleton an organelle found in the cells of most eukaryotes. Mitochondria are sometimes described as cellular "power plants" because their primary function is to manufacture adenosine triphosphate (ATP), which is used as a major source of cellular energy mitochondrion mitochondrion intron intron DNA sequences that interrupt the protein-coding sequence of a gene; introns are transcribed into mRNA but the sequences are eliminated from the RNA before it is used to make protein; junk DNA; in eukaryotic cells, a sequence of DNA that is contained in the gene but does not encode for protein. The presence of introns "splits" the coding region of the gene into segments called exons halocline the boundary where there is a marked change in salinity between surface fresh water and underlying saltwater in a stratified coastal environment halocline a behavior that once served its own purpose but has come to act as a signal about that purpose. For example, agonistic behaviors that substitute for physical contact and fighting, such as the erection of fins by fishes during displays, the yawn of baboons, the baring of teeth in dogs and wolves, the raising of fur in cats, and birds raising their feathers ritualized behavior ritualized behavior stenothermal pertaining to an aquatic organism that can withstand a narrow temperature range stenothermal coliform bacteria bacteria whose presence in water is an indicator of pollution and of potentially dangerous contamination coliform bacteria Arthropoda an animal phylum that contains lobsters, crabs, shrimp, mantis shrimp, barnacles and copepods, fairy shrimp (all crustaceans), insects, centipedes, millipedes, spiders, scorpions, horseshoe crabs, pycnogonids (sea spiders), ticks and mites. Approximately three quarters of a million species are described, many more than all the other animal phyla combined. The crustaceans are the arthropods associated with coral reefs Arthropoda information management the integration of a variety of activities designed to manage information and information resources throughout their life cycle. Activities include planning, budgeting, organizing, directing, training, promoting, and controlling the information and information resources throughout the process of collecting, processing, transmitting, disseminating, and disposing of information; the manipulation, reorganization, analysis, graphing, charting, and presentation of data for specific management and decision-making purposes information management hydrogen ion hydrogen ion an individual atom of hydrogen which is not attached to a molecule and therefore has a positive (+) charge pedunculate having a stem or stalk pedunculate the depth to which significant phytoplankton photosynthesis can take place. It is typically taken to be the depth at which PAR falls to 1 percent of its value just below the surface euphotic depth euphotic depth organ of locomotion and balance in fishes and some other aquatic animals; in fishes, fins are of two types: paired (pectoral and pelvic fins) and unpaired or median (dorsal, adipose, anal, and caudal fins and finlets). Fins of bony fishes contain hard spines and/or soft rays, which may be jointed and branched. The spines and rays are covered by integument. Counts of spines and rays are used as diagnostic characters in fish taxonomy; a membranous, finlike, swimming organ, as in pteropod (having the anterior lobes of the foot modified so as to form a pair of winglike swimming organs), and heteropod (where the foot developed into a median fin) mollusks fin fin meandroid colony meandroid colony a massive colony that has corallite mouths aligned in valleys, such that there are no individual polyps frequency of recombination the number of crossover events observed between two linked loci expressed as a proportion of the total number of meioses sampled frequency of recombination on June 11, 1998, President Clinton issued Executive Order 13089 directing all agencies to increase their efforts to protect our nation's coral reef resources. The executive order calls for the establishment of a U.S. Coral Reef Task Force, cochaired by the Secretaries of the Interior and of Commerce. The Task Force will develop and implement a comprehensive program of inventory, monitoring, and research to map and identify the major causes and consequences of degradation of coral reef ecosystems Executive Order 13089 Executive Order 13089 a pulmonate or opisthobranch gastropod in which the shell is absent, or reduced and buried within the mantle slug slug an organism that releases gametes directly into the sea for external fertilization broadcast spawner broadcast spawner an anthozoan of the subclass Octocorallia, commonly called sea fans and sea whips gorgonian gorgonian a reef-building coral with zooxanthellae in its tissues hermatypic coral hermatypic coral PADI ( Professional Association of Diving Instructors ) PADI ( Professional Association of Diving Instructors ) the world's largest scuba diving certification agency being primarily active at night nocturnal nocturnal a circular area of pigment spot spot ciliated epithelium any epithelium having motile cilia on the free surface ciliated epithelium subkingdom a taxonomic group comprising a major division of a kingdom subkingdom macerate to disintegrate tissues by means of cutting, soaking or enzymatic action to obtain a cell dissociation macerate pertaining to swamps or marshy habitats palustrine palustrine a coral reef occurring near and parallel to a coastline coastal reef coastal reef global warming global warming an increase in temperature that occurs globally the cultivation of marine organisms under controlled conditions; a synonym for marine aquaculture mariculture mariculture fore reef fore reef the portion of a reef seaward of reef crest. A synonym of reef slope psi (pounds per square inch) psi (pounds per square inch) a unit of air or water pressure expressed as pounds per square inch (psi) ecology ecology the study of the interrelationships between organisms and their environment, including the biotic and abiotic components a male or female that is genetically determined at birth or hatching and is not the result of sex change Primary male or female Primary male or female brown algae brown algae brown algae belong to the Division Phaeophycophyta, whose approximately 1,500 species are almost exclusively marine. They include the largest of the seaweeds and the kelps. The brown algae have chlorophyll a and c, as well as carotenes and xanthophylls, but the green chlorophyll coloration is masked by the brown and yellow pigments. Brown algae are among the largest photosynthetic organisms on earth. The largest kelps may grow to more than 60 meters in length, forming dense underwater forests in colder waters. Many microscopic brown algae grow as epiphytes on underwater vegetation, forming networks of branched filaments, or broad encrustations. All species are multicellular and do not form colonies. Their life cycles are complex, involving alternation of generations. In general, they are not free-floating organisms, but are attached to rock, coral, or other firm surfaces. Sargassum weed, however, is a floating brown algae that stays afloat by producing gas-filled bladders palatine palatine a bone in the roof of the mouth of fishes. The palatine is cartilaginous in some primitive bony fishes a website address, such as: www.coris.noaa.gov URL (Universal Resource Locator) URL (Universal Resource Locator) a protein produced by higher animals in response to the presence of a specific antigen antibody antibody the innermost layer of the Earth, consisting primarily of pure metals such as iron and nickel. The core is the most dense layer of the Earth, and is divided into the outer core, which is believed to be liquid, and the inner core, which is believed to be solid core (geology) core (geology) boss boss a columnar, flat-topped coral-algal growth or erosion structure usually found on the upper surfaces of spurs and buttresses cloned DNA cloned DNA exact copies of DNA segments prepared by using recombinant DNA technology a device for measuring the height (rise and fall) of the tide; especially an instrument for automatically making a continuous graphic record of tide height versus time tide gauge tide gauge white hole white hole an area along the spur and groove system (zone) where the sand channel widens considerably perturbation a disturbance or abnormality perturbation ooecium ooecium a brood chamber for developing embryos in the Ectoprocta (bryozoans); one of the special zooids of ectoprocts destined to receive and develop ova; an ovicell. periodically shed deciduous deciduous biochip biochip an electronic device that uses organic molecules to form a semiconductor; a microchip that uses tiny strands of DNA to latch onto and quickly recognize thousands of genes at a time; collection of miniaturized test sites (microarrays) arranged on a solid substrate that permits many tests to be performed at the same time in order to achieve higher throughput and speed. A biochip can perform thousands of biological reactions, such as decoding genes, in a few seconds. Biochips can also be used to rapidly detect chemical agents used in biological warfare so that defensive measures can be taken variance the population variance of a random variable is a non-negative number which gives an idea of how widely spread the values of the random variable are likely to be; the larger the variance, the more scattered the observations on average. It is a measure of the 'spread' of a distribution about its average value variance apparent shoreline in areas where the land is obscured by marsh grass, mangrove forests, cypress or similar marine vegetation, the actual shoreline can not be accurately represented. Instead, the outer limit line of the vegetation area is delineated (where it would appear to the eye as the shoreline) and is referred to as the apparent shoreline apparent shoreline altimetry altimetry a technique to measure the height of the sea surface from radar pulses transmitted from a satellite spermatium a non-motile male gamete produced by a spermatangium in red algae spermatium zygote zygote a fertilized egg with the diploid number of chromosomes formed by the union of the nuclei of male and female gametes anthocaulus anthocaulus a polyp that develops asexually on the skeletons of some coral species a coefficient measuring the rate of extinction, or diminution, with distance of transmitted light in sea water extinction coefficient extinction coefficient ebb current (ebb) ebb current (ebb) the movement of a tidal current away from shore or down a tidal river or estuary algal galls algal galls a response of gorgonia (Pseudoplexaura spp.) to tissue invasion by the algae, Entocladia endozoica, in Florida and Caribbean waters. The host gorgonia react to the algal filaments by producing capsules (galls) composed of skeletal elements that isolate the algae from the host tissue, at the expense of the skeletons' tensile strength and elasticity. The gorgonium readily breaks apart at the sites of the weakened skeleton. For more information and illustrations, see: http://www.coral.noaa.gov/coral_disease/algal_galls.shtml unused name unused name in taxonomy, an available senior synonym that is not known to have been used as a valid name in the past 50 years a globally complete reconstruction of of sea surface temperatures (SST) based on in situ measurements and satellite data produced at a monthly, 2 degree resolution ERSST (Extended Reconstruction of SST) data set ERSST (Extended Reconstruction of SST) data set a group or cluster of sporangia sorus sorus detrivore an animal that eats detritus detrivore in biology, any of the homologous segments lying in a longitudinal series that make up the body of certain animals, such as earthworms and lobsters. A metamere is also called a 'somite' metamere metamere radioactive isotope an unstable isotope of an element that decays or disintegrates spontaneously, emitting radiation radioactive isotope sea urchins are echinoderms in the class Echinoidea, that possess a hard calcareous shell (test) armed with spines, which may be long and pointed, or short and pointed, or dull. The spines are used for locomotion (along with tube feet), protection, and for trapping drifting food particulates, such as algae. Most sea urchins are algal grazers but some feed on sponges, ectoprocts and ascidians, and others on detritus. Sea urchins help to keep corals free of overgrowing algae sea urchin sea urchin the outermost part or region within a precise boundary periphery periphery number of parts of a substance found in one thousand parts of a particular gas, liquid, or solid parts per thousand (ppt) parts per thousand (ppt) the oxygen used in meeting the metabolic needs of aerobic microorganisms in water rich in organic matter (as water polluted by sewage) BOD (Biological (or Biochemical) Oxygen Demand) BOD (Biological (or Biochemical) Oxygen Demand) bipinnaria larva bipinnaria larva an early starfish larva with ciliated bands running about the periphery satellite a small celestial body orbiting a larger one; a man-made object designed to orbit a celestial body satellite pharmaco- pharmaco- pertaining to drugs a group of aquatic mammals pod pod the cavity within the mouth oral cavity oral cavity the larval stage of sea cucumbers immediately following the auricularia stage. It is cylindrical in shape and possesses five transverse bands of cilia doliolaria larva doliolaria larva Central Dogma (of molecular biology) Central Dogma (of molecular biology) the principal statement of the molecular basis of gene action. Genetic information is stored in and transmitted as DNA. Genes are expressed by being copied as RNA ( transcription), which is processed into mRNA (messenger RNA) via splicing and polyadenylation. The information in mRNA is translated into a protein sequence using a genetic code to interpret three-base codons as instructions to add one of twenty amino acids, or to stop translation; or more simply put, DNA carries the genetic information which is transcribed to RNA and subsequently translated to protein. Francis Crick, the co-discoverer of the double helix structure of DNA, coined the term "Central Dogma" in 1958 to characterize the all-important cellular processes whereby DNA is "transcribed" into RNA and RNA is "translated" into protein LED (light emitting diode) a very small light often used in electronic instrumentation LED (light emitting diode) counter shading counter shading protective body coloration where the dorsal surface (above) is dark and the ventral surface (below) is lighter starboard starboard the right side of a vessel to someone facing the bow or front sampling unit the sub-element of the total population selected for sampling sampling unit data mining data mining an information extraction activity whose goal is to discover hidden facts contained in databases. Using a combination of machine learning, pattern recognition, statistical analysis, modeling techniques and database technology, data mining finds patterns and subtle relationships in data and infers rules that allow the prediction of future results community community a naturally occurring assemblage of organisms that live in the same environment and are mutually sustaining and interdependent; a group of populations that interact in time and space air compressed to a pressure higher than the surrounding atmospheric pressure (ambient pressure) compressed air compressed air Gray's Reef National Marine Sanctuary Gray's Reef National Marine Sanctuary Gray's Reef comprises one of the largest nearshore sandstone reefs in the southeastern United States.It is located 32 kilometers (17.5 nautical miles) off Sapelo Island, Georgia. Designated in 1981, the Gray's Reef National Marine Sanctuary boundaries protect 17 square miles of open ocean. Sandstone outcroppings and ledges up to ten feet in height separate the sandy, flat-bottomed troughs in a reef that combines temperate and tropical flora and fauna. The rocky platform, some 60 to 70 feet below the surface, is covered by a carpet of attached organisms and is known locally as a "live bottom habitat." Gray's reef is not a coral reef. It is a consolidation of marine and terrestrial sediments (sand, shell, and mud) which was laid down as loose aggregate between 6 and 2 million years ago nucleotide one of the structural components, or building blocks, of DNA and RNA. A nucleotide consists of a base (one of four nitrogenous bases: adenine, thymine, guanine, and cytosine) plus a molecule of sugar and one of phosphoric acid nucleotide biological clock an internal biological mechanism which controls certain biological rhythms and biocycles, such as metabolism, sleep cycles, and photosynthesis biological clock zoarium zoarium the form of a bryozoan colony cadastral survey cadastral survey a survey which creates, marks, defines, retraces or reestablishes the boundaries and subdivisions of the public land of the United States. It is derived from the word cadastre, meaning a public record, survey, or map of the value, extent, and ownership of land as a basis of taxation pharyngeal arch one of several columns of mesenchyme found in the neck region of the developing vertebrate embryo. In lower vertebrates, blood vessels formed here become part of the gills; in higher vertebrates derivatives include portions of the jaw and middle ear; also known as branchial arches, gill arches, or visceral arches pharyngeal arch climax the final stage in ecological succession that is able to persist in the absence of environmental change climax the process by which two closely related species, with overlapping ecological requirements, interact so as to cause one or both of them to diverge evolutionarily in one or more traits. They differ more when they co-occur than when they do not character displacement character displacement numerical taxonomy numerical taxonomy study of the relationships of taxa by the application of numerical similarity values to characters so as to rank into categories based on degree of overall similarity marsh a soft, wet area periodically or continuously flooded to a shallow depth, usually characterized by a particular group of grasses, cattails and other low plants marsh coral assemblage a group of corals coral assemblage municipal discharge discharge of effluent from waste water treatment plants, which receive waste water from households, commercial establishments, and industries in the coastal drainage basin municipal discharge absolute zero the temperature at which all motion will cease (0 degrees Kelvin or -273.15 degrees C) absolute zero nautical mile the length of a minute of arc, 1/21,600 of an average great circle of the Earth. Generally one minute of latitude is considered equal to one nautical mile. The accepted United States value as of 1 July 1959 is 1,852 meters (6,076.115 feet) nautical mile Montastraea a genus of hard (stony) coral that includes the boulder coral and the great star coral Montastraea ecosystem based management (EBM) EBM integrates knowledge of ecological interrelationships to manage impacts within an ecosystem. Effective implementation of EBM should: (1) consider ecological processes that operate both inside and outside ecosystem boundaries, (2) recognize the importance of species and habitat diversity, and (3) accommodate human uses and associated benefits within the context of conservation requirements ecosystem based management (EBM) salinity a measure of the salt concentration of water salinity arrayed library arrayed library in genomics, Individual primary recombinant clones (hosted in phage, cosmid, YAC, or other vector) that are placed in two-dimensional arrays in microtiter dishes. Each primary clone can be identified by the identity of the plate and the clone location (row and column) on that plate. Arrayed libraries of clones can be used for many applications, including screening for a specific gene or genomic region of interest an instrument that identifies the molecular composition and concentrations of various chemicals in water and soil samples gas chromatograph/mass spectrometer (GC/MS) gas chromatograph/mass spectrometer (GC/MS) a general name for several species of halophyte belonging to different families of plants (including trees, shrubs, a palm tree and a ground fern) occurring in intertidal zones of tropical and subtropical sheltered coastlines and exceeding one half meter in height. The term is applied to both the individual and the ecosystem, the latter of which is termed mangal. Mangroves provide protected nursery areas for juvenile reef fishes, crustaceans, and mollusks. They also provide a feeding ground for a multitude of marine species. Many organisms find shelter either in the roots or branches of mangroves. Mangrove branches are nesting areas for several species of coastal birds. The root systems harbor organisms that trap and cycle nutrients, organic materials and other important chemicals. Mangroves also contribute to higher water quality by stabilizing bottom sediments, filtering water and protecting shorelines from erosion. They protect reefs from land runoff sedimentation. Conversely, coral reefs protect mangroves and seagrasses from erosion during heavy storms and strong wave action mangrove mangrove convergence come together and meet at a point convergence cycloid having a smooth-edged margin cycloid gulf a portion of an ocean or sea that extends into the land; a partially land-locked sea, e.g., the Gulf of Oman gulf sigmoid growth a growth rate trend characterized by an elongated S-shaped, or sigmoid curve. It is typical of population growth rate trends which begin rapidly at an exponential rate but slow as limiting factors are encountered until a limit is approached asymptotically sigmoid growth a type of connective tissue where the functional component is the rubbery intercellular matrix that is secreted by cartilage-producing cells called chondrocytes. Cartilage exists in several forms, from glassy to fibrous in appearance cartilage cartilage active during the day light hours diurnal diurnal mutualism in which one or both species in the association may survive and maintain populations in the absence of the other species facultative mutualism facultative mutualism leeward referring to the side of an island or reef that faces away from the prevailing wind leeward buffer buffer a solution or liquid whose chemical makeup neutralizes acids or bases without a great change in pH to replace a lost or damaged organ or part through formation of new tissues regenerate regenerate esthetasc a sensory seta covered by cuticle projecting from most antennules and antennae in crustaceans esthetasc the condition where organisms occur in aggregations patchiness patchiness a line with a lead weight on the end used to measure depth. The lead is dropped into the water and marks on the line are read to determine the current water depth. The lead usually has a cavity to return a sample of the bottom type (mud, sand, etc.) lead line lead line lacking a tail acaudal acaudal a taxonomic group that is between a genus and a species subgenus subgenus a chromatophore which contains black and brown pigments called melanin melanophore melanophore renewable resource renewable resource a resource or substance that can be replenished through natural or artificial means complement the complement of a nucleic acid sequence replaces each base by its complementary base: adenine (A) by thymine (T), cytosine (C) by guanine (G), and vice versa. In RNA, adenine is paired not with thymine but with uracil (U) complement rolled inwards fom the edges involute involute pertains to feeding on fecal matter coprophagous coprophagous decompression stop a specified time spent at a specific depth as a scuba diver ascends from a dive for purposes of releasing nitrogen gas from the tissues (nitrogen off-gassing) decompression stop subphylum subphylum a taxonomic group ranking that is between a phylum and a class climate long-term characteristics of weather climate a fertile blade in attached brown algae sporophyll sporophyll faro a rhomboid-shaped, steep-sided, continental shelf atoll faro fore reef terrace the uppermost portion of the fore reef; a flat plain beginning at the base of the buttress or mixed zone, at a depth of about 60 m fore reef terrace molten rock that forms naturally within the Earth. Magma may be either a liquid or a fluid mixture of liquid, crystals, and dissolved gases magma magma patchy necrosis patchy necrosis a disease of corals. Colonies with this condition have small (2-10 cm diameter) circular to irregular patches of denuded skeleton that will increase in diameter an additional 1-10 cm over a period of 5-7 days. The disease typically affects the top surface of elkhorn coral (Acropora palmata) branches. In most cases most of the affected tissue dies rapidly, and subsequent enlargement of the bare skeletal areas slows after a few days and eventually stops. A bacterium has been identified as a causal agent extreme environment an environment characterized by extremes in growth conditions, including temperature, salinity, pH, among others extreme environment critical value in statistics, the value of a test statistic at or beyond which the null hypothesis is rejected critical value a vascularized extra-embryonic membrane of amniote embryos that forms as a narrow outgrowth of the hind portion of the gut. In birds and reptiles, it stores waste products of embryonic metabolism. The allantois fuses with the chorion to form the chorio-allantoic membrane in birds and reptiles, and a part of the placenta in mammals allantois allantois environmental impact assessment environmental impact assessment detailed studies which predict the effects of a development project on the environment. They also provide plans for the mitigation of adverse impacts degrees of freedom in statistics, the number of independent comparisons that can be made between the members of a sample; in a contingency table it is one less than the number of row categories multiplied by one less than the number of column categories. The number of degrees of freedom is defined as the number of observations that can be chosen freely, i.e., an estimate of the number of independent categories in a particular statistical test or experiment degrees of freedom toxicant toxicant any substance which is potentially toxic reproductive isolation a species is an interbreeding natural population that is reproductively isolated from other such groups. Species are usually separated by discontinuities, which constitute barriers that prevent, or at least inhibit, an interspecific gene flow and gene exchange. Establishment of reproductive isolation is essential for development of a new species reproductive isolation a taxonomic group that is below a family but above a genus subfamily subfamily rhizome a horizontal stem rhizome a class of bony fishes comprising the ray-finned fishes, which make up about half of all vertebrate species known. They are found in most aquatic habitats from the abyssal depths of the ocean, greater than 10,000 m, to high altitude freshwater streams and ponds; a few species can even move about on land for short periods of time. Ray-finned fishes constitute a major human food source Actinopterygii Actinopterygii storm surge storm surge a rise above normal water level on the open coast due to the action of wind stress on the water surface bubblegum coral bubblegum coral a deep water gorgonian, Paragorgia arborea, found in the North Pacific and North Atlantic Oceans at depths that may exceed 1400m. It can grow to 5m in height and 8 m in width. It is called the bubblegum coral because because it is usually orange or pink in color, and has a lumpy surface texture to search for food forage forage anemone a cnidarian of the class Anthozoa that possesses a flexible cylindrical body and a central mouth surrounded by tentacles anemone a technique for separating different types of molecules based on their patterns of movement in an electrical field electrophoresis electrophoresis a dorsal fin containing only soft rays, or the soft-rayed hind part of the dorsal fin, if both spines and soft rays are present (as in squirrelfish) soft dorsal soft dorsal CaCO3 (calcium carbonate) CaCO3 (calcium carbonate) a molecule consisting of calcium, carbon and oxygen secreted by corals to their skeleton. It is also secreted by mollusks to form their protective shells a scuba diving partner. For safe diving, a pair of divers (buddies) stay close to each other in order to offer assistance if needed buddy buddy colonial a level of cellular organization intermediate between unicellular and multicellular; refers to organisms that occur in a fixed location, with one generation growing on top previous generations, as in coral reefs; types of animal that are organized into associations of incompletely separated individuals; eg, Portuguese man o' war, sponges and corals; in plants, describes cloning by asexual reproduction in which seemingly separate plants grew from rhizomes, stolons, or roots of a single or neighboring parent plant colonial a breathing gas mixture for scuba divers which has a percentage of oxygen greater than 21 percent as is found in normal air. This mixture allows longer bottom times at limited depths EANx ( Enriched Air Nitrox ) EANx ( Enriched Air Nitrox ) the number of items occurring in a given category frequency frequency a relationship between two species of organisms in which both members benefit from the association (mutualism), or where only one member benefits but the other is not harmed (commensalism), or where one member benefits at the expense of the well-being of the other (parasitism) symbiosis symbiosis one of the sensory receptors in some jellyfish (Scyphozoa), located on the margin of the bell. Rhopalia contain statocysts for equilibrium, and ocelli, which are photosensitive cells which allow the animal to respond to light stimulation rhopalium rhopalium in cnidarians, mesenchyme with sparse cellular components collenchyme collenchyme nonbiodegradable material a material that cannot be broken into simpler chemicals by living organismss nonbiodegradable material slender and/or threadlike filamentous filamentous composed of or containing a substance made of calcium carbonate calcareous calcareous shelf escarpment the edge of the bank/shelf where depth increases rapidly into deep oceanic water shelf escarpment a change from one ambient pressure to a lower ambient pressure as the scuba diver ascends. Decompression also occurs in a decompression chamber. Decompression results in a reduction of gas pressures within the body decompression decompression inferior inferior anatomically beneath, lower, or toward the bottom (e.g., the mouth is inferior to the nose) bacteriophage (phage) bacteriophage (phage) a virus that attacks and infects bacterial cells. Phages consist of a protein coat enclosing the genetic material, DNA or RNA, that is injected into the bacterium. Upon infection, synthesis of host DNA, RNA and proteins ceases and the phage genome is used to direct the synthesis of phage nucleic acids and proteins using the host's transcriptional and translational apparatus doppler radar radar that can measure radial velocity, the instantaneous component of motion parallel to the radar beam (i.e., toward or away from the radar antenna) doppler radar bimodal bimodal a distribution in which the frequency curve has two peaks. A single peak is called a mode refers to molecules that do not interact with water and are not soluble in water. Hydrophobic compounds do not dissolve easily in water, and are usually non-polar. Oils and other long hydrocarbons are hydrophobic hydrophobic hydrophobic Java a programming language created by Sun Microsystems which allows the user to create programs which run well in a networked environment (such as the World Wide Web). Java programs are commonly called "applets" and can be used to add anything from calculators to animated images to web sites Java a large-scale physical feature within the ecosystem. Reef zones are determined by currents, wave surge, exposure to sunlight and water depth, and may be comprised of a number of habitats zone zone tRNA (transfer RNA) short-chain RNA molecules present in the cell, in at least 20 varieties. Each variety is capable of combining with a specific amino acid, and attaches the correct amino acid to the protein chain that is being synthesized at the ribosome of the cell, according to instructions coded in the mRNA tRNA (transfer RNA) a feeding polyp of a bryozoan (Ectoprocta). Autozooids compose the majority of a bryozoan colony autozooid autozooid arborescent colony arborescent colony a coral colony with a tree-like growth structure selective pressure forces acting on populations that determine that some individuals are more reproductively successful or genetically fit than others, and contribute more descendants (or genes) to subsequent generations selective pressure denotes a disease of unknown cause or origin idiopathic idiopathic tissue a group of cells with a specific function in the body of an organism. Tissues are composed of nearly identical cells and their products, and are organized into larger units called organs tissue mini-atoll a ring-shaped patch reef with a central area (lagoon) containing sand mini-atoll a software program, such as Netscape Navigator or Microsoft Internet Explorer, that allows one to view pages on the Internet browser browser pixel pixel abbreviation of picture element the lower part of a cnidarian polyp, into which the distal portion of the polyp, the anthocodium (which includes the mouth and the tenacles) is withdrawn anthostele anthostele action potential the electrical signal which rapidly propagates along the membrane of the axon of nerve cells, as well as over the surface of some muscle and glandular cells. It is caused by change in membrane electrical potential, the underlying cause of which is a change in flow of ions across the membrane due to voltage-activated ion channels. It leads to an all-or-nothing action current, the nervous impulse action potential syntype syntype in taxonomy, each specimen of a type series from which neither a holotype nor a lectotype has been designated. The syntypes collectively constitute the name-bearing type nomen vetitum nomen vetitum in taxonomy, an impermissible name; an unavailable name published for divisions of the genus group other than genus and subgenus, which are not accepted by the International Code of Zoological Nomenclature in taxonomy, the International Code of Zoological Nomenclature. An authoritative document containing a system of rules and recommendations to be followed in giving a scientific name to an animal or animal group Code Code gas chromatography gas chromatography a method of separating chemical components of a mixture, which involves the passage of a gaseous sample through a column having a fixed adsorbent phase photographs taken from an aircraft or satellite utilized to interpret environmental conditions and geographic features aerial photography aerial photography Y-organ a gland situated near the external adductor muscles of the mandibleof some crustaceans that secretes the molting hormone Y-organ debris composed primarily of plastics, nets, lines, other fishing gear, glass, rubber, metal, wood and cloth. Sources of debris are people on beaches, storm drains, fishing boats, waste treatment sites, and industrial facilities. These materials have damaging effects on coral reefs marine debris marine debris nondegradable pollutant a polluting substance that is not broken down by natural processes nondegradable pollutant random sampling random sampling a sampling technique where a group of subjects (a sample) is selected for study from a larger group (a population). Each individual is chosen entirely by chance and each member of the population has a known, but possibly non-equal, chance of being included in the sample. By using random sampling, the likelihood of bias is reduced species that have a relatively narrow ecological niche specialist species specialist species a company or organization that provides access to the Internet Internet Service Provider (ISP) Internet Service Provider (ISP) an [-OH] or alcohol group on a larger molecule. The oxygen is single-bonded to the hydrogen and has one free bond to the rest of the molecule hydroxyl group hydroxyl group metanephridium metanephridium a type of excretory tubule in annelid worms. The metanephridium has internal openings called 'nephrostomes' that collect body fluids and conducts them to the outside through external openings, the 'nephridiopores' gastrolith A deposit of calcium salts made in the stomach of many crustaceans during the period between molts. It may be used to store calcium needed in the new exoskeleton gastrolith choanocyte chamber choanocyte chamber in sponges, a cavity lined with choanocytes and located between incurrent and excurrent systems halophile halophile an organism which lives in an environment of high salt concentration. Halophiles have special adaptations to permit them to survive under these conditions an enzyme that is able to synthesize DNA from information in RNA. It requires an RNA template and a DNA or RNA primer reverse transcriptase reverse transcriptase lophophore lophophore a feeding organ possessed by lophorates. It is a disk or horseshoe-shaped structure which surrounds the mouth and bears the tentacles of the Bryozoa (moss animals), Brachiopoda (lamp shells) and Phoronida (horseshoe worms). The tentacles are hollow (coelomic) and covered with cilia which generate water currents that draw food toward the mouth limu kohu the Hawaiian name for the red alga, Asparagopsis taxiformis, an edible species that is no longer common in the Main Hawaiian Islands, but is relatively abundant the shallow waters of some of the Northwestern Hawaiian Islands limu kohu sediments soil, sand, and minerals washed from land into water, usually after rain. They pile up in reservoirs, rivers, harbors, and coastal areas destroying habitats, and clouding the water so that sunlight cannot reach aquatic plants. Careless farming, mining, and building activities expose sediment materials, allowing them to wash off the land after rainfall sediments bacterial generation time bacterial generation time the time interval required for a bacterial cell to divide, or for a population of bacterial cells to double. Generation times for bacterial species growing in nature may be as short as 15 minutes or as long as several days a jelly-like substance formed by the coagulation of a colloidal liquid; a cytoplasmic phase gel gel hypothermia a condition when the body temperature is colder than normal (37 degrees C/98.6 degrees F in humans) hypothermia a satellite traveling in a near-polar orbit around the globe; civilian satellite program managed and operated by NESDIS polar-orbiting satellite polar-orbiting satellite intention movement an incomplete behavior pattern that provides information about the activity a particular animal is about to perform, and acts as a signal to others intention movement the rate of growth and the age structure of populations, and the processes that determine these properties demography demography bifacial bifacial describes plates which have corallites on both sides in cnidarians, a primitive "connective tissue" located between the epidermis and the gastrodermis. If it contains no cell components, it is termed "mesoglea"; undifferentiated cells of an embryo, derived from mesoderm, which give rise to connective tissue and the circulatory and lymphatics systems; amoebocytic cells often embedded in a gelatinous matrix mesenchyme mesenchyme a member of the pairs adenine-thymine, adenine-uracil, and guanine-cytosine that have the ability to hydrogen bond to one another complementary nucleotide complementary nucleotide autapomorphy autapomorphy an apomorphy (derived character differing from the ancestral condition) possessed by a species or clade that is shared with no other species or clade, i.e., a derived character found only in a terminal taxon anastomosis the union or connecting of branches forming a meshwork or a network anastomosis a regional, quasi-governmental group with authority to manage fisheries in federal waters, generally from three to 200 miles offshore fishery management council fishery management council barren zone the region of a coral reef seaward of the lower palmata zone and just landward of the buttress or mixed zone barren zone Cenozoic Cenozoic the current geologic era, which began 66.4 million years ago and continues to the present endosymbiotic endosymbiotic being symbiotic and living within the body of an individual of the associated species a line drawn on a map or chart joining points that receive the same amount of precipitation isohyetal line isohyetal line complete cleavage of the zygote. The cleavage furrows pass all the way through the zygote; typical of isolecithal and mesolecithal eggs holoblastic cleavage holoblastic cleavage P-value P-value in a statistical hypothesis test, the P value is the probability of observing a test statistic at least as extreme as the value actually observed, assuming that the null hypothesis is true. This probability is then compared to the pre-selected significance level of the test. If the P value is smaller than the significance level, the null hypothesis is rejected, and the test result is termed significant; the significance of a statistical test. P-values of less than 0.05 are generally considered to be an indicator that a statistical model is significant; a quantitative estimate of the probability that the observed difference between two groups could have happened by chance alone FISH (fluorescence in situ hybridization) hybridization of cloned DNA to intact chromosomes, where the cloned DNA has been labelled with a fluorescent dye. This is the major method of physical mapping of cloned DNA fragments on chromosomes FISH (fluorescence in situ hybridization) oxidant oxidant an oxidizing agent icon a small picture displayed on a computer monitor that identifies a command or file. icon mono- mono- a prefix meaning one adipocyte a fat cell adipocyte the depth in seawater below which carbon loss through respiration by phytoplankton exceeds carbon gain through photosynthesis; no net phytoplankton production occurs critical depth critical depth acontium a thread-like part of a coral polyp's or anemone's digestive system and employed as defensive or aggressive structures when extruded acontium micron (u) a unit of length equivalent to a micrometer (um), one-millionth of a meter or 0.00003937 inch micron (u) a subterranean layer of porous water-bearing rock, gravel, or sand capable of storing and conveying water to wells and streams aquifer aquifer watershed an area of land that drains downslope to the lowest point. The water moves through a network of subterranean and surface drainage pathways which converge into streams and rivers, eventually reaching an estuary and finally the ocean. Because water moves downstream, any activity that affects the water quality, quanity, or rate of movement at one location can affect locations downstream to the ocean and out to coral reefs watershed topotypical population topotypical population in taxonomy, a population occurring at the type locality a species that spawns in the ocean but lives parts of its life in fresh water, e.g., American eel catadromous species catadromous species circadian being, having, characterized by, or occurring in approximately 24 hour periods or cycles circadian protein sequencing the process of determining the amino acid sequence of a protein, or its component polypeptides protein sequencing Crustacea a subphylum of Arthropoda that includes shrimp, mantis shrimp, lobsters, crabs, water fleas, copepods, crayfish and wood lice. There are almost 40,000 described species of crustaceans. The Crustacea are mainly aquatic, but include some semi-terrestrial and terrestrial groups Crustacea avian avian of, relating to, or characteristic of birds rehabilitation the recovery of specific ecosystem components in a degraded ecosystem or habitat rehabilitation in litt. in correspondence or communicated in writing; used for an unpublished source of information (in litteris) in litt. endopinacocyte in sponges, a pinacocyte lining the incurrent and excurrent canals endopinacocyte green algae green algae green algae belong to the Division Chlorophycota. These algae contain photosynthetic pigments similar to those in higher plants (chlorophylls a and b, as well as secondary pigments: carotenes, lutein, and zeaxanthin) and have a green color. Green algae include unicellular forms, filamentous forms, and leaf-like thalluses. target in genomics, the DNA or RNA being hybridized to a microarray; for diagnostic tests, the molecule or nucleic acid sequence that is being sought in a sample target gustation pertains to the sense of taste gustation sampling sampling the probabilistic, systematic, or judgmental selection of a sub-element from a larger population, with the aim of approximating a representative picture of the whole theca the calcareous wall of the corallite theca genetic diversity genetic diversity the variety of different types of genes or alleles in a species or population endolithic growing within a rock or any other hard inorganic substratum endolithic Linnaean tautonymy Linnaean tautonymy in taxonomy,the identical spelling of a new genus-group name and a pre-Linnaean (i.e., before 1758) one-word name cited as a synonym of only one of the species or subspecies originally included in that genus shellfish shellfish a term that includes both molluscs, such as clams and oysters, and crustaceans, such as lobsters and shrimp Chaetodontidae Chaetodontidae a family of fishes (butterfly fish) whose number and behavior may serve as indicators of reef health in genomics, a tool for studying how large numbers of genes interact with each other and how a cell's regulatory networks control vast batteries of genes simultaneously. A robot is used to precisely apply tiny droplets containing functional DNA to glass slides. Researchers then attach fluorescent labels to DNA from the cell they are studying. The labeled probes are allowed to bind to cDNA strands on the slides. The slides are put into a scanning microscope to measure how much of a specific DNA fragment is present microarray microarray a group of cells or a single cell in animals or plants that is specialized to secrete a specific substance gland gland reverse transcription the synthesis of DNA on a template of RNA, accomplished by the enzyme, reverse transcriptase reverse transcription obligate mutualism a mutualistic relationship where one species cannot survive without the presence of the other obligate mutualism the anaerobic breakdown by microorganisms of complex organic substances, especially carbohydrates, to CO2 and alcohol; fermentation is also used to describe the process by which various chemical or pharmaceutical compounds can be made in large tanks, called fermenters, that contain microorganisms or plant or animal cells, and the nutrients they require to live and grow fermentation fermentation repetitive dive any dive within a certain time frame after a previous dive. Some dive tables consider any dive within 12 hours of a previous dive as repetitive repetitive dive culling the selective removal of animals from a population for conservation purposes culling homeostasis the ability to maintain a relatively constant internal environment homeostasis red algae belong to the Division Rhodophycota. Most of the over 4000 species are marine. They range in complexity from simple unicellular organisms to unbranched and branched filaments to complex multiaxial uprights and crusts. Their pigments include chlorophyll a and the phycobiliproteins, red phycoerythrin (often the dominant pigment) and blue phycocyanin, as well as carotenes, lutein, zeaxanthin. Most red algae have a complex life history with three phases: tetrasporophyte, gametophyte and carposporophyte red algae red algae maxilla pertains to mouth parts; the upper jaw maxilla magnetic north the direction a compass needle points when there are no local interfering influences magnetic north furcate furcate to divide into branches; to fork fistule fistule in sponges, a tubular structure on the upper surface, upon which the osculum is situated. A fistule is frequently found on species that burrow into mud or excavate coral a gene that controls the activity of other genes involved in the development of a body plan homeotic gene homeotic gene a multi-disciplinary approach to science that recognizes the limitations of traditional scientific inquiry in dealing with the complex reality of social institutions interacting with natural phenomena. Sustainability science seeks to improve on the substantial but limited understanding of nature-society interactions gained in recent decades. This has been achieved through work in the environmental sciences estimating and evaluating human impacts, and evidence from social and development studies that takes into account environmental influences on human well-being. Urgently needed is a better understanding of the complex dynamic interactions between society and nature so that the trend towards increasing vulnerability is reversed sustainability science sustainability science invertebrate invertebrate an animal that lacks a vertebral column (backbone) the order of amino acids as they occur in a polypeptide chain. This is referred to as the 'primary structure' of proteins amino acid sequence amino acid sequence poisonous an organism that contains poison in its tissues that can be harmful if the organism is ingested poisonous segments of chromosomal DNA known to be linked with heritable traits or diseases. Although the markers themselves do not produce the conditions, they exist in concert with the genes responsible and are passed on with them DNA marker DNA marker a sand covered, gradual or sharply descending slope; the next-to-deepest part of the fore reef fore reef slope fore reef slope an animal phylum synonymous with Ectoprocta that contains approximately 5,000 living species. They are all sessile colonial forms composed of zooids. Zooids are tubular, oval or box-like structures that contain a lophophore, which is a circular or horseshoe-shaped fold of the body wall that encircles the mouth and bears numerous ciliated tentacles. Most species form erect or encrusting colonies. They occur in many different habitats, including coral reefs Bryozoa Bryozoa hapteron hapteron a single branch within a holdfast pertaining to the mouth oral oral nanobiology nanobiology biological studies at the extremely small to molecular levels. Many fundamental biological functions are carried out at the level of molecular machineries that have the sizes of 1-100 nm. The emergence of nanobiology allowed understanding of the functions of these machineries, with the invention of nano- technology, e.g., scanning probe microscopy, modern optical techniques, and micro- manipulating techniques pectinate pectinate comb-like; in mollusks, it refers to the comb-like lamellae of the ctenidia (gills) onshore onshore a direction landward from the sea delta the fan-shaped area at the mouth or lower end of a river formed by eroded material that has been carried downstream and dropped in quantities larger than can be carried off by tides or currents delta a member of the animal phylum Ctenophora. A small phylum (about 50 species) whose members, known as comb jellies and sea walnuts, superficially resemble jelly fishes. These planktonic organisms are thought to have evolved from a medusoid cnidarian ctenophore ctenophore in sponges, an amoeboid cell capable of phagocytosis. Archaeocytes are totipotent, having the capability of differentiating into other types of sponge cells archaeocyte archaeocyte sand flat sandy areas found in depressions and gullies in a coral reef, or between patch reefs, or in deeper areas below or beyond the reef. Seemingly near barren during the day, at night sand flats teem with biological activity; also a sandy tidal flat barren of vegetation. A tidal flat is an extensive, nearly horizontal, marshy or barren tract of land that is alternately covered and uncovered by the tide. It consists of unconsolidated sediment (mostly mud and sand) sand flat offspring from the same parental group going through their life cycle together generation generation in evolution, an attribute of taxonomic group which all members of the group possess, i.e., the more common shared characters of a given group of organisms. Primitive characters are also called 'plesiomorphies' primitive character primitive character having to do with living or being located on the edges or banks of streams or rivers riparian riparian an absolute scale of temperature in which each degree equals one kelvin. Water freezes at 273.15 K and boils at 373.15 K Kelvin scale Kelvin scale fluorescent pigment a pigment that absorbs light at one wavelength and emits it at a different wavelength. The emitted light usually has a lower energy than the light absorbed by the pigment fluorescent pigment fecundity the productiveness or potential productiveness of an organism, measured in the number of viable offspring it may produce; the number of eggs an animal produces each reproductive cycle; the potential reproductive capacity of an organism or population fecundity may be conveniently summarized as: encrusting (lichen-like); branched (staghorn-like); massive (rock-like); sub-massive (pillar-like); tabulate (table-like); foliose (scroll-like); and solitary hard coral forms hard coral forms ITIS (Integrated Taxonomic Information System) ITIS (Integrated Taxonomic Information System) a partnership of U.S., Canadian, and Mexican agencies, other organizations, and taxonomic specialists cooperating on the development of an online, scientifically credible, list of biological names. ITIS is also a participating member of Species 2000, an international project indexing the world's known species cytoplasm cytoplasm the protoplasm of a cell exclusive of that of the nucleus. It consists of a continuous aqueous solution (cytosol) and the organelles and inclusions suspended in it. The cytoplasm is the site of most of the chemical activities of the cell Placozoa Placozoa a phylum of extremely simple and cryptic marine animals, for which only two species have been described, Trichoplax adhaerens and Treptoplax reptans. These tiny animals were discovered in Europe in the late 1800's living on the glass walls of an aquarium. Since then, most of what has been learned about their biology has come from studying cultures kept in various laboratories around the world. Their bodies are made up of only a few thousand cells of just four types. They also have the smallest amount of DNA measured for any type of animal. They lack tissues, organs and organ systems.They reproduce asexually, but it is not known if they can also reproduce sexually. Practically nothing is known about them in nature. Some scientists believe they emerged early in metazoan evolution, either before or just after the sponges (Porifera). However, recent DNA studies lead others to believe they emerged after the Cnidaria. Of the two species described, Treptoplax reptans has never been seen since its description in 1896, causing some to doubt its existence. However Trichoplax adhaerens has been reported from the Mediterranean and many tropical and subtropical locations around the world. It may be that Trichoplax adhaerens actually consists of more than a single species luciferase the enzyme which activates luciferin, in the presence of ATP, to produce bioluminescence luciferase byte a memory and data storage unit composed of contiguous bits, usually eight. For example, file sizes are measured in bytes or megabytes (one million bytes). Bytes contain values of 0 to 255 and most often represent integer numbers or ASCII characters byte lipase lipase an enzyme, secreted by the pancreas and the glands of the small intestine, that breaks down fats into glycerol and fatty acids during digestion in taxonomy, a situation where a genus group taxon is established with only one immediately subordinate taxon, e.g., a genus containing only one species monotype monotype CORDIO (Coral Reef Degradation in the Indian Ocean) CORDIO is an international program created to respond to the degradation of coral reefs throughout the Indian Ocean. In the western Indian Ocean region coral reefs are key ecosystems that support large sectors of the countries' populations and economies, through artisanal fisheries, tourism and large-scale investments. Projects within CORDIO focus on determining a) the biophysical impacts of coral degradation as a result of bleaching and other disturbances, and the long term prospects for recovery, b) the socio-economic impacts of coral mortality and options for mitigating these through management and development of alternative livelihoods, and c) the prospects of restoration and rehabilitation of reefs to accelerate the ecological and economic recovery. CORDIO (Coral Reef Degradation in the Indian Ocean) brooding brooding parental care of young the development of larvae within the gastrovascular cavity of an adult coral polyp inner cell mass the cluster of cells inside the mammalian blastocyst. These cells give rise to the embryonic disk of the later embryo and, ultimately, to the fetus inner cell mass megabyte (mb) megabyte (mb) a measure of storage space. One megabyte roughly translates to a million characters of text, or 180,000 words a proposal to reduce or alleviate potentially harmful impacts mitigation plan mitigation plan filiform filiform thread-shaped abdomen abdomen in higher animals, the portion of the body that contains the intestines and other viscera other than the lungs and heart; in arthropods, the rearmost segment of the body, which contains part of the digestive tract and all the reproductive organs senior homonym in taxonomy, the older, or earliest established taxonomic name senior homonym the production of offspring (hybrids) from genetically dissimilar parents hybridization hybridization endangered taxa endangered taxa taxa in danger of extinction and whose survival is unlikely if causal factors continue operating. Included are taxa whose numbers have been drastically reduced to a critical level or whole habitats have been so drastically impaired that they are deemed to be in immediate danger of extinction. Also included are those that possibly are already extinct, in so far as they have not been seen in the wild in the past 50 years aboral situated opposite to, or away from the mouth; normally used to describe radially symmetrical animals, such as starfishes, sea urchins, and jellyfishes aboral solvent the liquid in which a solute is dissolved to form a solution solvent a supportive or protective structure or framework of an animal, a plant, or part of an animal or plant. In animals it is an external (exoskeleton) or internal (endoskeleton) support structure, against which the force of muscles acts. Vertebrates have a skeleton of bone or cartilage; arthropods have one made of chitin; corals have one of calcium carbonate: sponges have a mass of spicules; many other invertebrates use a hydrostatic skeleton, which is an incompressible fluid-filled region of their body. In plants, the skeleton may be a rigid protective covering, as in the shell of a diatom, or the vascular system of a vascular plant skeleton skeleton pertaining to the tail; denoting a position more toward the tail of an animal, e.g., the tail fin of a fish is called the caudal fin. Caudal vertebrae are the vertebrae which extend into the tail of an animal caudal caudal strobila a stage in the jellyfish life cycle. Free-swimming scyphozoan (true jellyfishes) medusae produce gametes which give rise to small polyps called scyphistomae. After a period of growth, a scyphistoma divides transversely to become a strobila that resembles a stack of discs. Each of the "discs" becomes an ephyra larva, detaches from the strobila and swims freely in the plankton. The ephyra larva will eventually grow into an adult medusa strobila a submarine mountain, usually conical in shape and volcanic in origin, that rises 1000 meters or more above the sea floor. Some definitions of seamounts do not include the height criterion seamount seamount biome biome a community of animals and plants occupying a climatically uniform area on a continental scale the pygmy goby, Eviota sigillata, has the shortest life span of any known vertebrate on Earth, with a maximum life expectancy of 59 days. Eviota sigillata is a small cryptic coral reef fish distributed in the Indo-West Pacific: Seychelles to the Great Barrier Reef and Micronesia, north to the Ogasawara Islands pygmy goby pygmy goby zooid of the distinct individuals forming a colonial invertebrate animal, such as a hydrozoan zooid CREIOS (Coral Reef Ecosystems Integrated Observing System) The Coral Reef Ecosystem Integrated Observing System (CREIOS) will provide a diverse suite of long-term ecological and environmental observations and information products over a broad range of spatial and temporal scales. The CREIOS goal is to understand the condition and health of, and processes influencing, coral reef ecosystems, to assist stakeholders in making improved and timely ecosystem-based management decisions to conserve coral reefs CREIOS (Coral Reef Ecosystems Integrated Observing System) subspecies subspecies a taxonomic group that is a division of a species. It usually evolves as a consequence of reproductive isolation of one or more populations within a species reef flat the shallow area between the shoreline intertidal zone and the reef crest of a fringing reef reef flat GBIF (Global Biodiversity Information Facility) GBIF (Global Biodiversity Information Facility) an international non-profit organization that provides free and universal access to data regarding the world's biodiversity. A wide range of countries and organizations participate in GBIF and have made their data available through the GBIF web site (http://www.gbif.org) bar a thick, pigmented vertical marking that does not encircle the body of an organism; an elongate submarine shoal bar a mass of cytoplasm containing several nuclei and enclosed in a membrane, but having no internal cell boundaries, e.g., skeletal muscle cells syncytium syncytium data sets from previous studies historical data historical data estimate estimate the best guess arrived at after considering all the information given in a problem class class in taxonomy, a category just beneath the phylum and above the order; a group of related orders correlation coefficient a measure of the relationship between variables correlation coefficient egg a female sex cell or gamete with the haploid number of chromosomes. It may be fertilized by a sperm cell to produce a zygote with the diploid number of chromosomes for that particular species. The eggs of some species may develop into multicellular individuals without being fertilized by a sperm cell. This is the process of parthenogenesis egg a virus that contains the enzyme, reverse transcriptase. This enzyme converts the viral RNA into double-stranded DNA copies of their genome, (by using reverse transcription), which can combine with the DNA of the host cell and produce more viral particles. Many naturally occurring cancers of vertebrates are caused by retroviruses retrovirus retrovirus The CFS compares the fauna of one area with that of another. CFS = 2C/(a+b), where C = the number of species in common between two areas, a = the number of species in the first area, and b = the number of species in the second area. The higher the CFS, the greater the resemblance coefficient of faunal similarity (CFS) coefficient of faunal similarity (CFS) the purposeful introduction of members of a species into an appropriate habitat, foreign to the "home" habitat or area, for the purposes of conservation of that species benign introduction benign introduction allopolyploid a type of polyploid species resulting from two different species interbreeding and combining their chromosomes allopolyploid species which are protected by federal legislation such as the Endangered Species Act, Mammal Protection Act, and Migratory Bird Treaty Act protected species protected species scavenger scavenger an animal that feeds on dead or decaying organic matter auricularia larva auricularia larva larva of a sea cucumber; an early bipennaria larva of a starfish bow bow the front part of a vessel standard deviation a measure of the spread or dispersion of a set of data. It is calculated by taking the square root of the variance standard deviation a class of Mollusca that includes clams, oysters and mussels Pelecypoda (Bivalvia or Lamellibranchia) Pelecypoda (Bivalvia or Lamellibranchia) gametocyte a reproductive cell capable of dividing by meiosis to produce gametes, e.g., a spermatocyte or oocyte gametocyte a high-speed particle, identical to an electron, emitted from an atomic nucleus beta particle beta particle oviparity the reproductive mode where eggs are released from the body and later hatch oviparity NOAA Diving Program the NOAA Diving Program is administered by NOAA and is headquartered at the NOAA Diving Center in Seattle, WA. The Program trains and certifies scientists, engineers and technicians to perform the variety of tasks carried out underwater to support NOAA's mission. With more than 300 divers, NOAA has the largest complement of divers of any civilian federal agency. In addition, NOAA's reputation as a leader in diving and safety training has led to frequent requests from other governmental agencies to participate in NOAA diver training courses NOAA Diving Program a troughlike depression with vertical to overhanging walls which cut across the reef front at right angles submarine groove submarine groove competition between individuals of the same species intraspecific competition intraspecific competition cell line cell line cells that have been extracted from human or animal tissue and now grow and replicate continuously outside the living organism a circulatory system in which blood flows through blood vessels at all times. Blood flows from arteries to capillaries and through veins, but the tissues surrounding the vessels are not directly bathed by blood. Some invertebrates and all vertebrates have closed circulatory systems closed circulatory system closed circulatory system retractable capable of being drawn or pulled back retractable antigen antigen a foreign macromolecule introduced into a host organism that elicits an immune response aragonite skeleton aragonite skeleton skeletons primarily composed of the aragonite form of calcium carbonate flotsam flotsam wreckage or discarded material, e.g. garbage, found floating on the surface of the ocean or washed up on the beach Late gastrula. This photograph is a dorsal view of the embryo, with the anterior being toward the animal pole and the posterior toward the vegetal pole. Note the beginning of the formation of enterocoelic (mesodermal) pouches, from which the mesoderm is derived, on the right and left side of the anterior end of the gastrocoel. A Late gastrula. This photograph is a dorsal view of the embryo, with the anterior being toward the animal pole and the posterior toward the vegetal pole. Note the beginning of the formation of enterocoelic (mesodermal) pouches, from which the mesoderm is derived, on the right and left side of the anterior end of the gastrocoel. A mesoderm; B the MPRSA (1972) provides protection for many coral reefs by authorizing NOAA to designate areas as marine sanctuaries and promulgate regulations for the conservation and management of those areas. Since the Act was passed, thirteen sanctuaries have been designated, several of which contain coral reef communities. Coral research, monitoring, and management activities are conducted in these sanctuaries, as well as in the Northwestern Hawaiian Islands Coral Reef Ecosystem Reserve, which is currently (June 2004) under consideration to become the nation's fourteenth sanctuary MPRSA (Marine Protection, Research, and Sanctuaries Act) MPRSA (Marine Protection, Research, and Sanctuaries Act) a text file containing a sequence of commands that can be executed as one command. macro macro particulate material of biological origin that is suspended in water particulate organic matter particulate organic matter change of body shape, e.g., the change from a larval form to a juvenile or adult form metamorphosis metamorphosis a process of fusion of the nuclei of two sex cells or gametes; the second step in syngamy karyogamy karyogamy fatty acid any of a class of saturated aliphatic monocarboxylic acids that form part of a lipid molecule; a product of fat hydrolysis fatty acid Fishery Conservation and Management Act the federal law that created the regional councils and is the federal government's basis for fisheries management in the EEZ. Also known as the Magnuson Act after a chief sponsor, Senator Warren Magnuson of Washington State Fishery Conservation and Management Act clathrate clathrate resembling an open latticework siphonoglyph a groove in the pharynx of some cnidarians that is lined with cilia which pump water into the animal's gastrovascular cavity.This water current inflates the body, circulates fluids, and provides a volume of water to act as a hydrostatic skeleton siphonoglyph a gene pair having different alleles in the two chromosome sets of the diploid individual, for example, Aa heterozygous gene pair heterozygous gene pair a method for gathering data pertaining to ecologically significant biological components of a reef habitat over small spatial scales. Because the method provides a quick "snapshot" of major reef biota during a single dive or snorkel survey, it is particularly useful in assessing remote areas that are only rarely visited and where little time can be spent. REA is usefully employed by Coral Reef Ecosystem Division (CRED) at the NMFS Pacific Island Fisheries Science Center. During research cruises to these remote areas, teams of CRED divers survey the reef communities in a comprehensive manner, recording species abundance, diversity, and spatial distribution simultaneously for four key components of the ecosystem: fishes, corals, other invertebrates, and algae. Specific protocols are followed for field work and subsequent laboratory analyses Rapid Ecological Assessment (REA) Rapid Ecological Assessment (REA) lacking cross walls (septa); also termed "aseptate" nonseptate nonseptate trophic group a group of organisms consuming resources from a similar level in the energy cycle trophic group SHOALS is a laser-based scanning LIDAR bathymeter which collects high-resolution bathymetric data in shallow, offshore areas. Map products provide a view of sea-floor topography. In areas with coral reefs, this includes not only the top surface of the reef but also associated channels and sand flats SHOALS (Scanning Hydrographic Operational Airborne Lidar Survey) SHOALS (Scanning Hydrographic Operational Airborne Lidar Survey) in taxonomy, the first person after a taxon was proposed to select one of the names over the other (or one nomenclatural act over another) when both names (or acts) were published at the same time. Also applies to first selection of multiple original spellings first reviser first reviser captive breeding raising animals (or plants) in controlled conditions to produce stock for subsequent release into the wild captive breeding a type of asexual reproduction in some sea anemones in which parts of the pedal disc break off and are left behind as the anemone moves pedal laceration pedal laceration compound chromatophore a chromatophore that contains more than one kind of pigment compound chromatophore class interval class interval one of the ranges into which data in a frequency distribution table (or histogram) are binned. The ends of a class interval are called class limits, and the middle of an interval is called a class mark. In plotting a histogram, begin by dividing the range of all values into non-overlapping class intervals, in such a way that every piece of data is contained in some class interval photophile an organism which grows or thrives in lighted conditions photophile pseudocoelomate any of a group of triploblastic invertebrates that has a fluid-filled body cavity, the pseudocoelom, lying between the endoderm and the mesoderm The pseudocoelom is contrasted with the coelom of mollusks, annelid worms, and the more complex animals, including vertebrates, by lacking an endothelial lining. Pseudocoelomates lack a circulatory system, using the pseudocoelom to transport nutrients. The hydrostatic pressure of the pseudocoelom gives the body a supportive framework that acts as a skeleton. Nematodes (roundworms), rotifers, acanthocephalans (spiny-headed worms), kinorhynchs, and nematomorphs (horsehair worms) are pseudocoelomate groups pseudocoelomate agar agar a gelatinous material extracted from the walls of some red algae, mainly species of Gelidium and Gracilaria. Agar is used as a support medium, when supplemented by appropriate buffers and/or nutrients and other ingredients, for cultures of microrganisms and tissues, electrophoresis, etc branchiostegal branchiostegal one of the dermal bony or cartilaginous struts that support the branchiostegal membranes of fishes. Sometimes called branchiostegal rays, but not to be confused with the fin rays mitigation the act of making less severe or intense; measures taken to reduce adverse impacts on the environment mitigation the number or weight of organisms in a population that can be harvested without reducing the population biomass from year to year, assuming that environmental conditions remain the same sustainable yield sustainable yield a triplet of nucleotide bases (codon) in tRNA (transfer RNA) that pairs with (is complementary to) a triplet in mRNA (messenger RNA). For example, if the codon is UCG, the anticodon is AGC anti-codon anti-codon geostrophic current geostrophic current a flow that sustains a balance between Coriolis deflection and a pressure gradient a network of fiber-like microtubules that forms in a cell's nucleus during mitosis (nuclear division) which connects the centrosomes to the kinetochores and helps move the chromosomes around mitotic spindle mitotic spindle opisthobranch opisthobranch a marine gastropod, many of which have lost or reduced their shell, mantle and gills ephyra larva ephyra larva a jellyfish (Scyphozoa) larval stage that develops into the adult medusa or jellyfish tentacle-tube-foot suspension feeder tentacle-tube-foot suspension feeder a suspension feeder that traps particles on distinct tentacles or tube feet (in echinoderms) the process of controlling the amount of water in tissues and cells osmoregulation osmoregulation vestigial structure vestigial structure an incompletely or ineffectively developed structure which is greatly reduced from the original ancestral form and is no longer functional an animal which exhibits parental behavior towards another animal's offspring alloparent alloparent veliger veliger a molluskan larva in which the foot, mantle and shell first make their appearance euphotic zone euphotic zone the layer of the ocean that receives sufficient sunlight for photosynthesis. The depth to which 1% of incident light penetrates (1% is the minimum amount of light required for photosynthesis) dorsoventral an axis extending from the dorsal to ventral surface of an animal body dorsoventral white-band disease a coral disease characterized by complete coral tissue degradation of Caribbean acroporid corals.-Two species of Acroporidae are affected, the elkhorn coral, Acropora palmata, and the staghorn coral, A. cervicornis. The disease exhibits a sharp demarcation between apparently healthy coral tissue and exposed coral skeleton.- These signs are identical to plague, except that white band is acroporid specific (and plague has not been found on acroporids).- Tissue loss usually proceeds- from the base of the colony branch to the tip, although it can begin in the middle of a branch in A. cervicornis. White band disease affects acroporid corals throughout the Caribbean and has decimated populations at a regional scale.The infective agent has not yet been isolated. For more information and illustrations, see: http://www.coral.noaa.gov/coral_disease/white_band.shtml white-band disease one of the threadlike "packages" of genes and other DNA in the nucleus of a cell. Different species of organisms have different numbers of chromosomes. In sexually reproducing species, each parent contributes one chromosome of each pair, so offspring get half of their chromosomes from the maternal parent and half from the paternal parent. Bacterial cells do not possess a nucleus, therefore their chromosomes are located in the cellular cytoplasm chromosome chromosome stolon a type of stalk that lies in contact with the substrate; in corals, a horizontal polyp outgrowth from which daughter polyps are budded stolon a measure of a systems capacity to oxidize material; the energy gained by transferring 1 mole of electrons from an oxidant to H2. It is measured in volts relative to a hydrogen electrode which is at zero redox potential (Eh) redox potential (Eh) TIFF (Tag Image File Format) TIFF (Tag Image File Format) a common format for exchanging raster graphics (bitmap) images between application programs, including those used for scanner images proteinaceous proteinaceous any structure composed of proteins the role of an organism in an ecological community; the environmental requirements and tolerances of a species; sometimes seen as a species' "profession" or what it does to survive niche niche medusa medusa the free swimming stage of some corals, jellyfish, anemones, hydroids and comb jellies, shaped like a bell or umbrella and swims by pulsations of the body the systematic collection of data over time monitoring monitoring mantle mantle a membranous or muscular structure in mollusks that surrounds the visceral mass and secretes a shell if one is present the addition of a phosphate group to a compound phosphorylation phosphorylation proxy signal proxy signal paleoclimatic evidence that can be used to indirectly infer or estimate some aspect of the paleoenvironment, such as precipitation or temperature ascidian a solitary or colonial sea squirt of the phylum Chordata, class Ascidiacea. The adult form does not resemble vertebrate chordate animals but the larval stage possesses all basic chordate characteristics. Adult ascidians are sedentary, filter-feeding, cylindrical or globular animals, usually found attached to a substrate. The soft body is surrounded by a thick gelatinous to leathery test, or tunic (which also gives them the name of tunicate), often transparent or translucent. The test is secreted by the body wall of the adult animal. It is composed of cellulose, a carbohydrate unique in the animal kingdom ascidian the retention of juvenile features in an adult organism paedomorphy paedomorphy anterior concentration of nervous tissue in several invertebrate groups, such as mollusks, annelid worms, sipunculids (peanut worms), and echiurans (spoon worms or innkeeper worms) circumesophageal nerve ring circumesophageal nerve ring population a group of individuals of the same species living in the same area at the same time and sharing a common gene pool; a group of potentially interbreeding organisms in a geographic area population neuroscience the scientific disciplines concerned with the development, structure, function, chemistry, pharmacology, clinical assessments and pathology of the nervous system neuroscience a small population that is just beginning to reproduce and become established in an area or community incipient population incipient population isometric contraction isometric contraction a muscular contraction in which tension increases while the length of the muscle remains constant having a large compact structure without a definable shape massive massive Anthozoa a class of Cnidaria that includes the stony corals, soft corals, sea anemones, gorgonians, and corallimorpharians Anthozoa a reef that develops adjacent to deeper waters, often in association with oceanic islands oceanic reef oceanic reef virology virology the study of viruses prevailing winds prevailing winds the typical winds for a particular region and time of year a type of mimicry which results in a deceived species being preyed upon or parasitized by a predator species. The mimic's cues may be visual, auditory, olfactory or behavioral aggressive mimicry aggressive mimicry calyx calyx the upper or open end of the corallite or coral polyp cup; the central body of entoprocts (goblet worms) or crinoids (sea lilies and feather stars) cup-shaped caliculate caliculate the pressure that is needed to counteract the osmotic passage of water molecules across a semipermeable membrane into the more concentrated solute osmotic pressure osmotic pressure suppressor gene suppressor gene a gene that can reverse the effect of a mutation in other genes, i.e., a gene that suppresses the phenotypic expression of another gene, especially of a mutant gene herbivore an animal that feeds on plants herbivore a cell that discharges a sticky filament upon contact with a prey organism. Colloblasts are found in the tentacles of ctenophores (comb jellies). As the tentacles are dragged through the water, the colloblasts discharge and capture prey colloblast colloblast prime meridian an imaginary line running from north to south through Greenwich, England, used as the reference point for longitude prime meridian a branch of biology that deals with the geographical distribution of organisms biogeography biogeography barophile a microorganism which grows best (or can only grow) in high-pressure environments, such as deep-sea environments barophile to produce or deposit eggs; the eggs of aquatic animals; the mass of eggs deposited by fishes, amphibians or mollusks; offspring in great numbers or masses; to give forth young in large numbers spawn spawn maritime climate maritime climate a climate strongly influenced by an oceanic environment, found on islands and the windward shores of continents. It is characterized by small daily and yearly temperature ranges and high relative humidity raster map raster map a map or chart encoded in the form of a regular array of cells oolitic limestone rock composed primarily of petrified corals or the skeletons of other calcareous animals oolitic limestone kingdom in taxonomy, the highest ranked category in the taxonomic hierarchy. All organisms are classified into one of five kingdoms: Monera (the prokarytic Kingdom. Includes archaebacteria, eubacteria and cyanobacteria); Protista (unicellular eukaryotes); Fungi (yeasts and mushrooms); Plantae (plants); and Animalia (animals). Some scientists recognize slightly different classification schemes kingdom habituation habituation in animal behavior, the temporary waning or disappearance of an innate response when it is elicited many times in succession atrial siphon in tunicates, the opening that carries water, wastes, and gametes from the organism. Also called the excurrent or exhalent siphon/canal atrial siphon DNA library DNA library a collection of cloned DNA fragments that collectively represent the genome of an organism a feeding polyp of a colonial hydrozoan. It bears tentacles armed with nematocysts, a mouth and a thin outer covering, the hydrotheca hydranth hydranth abductor abductor a type of muscle whose function is to move an appendage or body part away from the body of an animal. Abductors work antagonistically with adductors in a diploid organism, a chromosome in which both alleles at every locus are identical on both copies isogenic chromosome isogenic chromosome keystone predator the dominant predator or the top predator that has a major influence on community structure keystone predator paliform lobe paliform lobe an upright skeletal rod or plate at the inner margin of septa formed by upward growth of the septum ecotype ecotype a genetically differentiated subpopulation that is restricted to a specific habitat an order of corals which contains the black and horny corals Antipatharia Antipatharia a surface which is rocky and steep craggy craggy a unit of length which constitutes the basis of the Metric System. It is one ten-millionth part of the distance measured on a meridian of the Earth from the equator to the pole. One meter equals 39.37 inches meter meter Charles Law Charles Law under conditions of constant pressure and quantity, there is a direct relationship between the volume and absolute temperature for an ideal gas cleavage the early mitotic cellular divisions of the fertilized egg (zygote) cleavage a protein that has all of the essential amino acids and in the correct proportions complete protein complete protein phylogenetics phylogenetics the field of biology that deals with the relationships among organisms aggregate a collection of units or particles forming a body or mass (noun); to form such a body or mass (verb) a group of species, other than a subgenus, within a genus, or a group of subspecies within a species. An aggregate may be denoted by a group name aggregate branchial pertaining to gills branchial a narrow ridge, 1-2 m high, built by waves along the seaward edge of a reef flat. It consists of boulders, shingle, gravel or reef rubble, commonly capped by dune sand rampart rampart a cell that engulfs and digests debris and invading microorganisms phagocyte phagocyte a disease that has its origin in changes to the genetic material. Genetic diseases usually refer to diseases that are inherited in a Mendelian fashion, although non-inherited forms may also result from genic (DNA) mutation genetic disease genetic disease superficial cleavage superficial cleavage a type of cleavage, typical of centrolecithal eggs found in most arthropods, in which karyokinesis (nuclear division) occurs without cytokinesis (cytoplasmic division), resulting in a syncytium. Cleavage furrows form to separate the nuclei scientific law scientific law a statement of a scientific fact or phenomenon that is invariable under given conditions. A law may be either quantitative (including measurement) or qualitative (general characteristics). It must describe evidence that has been gathered using acceptable scientific standards of reproducibility. Examples of scientific laws: Faraday's Law of electromagnetic induction, Coulomb's Law of electrostatic attraction, Dalton's Law of partial pressures, and Boyle's Gas Law chimera the individual produced by grafting an embryonic part of one individual onto an embryo of either the same or of a different species chimera radiocarbon time regular known rates of radiocarbon decay that are used to determine the exact ages of carbon-based life radiocarbon time filter feeder an organism that feeds by capturing particles suspended in the water column. A synonym of suspension feeder. filter feeder a quality of light, depending on its wavelength. Perceived color (or visual color) is the quality of light emission as conveyed by the eye, i.e., the visual perception of light that enables humans and other organisms to differentiate between wavelengths of the visible spectrum color color polyculture polyculture the cultivation of more than one species of organism in an aquaculture system an overt, measurable activity generated by some internal oscillator (or 'clock') biological rhythm biological rhythm composed of silicon or primarily of silicon siliceous siliceous EST (expressed sequence tag) EST (expressed sequence tag) a small part of the active part of a gene, made from cDNA which can be used to fish the rest of the gene out of the chromosome by matching base pairs with part of the gene. The EST can be radioactively labeled in order to locate it in a larger segment of DNA a cluster of reefs reef system reef system a physiological variety or a group of individuals having distinctive genetic characters in common biotype biotype feces egested undigested food wastes feces echolocation the sonar-like ability used by bats, dolphins, some whales, and two groups of cave-dwelling birds to detect objects in their environment. Using echolocation, the animal emits high-frequency sounds that reflect off of an object and return to the ears or other sensory receptors echolocation cell culture cell culture the in vitro growth of cells derived from multicellular organisms. The cells are usually of one type an amino acid which can be synthesized by the organism's body, and not required in the nourishment source. Humans can make 13 nonessential amino acids nonessential amino acid nonessential amino acid infraspecific name infraspecific name in taxonomy, a general term for any name below the rank of species. The term includes subspecific and infrasubspecific names regression analysis regression analysis a statistical technique applied to data to determine the degree of correlation of a dependent variable with one or more independent variables, in other words, to see if there is a strong or weak cause and effect relationship between things; a statistical process for fitting a line through a set of data points. It gives the intercept and slope(s) of the "best fitting" line. It tells how much one variable (the dependent variable) will change when other variables (the independent variables) change inflated inflated swollen or expanded the sudden death of fishes due to the introduction of pollutants, toxic blooms, or the reduction of the dissolved oxygen concentration fish kill fish kill isoenzyme one of a group of enzymes that are very similar in catalytic properties, but may be differentiated by variations in physical properties, such as isoelectric point or electrophoretic mobility; also called 'isozyme' isoenzyme mycelium the mass of filamentous growth (hyphae) from which the vegetative part of a fungus develops mycelium an older name for the phylum Cnidaria Coelenterata Coelenterata in fishes, teeth located on the bones in the pharynx, which is the posterior part of the oral cavity pharyngeal teeth pharyngeal teeth Ekman layer the thin horizontal layer of water riding on top of the ocean that is affected by wind Ekman layer decapod crustacean a members of the Order Decapoda, Class Malacostraca, Superclass Crustacea, Phylum Arthropoda; has five pairs of thoracic legs. Examples are shrimps, lobsters, crabs, and hermit crabs decapod crustacean global change global change a transformation which occurs on a worldwide scale (for example, an increase in CO2 in the atmosphere) or exhibits sufficient cumulative effects to have worldwide impact (for example, local species extinction resulting in global loss of biodiversity) chloroplast chloroplast a disk-like organelle with a double membrane, found in some protists and all green plant cells, that contains chlorophyll and is the site of photosynthesis manta tow technique manta tow technique a technique used to provide a general description of large areas of reef and to gauge broad changes in abundance and distribution of organisms on coral reefs. The technique, widely used in Australia, involves towing a snorkel diver (observer) at a constant speed behind a boat. The observer holds on to a 'manta board' attached to a small boat by a 17-meter length of rope. This person makes a visual assessment of specific variables during each manta tow (2 minutes duration), and records these data when the boat stops, on a data sheet attached to the manta board. The manta tow technique is used to provide a general description of large areas of reef and to gauge broad changes in abundance and distribution of organisms on coral reefs. The advantage of manta tow over other survey techniques is that it enables large areas of reefs to be surveyed quickly and with minimal equipment a waste product of metabolism eliminated via the kidneys. In elasmobranchs (sharks, rays, skates), urea is found in the blood where it helps to maintain osmotic balance urea urea CLEO (Coral Literature, Education & Outreach) CLEO (Coral Literature, Education & Outreach) the CLEO project is designed to provide easy access to gray literature and pre-1990's literature on the coral reef environments near the Coral Reef Early Warning System (CREWS) monitoring stations to support education, research and management objectives. The Education modules leverage techniques developed at NOAA/AOML in the Explorer of the Seas, Coral Health and Monitoring and CREWS programs under which knowledge transfer of oceanographic instrumentaion and coral reef processes have been developed. Education modules for middle school students engage the students in oceanographic instrumentation, classroom experiments and use of data, and the live Coral Cam observations the large-scale movement of a population for some specific purpose migration migration protogyny a state in hermaphroditic systems characterized by the development of female reproductive organs, or maturation of their gametes, before the appearance of the corresponding male product, thus insuring against self-fertilization protogyny that portion of a gene which directly specifies the amino acid sequence of its protein product coding sequence coding sequence the sum of all the physical and chemical processes by which living organised materials are produced and maintained (anabolism), and also the destructive transformation processes by which energy is made available for the uses of the organism (catabolism) metabolism metabolism ribose ribose a monosaccharide containing five carbon atoms per sugar molecule, C5H10O5. Ribose is a major component of ribonucleic acid (RNA) tsunami a long-period gravity wave generated by a submarine earthquake or volcanic event tsunami modifier gene a gene that modifies the effect produced by another gene modifier gene biramous appendage biramous appendage a type of appendage that is characteristic of crustaceans. It forks from the basal protopodite to form two branches, the inner endopodite and the outer exopodite. Each of these branches can be composed of either one or more segments. There are many variations on this generalized structure; the branches often possess highly specialized extensions cellulolytic enzyme cellulolytic enzyme an enzyme that acts upon cellulose pluteus larva pluteus larva a free-swimming, bilaterally symmetrical, ciliated larva of some echinoderms, such as sea urchins and brittlestars one of the four nitrogenous bases in DNA that make up the letters ATGC. Cytosine is the "C". The others are adenine, guanine, and thymine. Cytosine always pairs with guanine cytosine cytosine lumisome lumisome in some cnidarians, a small, intracellular membrane-enclosed vesicle which contains all the proteins necessary for bioluminescence a lepton with no electric charge. Neutrinos participate only in weak (and gravitational) interactions and therefore are very difficult to detect. There are three known types of neutrino, all of which have very low or possibly even zero mass neutrino neutrino chemiluminescence chemiluminescence a chemical reaction that gives off energy in the form of light instead of heat guanine guanine one of the four nitogenous bases in DNA and RNA that make up the letters ATGC, guanine is the "G". The others are adenine, cytosine, and thymine. Guanine always pairs with cytosine a substrate formed by the deposition of calcium carbonate by reef building corals and other organisms or existing as bedrock or volcanic rock usually of minimal relief hard bottom hard bottom compression compression in information technology, decreasing the size of stored information by reducing the representation of the information without significantly diminishing the information itself, usually by removing redundancies. The information requires decompression upon retrieval. Lossless compression allows the original data to be recreated exactly. Lossy compression sacrifices some accuracy to achieve greater compression the evolutionary process that gives rise to a new species speciation speciation articulated jointed, as in for example, the soft fin rays of fishes articulated refers to the interstices or pore spaces in rock, soil, or other material subject to filling by water; fluid-filled spaces between cells in tissues interstitial interstitial of the same species conspecific conspecific petrochemical a chemical derived from petroleum or natural gas petrochemical biodegradable capable of undergoing rapid decomposition by microorganisms under aerobic and/or anaerobic conditions. Most organic materials are biodegradable biodegradable replacement name replacement name in taxonomy, a new taxonomic name expressly proposed for an already established one prevalence prevalence the number of disease cases within a population over a given period of time a chemical substance produced by one organism that is toxic or inhibitory to the growth or well being of another allelochemical allelochemical a finger-like evagination of the body wall. Tentacles surround the mouths of coral polyps, anemones and other invertebrates. They are used for capturing prey, defense, reproduction, gas exchange, and light absorption tentacle tentacle in genetics, the process by which offspring derive a combination of genes different from that of either parent. In higher organisms, this can occur by crossing over recombination recombination a perforated platelike structure in most echinoderms that forms the intake for their water vascular systems madreporite madreporite bank/shelf deepwater area extending offshore from the seaward edge of the fore reef to the beginning of the escarpment where the insular shelf drops off to the deep, oceanic water. If no reef crest is present, it is the flattened platform between the fore reef and the deep ocean waters or between the intertidal zone and open ocean bank/shelf a thermometric scale on which the freezing point of water is at 32 degrees F (Fahrenheit) above the 0 degree (F) mark on the scale, and the boiling point of water is at 212 degrees F Fahrenheit temperature scale Fahrenheit temperature scale having a global distribution cosmopolitan cosmopolitan the number of organisms per unit area or volume population density population density viral DNA DNA (deoxyribonucleic acid) that makes up the genetic material of viruses viral DNA kinetics kinetics the study of acceleration, motion, or rate of change deposit deposit material left in a new position by a natural transporting agent, such as water, wind, ice, or gravity, or by human activity Archaea a group of organisms that resemble bacteria. However, these organisms are biochemically and genetically different from bacteria. Some species live in the most extreme environments found on Earth Archaea phenotype phenotype the total characteristics of an individual, i.e., its appearance, resulting from interaction between its genotype (genetic constitution) and its environment one of the several classes of enzymes that degrade nucleic acid; an enzyme that can degrade DNA or RNA by breaking phosphodiester bonds that link adjacent nucleotides nuclease nuclease v. et. v. et. see also (vide etiam) instar a discreet, in-between molt stage, during the metamorphosis of an arthropod from larva to adult instar off-reef off-reef a synonym of reef slope a periodic environmental signal that entrains a biological rhythm. For example, a cycle for a circadian rhythm, but may also be a temperature or even social cycle zeitgeber zeitgeber the process of combining all aspects of the human, physical and biological aspects of the coastal zone within a single management framework integrated coastal zone management integrated coastal zone management anonymous work according to the International Code of Zoological Nomenclature, a published work that does not state the name of the author(s) anonymous work species recovery plan species recovery plan a plan for restoration of an endangered species through protection, habitat management, captive breeding, disease control, or other techniques that increase populations and encourage survival gill raker one of a series of knob- or comb-like projections on the front edge of the gill arch. Gill rakers aid in the fish's feeding. Their shape and number are a good indication of the diet of the fish. Fishes which eat large prey, such as other fishes, have short, widely spaced gill rakers that prevent the prey item from escaping between the gills. Fishes which eat smaller prey have longer, thinner and more numerous gill rakers. Species which feed on plankton have the longest, thinnest and most numerous gill rakers. Gill rakers also protect and clean the gill fillaments. Counts of gill rakers are used as taxonomic characters gill raker a rise in the sea surface on an open coast, often resulting from a hurricane hurricane surge hurricane surge aggressive, negative behaviors, such as fighting, threatening, and fleeing agonistic behavior agonistic behavior an abstraction of the real world where spatial data is expressed as a matrix of cells or pixels, with spatial position implicit in the ordering of the pixels. With the raster data model, spatial data is not continuous but divided into discrete units. This makes raster data particularly suitable for certain types of spatial operation. The term may also refer to the region of a CRT (cathode-ray tube) or LCD (liquid crystal display) monitor that is capable of rendering images raster raster diploid the condition in which a cell contains a nucleus with two complete sets of chromosomes, one set inherited from each parent. The diploid condition is often abbreviated as 2n. Most plants and animals are diploid. The term also represents the number of chromosomes in most cells except the gametes, which are haploid in chromosome number diploid sea state sea state a description of the sea surface with regard to wave action spur and groove spur and groove a system of shallow ridges (spurs) separated by deep channels (grooves) oriented perpendicular to the reef crest and extending down the upper seaward slope the proboscis of a jellyfish: a tubular structure that connects the mouth to the digestive cavity manubrium manubrium a structure extending into the ocean to influence the current or tide in order to protect harbors, shores, and banks jetty jetty any pathological or traumatic discontinuity of tissue, or loss of function of a part lesion lesion detritus the particulate decomposition or disintegration products of plankton, including dead cells, cell fragments, fecal pellets, shells, and skeletons, and sometimes mineral particles in coastal waters detritus gonochoric gonochoric having separate sexes. Individuals within the species contain only one or the other of male and female reproductive systems protandry a state in hermaphroditic systems characterized by the development of male reproductive organs, or maturation of their gametes, before the appearance of the corresponding female product, thus insuring against self-fertilization protandry Reef Environmental Education Foundation (REEF) Reef Environmental Education Foundation (REEF) REEF is a grass-roots, non-profit organization of recreational divers who regularly conduct fish biodiversity and abundance surveys during their dives luciferin a compound whose activated form emits light. In the presence of the enzyme luciferase and ATP, luciferin is oxidized to produce oxyluciferin and energy given off as cold light (bioluminescence) luciferin medusa bud medusa bud one of the buds of a hydroid, destined to develop into a gonophore or medusa. Medusa buds are released from the gonangium through a central opening, the gonopore a circular shelf of tissue attached to the underside of the umbrella in a hydrozoan mesusa. It functions in locomotion velum velum photic zone photic zone the vertical zone in the ocean extending from the surface to that depth permitting photosynthetic activity continental margin the water-covered edges of continents consisting of the continental shelf, the continental slope, and the continental rise continental margin depressed a body shape which is flattened dorso-ventrally, e.g., a ray, skate, monkfish depressed organic refers to those substances produced by the metabolism of a living organism, especially carbon-containing compounds organic prialt an analgesic drug made from the venom of a species of cone shell snail, Conus magus. The particular anagesic substance in the venom is a conopeptide, one of the first pharmaceuticals that demonstrate the promise of "drugs from the sea" prialt periderm an external layer of secreted cuticular material in many Anthozoa. The term is synonymous with "cuticle." In woody plants, the periderm is a protective secondary tissue produced by the cork cambium periderm a record of climatic events found by examining the natural environment (e.g., coral growth bands, tree rings, layers of ice in glaciers) natural climate record natural climate record database database a structured file of information or a set of logically related data stored and retrieved using computer-based means light produced by organisms as a result of conversion of chemical energy to light energy bioluminescence bioluminescence exocrine gland exocrine gland a gland that secretes its product through a duct a class of vertebrates that consists of frogs, toads, newts, salamanders, and caecilians. These organisms live at the land/water interface and spend most of their life cycle in water. With exception of some tree frogs, all must reproduce in water or otherwise moist conditions. Amphibians are not typically marine Amphibia Amphibia metadata metadata information about data or other information. Metadata or "data about data" describe the content, quality, condition, and other characteristics of data gene expression the conversion of information from gene to protein via transcription and translation gene expression auxotroph a polyploid formed from the doubling of a single genome an organism which is unable to synthesize a particular organic compound required for its growth. An auxotrophic alga, for example, is one which requires a few organically derived substances, such as vitamins, along with dissolved inorganic nutrients for photosynthesis; in microbiology, a mutant strain that requires a new nutrient for growth auxotroph siphonozooid siphonozooid a specialized polyp found in colonial soft corals, such as sea pens and sea pansies, which functions as as intake for water, which circulates within the colony and helps keep it upright repressor repressor a protein that binds to an operator adjacent to a structural gene, inhibiting transcription of that gene radial cleavage radial cleavage a type of cleavage characteristic of deuterostomes. When changing from a four-cell stage to an eight-cell stage embryo, the cells divide such that each cell in the top four cell plane is directly over one other cell in the bottom plane a pore in a cell membrane, formed by an integral protein, that selectively regulates the diffusion of ions into and out of the cell. An ion channel switches between open and closed when the protein undergoes a conformational change. Ion channels are usually selective for a specific ion type (e.g., Na, or K, or Cl, or Ca) ion channel ion channel a phagocytic cell found circulating in the body cavity of coelomates, particularly annelids and mollusks, or crawling by amoeboid movement through the interstitial spaces of sponges; an amoeboid cell in sponges that transports nutrients and is found in the matrix between the epidermal and collar cells; any cell having the shape or properties of an amoeba amoebocyte amoebocyte ostium ostium in sponges, a microscopic pore through which water enters the sponge body autopolyploid a polyploid formed from the doubling of a single genome autopolyploid the maximum number of a food or game population that can be harvested without harming the population's ability to grow back; the largest average catch or yield that can continuously be taken from a stock under existing environmental conditions maximum sustainable yield maximum sustainable yield a sponge larva that appears as a hollow ball with anterior flagellated cells and posterior larger and nonflagellated cells (megascleres) amphiblastula amphiblastula autoradiography a technique that uses X-ray film to visualize radioactively labeled molecules or fragments of molecules; it is used in analyzing length and number of DNA fragments after they are separated by gel electrophoresis autoradiography an open atoll in the Northwest Hawaiian Islands (NWHI) that consists of a large, crescent-shaped reef surrounding numerous small, sandy islets. While the land area is only one-fourth square kilometer (67 acres), the total coral reef area of the shoals is over 938 square kilometers (232,000 acres). The reef system associated with French Frigate Shoals supports the greatest variety of coral species in the NWHI, with 41species of stony corals documented. It also supports more than 600 species of invertebrates, many of which are endemic to the area, over 150 species of algae, and many species of fishes. Hundreds of green sea turtles travel to the shoals for safe nesting. The many small islets of French Frigate Shoals also provide refuge to the largest sub-population of endangered Hawaiian monk seals French Frigate Shoals French Frigate Shoals tabulate tabulate having a flat surface the branch of biology that is concerned with the study of functions of particular structures or organs of organisms physiology physiology a multi-agency, multi-year effort that began in 2000. NOWRAMP's objective is to rapidly evaluate and map the shallow water reef habitats in the NWHI. The agencies which contribute to NOWRAMP are: NOAA, the U.S. Fish and Wildlife Service, the State of Hawai'i Department of Land and natural Resources, the University of Hawai'i, the Bishop Museum, the Hawai'i Maritime Service, the U.S. National Park Service, and scientists from the University of California at Santa Cruz NOWRAMP (Northwestern Hawaiian Islands Coral Reef Assessment and Monitoring Program) NOWRAMP (Northwestern Hawaiian Islands Coral Reef Assessment and Monitoring Program) hypha one of the long, branching filaments that forms the mycelium of a fungus hypha gap analysis a Geographic Information System (GIS) methodology to identify the distribution of biodiversity over large spatial areas. It was developed in 1988 by the U.S. Geological Survey in an effort to ensure that regions rich in species diversity are conserved with the hope that this will eliminate the need to list species as threatened or endangered in the future. The gap analysis approach uses maps of vegetation and predicted animal distributions to locate centers of species richness outside areas currently managed for biodiversity protection. These are considered the "gaps" of gap analysis. Thus far, its use primarily has been in the terrestrial sphere gap analysis the Northwestern Hawaiian Islands (NWHI) are a chain of small islands, atolls, submerged banks, and reefs beginning approximately 120 nautical miles west of the main Hawaiian islands, and stretching northwest for more than 1,079 nautical miles or 2,000 kilometers. This vast archipelago is uninhabited (except for Midway Island) and is surrounded by some of the most extensive and pristine coral reefs in U.S. waters NWHI (Northwestern Hawaiian Islands) NWHI (Northwestern Hawaiian Islands) sea cucumber sea cucumber an echinoderm in the class Holothuroidea. Sea cucumbers possess a flexible, elongated body and leathery skin, and tentacles surrounding the mouth. Although they don't superficially resemble other members of the phylum Echinodermata, they retain pentameral (five-rayed) symmetry, with five rows of tube feet running from the mouth down along the sides of the body. Sea cucumbers are an abundant and diverse group that are found in nearly every marine environment, but are most diverse on tropical, shallow-water coral reefs.They are economically important in two main ways. They produce chemical compounds that are of interest to pharmaceutical firms, and as a food item in Asia, they form the basis of a multimillion-dollar industry that processes the body wall for sale as beche-de-mer or trepang organic enrichment organic enrichment the addition of nutrients from organic matter atom the smallest component of an element, made up of neutrons, protons, and electrons atom ribbed describes a surface with a series of ridges ribbed base sequence the order of nucleotide bases in a DNA molecule base sequence radiocarbon dating a dating method used to determine the age of samples containing carbon. The method measures the disintegration of the 14C atom. 14C is produced in the atmosphere by cosmic ray bombardment, and has a half-life of 5,570 years, making it useful for dating samples in the range of 0-40,000 years radiocarbon dating transfer of genetic material from one cell to another by means of a virus or phage vector transduction transduction the evolutionary relationships among organisms phylogeny phylogeny cetacean cetacean a marine mammal of the Order Cetacea. The Cetacea includes whales, dolphins and porpoises classification based on degree of overall similarity phenetic classification phenetic classification impact a change, caused by external sources, in the chemical, physical (including habitat) or biological quality or condition of a habitat or environment impact measurements made at the actual location of the object or material measured, in contrast to remote sensing in situ data in situ data food pyramid pyramid-shaped diagram which shows feeding relationships within a food chain, e.g. that herbivores are smaller, more numerous and faster breeding than the predators that feed on them food pyramid the alimentary canal or the gut of an embryo. Some structures of the enteron may not be completely developed or differentiated in early embryonic growth enteron enteron dependent variable the variable being measured dependent variable acellular acellular describes the construction of an organism or tissue that is a mass of protoplasm which is not divided into cells, e.g., some structural parts of slime molds and fungi epistasis epistasis the prevention or masking of the expression of an allele at one locus by an allele at another locus Pangea Pangea a supercontinent that existed from about 300 to 200 million years ago. It included most of the continental crust of the Earth trade winds trade winds a system of relatively constant low level winds that occur in the tropics. The trade winds blow from the northeast to the equator in the Northern Hemisphere and from the southeast to the equator in the Southern Hemisphere the external surface of a sponge, lined with pinacocytes in a single cellular layer pinacoderm pinacoderm an organism whose habitat is on or near the bottom of a stream, lake, or ocean benthic organism (benthos) benthic organism (benthos) radial velocity component of motion toward or away from a given location radial velocity egestion egestion the elimination of undigested food materials from an organism epibiont epibiont an organism that lives on the outside of another organism oxygen isotopes oxygen atoms that have the same atomic number (protons) but different mass numbers (and different numbers of neutrons). The two stable isotopes of oxygen are 16O and 18O oxygen isotopes Pseudostratified ciliated columnar epithelium Pseudostratified ciliated columnar epithelium the ciliated epithelium that lines the trachea (windpipe) of mammals. (Photo courtesy of Dr. Franklin S. Carman III, donated from URL: http://tooldoc.wncc.edu) upstream toward the source or upper part of a stream or current; against the current upstream elastic capable of returning to an initial form or shape after deformation; resilient elastic water pure water consists of hydrogen and oxygen, H2O. It is a binary compound that occurs at room temperature as a colorless, odorless, tasteless, transparent liquid which is very slightly compressible. It freezes at 0 degrees C and boils at 100 degrees C. It is the most important natural solvent, and frequently contains impurities, which are mostly removed by distillation water in evolution, a shared derived character synapomorphy synapomorphy pleurite one of the external lateral processes of a somite (body segment) of a crustacean; also called a 'pleuron' pleurite a systematist who attempts to classify life forms according to their evolutionary relationships, not just overall similarity cladist cladist transducer transducer the electromechanical component of a sonar system that is mounted underwater and converts electrical energy to sound energy and vice versa primary production primary production a synonym of primary productivity intersex intersex an organism which possesses a mixture of male and female characteristics a gaseous molecule that contains three oxygen atoms (O3), instead of the usual two (O2). Ozone can exist either high in the atmosphere (stratosphere), where it shields the Earth against harmful ultraviolet rays from the sun, or close to the ground (troposhere), where it is the main component of smog. Ground-level ozone is a product of reactions involving hydrocarbons and nitrogen oxides in the presence of sunlight. Ozone is a potent irritant that causes lung damage and a variety of respiratory problems ozone ozone tongue-shaped linguiform linguiform a gene found in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution ortholog ortholog fixed action pattern fixed action pattern in ethology or animal behavior, a complex behavioral response which once released by a key stimulus, runs to completion pustule a pimple- or wart-like projection; a bump or raised knob on the outside surface of a mollusk shell pustule acantho- acantho- a prefix meaning "with spines" consisting of dissimilar elements, parts or forms; having non-uniform structure or composition heterogeneous heterogeneous a pattern or model that provides a framework for interpreting observations paradigm paradigm a photosynthetic pigment which absorbs light and transfers energy to chlorophylls during photosynthesis accessory pigment accessory pigment quantitative inheritance inheritance of measurable traits (height, weight, color intensity, etc.) that depend on the cumulative action of many genes. quantitative inheritance vernacular name the colloquial or common name of a taxon, i.e., in any language or form other than that of biological nomenclature. Vernacular names have no status in nomenclature vernacular name uptake of material into a cell by the formation of a membrane-bound vesicle endocytosis endocytosis a scuba diving certifying and instruction agency NAUI ( National Association of Underwater Instructors) NAUI ( National Association of Underwater Instructors) histology histology the branch of biology that studies the microscopic structure of animal or plant tissues. The four basic types of animal tissues are: epithelial tissue, nervous tissue, muscular tissue and connective tissue (bone, cartilage, blood, fat, and areolar (fibrous). The three basic plant tissues are: dermal tissue, ground tissue, and vascular tissue a taxonomic group that is below an order but above a family superfamily superfamily gut the digestive tube formed between the mouth and anus in which food is digested and nutrients absorbed; it consists of the mouth, pharynx, esophagus, stomach, intestine, and anus, though some animals do not have all these regions gut phaceloid coral a coral that has corallites of uniform height which are adjoined toward their base phaceloid coral paleoecology paleoecology the study of the relationship of extinct organisms or groups of organisms to their environments palus one of several upright slender calcareous processes which surround the central part of the calicle of certain corals; vertical radially arranged plates forming one or more cycles between the septa and the central axis in the scleractinian skeleton palus oligomer oligomer a molecule of intermediate relative molecular mass, the structure of which essentially comprises a small plurality of units derived, actually or conceptually, from molecules of lower relative molecular mass; a polymer that consists of two, three, or four monomers living or moving in a group with others of its kind, as in a flock of birds or school of fish gregarious gregarious a non-inherited character, of function or structure, developed in an organism as a result of environmental influences during the individual's life acquired character acquired character a shell divided into smaller chambers, as in the chambered nautilus (Cephalopoda-Mollusca) septate shell septate shell subset subset in mathematics, a subset of a given set is a collection of things that belong to the original set pertaining to the lips labial labial fan-shaped, paired posterior abdominal appendage in certain crustaceans, e.g., lobsters or shrimp, that are used for swimming uropod uropod a relatively level area of fine silt along a shore (as in a sheltered estuary) or around an island, alternately covered and uncovered by the tide, or covered by shallow water mud flat mud flat iridescent iridescent exhibiting rainbow colors percentile percentile one of the division points that divides a set of ranked data into one hundred equal points; a value on a scale of zero to one hundred that indicates the percent of a distribution that is equal to or below it. A score in the 95th percentile is a score equal to or better than 95 percent of all other scores turbinate turbinate resembling an inverted cone isogamous having haploid gametes that are similar in size, structure and motility. An isogamete can unite with another to form a zygote isogamous fish eggs or egg-filled ovary; the egg mass or spawn of certain crustaceans, such as lobsters roe roe endothermic an animal that is able to maintain a body temperature that varies only within narrow limits by means of internal mechanisms. Most birds and mammals are considered endothermic; also called homeothermal or "warm blooded" endothermic living in a natural state; living in nature wild wild the force per unit area exerted by the weight of water. Each 33 feet of sea water exerts a pressure equivalent to one atmosphere, or 14.7 psi water pressure water pressure a permanent structural alteration in DNA. In most cases, DNA changes either have no effect or cause harm, but occasionally a mutation can improve an organism's chance of surviving and passing the beneficial change on to its descendants genetic mutation genetic mutation pristine an area having its original purity, not contaminated or corrupted by human intervention; the original or pure condition or state of something; unspoiled pristine any geographical region characterized by a distinctive biota bioregion bioregion decomposition decomposition the breakdown of organic matter by bacteria and fungi a taxonomic group that is below a class and above an order subclass subclass innate innate not established by conditioning or learning; "an unconditioned reflex"; a genetic behavior pattern growth that occurs at the same rate for all parts of an organism so that its shape is consistent throughout development isometric growth isometric growth nucleus a central cell structure that contains the chromosomes, and as such, controls the activities of the cell; the center of an atom, containing protons, neutrons, and most of the mass nucleus a component part of a complex molecule moiety moiety the internal, usually calcium carbonate skeletal rod of sea fans (Gorgonacea) and sea pens (Pennatulacea) axis axis pyramid of biomass in ecology, the total biomass of all organisms at each trophic level in a food chain; typically biomass declines with successively higher trophic levels pyramid of biomass a layer of calcium carbonate that grows outside corallite walls epitheca epitheca ecoregion ecoregion a geographic area of relative homogeneity in ecological systems or in relationships between organisms and their environment; a relatively large area of land or water that contains a geographically distinct assemblage of natural communities a fishing net used to encircle surface schooling fish. During retrieval the bottom of the net is closed or pursed by drawing a purse line through a series of rings to prevent the fish from escaping. The catch is deposited on the fishing boat. The purse seine is operated by two boats, a large boat that surrounds the catch with the net and a smaller boat which anchors the net. Purse seines may be of up to 1 km length and 300 m depth purse seine purse seine having a pH of more than 7. Alkaline solutions are also said to be basic alkaline alkaline abiotic abiotic refers to nonliving objects, substances or processes of the same sex consexual consexual a codon in mRNA for which there is no corresponding tRNA molecule to insert an amino acid into the polypeptide chain. Protein synthesis is terminated and the completed polypeptide is released from the ribosome. Three stop codons are known: UAA, UAG, and UGA. Mutations which generate any of these three codons in a position which normally contains a codon specifying an amino acid are known as 'nonsense mutations'; also called 'nonsense codons.' A stop codon signals the end of the amino acid chain in protein synthesis stop codon stop codon chemical evolution the chemical changes that transformed simple atoms and molecules into the more complex chemicals needed for the origin of life chemical evolution having benefit for one member of a two-species association but neither positive nor negative effect on the other commensal commensal a short sequence (usually 2-50 bases) of DNA. Oligonucleotides of up to 30 bases are routinely synthesized for use as PCR primers or as probes for their sequence compliments in a complex mixture of DNA oligonucleotide oligonucleotide amphimixis amphimixis sexual reproduction involving the fusion of male and female gametes and the formation of a zygote an extracellular, protective external body covering, secreted by the epidermis, of some invertebrate animals, usually composed of fibrous material, such as chitin or collagen; the waxy layer of epidermal cells of plant parts, such as leaves, stems, and fruit cuticle cuticle bioassay bioassay an assay for the activity or potency of a substance that involves testing its activity on living materials entropy the measure of the disorder or randomness of energy and matter in a system entropy ionizing radiation high-energy radiation capable of producing ionization in substances through which it passes, i.e., radiation that has enough energy to eject electrons from electrically neutral atoms, leaving behind charged atoms or ions; examples are alpha particles (helium nuclei), beta particles (electrons), neutrons, and gamma rays (high frequency electromagnetic waves, x-rays) ionizing radiation greenhouse gases atmospheric gases, primarily carbon dioxide, methane, and nitrous oxide restricting some heat-energy from escaping directly back into space greenhouse gases venomous pertaining to an organism that has a venom, usually secreted by a gland, that is injected through hollow spines or teeth venomous coelom coelom an internal fluid-filled body cavity within a coelomate organism. It lies between the gut and the outer body wall, and is lined entirely with tissue (peritoneum) derived from the mesoderm. Most internal organs are located within the coelom. The structure and development of the coelom is an important taxonomic character for recognizing major groups of animals a subclass of the Anthozoa that contains the sea pens, sea pansies, sea fans, whip corals, and pipe corals. Octocorals always possess 8 tentacles and 8 complete septa (hard corals and anemones possess 12 or more tentacles and septa). They are colonial cnidarians whose polyps are connected by a tissue mass called the coenenchyme. This tissue connects the gastrovascular (digestive) cavities of all the polyps in the colony Octocorallia Octocorallia Late-stage auricularia of Stichopus californicus ca. 17-18 days old, raised in culture by T.H.J. Gilmour. (Photo: University of Saskatchewan Archives) Late-stage auricularia of Stichopus californicus the process of nuclear division in eukaryotic cells that produces two daughter cells from one mother cell, all of which are genetically identical to each other. See cell division - mitosis mitosis megabase (Mb) megabase (Mb) unit of DNA or RNA sequence equal to one million (10) pairs of nucleotide bases. Abbreviated Mb aculeiform having a sharp point; needle-shaped aculeiform thermoreceptor a neurological receptor that detects changes in temperature thermoreceptor a small electronic sensor and calculator, carried by the scuba diver, that calculates and displays the basic information needed during a dive, i.e., depth, time, decompression status and tank pressure. By constantly monitoring depth and bottom time, dive computers automatically recalculate the diver's no-decompression status, giving longer dive times while still keeping the diver within a safe envelope of no-decompression time. Computers also monitor ascent rates, logs dives, and measures time intervals between dives dive computer dive computer ossified ossified made or converted into bone any steady back and forth movements oscillation oscillation Foraminifera planktonic and benthic protozoan protists that have a test (shell) composed of calcium carbonate Foraminifera oxidation the combination of a substance with oxygen. Oxidation can also describe a type of reaction in which the atoms in an element lose electrons and the valence is correspondingly increased oxidation Aquarius is an underwater ocean laboratory located in the NOAA Florida Keys National Marine Sanctuary. The laboratory is deployed three and half miles offshore, at a depth of 60 feet, next to spectacular coral reefs. Scientists live in Aquarius during ten-day missions using saturation diving to study and explore the coastal ocean. Aquarius is owned by NOAA and is operated by the National Undersea Research Center at the University of North Carolina at Wilmington Aquarius Aquarius neo-Darwinism neo-Darwinism the unification of natural selection and Mendelian genetics; also called the Modern Synthesis ophiopluteus larva larva of a brittle star (phylum Echinodermata) ophiopluteus larva having genetic material (DNA) from another species. This term can be applied to an organism that has genes from another organism transgenic transgenic sonograph a hard copy display of sound data generated either in real time or from recorded data. Also known as a sonogram sonograph allorecognition, followed by the immune effector mechanisms generated by the recognition process alloresponse alloresponse horse latitudes horse latitudes two belts or regions of subtropical high-pressure areas, located between 30-35 degrees north and south, in which the wind is light and varied and weather is hot and dry fingerling a young or small fish fingerling sex-linked gene sex-linked gene a gene coded on a sex chromosome, such as the X-chromosome-linked genes burrower burrower an animal that makes a hole or burrow in the substratum and lives in it. For example, a fidler crab fan palm the only species of tree (Pritchardia remota) on the island of Nihoa in the Northwestern Hawaiian Islands fan palm serpulid worm a marine polychaete worm in the family Serpulidae which secretes and lives in a rigid calcareous tube serpulid worm species which are now living extant species extant species territoriality the defense of a given area territoriality the protein substance of the collagenous fibers (white fibers) of skin, tendon, bone, cartilage and all other connective tissue. Collagen also serves as skeletal support in some sponges collagen collagen perradial canal one of four branched ciliated canals that originates directly from the stomach of scyphozoan medusae and moves partially digested food materials from the ring canal to the stomach perradial canal a prefix meaning 'ultimate beginning' arch- arch- Karst cave Karst cave a cave caused by dissolution of limestone by water see North Star Polaris Polaris gross primary production gross primary production the total amount or weight of organic matter created by photosynthesis over a defined time period (total product of photosynthesis) rural area an area in which most residents depend on agriculture or the harvesting of natural resources for their livelihood rural area edge effect habitat conditions created at or near the more-or-less well-defined boundary between ecosystems (ecotone). Typically there is an increased richness of organisms resulting from the mixing of two communities where they join edge effect environmental stress environmental stress severe environmental effects on the natural ecosystem the Web Reef Advisory System (WRAS) was developed by ReefBase and Reef Check, in collaboration with the Coastal Resources Center at the University of Rhode Island and the Department of Biological Sciences at the University of Southern California, as "an online application to input, view, and analyze Reef Check survey data. It calculates indicators of how good or bad a shape a particular reef is in, and what the underlying causes may be, based on Reef Check surveys." WRAS allows users to view, analyze, and add data. The file location is: www.reefcheck.org/datamanagement/ Web Reef Advisory System (WRAS) Web Reef Advisory System (WRAS) background level the concentration or level of a substance or other factor in an environment that is not the result of human activities, e.g., background levels of chemicals, light, sound, etc background level the movement of particles from an area of higher concentration to an area of lower concentration diffusion diffusion structural complexity structural complexity as pertaining to coral reef ecosystems, a measure of the amount of coral surface area in relation to linear area. For example, branching coral reef habitats will have a higher structural complexity than encrusting coral reef habitats a depression formed in an area either by dissolving of the surface limestone or by collapse of underlying cavities sinkhole sinkhole a raised bump or nipple-like projection on a tissue surface; a cellular outgrowth. Papillae have the appearance of little bumps or fingers on the surface of cells papilla papilla AIMS (Australian Institue of Marine Science) AIMS (Australian Institue of Marine Science) the Australian Institute of Marine Science (AIMS) was established by the Commonwealth government in 1972 to generate and transfer the knowledge needed for the sustainable use and protection of the marine environment through innovative, world-class scientific and technological research. It is a federally-funded and independent statutory authority governed by a Council appointed by the Australian government. AIMS has its headquarters at Cape Ferguson, 25km east of Townsville in North Queensland fin (scuba) fin (scuba) a rubber or plastic shoe-like device attached to the feet to increase surface area for greater thrust while swimming; they may be open heeled or full-footed. Scuba divers prefer the open heel style, usually worn with booties fertilization fertilization the process where a spermatozoan (sperm cell) penetrates the cell membrane of an egg cell and the nuclei of the sperm and egg cells join together and their chromosomes combine to form a diploid zygote least squares least squares a statistical criterion for the estimation of the goodness of fit in correlation analysis. Least squares methods aim to minimize the sum of squared differences between the observations and the predictions from a model monophyletic group a group of organisms descended from a common ancestor monophyletic group saturation diving the situation where a diver is at a depth or pressure for a long enough period of time (12 hours or longer) to have the partial pressures of the dissolved gases in the body at equilibrium with the partial pressure of the gases in the surrounding environment. Scientists are able to live in and work around underwater habitats for extended periods without the risk of developing decompression sickness (the bends). Divers breathe compressed air mixed with light, inert gases, such as helium. When the diver's blood becomes saturated with helium, the time required for decompression, even if the diver returns to the surface after a period of weeks, is no greater than that required after a dive lasting just a few hours saturation diving xanthochromic yellow or golden color xanthochromic gale gale a storm with wind speeds between 34 to 40 knots mycophage an animal which primarily eats fungi mycophage adaptive radiation adaptive radiation the evolution of a single evolutionary stock into a number of different species a solution in which water is the solvent aqueous solution aqueous solution biophysics the scientific study of the physics of organisms, their biological structure and processes biophysics plication plication a fold referring to water with a salinity lower than that of natural seawater hyposaline hyposaline statistic an estimate based on a sample or samples of a population, providing an indication of the true population parameter statistic canopy canopy the more or less continuous cover of branches and foliage formed collectively by the tops, or crowns, of adjacent trees a condition in which an organism mounts an immune response against one of its own organs or tissues; i.e., an organism's immune system attacking its own body autoimmunity autoimmunity atoll a horseshoe or circular array of reef islets, capping a coral reef system that encloses a lagoon, and perched around an oceanic volcanic seamount atoll Acrobat Reader is a software product from Adobe, designed to view .pdf (portable document format) documents downloaded from the World Wide Web Adobe acrobat Adobe acrobat cyclone an area of low pressure. Circulation is counterclockwise around a low pressure system in the Northern Hemisphere and clockwise in the Southern Hemisphere cyclone coralline algae algae that form solid calcium carbonate accretions coralline algae a measure of the genetic similarity between any pair of populations. Such distance may be based on phenotypic traits, allele frequencies or DNA sequences genetic distance genetic distance the primitive endoderm-lined gut of an animal embryo formed during gastrulation. It is formed by the invagination of blastula cells (blastomeres) into the blastocoel. The archenteron develops into the digestive tract of the adult animal archenteron archenteron crypsis protective camouflage coloration where the individual resembles its backgound crypsis pheromone a hormone-like substance that is secreted by an organism into the environment as a specific signal to another organism, usually of the same species pheromone exposure contact with infectious agents such as bacteria or viruses in a manner that promotes transmission and increases the likelihood of disease exposure pertaining to concealment, usually in reference to color pattern or behavior (e.g., hiding in reef crevices) cryptic cryptic sudden increase in the number of individuals found in a population because of an abundance of useable environmental resources population explosion population explosion Annual Composite HotSpot map Annual Composite HotSpot map a map that composites all of the average monthly HotSpot (see HotSpot) images for a given year a group of species with a common evolutionary ancestry clade clade relatively minor change in the composition of a species' gene pool over time microevolution microevolution cancellous cancellous possessing a spongy or porous surface radiocarbon age radiocarbon age the age of plant or animal remains, determined by measuring the remaining activity of the 14C atoms in the sample: A=A0 e-t where A is the measured activity, A0 is the initial activity, e is the decay constant, and t is the sample age sediments deposited by erosional processes, usually by streams alluvium alluvium controlled experiment controlled experiment a scientific experiment, in which results from an experimental group with variable conditions, is compared with a control group with nonvariable conditions visible radiation energy at wavelengths from 400 visible radiation Law a description of how a natural phenomenon will occur under certain circumstances; a statement that summarizes the results observed in an experiment that is repeated many times by many different scientists. A scientific law is widely accepted as true or as a fact, such as Newton's Laws of Gravitation Law determinate cleavage cleavage resulting in blastomeres each capable of developing only into a particular embryonic structure, not into a complete organism determinate cleavage zoospore a motile, flagellated spore zoospore biometrics biometrics the use of statistics for the study of biological events the 'Washington' Convention on International Trade in Endangered Species of Wild Fauna and Flora, more commonly known as CITES, aims to protect certain plants and animals by regulating and monitoring their international trade to prevent it reaching unsustainable levels. There are more than 150 Parties to the Convention. The CITES Secretariat is administered by the United Nations Environment Programme (UNEP). CITES regulates international trade in over 30,000 species, of which approximately 25,000 are plants CITES (Convention on International Trade in Endangered Species) CITES (Convention on International Trade in Endangered Species) duplex DNA duplex DNA double-stranded DNA population (statistics) any entire collection of animals, plants, people, or things from which we may draw a sample and collect data. It is the entire group we are interested in, which we wish to describe or draw conclusions about. In order to make any generalizations about a population, a sample, that is meant to be representative of the population, is often studied. For each population there are many possible samples. A sample statistic gives information about a corresponding population parameter. For example, the sample mean for a set of data would give information about the overall population mean population (statistics) fat fat a triglyceride (lipid) that is usually solid at room temperature viroid an infectious particle similar to a virus, but smaller. It consists only of a strand of nucleic acid without the protein coat (capsid) characteristic of a virus viroid shore bird shore bird any of various species of bird, such as the sandpiper, plover, or snipe, that frequents the shores of coastal or inland waters a haploid spore in the red algae life cycle which is the meiotic product of the tetrasporangium of a diploid tetrasporophyte. The tetraspores are released, settle, and grow into gametophytes tetraspore tetraspore blastula blastula a stage of embryonic development of animals near the end of cleavage (cell division), but before gastrulation. In animals where cleavage involves the whole egg, the blastula usually consists of a hollow ball of cells (blastomeres) surrounding a fluid-filled central cavity, the blastocoel notochord a flexible rodlike structure that forms the supporting axis of the body in the lowest chordates, (e.g., tunicates and lancelets) and lowest vertebrates (e.g., lampreys), and in the embryos of all higher vertebrates, where it is replaced by the vertebral column; a prime defining characteristic of the phylum Chordata notochord motu motu a coral island in the lagoon of an atoll monk seal an endangered species of seal (Monachus schauinslandi) normally found on the leeward (southwest) sides of the Northwestern Hawaiian Islands, and occasionally sighted in the Main Hawaiian Islands. It is estimated that fewer than 1500 Hawaiian monk seals exist today. The Hawaiian monk seal was officially designated endangered 1976 and is protected by the Endangered Species Act and the Marine Mammal Protection Act. It is illegal to kill, capture or harass monk seals. A critically endangered species of monk seal (Monachus monachus) is found in the Mediterranean Sea. The Caribbean monk seal (Monachus tropicalis) is thought to be extinct monk seal the emission of light from a substance caused by exposure to radiation from an external source fluorescence fluorescence flux the rate of flow of energy or particles across a given surface flux extensions of the water-vascular system of echinoderms, protruding from the body and often ending in suckers. They may be used for locomotion and/or for maintaining a tight grip on prey or on the substrate tube feet tube feet the metabolic processes that consumes energy and involve the synthesis of larger, complex molecules from simpler ones anabolism anabolism epidemic spawning the simultaneous shedding of gametes by a large number of individuals epidemic spawning the canal, including the stomach and intestines, leading from the mouth to the anus alimentary canal alimentary canal refers to molecules with both hydrophobic and hydrophilic regions. Proteins and lipids may be amphipathic amphipathic amphipathic one of the paired, flexible, and jointed sensory appendages on the head of a crustacean, an insect, or a myriapod (e.g., a centipede) antenna antenna the non-centralized, disorganized network of nerve cells under the epidermis, and sometimes the gastrodermis, of cnidarians. It is comprised of multipolar cells with multiple synaptic junctions, but no polarization. Impulses pass either way across the synapse. Both neuron endings of a synapse have secretory vesicles nerve net a diffuse, two-dimensional plexus of interconnected bipolar or multipolar neurons with no central control organ; found in cnidarians nerve net blood a circulating tissue composed of a fluid portion (plasma) with suspended formed elements (red blood cells, white blood cells, and platelets) that delivers nutrients and hormones to cells and removes wastes; In some invertebrates, the blood is called the haemolymph blood a social group of fishes (and some other aquatic animals), usually of the same species, which tends to orient and move in the same direction school school sol sol a liquid colloidal dispersion; a cytoplasmic phase (the other phase is a gel) an animal, such as a parasitic tapeworm, that absorbs digested food products through the body wall absorptive feeder absorptive feeder coefficient coefficient a number expressing the amount of some change or effect under certain conditions Type I error Type I error the error of rejecting the null hypothesis when it is true habitat complexity habitat complexity the areal extent and number and diversity of habitat types and distinct ecological zones within a specified area age class a group of individuals of a species all of the same age age class a linear spicule in sponges; a single rod or ray with a pointed, hooked, or knobbed end monaxon monaxon cilia cilia short, motile, generally microscopic, hairlike projections found on many protists and larvae of some invertebrates. Cilia are used for locomotion, the generation of a current, or filter feeding; A cilium is made up of microtubules and has basically the same internal structure as a flagellum. Movement is caused by the interactions of the microtubules. In higher animals, cilia are found projecting from cells that line certain tubes and passages, such as the tracheae (windpipe) of mammals water that has been on land and moves seaward as a result of rain, flooding, irrigation or flushing . Runoff is frequently high in nutrients and suspended sediments, as well as toxicants runoff runoff tetrodotoxin (TTX) tetrodotoxin (TTX) is an especially potent marine neurotoxin, named after the order of fish from which it is most commonly associated, the Tetraodontiformes (includes the puffers, porqupine fish, blowfish, cowfish, boxfish).The toxin appears in high concentrations in the gonads, liver, intestines and skin of pufferfish. The fatality rate when injested may be as high as 60 percent. Tetradotoxin is more than 10,000 times deadlier than cyanide. Other marine and terrestrial organisms have been found to store TTX, for example, the Australian blue-ringed octopus, parrotfish, triggerfish, gobies, angelfish, ocean sunfish, globefish, seastars, starfish, xanthid and other crabs, a horseshoe crab, a number of marine snails, flatworms, tunicates, ribbonworms, mollusks and marine algae (Jania spp.) Terrestrial organisms include the Harlequin frogs (Atelopus spp.), three species of California newt and other eastern salamanders tetrodotoxin (TTX) gradient analysis gradient analysis an intuitive method to portray variation along a single or multiple environmental gradients. The plots display species or community abundance in response to a known environmental gradient, i.e., the analysis of species composition along a gradient of environmental conditions a complex red organic pigment containing iron and other atoms to which oxygen binds heme heme rhinophoral sheath rhinophoral sheath in sea slugs, the upstanding flange from the antero-lateral part of the mantle into which a rhinophore can be contracted cyanide fishing cyanide fishing a destructive fishing technique in which sodium cyanide or some other cyanide compound is used to stun and capture coral reef fishes for the aquarium and live food trade Batesian mimicry Batesian mimicry a type of mimicry in which a harmless species resembles a different species that is unpalatable, poisonous, or otherwise noxious or harmful to a predator microsclere a small spicule in sponges microsclere nociceptor a sensory receptor which responds to potentially harmful stimuli; produces a sensation of pain nociceptor endogenous rhythm a metabolic or behavioral rhythm that originates within the organism and persists regardless of external conditions endogenous rhythm scattered islands of the central and southern Pacific Ocean roughly between New Zealand in the southwest, Hawaii in the north, and Easter Island in the southeast. The larger islands are volcanic, the smaller ones are generally coral formations Polynesia Polynesia wedge shaped wedge shaped a form that is thick at one edge and tapered to a thin edge at the other a transitional area between two adjacent ecological communities ecotone ecotone tubercle any small, usually hard, knobby excrescence or lump. In pycnogonids and some cheliceramorph arthropods, the central eyes are carried on a tubercle tubercle stakeholder stakeholder an individual or group with an interest in the success of an organization in delivering intended results and maintaining the viability of the organization's products and services. Stakeholders influence programs, products, and services biotechnology biotechnology biological techniques used in applied research research and product development. In particular, the use by industry of recombinant DNA, cell fusion, and new bioprocessing techniques; any technology that is applied to living organisms to make them more valuable to humans the cell cycle phase during which the DNA doubles with replication of the chromosomes S phase S phase the pressure surrounding an organism. On land, it results from the weight of the atmosphere. At depth, it comes from the weight of the water plus the weight of the atmosphere ambient pressure ambient pressure platform reef a large reef of variable shape lacking a lagoon, seaward of a fringing reef and/or a barrier reef, for which the width is more than half its length platform reef diastema diastema a space; a gap Caribbean Coral Reef Institute (CCRI) NOAA's Caribbean Coral Reef Institute (CCRI), inaugurated in May, 2005, is located at the the University of Puerto Rico-Mayaguez. The CCRI focuses exclusively on the acute problems of Caribbean coral reefs. Its main objective is to aid in the management and conservation of Puerto Rico's coral reefs by providing timely, relevant information to the Puerto Rico Department of Natural and Environmental Resources and the scientific community at large. CCRI projects include conducting habitat mapping of the western shelf of Puerto Rico, assessing the status of reef resources, and assessing fishery impacts Caribbean Coral Reef Institute (CCRI) the inhibition of growth of a microorganism by a substance produced by another microorganism antibiosis antibiosis a ciliated larva of echinoderms, such as sea lillies (Crinoidea), some sea cucumbers (Holothuroidea), and brittle stars (Ophiuroidea) vitellaria larva vitellaria larva an assessment of the short-term and long-term costs (losses) and benefits (gains) that arise from an economic decision. If the calculated benefits exceed the calculated costs, the decision to buy an economic good or provide a public good is considered profitable cost-benefit analysis cost-benefit analysis endothecal dissepiment one of many horizontal partitions across the corallite within the corallite wall endothecal dissepiment describes a branch with compact radial sub-branches bottlebrush branching bottlebrush branching server a computer which is designed to be accessed by many other computers. Servers can be attached to local area networks and/or be hooked up to the internet. With the proper software and connections, servers can control the distribution of email, store World Wide Web documents, and provide access to files that are shared by many users server plate like resembling thin, flat sheets of uniform thickness plate like tide tables tide tables tables which give daily predictions of the times and heights of high and low waters. These predictions are usually supplemented by tidal differences and constants through which predictions can be obtained for numerous other locations gastric filaments gastric filaments in scyphozoan medusae, a fringe of short, threadlike filaments whose secretory cells secrete digestive enzymes. They are located on the floor of each gastric pouch pinnacle reef pinnacle reef a nearly cylindrical reef with vertical sides; may be up to 200 m diameter and 50 m in height the fluid, less structured part of the cytoplasm of a cell, excluding organelles and membranous structures; the portion of the cytoplasm which remains after removal of particulate components cytosol cytosol pyrimidine pyrimidine a nitrogen-containing, double-ring, basic compound that occurs in nucleic acids. The pyrimidines in DNA are cytosine and thymine. The pyrimidines in RNA are cytosine and uracil biogenous sediment sediment that is composed of the skeletons and shells of marine organisms, primarily plankton biogenous sediment a DNA sequence that forms the blueprint for the synthesis of a polypeptide, such as an enzyme structural gene structural gene an analytical technique where ions are separated according to their ratio of charge to mass. The atomic weight of the particle can be obtained from the mass spectrum produced mass spectrometry mass spectrometry etiology the science that is concerned with origins and causes of disease etiology coelenteron coelenteron the gastrovascular (digestive) cavity of a cnidarian or ctenophore visualization tool a method of visually displaying data, such as a visualization theater, computer display, and map and chart visualization tool homocercal homocercal a caudal fin with upper and lower lobes that are approximately equal in size; characteristic of most bony fishes noncoding DNA noncoding DNA DNA that does not encode any product (RNA or protein). The majority of the DNA in plants and animals is noncoding an environmental remnant of the past (pollen grains, tree rings, lake sediments, pack rat middens, ice cores, coral skeletons) used to assist researchers in deciphering past climatic conditions paleoenvironmental proxy paleoenvironmental proxy the act of moving, or the ability to move, from place to place locomotion locomotion epilithic epilithic growing on rock or stone. Epilithic organisms live attached to rocks describes a form that is similar to a flower petal petaloid petaloid alluvial alluvial relating to mud and/or sand deposited by flowing water habitat habitat the place or environment where a particular organism, population, or species lives glutinous sticky glutinous Clean Water Act (CWA) Clean Water Act (CWA) an act passed by the U.S. Congress to control water pollution. Growing public awareness and concern for controlling water pollution led to enactment of the Federal Water Pollution Control Act Amendments of 1972. As amended in 1977, this law became commonly known as the Clean Water Act. The Act established the basic structure for regulating discharges of pollutants into the waters of the United States. It gave EPA the authority to implement pollution control programs such as setting wastewater standards for industry. The Clean Water Act also continued requirements to set water quality standards for all contaminants in surface waters. The Act made it unlawful for any person to discharge any pollutant from a point source into navigable waters, unless a permit was obtained under its provisions. It also funded the construction of sewage treatment plants under the construction grants program and recognized the need for planning to address the critical problems posed by nonpoint source pollution the study of the physical, chemical, meteorological and biological aspects of fresh waters limnology limnology GIS (Geographic Information System) a system that allows automatic location of information suitable for mapping. Usually involves a software system that takes geographic position data and other data (e.g., type of bottom sediment) in order to create a map. Data on processes (e.g., current speed) can be incorporated to make a geographic model of flow GIS (Geographic Information System) euryphagous describes an organism which gains its nourishment from a large variety of foods euryphagous progenitor an ancestor or precursor progenitor mesolamella a collagenous layer that separates the choanochambers of hexactinellid sponges (glass sponges) mesolamella the origin and development of disease pathogenesis pathogenesis a small conspicuous constellation in the southern hemisphere in the Milky Way near Centaurus Southern Cross Southern Cross a planktonic larva that gains its nutrition from yolk (semi-crystalline phospholipoprotein granules). In most bony fishes, yolk is supplied by the yolk sac, a bag-like ventral extension of the gut containing yolk granules lecithotrophic larva lecithotrophic larva the outer solid part of the earth, including the crust and uppermost mantle. The lithosphere is about 80-100 km thick, although its thickness is age dependent The lithosphere below the crust is brittle enough at some locations to produce earthquakes by faulting, such as within a subducted oceanic plate lithosphere lithosphere ctenoid comb-shaped; with a comb-like margin ctenoid euryhaline euryhaline pertaining to an aquatic organism that can withstand a broad salinity range undercurrent undercurrent a current below another current, or beneath the surface a specific region of an enzyme where a substrate binds and catalysis takes place active site active site Agnatha agnathans are the most primitive and ancient of the vertebrates. As the name "Agnatha" implies, they lack jaws. Paired fins are also generally absent, and the the adult retains the notochord. The skeleton is cartilaginous. The agnathans include the lampreys and hagfishes Agnatha vitamin B complex a large group of water soluble vitamins that function as co-enzymes vitamin B complex bleaching outbreaks development of bleaching events bleaching outbreaks IKONOS satellite IKONOS satellite high-resolution (1-2 meter resolution) imaging satellite; the world's first commercial satellite for imagery of this type haplotype haplotype a set of closely linked genes that tends to be inherited together as a unit; a particular set of alleles at linked loci that are found together on a single homolog in genetics, one member of a chromosome pair. Homologous chromosomes have corresponding DNA sequences and come from separate parents, i.e., one homolog comes from the maternal parent and the other comes from the paternal parent; in evolution, a characteristic that is similar in different species because it evolved from a common ancestor homolog homolog coral growth line a minute growth line on the outer surfaces of corals that have a calcified outer wall. The carbonate is produced by zooxanthellae which create a series of diurnal growth increments coral growth line phyllopod any of various branchiopod crustaceans having swimming and respiratory appendages that resemble leaves phyllopod an instrument that measures particle size distribution from the change in electrical conductivity as particles flow through a small opening Coulter counter Coulter counter a weight at the bottom of the boat to help keep it stable. Ballast can be placed inside the hull of the boat or externally in a keel. Water picked up as ballast in one location may be released in another, and in doing so, may introduce non-native species ballast ballast respiratory tree respiratory tree a respiratory organ of sea cucumbers (Holothuroidea-Echinodermata) an isotope of a chemical element which is not spontaneously radioactive. Elements can exist in both stable and unstable (radioactive) forms. Most elements of biological interest (including C, H, O, N, and S) have two or more stable isotopes, with the lightest of these present in much greater abundance than the others. Among stable isotopes the most useful as biological tracers are the heavy isotopes of carbon and nitrogen. These two elements are found in the earth, the atmosphere, and all organisms stable isotope stable isotope bioerosion bioerosion erosion of the physical/geological environment by organism activities such as boring, scraping, etching, etc. the rear (back) end of a vessel stern stern bioturbation the rearrangement of sediments by organisms that burrow through them and ingest them bioturbation display in animal behavior, visual messages or body language, used by animals primarily to communicate anger, fear, and other basic emotions. Displays are strong indications of an animal's emotional state display the marine component of the Global Biodiversity Information Facility. It links marine databases around the world to provide an internet accessible, dynamic interface for comparing species level, geo-referenced biodiversity data in relation to ocean habitats. All Census of Marine Life (CoML) field project data will be managed in and accessible through OBIS (www.iobis.org) OBIS (Ocean Biogeographic Information System) OBIS (Ocean Biogeographic Information System) the left side of a vessel to someone facing the bow or front port port biomagnification biomagnification the accumulation and amplification of chemical substances at each succeeding trophic level dextral dextral right, as opposed to sinistral, or left globular globular globe-shaped; having the form of a sphere, or nearly so in statistics, the difference between an actual observation and the mean of all observations deviation deviation pycnogonid pycnogonid pycnogonids, or sea spiders, are benthic, marine arthropods, with a superficial resemblance to true spiders, to which they are probably only distantly related. They are carnivores and use a muscular pharynx to suck soft food into the gut. The mouth is at the end of a large proboscis. Digestion is intracellular and most feed on sponges, cnidarians, or bryozoans from which they suck fluids. There are no excretory organs, respiratory organs, or body cavity (coelom) antibiotic a chemical substance, e.g., penicillin, that kills or inhibits the growth of bacteria antibiotic the relationship of any two characters that have descended from a common ancestor. The term can apply to a morphological structure, a chromosome, an individual gene, or a DNA sequence homology homology oscillator oscillator the internal biological clock mechanism that produces a measurable biological rhythm in an organism a membrane-bound organelle in plant cells that functions in storage (of food or pigments) or food production. Chloroplasts contain the pigments for photosynthesis plastid plastid lobate lobate lobe-shaped a molecule that contains one or more carbon atoms organic molecule organic molecule the description of new taxa or alterations to the concept of previously described taxa which involve changes in the names of taxa nomenclature nomenclature net-like reticulate reticulate catalysis catalysis the acceleration of a chemical reaction by a catalyst. pore water pore water water between the grains of a sediment; also called interstitial water a tubelike structure in the body of a shelled cephalopod, such as the chambered nautilus, extending through the partitions of each chamber of the septate shell; the term is also used to describe tubular structures that direct water flow, or as a feeding siphon of several different kinds of invertebrates siphuncle siphuncle worldwide distribution within habitat limits cosmopolitan distribution cosmopolitan distribution biolimiting relating to the environmental factors determining or restricting the growth of a particular life form biolimiting ovoviviparity the reproductive mode where the eggs hatch and develop in the female's reproductive tract (or a specialized pouch in the males of some species), are not nourished in any way by the female, and are free-swimming when released from the parent ovoviviparity nuchal nuchal pertaining to the neck costa costa the extension of the septa outside the calyx into the coenosteum of a taxon: having living representatives; of a specimen: still in existence extant extant species in sexually reproducing organisms, a species is a group of genetically related organisms, usually similar in physical appearance, that actually or potentially interbreed and are reproductively isolated from other groups species mangal mangal relating to a shoreline ecosystem dominated by mangrove trees, with associated mud flats everything external to the organism environment environment liveaboard a commercial dive boat with sleeping and eating accommodations. Scuba divers live aboard the boat for several days and usually visit dive locations unaccessible to other divers liveaboard a coral which does not have symbiotic zooxanthellae in its tissues azooxanthellate coral azooxanthellate coral blastocyst a preimplantation embryo. The blastocyst consists of a sphere made up of an outer layer of cells (trophectoderm), a fluid-filled cavity (blastocoel), and a cluster of cells on the interior (inner cell mass) blastocyst chlorosis chlorosis the yellowing or bleaching of plant tissues due to the loss of chlorophyll or failure of chlorophyll synthesis. It can be caused by insuffient light or nutrients, and also by certain diseases Reef Check Reef Check a volunteer, community-based monitoring protocol designed to measure the health of coral reefs on a global scale. Reef Check is active in over 60 countries and territories throughout the tropics the process of ovum (egg) development in female animals, in which the diploid number of chromosomes is reduced by half to the haploid number in the ovum oogenesis oogenesis erythrophore a chromatophore which contains reddish pigments found in carotenoids and pteridines erythrophore development the chronological series of changes, from a lower to a higher state of organization, which multicellular organisms undergo from the fertilized egg (zygote) to maturity development in situ in the natural or original position in situ heterochrony a change in the timing of ontogenetic events between two species. These can be the result of relatively small genetic changes between an ancestor and its descendant species heterochrony the science and methodology of classifying organisms based on physical and other similarities. Taxonomists classify all organisms into a hierarchy, and give them standardized Latin or Latinized names. There are seven main levels of classification in the hierarchy. They are, from most to least inclusive: Kingdom; Phylum (or Division for algae, fungi, and plants); Class; Order; Family; Genus; and Species. Taxonomists describe new species, classify organisms, and study speciation, the evolution of new species taxonomy taxonomy thermocline thermocline the region below the surface layer of the ocean or lake, where the temperature gradient increases abruptly (i.e. where temperature decreases rapidly with increasing depth). A thermocline may reach the surface and become a front. It is usually an ecological barrier and its oscillations have significant consequences on population distribution and ocean productivity simultaneous hermaphrodite a form of hermaphroditism where individuals simultaneously possess functional testes and ovaries, and can release either male or female gametes during spawning simultaneous hermaphrodite minute particulate material moving in water that is composed of both living organisms, such as plankton, and non-living matter such as plant debris and suspended soil particles seston seston salt marsh salt marsh a marsh periodically flooded by marine water membranes possessed by amniote (reptiles, birds, and mammals) embryos that allow these classes of vertebrates to be free of aquatic habitats for reproduction, and in their evolution, occupy terrestrial habitats. The membranes are the amnion, yolk sac, allantois and chorion extra-embryonic membrane extra-embryonic membrane the presence of a species (or other taxonomic unit) in two widely separated geographic areas bicentric distribution bicentric distribution radial canal a part of the water vascular system of echinoderms. Specifically, a branch off of the ring canal that leads to an arm (ray) and gives rise to the tube feet. In hydrozoan medusae, the radial canal is part of the gastrovascular cavity. it is one of four extensions leading from the mouth to the outer margin of the bell radial canal stellate star-shaped stellate cement the chemically precipitated calcium carbonate present in spaces within skeletons or between grains of internal sediment cement osmosis osmosis the passage of water through a semipermeable membrane from a solution with a lower concentration of solute to one with a higher concentration of solute in sponges, a cell surrounding a pore (ostium) porocyte porocyte artificial reef artificial reef an artificial structure placed on the ocean floor to provide a hard substrate for sea life to colonize. Artificial reefs are constructed by sinking dense materials, such as old ships and barges, concrete ballasted tire units, concrete and steel demolition debris and dredge rock on the sea floor within designated reef sites translucent or transparent hyaline hyaline key key a small, low coastal island or emergent reef of sand or coral; flat mound of sand and admixed coral fragments built upon a reef flat or just above high tide level. A synonym of cay definitive host in a parasite's life cycle, it is the host organism in which the parasite reproduces sexually definitive host the growing of aquatic organisms in controlled environments for any commercial, recreational, or public purpose; sector of fisheries that includes the rearing or raising under controlled conditions of aquatic products such as fishes, mollusks, crustaceans, sea weeds and other aquatic resources in sea, lakes and rivers. Examples are fish ponds, fish pens, and fish cages. Aquaculture is widespread, and in tropical countries has been a significant source of pollution in coastal waters and also contributes to the destruction of mangrove forests aquaculture aquaculture allotype in taxonomy, a paratype of the opposite sex to the holotype allotype allochthonous population an organism or a population of organisms foreign to a given ecosystem; they have arrived from elsewhere allochthonous population a phylum of marine invertebrates that superficially resemble bivalve mollusks because of their hinged bilaterally symmetrical shells.They are commonly known as "lampshells" Brachiopoda Brachiopoda zonate divided by parallel planes, e.g., zonate tetraspores, found in certain species of red algae zonate dive table dive tables present dive times for specific depths, adherence to which, the scuba diver can avoid contracting decompression sickness (the bends). The theory behind dive tables is based on our understanding of how nitrogen is taken up on compression (descent) and given off on decompression (ascent). The first dive tables were devised by John S. Haldane in the period 1906-1908 dive table allelopathic substance allelopathic substance a substance produced by one organism that adversely affects another organism blastomere an undifferentiated cell of a cleaving embryo, and of the morula and blastula stages of embryonic development blastomere shore reef shore reef a synonym of fringing reef NOAA and the Florida Institute of Oceanography (FIO) supply daily and historical enhanced Coastal-Marine Automated Network (C-MAN) data via the SEAKEYS program. Since 1992, SEAKEYS has provided hourly data from up to seven meteorological and oceanographic monitoring stations situated throughout the Florida Keys National Marine Sanctuary and Florida Bay. These stations measure the usual C-MAN meteorological parameters, such as wind speed, gusts and barometric pressure, but are enhanced with oceanographic instruments measuring salinity, sea temperature, fluorometry and turbidity These data are collected and presented via email and the Web daily, and are supplied through a historical database on the Web. Unique software developed for SEAKEYS data operates in near real-time and provides alerts as to conditions conducive to natural events such as coral bleaching (Coral Reef Early Warning System [CREWS]), larval conch survival, and in the future, harmful algal blooms SEAKEYS SEAKEYS developmental response morphological and physiological characteristics an organism developed in response to prolonged exposure to environmental conditions developmental response contour interval the difference in surface values between contours contour interval the kingdom of multicellular heterotrophic eukaryotes that are capable of motility during some stage of their life history Animalia Animalia diatomaceous pertaining to diatoms or their fossil remains diatomaceous bathymetry the science of measuring ocean depths to determine the topography of the sea floor bathymetry linear regression linear regression regression in which the relationship is linear stomadaeum the pharynx in anthozoans; foregut of higher animals; the anterior or oral portion of the alimentary canal of an embryo stomadaeum an organism that utilizes oxidation of inorganic chemicals for its energy and carbon from inorganic carbon dioxide for cell growth; these organisms are also called chemolithotrophs chemoautotroph chemoautotroph the direction towards center of the body; opposite of distal proximal proximal a coral colony that is solid and typically hemispherical in shape massive colony massive colony carposporophyte carposporophyte the diploid stage of red algae which develops after fertilization of the carpogonium hydrology hydrology the science dealing with the properties, distribution and circulation of water and snow basilar basilar forming a foundation paresthesia abnormal neurological sensations which include: numbness, tingling, burning, prickling and hyperesthesia (increased sensitivity); one possible symptom of ciguatera poisoning paresthesia stiff hairs bristles bristles gill gill a highly vascularized respiratory organ with a large surface area in aquatic animals. Gills are in direct contact with the surrounding water for gas exchange dactylozooid a colonial hydrozoan polyp that possesses a large, nematocyst-bearing fishing tentacle, and functions in defense and in food capture dactylozooid the cycling of carbon in the form of carbon dioxide, carbonates, organic compounds, etc., between various reservoirs, e.g., the atmosphere, the oceans, land and marine biota and, on geological time scales, sediments and rocks carbon cycle carbon cycle str (short tandem repeats) str (short tandem repeats) repetitive segments of DNA of a pattern of length from 2 to 10 bp, scattered throughout the genome in the non-coding regions between genes or within genes (introns), often used as markers for linkage analysis because of high variability in repeat number between individuals. These regions are inherently unstable and susceptible to mutations daughter cell daughter cell one of the two cells formed by the division of a parent cell shoal shoal a submerged expanse of coral reef, surrounded by deep water, which does not form a part of a barrier or fringing reef cleavage where the fate of the resulting daughter cells is not determined after the initial divisionof a fertilized egg. If the cells separate, each has the potential to develop into an entire organism and the resulting individuals are genetically identical (identical twins). Inderterminate cleavage is characteristic of deuterostomes indeterminate cleavage indeterminate cleavage genes that are so closely associated on a chromosome that the allelic forms found on a chromosome are inherited together by an offspring at least 80 percent or more of the time linked genes linked genes small vesicles and pores around the head of a shark that form part of an extensive subcutaneous sensory network system that detects weak magnetic fields produced by other fishes, at least over short ranges. This enables the shark to locate prey that are buried in the sand, or orient to nearby movement. The ampullae may also allow the shark to detect changes in water temperature ampullae of Lorenzini ampullae of Lorenzini polyclad flatworm a free-living flatworm belonging to the order Polycladida (Class Turbellaria; Phylum Platyhelminthes). Many species are coral reef inhabitants polyclad flatworm the separation of one cell into two daughter cells, involving both nuclear division (karyokinesis) and subsequent cytoplasmic division (cytokinesis). Genetically, the daughter cells are identical to the mother cell (mitosis); however, in gametogenesis (meiosis), the resultant daughter cells (gametes) have the chromosome number reduced by one-half cell division cell division caridean shrimp caridean shrimp caridean shrimps can be distinguished from other shrimp-like creatures by the way in which the plate of the second abdominal segment overlaps the segments both in front and behind, forming a saddle. They are found in marine, brackish and freshwater habitats from the tropics to the polar regions. Carideans are taxonomically and ecologically diverse, with many remarkable adaptations for survival and reproduction.These crustaceans are placed in the infraorder Caridea, order Decapoda, and class Malacostraca a type of hydrocarbon, such as benzene or toluene, with a specific type of ring structure aromatic aromatic a highly developed chewing apparatus used for feeding in some sea urchins Aristotle's lantern Aristotle's lantern the relation that exists when things occur at the same time synchrony synchrony a single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle single-stranded DNA single-stranded DNA gonophore a sexual zooid produced as a medusa bud upon a hydroid, sometimes becoming a free hydromedusa and sometimes remaining attached gonophore interspecific between members of different species interspecific inquilinism a symbiotic association in which one symbiont lives in close association with another, generally in its shell, tube or burrow, or actually within a body cavity of the host inquilinism gonotheca a thin membrane covering the body of a gonangium, the reproductive polyp of a colonial hydrozoan gonotheca those wavelengths of light that can be absorbed by chlorophyll or other light harvesting pigments PAR (Photosynthetically Active Radiation) PAR (Photosynthetically Active Radiation) maternal mRNA maternal mRNA messenger RNA found in oocytes and early embryos that is derived from the maternal genome during oogenesis shoal (biol.) shoal (biol.) a social group of fishes of the same species that are not always similar in size or equal in social status. The shoal does not usually move in a highly coordinated fashion, as does a school. Shoals are typically found in shallow water or at the surface. Some consider shoals to be schools in shallow water benchmark benchmark a measurement or standard that serves as a point of reference by which process performance is measured sex chromosome sex chromosome a heteromorphic chromosome that plays a role in sex determination, such as the X and Y chromosomes, whose distribution in a zygote determines the sex of the organism; a chromosome whose DNA determines sexual characteristics in females (X)-and males (Y) a bacterium with a spherical shape coccus coccus pertains to an organism that inhabits the empty living space or shell of another organism xenoecic xenoecic a fingerlike projection from a gill arch through which respiratory gases enter and leave the blood gill filament gill filament the strand of duplex DNA which contains the same base sequence (after substituting Uracil for Thymine) found in the mRNA molecule resulting from transcription of that segment of DNA., known as the sense strand. The mRNA molecule is transcribed from the other strand, known as the template or antisense strand coding strand coding strand a traditional Hawaiian place of worship; a religious shrine heiau heiau united by means of a moveable joint articulating articulating intermediate form a fossil or modern species that possesses characters definitive of two or more different taxa, or that displays characters morphologically intermediate between two different taxa intermediate form androgenesis male parthenogenesis, i.e., the development of a haploid embryo from a male nucleus. The maternal nucleus is eliminated or inactivated subsequent to fertilization of the ovum, and the haploid individual (referred to as androgenetic) contains the genome of the male gamete only in its cells androgenesis reproduction or duplication; in genetics, the synthesis of duplex (double-stranded) DNA by copying from a single-stranded template, i.e., the synthesis of an informationally identical macromolecule from a template molecule replication replication the pressure exerted by a single component of a gas within a gas mixture, or dissolved in a liquid partial pressure partial pressure pelvic fin pelvic fin the paired fin located ventrally beneath, in front of, or behind, the pectoral fin the ventral plate (or sclerite) of each segment of the body of an arthropod sternite sternite abaxial away from, or distant from the axis abaxial Chondrichthyes the class of cartilaginous fishes that includes sharks, rays, skates, and chimaeras. Their skeleton is composed of cartilage, not bone Chondrichthyes ArcIMS ArcIMS ESRI software that allows for centrally hosting and serving GIS maps, data, and applications for use on the Internet analytical procedures for the determination of the sequential order of amino acids in a polypeptide chain or nucleotides in a DNA or RNA molecule sequencing sequencing the establishment of a population, species or other taxonomic unit in several widely separated geographic places polycentric distribution polycentric distribution the time it takes the Earth to make one orbit around the Sun; approximately 365.2422 days solar year solar year habitat distribution habitat distribution the structure and spatial characterization of all habitat types in a specified area the functional and physical unit of heredity passed from parent to offspring. Genes are pieces of DNA, and most genes contain the information for making a specific protein gene gene having two margins which are toothed, like a comb; descriptive of the gills (ctenidia) of aquatic mollusks bipectinate bipectinate the return of an ecosystem or habitat to its original community structure, natural complement of species, and natural function restoration restoration motile motile capable of self-locomotion in organisms the study of sickness, injuries and other abnormalities in the health of ancient organisms paleopathology paleopathology sustainable development sustainable development those efforts to guide economic growth in an environmentally sound manner with an emphasis on natural resource conservation terminal terminal at the end position cross cross in genetics, the mating of two individuals or populations the Flower Garden Banks National Marine Sanctuary was designated as a national marine sanctuary on January 17, 1992. The sanctuary is located about 110 miles off the coasts of Texas and Louisiana, and harbors the northernmost coral reefs in the United States and serves as a regional reservoir of shallow water Caribbean reef fishes and invertebrates. The coral reefs rise to within 66 feet of the surface. The area containing both the East and West Banks is 41.7 square nautical miles in size and contains 350 acres of reef crest. In October 1996, Congress expanded the sanctuary by adding a small third bank, Stetson Bank, located about 70 nautical miles south of Galveston, Texas. Environmental conditions at Stetson Bank do not support the establishment and growth of coral reefs Flower Garden Banks National Marine Sanctuary Flower Garden Banks National Marine Sanctuary captaculum captaculum a filamentous tactile organ with an adhesive, sucker-like end near mouth of a tusk shell (mollusks in the class Scaphopoda).The captacula are used to gather small particles of food in the sand and pass them to the mouth a discarded material which contains substances known to be toxic, mutagenic, carcinogenic, or teratogenic to humans or other life; ignitable, corrosive, explosive, or highly reactive alone or with other materials hazardous waste hazardous waste chiton a marine mollusk of the Subclass Polyplacophora, which contains about 600 species of sedentary animals commonly known as chitons.They are found from shallow waters to depths of about 400 m. A chiton has a broad foot and a shell consisting of eight overlapping plates chiton a blue, water soluble pigment found in red algae and cyanobacteria phycocyanin phycocyanin restriction fragment a fragment of DNA produced by cleaving (digesting, cutting) a DNA molecule with one or more restriction endonucleases restriction fragment Kure Atoll the most remote of the Northwestern Hawaiian Islands, and the northern-most coral atoll in the world, located at the extreme northwest end of the Hawaiian archipelago. The atoll has almost 80,000 acres of coral reef habitat with 28 species of stony corals so far documented. Kure Atoll is an important pupping and resting area for Hawaiian Monk seals. The island is also a nesting area for smany species of sea birds, and a wintering area for a variety of migratory bird species from North America and Asia Kure Atoll cloning cloning the process of asexual reproduction in an otherwise multicellular organism plague (white plague disease) plague (white plague disease) a coral disease characterized by a sharp line between apparently healthy coral tissue and freshly exposed coral skeleton.-There is no obvious microbial band present.-The infective pathogen is a bacterium. Plague is currently epidemic throughout the Caribbean, and affects stony corals. For more information and illustrations, see: http://www.coral.noaa.gov/coral_disease/white_plague.shtml regulatory gene a gene that acts to control the protein-synthesizing activity of other genes; also called a 'regulator gene' regulatory gene in sponges, a surface lined with endopinacocytes endopinacoderm endopinacoderm Fagatele Bay National Marine Sanctuary Fagatele Bay, located on Tutuila, the largest island of American Samoa, was designated as a National Marine Sanctuary in 1986. It is the smallest and most remote of all the national marine sanctuaries encompassing only 163 acres (.25 sq. mi.). Fagatele is the only true tropical coral reef in the National Marine Sanctuaries Program Fagatele Bay National Marine Sanctuary metric system a decimal system of measures and weights with the meter and the gram as bases metric system necrolysis necrolysis the decomposition of an organism's body after it dies hard coral hard coral a coral in the anthozoan order Scleractinia. Also known as the stony corals, these organisms possess a hard external calcareous skeleton. A synonym of stony coral the posterior opening of the intestine, gonads, and kidney ducts. The vent is located just anterior to the anal fin in fishes vent vent sclerodermite the basic unit of coral skeletal microstructure. A center of calcification from which bundles of acicular aragonite crystals radiate outward; the hard integument of Crustacea. sclerodermite proliferation to reproduce or increase rapidly and repeatedly proliferation the most anterior of three coelomic spaces that appear during larval development of echinoderms axocoel axocoel conspicuous warning coloration aposematism aposematism gestation period gestation period the period of development of the young in viviparous animals, from the time of zygote formation (fertilization) until birth pandemic an epidemic that is geographically widespread; occurring throughout a region or even throughout the world pandemic plate tectonics plate tectonics the theory that the Earth's lithosphere consists of large, rigid plates that move horizontally in response to the flow of the asthenosphere beneath them, and that interactions among the plates at their borders cause most major geologic activity, including the creation of oceans, continents, mountains, volcanoes, and earthquakes the process of formation of specific organs in a plant or animal involving morphogenesis and differentiation organogenesis organogenesis the sequence of events whereby embryos develop from somatic cells asexual embryogenesis asexual embryogenesis calcareous ooze a biogenous sediment that is made of the calcium carbonate shells and skeletons of marine organisms calcareous ooze a small antenna, especially the first pair of antennae in crustaceans antennule antennule ester ester a chemical compound formed by the reaction of an organic or inorganic acid with an alcohol, with the elimination of water a form of reproduction where the offspring are nourished in the reproductive tract of the female (other than by a yolk sac) and then expelled from the mother as free-swimming young. Mangrove reproduction by means of propagules is also a form of viviparity in plants viviparity viviparity mouthparts mouthparts a collective term for the appendages around the mouth of crustaceans which are concerned with feeding: mandibles, maxillae and maxillipeds a taxonomic group containing one or more genera family family Weberian apparatus Weberian apparatus the four anterior vertebrae and associated tissues in some fishes (catfishes, loaches, minnows, suckers) that connect the gas bladder to the inner ear, conveying pressure changes and sound the organ-pipe coral, Tubipora musica, is a reef-building (hermatypic) octocoral organ-pipe coral organ-pipe coral isotope isotope one of two or more species of atoms of the same chemical element that have the same atomic number and occupy the same position in the periodic table. They are nearly identical in chemical behavior, but they differ in atomic mass or mass number. Therefore, they behave differently in the mass spectrograph, in radioactive transformations, and in physical properties, and may be separated or detected by means of these differences to check or adjust the graduations of a quantitative measuring instrument calibrate calibrate brood all of the offspring that hatch from a single clutch of eggs or the offspring of a single birth; to incubate eggs brood Fungi the Kingdom of usually multicellular, heterotrophic eukaryotes that have multinucleated cells enclosed within cell walls. Nutrition is obtained by decomposing dead and dying organisms and absorbing the decomposition products Fungi setose bearing setae setose in taxonomy, the relationships between different names applied to the same taxon; a chronological list of taxonomic names which have been applied to a single taxon, including authors and dates synonymy synonymy immersed corallite a corallite that is embedded in the surrounding coenosteum immersed corallite centrolecithal a type of egg cell that has its yolk in the very center of the cytoplasm, such that the initial meroblastic cleavage of the zygote happens all around the embryo. Most arthropods have centrolecithal eggs centrolecithal gene mapping gene mapping determination of the relative locations of genes on a chromosome a contractile, collagen-secreting amoebocyte in sponges collencytes collencytes baseline data baseline data a quantitative level or value from which other data and observations of a comparable nature are referenced polysaccharide any of a class of carbohydrates whose molecules contain chains of monosaccharide molecules - polysaccharide vegetal coloration a resemblance to vegetation which allows organisms to conceal themselves from predators or prey vegetal coloration common ancestor the most recent ancestral form or species from which two different species evolved common ancestor ATPase ATPase an enzyme that functions in producing or using adenosine triphosphate (ATP) sea cow sea cow a large, herbivorous aquatic mammal of the order Sirenia that contains two Recent families: Dugongidae for the genera Dugong (dugong, one species) and Hydrodamalis (Steller's sea cow, one species hunted to extinction); and Trichechidae for the single genus Trichechus (manatees, three species). The dugong inhabits coastal regions in the tropical parts of the Old World, and some individuals go into estuaries and rivers. Steller's sea cow inhabited the Bering Sea, and was the only Recent member of this order adapted to cold waters. Manatees live along the coast and in coastal rivers in the southeastern United States, Central America, the West Indies, northern South America, and western Africa basket star basket star a basket star is a specialized type of brittle star (Echinodermata). It has a series of complexly branched arms which are used to capture plankton gradualism a model of evolution that assumes slow, steady rates of change, as contrasted with punctuated equilibrium, an evolutionary model in which change occurs in relatively rapid bursts gradualism Content Standard for Digital Geospatial Metadata Content Standard for Digital Geospatial Metadata provides a common set of terminology and definitions for the documentation of digital geospatial data. The standard establishes the names of data elements and compound elements (groups of data elements) to be used for these purposes, the definitions of these compound elements and data elements, and information about the values that are to be provided for the data elements Mammalia a class of warm blooded animals (mammals) whose common characteristics include the presence of hair, milk-secreting glands, a muscular diaphragm between the abdominal and pleural and mediastinal cavities, a lower jaw composed of a single pair of bones, a middle ear containing three bones, and the presence of only a left systemic arch Mammalia phycoerythrin a red, water soluble pigment found in red algae and cyanobacteria phycoerythrin RACE (Rapid Amplification of cDNA Ends) RACE (Rapid Amplification of cDNA Ends) a technique used to obtain the 3' and 5' end of a cDNA. The technique involves three sequential enzymatioc steps: reverse transcription, addition of homopolymeric tails, and polymerase chain reaction (PCR) arterial gas embolism arterial gas embolism a hazardous condition for scuba divers that is characterized by air bubbles released from ruptured lung air pockets (alveoli) into the pulmonary circulation. The bubbles then travel to the arterial circulation, where they may block blood flow in the small arteries or capillaries of the brain or heart. The results may be fatal. Arterial gas embolism in divers may be caused by holding one's breath during an ascent, wherein the lungs expand to the danger point a cell whose cytoplasm contains pigment granules that can be rapidly concentrated or dispersed, producing an overall effect of altering the color, color pattern or tone of the whole or part of an animal chromatophore chromatophore the nonliving particulate matter in bodies of water tripton tripton poacher a person who hunts or fishes illegally; a family (Agonidae) of small bottom-dwelling cold-water marine fishes poacher an instrument that detects infrared radiation and converts the detected energy to an electrical signal for recording on another medium infrared scanner infrared scanner RNA (Ribonucleic acid) a single-stranded nucleic acid found in the nucleus and cytoplasm of a cell. It is a polymer of the sugar ribose, phosphate, purine and pyrimidine bases. RNA is very similar to DNA, but substitutes the nucleotide, uracil, for thymine. It acts as a "middle-man", converting genetic information from DNA to proteins. There are three types of RNA: mRNA (messenger RNA), which contains the specific sequence of nucleotides necessary to dictate amino acid sequence in proteins; tRNA (transfer RNA), which serves as the "adaptor" to position the appropriate amino acid next to a growing polypeptide chain during protein synthesis; and rRNA (ribosomal RNA), which is the RNA component of ribosomes. In some viruses, RNA is the genetic material RNA (Ribonucleic acid) photophilous photophilous thriving in conditions of strong light water table the level or depth below the ground that is saturated with water water table the level below the earth's surface at which the ground becomes saturated with water. The water table is set where hydrostatic pressure equals atmospheric pressure; the surface between phreatic water which completely fills voids in the rock and ground air which partially fills higher voids foliaceous leaf-like; also foliose foliaceous a synonym of hard coral stony coral stony coral uniramous appendage uniramous appendage a type of appendage that is characteristic of insects and other members of the arthropod subphylum Uniramia. It consists of an unbranched series of segments heliox heliox a breathing gas mixture for scuba divers that contains only oxygen and helium, used for deep diving to remove the narcotic effect of nitrogen androgen androgen a principal male steroid hormone, such as testosterone, which stimulates the development and maintenance of the male reproductive system and secondary male sexual characteristics extirpated species a species that has been destroyed or removed completely from a particular area, region, or habitat extirpated species supergene a group of neighboring genes on a chromosome that tend to be inherited together and sometimes are functionally related supergene sporangium an organ containing or producing spores in some algae and fungi sporangium the evolutionary termination of a species caused by the failure to reproduce and the death of all remaining members of the species; the natural failure to adapt to environmental change extinction extinction geo-referenced data refers to data with geographic location information included, such as latitude and longitude geo-referenced data distinct clearly defined and easily recognized distinct attached to the scuba tank, the first stage regulator reduces the high tank pressure to an intermediate pressure of 100 to 150 psi above the surrounding water pressure first stage regulator first stage regulator PowerPoint: a program in the Microsoft Office suite which allows users to create presentations and handouts. By creating PowerPoint "slides," users can add color, images, sounds, and movies to their text presentations PowerPoint: the discontinuous or separated geographical distribution of a species or other taxonomic unit disjunct distribution disjunct distribution flora flora the entire group of plants found in an area isthmus a narrow strip of land connecting two larger land masses, such as the isthmus of Panama isthmus the location of a gene on a genetic map, deduced from recombination frequencies genetic map position genetic map position stromatolite a layered, fossilized deposit, mainly of limestone, formed by photosynthesizing colonial cyanobacteria and other microbes. They are the oldest known fossils, dating back more than 3 billion years. Stromatolites are prokaryotes that thrived in warm aquatic environments and built reefs much the same way as coral does today. They were common in Precambrian time (i.e., more than 540 million years ago). Although stromatolites continue to form in certain areas of the world today, they grow in greatest abundance in Shark Bay in western Australia stromatolite pyramid of energy pyramid of energy in ecology, the total energy content of all organisms at each trophic level in a food chain; the energy content declines at successively higher trophic levels intromittent organ intromittent organ a copulatory structure employed by the males of species that practice internal fertilization to transfer sperm cells into the reproductive tube of the female, e.g., the clasper of a shark, skate or ray; penis; modified anal fin (gonopodium) of live-bearer fishes radiant flux the rate of flow of radiant energy (electromagnetic waves) radiant flux activator activator a substance or physical agent that stimulates transcription of a specific gene or operon water column water column the water mass between the surface and the bottom aciculate aciculate needle-like or having needle-like parts a bluish, copper-containing respiratory pigment with an oxygen-carrying function similar to that of hemoglobin that is present in the blood of certain mollusks and arthropods hemocyanin hemocyanin an organism that feeds by capturing particles suspended in the water column. A synonym of filter feeder suspension feeder suspension feeder effluent effluent a discharge of pollutants into the environment, partially or completely treated or in its natural state. Generally used in regard to discharges into waters; in contrast to an emmission, which is generally used in regard to discharges of pollutants into the air carboxyl group the -COOH functional group, acidic in nature, found in all amino acids; the acid group of organic molecules carboxyl group siphonophore siphonophores are "colonial jellyfish" which have swimming bells at the top, and tentacles with stinging cells below that help them to catch their prey. Each individual of the colony is specialized for a different function, such as swimming, feeding and reproduction. Some siphonophores can be more than 10 meters long. They are in the phylum Cnidaria, class Hydrozoa and order Siphonophora siphonophore in response to the dramatic increase of coral diseases observed over recent years, the U.S. Coral Reef task force (2002) recommended the creation of the CDHC from a cross-section of internationally recognized experts in coral diseases, biomedical and veterinary sciences, pathology, chemistry, biology, biotechnology, and marine management. It organizes and coordinates the scientific resources of the U.S. and its territories to meet the challenge of globally declining coral reefs CDHC (Coral Disease and Health Consortium) CDHC (Coral Disease and Health Consortium) all multicellular animals excluding the sponges eumetazoa eumetazoa video transect a nondestructive, repeatable procedure for assessing and monitoring diurnally active fishes and other macroscopic marine organisms. Videotaping along a linear transect reduces the variance in error inherent with visual observations made by a diver or snorkeler, and allows virtually unlimited time for study of the images by many individuals video transect zooecium the skeleton of a bryozoan zooid zooecium communication network telecommunications infrastructure that transfers data from observing systems to data centers, and then to end users communication network regression line regression line a line fit to a set of data points (scatterplot) using least-squares regression; a graph of the mathematical relationship between two variables a group or network of intersecting nerves and/or blood vessels plexus plexus ctenidium a comb-like structure; the respiratory organ of a mollusk (ctenidial gill) ctenidium any segment of embryonic mesoderm that develops into skeletal (voluntary) muscle in the adult; any of the segmentally arranged blocks of muscle in lower vertebrates, such as fishes myotome myotome brachy- a prefix from the Greek, meaning "short" brachy- basic research research conducted with the sole goal of obtaining knowledge; in contrast with applied research basic research nucleic acid isolation nucleic acid isolation a prerequisite for molecular genetic studies is, by definition, the ability to isolate nucleic acids (DNA and RNA) classification a system of nested hierarchical categories used to efficiently store information about biological diversity classification a corallite on a side of a branch as opposed to an axial corallite on the tip of the branch radial corallite radial corallite vegetal hemisphere the half of an oocyte or egg with more yolk, or the corresponding half of an early embryo with the slower dividing yolk-laden cells vegetal hemisphere outer slope a synonym of reef slope. It is sometimes used to represent the lower reef slope outer slope wild type the form of an organism that occurs most frequently in nature wild type five prime and three prime ends (5' and 3' ends) five prime and three prime ends (5' and 3' ends) a double stranded DNA (the double helix) always has an orientation or directionality. Because of this directionality, the nucleotides along one strand are heading in one direction (e.g. the 'ascending strand') and the others are heading the other (e.g. the 'descending strand'). For reasons of chemical nomenclature, the asymmetric termini of each strand are called the 5' and 3' ends (pronounced "five prime" and "three prime"). Nucleotide sequences are read by enzymes in the "5' to 3' direction". In a vertically oriented double helix, the 3' strand is said to be ascending while the 5' strand is said to be descending a nonspecific term for small organisms that can be seen only with the aid of a microscope. The term encompasses viruses, bacteria, yeasts, molds,and protists. The term, however, is used most frequently in refererence to bacteria microbe microbe chi-square test chi-square test a statistical test based on the comparison of a test statistic to a chi-square distribution. It is used to reject or not reject the hypothesis that two or more population distributions do not differ from one another nacre the irridescent innermost layer of a molluscan shell that is secreted by the mantle. It is also called the mother-of-pearl layer nacre endosymbiont endosymbiont an organism which lives within the body of another organism as part of a symbiotic relationship. The relationship may be mutualistic or commensalistic; also called an 'endobiont' vertebrate an animal that possesses a vertebral column (back bone), such as fishes, amphibians, reptiles, birds and mammals vertebrate surface interval surface interval the length of time that a scuba diver spends on the surface between two consecutive dives a document used by an organization to align its organization and budget structure with organizational priorities, missions, and objectives. A strategic plan should include a mission statement, a description of the agency's long-term goals and objectives, and strategies or means the agency plans to use to achieve these general goals and objectives strategic plan strategic plan any of several light-colored burrowing crabs of the genus Ocypoda frequenting the tide line along sandy shores from the northeast United States to Brazil. Ghost Crabs have a relatively thin, light exoskeleton and two large black eyes that stand up like periscopes. They are called ghosts because of their ability to instantly disappear from sight, moving at speeds at speeds up to 10 miles per hour, while making sharp directional change and disappearing into their burrows ghost crab ghost crab incurrent canal in sponges, an inpocket of the epidermis (pinacoderm) which opens into a choanocyte chamber via a small opening, the prosopyle incurrent canal all of the changes that occur to a deposited sediment during its conversion to rock; includes changes that result from chemical, physical as well as biological processes diagenesis diagenesis conjugation a process of sexual reproduction whereby two cells come in contact and exchange genetic material. In prokaryotes and unicellular agae, the transfer is a one-way process. The union of two bacterial cells, during which chromosomal material is transferred from the donor to the recipient cell. Conjugation in protozoans is a two-way process, genetic material is passed between each conjugant conjugation accuracy the closeness by which a set of measurements approaches the true value accuracy corrugated corrugated having a surface with alternating parallel ridges and grooves an animal phylum containing four classes of flatworms. Three are parasitic (tapeworms, flukes) and one, the Turbellaria, is free-living and contains coral reef inhabiting species Platyhelminthes Platyhelminthes yeast a single-celled fungus that reproduces by budding yeast gonozooid a reproductive polyp of a colonial hydrozoan gonozooid clone clone an individual genetically identical to the parent organism, created by the splitting off or budding of cells from the parent organism a taxonomic group containing one or more species genus genus an aggregate of colloidal droplets held together by electrostatic forces. Coacervate droplets may contain a mixture of organic compounds. One theory of the evolution of life is that the formation of coacervates in the primeval soup was a step towards the development of cells coacervate coacervate zoea zoea a free-swimming larval stage of various crustaceans double helix double helix the normal structural configuration of DNA consisting of two helices winding about the same axis. The structure of DNA was first proposed by Watson and Crick (1953) with two interlocking helices joined by hydrogen bonds between paired bases a polygynous mating system where a number of males aggregate at a particular site during the breeding period and engage in courtship behavior, especially displays. Females attracted to the site "select " males for mating and subsequent fertilization of eggs. Once mated, the females usually go elsewhere to lay their eggs or to complete gestation. Lekking behavior (also called arena behavior) has been observed among cuttlefish, fishes, birds, antelope, and insects. Lekking species tend to stay at a single lek throughout a breeding season and to return to the same lek site from breeding period to breeding period lek lek nutrient regeneration the release of nutrients from organic matter by decomposer organisms nutrient regeneration flabellate fan-shaped flabellate ecological species ecological species a concept of species, in which a species is a set of organisms adapted to a particular ecological niche ancestor any organism, population, or species from which some other organism, population, or species is descended ancestor region in which the climate undergoes seasonal change in temperature and moisture. Temperate regions of the earth lie primarily between 30 and 60 degrees latitude in both hemispheres temperate temperate ocellus ocellus an eye-like spot, usually surrounded with a ring of a lighter color, e.g. the ocellus toward the caudal peduncle of some butterflyfish. It may function to deflect attacks to the eyes in agonistic encounters.Ocelli are also present in other animal groups, especially insects open circulatory system open circulatory system a circulatory system, characteristic of some invertebrates, e.g., arthropods, in which blood flows through an interconnected system of open sinuses rather than blood vessels. The tissues and cells are directly bathed by the blood for gaseous exchange and nutrient uptake. The circulatory fluid is called the hemolymph the collection of information about an object or event without being in physical contact with the object or event. Remote sensing is restricted to methods that record the electromagnetic radiation reflected or radiated from an object, which excludes magnetic and gravity surveys that record force fields remote sensing remote sensing guano guano the manure of birds and bats that is often used as fertilizer catenation catenation linking of multiple copies of a macromolecule to each other a method for differential staining of bacteria; Gram-positive cells stain purple-black and Gram-negative cells stain pink; useful in bacterial taxonomy and identification Gram's stain Gram's stain a mathematical index of species diversity within a community diversity index diversity index the outer germ layer of cells in an embryo that gives rise to the outer layer of skin (epidermis) and neural tissue ectoderm ectoderm umbrella umbrella describes the body of a jellyfish or medusa the area comprising the reef flat and reef crest reef top reef top a method of structuring data as collections of tables that are logically associated to each other by shared attributes. Any data element can be found in a relation by knowing the name of the table, the attribute (column) name, and the value of the primary key relational database relational database alternative hypothesis alternative hypothesis in statistics, the hypothesis that is adopted when the null hypothesis is rejected the central body cavity of sponges, which opens to the outside by way of the osculum. spongocoel spongocoel a NOAA program whose mission is to provide services to help improve and sustain coral reef health throughout the world. Long term goals are: establish an international network of coral reef researchers for the purpose of sharing knowledge and information on coral health and monitoring; provide near real-time data products derived from satellite images and monitoring stations at coral reef areas; provide a data repository for historical data collected from coral reef areas; and add to the general fund of coral reef knowledge CHAMP (Coral Health And Monitoring Program ) CHAMP (Coral Health And Monitoring Program ) c-card c-card a scuba diving certification card from scuba certifying agencies, such as NAUI, BSAC, NOAA, PADI, etc. a coral that lacks zooxanthellae and does not build reefs ahermatypic coral ahermatypic coral mutualistic behavior in which larger animals, usually fishes, permit smaller animals, usually other species of fishes or invertebrates, to clean them of external parasites cleaning behavior cleaning behavior electromagnetic receptor electromagnetic receptor a neurological receptor that responds to light, electricity, and magnetism. Photoreceptors respond to light and electroreceptors detect electrical energy imbricate with overlapping parts, such as scales imbricate axial axial refers to the head and trunk of an individual a root that originates from any part of the plant other than the root system adventitious root adventitious root animated GIF (Graphics Interchange Format) file animated GIF (Graphics Interchange Format) file a graphic image on a Web page that moves tritoniid a member of a family of nudibranchs (Tritoniidae) which feed on soft corals, gorgonians, and other anthozoans. A characteristic common to the tritoniids are the dorsilateral branched cerata, used as gills and located in the edges of the dorsal surface tritoniid iridiophore iridiophore a colorless chromatophore which contains purines, mostly guanine in the form of large, nonmotile crystals microbiota organisms which are invisible, or nearly so, to the naked eye microbiota surf surf a collective term for "breakers"; the wave activity in the area between the shore line and the outermost limit of breakers. In literature, surf usually refers to the breaking waves on shore and on reefs saprotroph an organism which feeds on dead and decaying organisms, allowing the nutrients to be recycled into the ecosystem. Fungi and bacteria are two groups with saprophytic members saprotroph a basket-like structure formed midventrally by overlapping branchiostegals in some families of eels jugostegalia jugostegalia a species that is disproportionately important in the maintenance and balance of its community integrity keystone species keystone species peptide two or more amino acids joined by a peptide bond peptide split spawning spawning occurring over consecutive nights or consecutive lunar cycles within a reef split spawning hookah hookah "hookah" refers to diving where the diver is supplied with breathable air from the surface via an air compressor and an airline (hose). This type of diving is ideal for shallow water commercial applications long term monitoring the repeated surveying of organisms, populations, communities, or environmental parameters over time to help us understand a variety of natural processes long term monitoring photosynthetic pigment photosynthetic pigment a pigment that efficiently absorbs light within the 400-700 nm range and is essential for photosynthesis magmatic hotspot in geology, a hotspot is a location on the Earth's surface that has had volcanism for a long period of time. Geologists have identified some 40-50 such hotspots magmatic hotspot that period of tide between a high water and the succeeding low water; falling tide ebb tide ebb tide transforming gene transforming gene a gene that causes normal cells to change into cancerous tumor cells; also called an 'oncogene' coral product any living or dead specimens, parts, or derivatives, or any product containing specimens, parts, or derivatives, of any species of coral in the cnidarian Orders: Antipatharia (black corals), Scleractinia (stony corals), Gorgonacea (horny corals), Stolonifera (organpipe corals and others), Alcyanacea (soft corals), and Coenothecalia (blue coral), of the Class Anthozoa; and all species of the Order Hydrocorallina (fire corals and hydrocorals) of the Class Hydrozoa coral product milt milt the testes of fishes when filled with semen; fish seminal fluid prostrate colony a coral colony which sprawls horizontally over the substrate prostrate colony infection of a cell with nucleic acid from a virus, resulting in replication of the complete virus; gene transfer into eukaryotic cells transfection transfection microflora microflora plants which are invisible, or nearly so, to the naked eye Cell division by mitosis. A-B: Prophase Cell division by mitosis. A-B: Prophase the replicated (daughter) chromosomes (chromatids) undergo extensive condensation. They are greatly thickened and shortened but are still contained within the nuclear membrane. Prophase ends with the sudden beakdown of the nuclear membrane. C: Metaphase a nerve ending, cell, or group of cells specialized to sense or receive light photoreceptor photoreceptor a bundle of neurons (nerve cells); specifically, a bundle of axons which are the motor processes of neurons which carry nervous impulses in the direction away from the cell bodies nerve nerve the National Oceanic and Atmospheric Administration (NOAA) is a federal agency within the US Department of Commerce that is dedicated to predicting and protecting the environment. NOAA's overall mission is to understand and predict changes in the Earth+s environment, protect life and property, provide decision makers with reliable scientific information, conserve and manage the Nation+s living marine and coastal resources to meet our Nation+s economic, social, and environmental needs, and foster global environmental stewardship. To achieve its mission, NOAA+s focus through 2008 will be on four mission goals: NOAA (National Oceanic and Atmospheric Administration) NOAA (National Oceanic and Atmospheric Administration) epizootic a temporal pattern of disease occurrence in an animal population in which the disease occurs with a frequency clearly in excess of the expected frequency in that population during a given time interval; an outbreak (epidemic) of disease in an animal population epizootic a form of associative learning. Trial and error learning occurs when an animal connects its own behavior with a particular environmental response. If the response has a positive reinforcement, or it is favorable to the animal, the animal will repeat the behavior in order to receive the same response again, possibly to receive a reward. If the response is unfavorable, such as causing pain, the animal will avoid the behavior trial and error learning trial and error learning GPS (Global Positioning System) a network of satellites and receiving devices used to compute accurate geographical positions on the Earth. A GPS is used in navigation, and its precision supports cadastral surveying GPS (Global Positioning System) the amount of time and fishing power used to harvest fish. Fishing power includes gear size, boat size, and horsepower effort effort tunic the outer covering of a tunicate (Urochordata). The tunic is mostly composed of a protein and carbohydrates tunic pertains to a reproductive cycle that alternates between sexual and asexual phases metagamy metagamy the coating protein that encloses the nucleic acid core of a viral particle; the capsid coat protein coat protein the occurrence of single species or groups of species in recognizable bands that might delineate a range of water depth or a range of height in the intertidal zone zonation zonation taxonomic key a tabulation of diagnostic characters of taxa in dichotomous couplets to facilitate rapid identification taxonomic key Porites an important and dominant genus of hermatypic coral. Porites brood or release live young rather than sperm and egg packets like most corals Porites in probability, an event is an occurrence or the possibility of an occurrence that is being investigated event event framework framework a rigid, wave resistant calcareous structure constructed by sessile organisms such as sponges, corals, and bryozoans, in a high energy environment prokaryote an organism whose chromosomes are not enclosed within a nuclear membrane, e.g., a bacterium or cyanobacterium prokaryote point mutation a mutation in which a single nucleotide in a DNA sequence is substituted by another nucleotide point mutation the outer portion (layer) of an organ cortex cortex weight belt a belt worn during scuba diving that contains lead weights, either solid masses or as shot in pouches. The weight belt allows a diver to descend in the water column against the forces buoying the diver upwards weight belt neuropodium neuropodium a lobe of the parapodium closer to the ventral side in polychaete worms a small bryozoan heterozooid in which the zooecium and operculum form a beak-like, snapping structure that deters small predators avicularium avicularium a delta formed at both sides of a tidal inlet tidal delta tidal delta a deep channel in the windward side of a coral reef through which water moves in and out of the reef surge channel surge channel coenzyme coenzyme an organic nonprotein molecule that binds with the protein molecule to form the active enzyme the narrowest portion of a fish's body, located just posterior to the anal fin and just anterior to the caudal fin caudal peduncle caudal peduncle a taxonomic group that is below a phylum and above a class superclass superclass catabolism a destructive metabolic process by which organisms convert substances into excreted compounds catabolism cladistic species cladistic species the concept of species in which a species is a lineage of populations between two phylogenetic branch points (speciation events) in taxonomy, one of two or more scientific names that are spelled differently, but refer to the same organism synonym synonym when a sperm cell and ovum from the same organism fuse and form a zygote self-fertilization self-fertilization water that is safe for drinking by humans. Specifically, freshwater that generally meets the standards in quality as established in the U.S. Environmental Protection Agency (EPA) Drinking Water Standards potable water potable water nomen nullum in taxonomy, a null name, i.e.,an unavailable name which, as defined by the International Code of Zoological Nomenclature, is a non-demonstrably intentional change of an original spelling, i.e. a form of incorrect subsequent spelling nomen nullum nomen novum in taxonomy, a new name which is published to replace an earlier name (and valid only if the latter is preoccupied) and which is expressly proposed as a replacement name; a new name, not to be confused with a new species, or a new genus, etc., which represent new taxa. It is commonly applied to names proposed to replace junior homonyms nomen novum pain or discomfort in an enclosed space (sinuses, middle ears, inside a face mask) experienced by scuba divers on descent and ascent, caused by barotrauma to the affected area squeeze squeeze is a unit of length often used to measure depth of water and is equivalent to 6 feet or 1.8 meters fathom fathom blue coral blue coral the blue coral, Heliopora coerulea, is an octocoral that has a massive aragonite skeleton and is an important reef builder in some areas geographical isolation a form of reproductive isolation in which members of a population become separated from another population by geographical barriers that prevent the interchange of genes between the separated populations geographical isolation linear reef a linear coral formation that is oriented parallel to the shore or the shelf edge linear reef homeotic mutation a mutation that causes a body part of an organism to develop in an inappropriate position homeotic mutation an animal that lives on the surface of another organism epizoite epizoite algaestat algaestat a chemical agent which retards and prevents the reproduction and growth of algae immunogen immunogen any substance that can elicit an immune response a natural, interbreeding unit of sexually reproducing organisms sharing a common gene pool Mendelian population Mendelian population immature describes an animal that has not reached sexual maturity, regardless of size or age immature the amount of oxygen taken up by microorganisms that decompose organic waste matter in water. It is therefore used as a measure of the amount of certain types of organic pollutant in water. A high BOD indicates the presence of a large number of microorganisms, which suggests a high level of pollution biochemical oxygen demand (BOD) biochemical oxygen demand (BOD) a form of hermaphroditism where individuals can change sex, but the sexes are separate sequential hermaphrodite sequential hermaphrodite a polychaete worm (Palola viridis) that burrows in the coral reefs of some Pacific Islands. Just before the last quarter of the moon in October and November, they swarm and breed in vast numbers at the sea surface. They are gathered and highly esteemed as food by the islanders. An allied species inhabits the tropical Atlantic and swarms in June or July palolo palolo Porifera an animal phylum that contains the sponges. They are the most primitive of the multicellular animals. Sponges assume many sessile body forms, such as finger, branching, bushy, spherical, tubular, vase and tube-like, encrusting, amorphous and massive. Some bore into coral and mollusk shells. Many of the 5,000 species are colorful and prominent inhabitants of coral reefs Porifera allotopic allotopic refers to species with overlapping ranges but do not occupy the same space. They do not "live together" supraorbital an area above the eye supraorbital the breaking down of a compound into fragments by the addition of a molecule of water. The hydroxyl group is incorporated in one fragment and the hydrogen atom in the other hydrolysis hydrolysis brittle star brittle stars are echinoderms (class Ophiuroidea) which are closely related to sea stars (starfish). They possess radial symmetry with a central body disc from which five highly flexible snake-like arms protrude. There is no replication of internal organs,as in the arms of sea stars, just one set in the central disk. Compared to starfish, brittle stars have a much smaller central disc and no anus. Wastes are eliminated through the mouth, which is situated on the undersideof the disc. The name is derived from their arms breaking off as a means of defense. New arms are easily regenerated. They are also called serpent stars because of the snakelike movements of the five arms brittle star the building block of a protein. Twenty different amino acids are used to synthesize proteins. The shape and other properties of each protein is dictated by its precise sequence of amino acids. Humans must include adequate amounts of 9 of the 20 amino acids in their diet. These "essential" amino acids cannot be synthesized from other precursors amino acid amino acid cryptogenic species cryptogenic species species whose endemic or alien status is unclear. For many species, data are lacking on their original geographic distribution, and it cannot be determined whether they are native or introduced into a particular location lepton a class of subatomic particles that constitute matter which have no measurable size and do not interact with the strong nuclear force. The charged leptons are the electron, the muon, the tau and their antiparticles. Neutral leptons are called neutrinos lepton eelgrass eelgrass a common seagrass (Zostera marina) distributed from Greenland to Florida that serves as an important habitat for fishes and shellfish. Unfortunately, approximately 90 percent of all eelgrass throughout its range along the Atlantic coast has been destroyed vertebra one of the bony segments of the vertebral column of vertebrate animals; in brittlestars (Echinodermata-Ophiuroidea), a vertebra is one of the many articulated ossicles that join together along the length of the arms. They occupy most of the interior of each arm, and have sockets by which they connect to each other vertebra Darwin point Darwin point the latitude at which reef growth just equals reef destruction by various physical forces operator gene a region of the chromosome, adjacent to the operon, where a repressor protein binds to prevent transcription of the operon operator gene refers to the side of an island or reef that faces the prevailing wind windward windward objects that have been thrown overboard in order to lighten a ship when it is in trouble jetsam jetsam social behavior any kind of interaction between two or more animals, usually between animals of the same species social behavior fissure fissure a deep and narrow depression cutting across the reef front with origins relating to jointing planes in the reef limestone or non-limestone bedrock ciguatoxin ciguatoxin a toxin found in flesh of marine animals, especially some fishes, at some times, in some localities. It is probably of algal origin and causes paresthesia, gastrointestinal symptoms, neuromuscular blockade, and respiratory paralysis due to interference with membrane function centromere the center part of a chromosome that appears 'pinched', in between the short arm (p) and the long arm (q). The centromere holds the two chromatids together, and during cell division (mitosis) it is the site of attachment for the spindle fibers centromere correlogram a graph illustrating the auto-correlations between members of a time series (vertical axis) for different separations in time (horizontal axis) correlogram type series in taxonomy, the series of specimens which either constitutes the name-bearing type (syntypes) of a nominal species or subspecies or from which the name-bearing type has been or may be designated type series aerial roots (pneumatophores) of mangroves contain spongy tissue connected to the exterior of the root via small pores called lenticels. During low tide, when lenticels are exposed to the atmosphere, oxygen is absorbed from the air and transported to and even diffused out of the roots below ground. This diffusion of oxygen maintains an oxygenated microlayer around the roots that enhances nutrient uptake. lenticel lenticel a larval form of some echinoderms echinopluteus larva echinopluteus larva Lacey Act Lacey Act the Lacey Act, passed in 1900, and amended several times, makes it unlawful to import, export, transport, sell, buy, or possess fish, wildlife, or plants taken, possessed, transported, or sold in violation of any federal, state, foreign, or Native American tribal law, treaty, or regulation the locomotor structure of ctenophores (comb jellies) made up of cilia arranged into flattened plates. The ctenes are arranged into eight longidutinal bands, from the aboral to the oral surface ctene ctene hydrocarbon an organic molecule, such as methane (CH4), which consists only of carbon and hydrogen atoms hydrocarbon an organism that can live in the absence of oxygen anaerobe anaerobe odontophore a tooth-bearing structure found in most mollusks, except bivalves. It consists of several muscles and a cartilage which support the radula and radula sac; the term is also applied to the radula alone odontophore verruca verruca a wart-like projection; a small cylindrical projection arising from the corallum that contain calices chronology the age-depth relationship in ice, sediment, or another deposit. Ages are usually measured for discrete samples, and the ages of intermediate samples are interpolated between samples with measured ages chronology biomass an estimate of the amount of living matter per some unit volume or area biomass refers to water bodies with low concentrations of nutrients oligotrophic oligotrophic MAREPAC (Marine Resources Pacific Consortium) MAREPAC (Marine Resources Pacific Consortium) MAREPAC is a consortium made up of representatives from nine islands in Micronesia (Marshall Islands, Federated States of Micronesia, Northern Marianas, Guam, Palau, and American Samoa). MAREPAC's mission is to develop regional capabilities, foster collaboration, and disseminate accurate information in support of sound policy development on sustainable use of marine resources of cultural, economic, and scientific value arenaceous arenaceous a condition of skeletal architecture in sponges in which sand and/or foreign spicule debris partly or completely replaces native spicules within the sponge skeleton; resembling or containing sand; or growing in sandy areas a planktonic larva of tube anemones (Ceriantharia) arachnactis arachnactis animal pole the pole of a spherical oocyte or egg that is closest to the nucleus and contains most of the cytoplasm. The opposite pole is the vegetal pole, which, depending upon the type of egg, contains most of the nutritive or yolk granules. There is a graded distribution of cytoplasm and yolk along an axis between the poles that passes through the nucleus. After the fertilized egg undergoes cleavage and develops into a blastula, the same "geographic" points or reference are used animal pole the material making up the base upon which an organism lives or to which it is attached substrate substrate osmotroph an organism that obtains nutrients through the active uptake of soluble materials across the cell membrane osmotroph water mass a large body of water whose density characteristics are distinct from the surrounding aquatic environment because of inherent temperature or salinity differences water mass vibraculum a bryozoan heterozooid that possesses long setae, or bristles, and may function in cleaning the colony vibraculum allozyme allozyme a form of an enzyme that differs in amino acid sequence from other forms of the same enzyme and is encoded by one allele at a single locus - a pefix meaning other, or differing from the normal or usual allo allo behavioral isolating mechanism behavioral isolating mechanism a difference in behavior (usually reproductive behavior) that prevents genetic exchange between members of different populations or species visible representation of objects and (or) phenomena as sensed or detected by cameras, infrared and multispectral scanners, radar, and photometers imagery imagery an organism at the top of the food chain, relying on smaller organisms for food apex predator apex predator the direction in which a vessel is pointed at any given moment heading heading MAC (Marine Aquarium Council) an international, not-for-profit organization that brings marine aquarium animal collectors, exporters, importers and retailers together with aquarium keepers, public aquariums, conservation organizations, and government agencies. Its mission is to conserve coral reefs and other marine ecosystems by creating standards and certification for those engaged in the collection and care of ornamental marine life from reef to aquarium MAC (Marine Aquarium Council) zoonose zoonose a disease of non-human animals that may be transmitted to humans, or may be transmitted from humans to non-human animals gnathic gnathic pertaining to the jaw a tool to help identify taxa. It is made up of pairs of choices. Each choice is between statements describing specific traits of the taxa under consideration. Only one statement will be true for each choice. Each choice points to another set of choices until finally only one choice remains dichotomous key dichotomous key gene product the product, either RNA or protein, that results from expression of a gene. The amount of gene product reflects the activity of the gene gene product a crack or fracture in the Earth's crust accompanied by a displacement of one side of the fracture. Movement along the fault can cause earthquakes or, in the process of mountain-building, can release underlying magma and permit it to rise to the surface fault fault histogram a bar graph in which the area over each class interval is proportional to the relative frequency of data within this interval histogram optical oceanography optical oceanography the subdiscipline of oceanography concerned with the propagation and interaction of radiation, typically at wavelengths between about 350 and 750 nm, with seawater Darwin Mounds Darwin Mounds two areas of hundreds of sand and cold-water coral mounds at depths of about 1,000 m, in the northeast corner of the Rockall Trough, approximately 185 km northwest of the northwest tip of Scotland. The Darwin Mounds cover an area of approximately 100 sq. km. The tops of the mounds are covered with Lophelia pertusa corals and coral rubble amplification in genomics, the process of increasing the number of copies of a particular gene or chromosomal sequence amplification columnar colony columnar colony a coral colony formed into one or more columns equinox equinox either of the two times during a year when the sun crosses the celestial equator and the length of day and night are equal bioacoustics a discipline of zoology that is concerned with sounds of biological origin: their mechanisms of production, physical properties, receptors and reception physiology, and the role of the sounds in behavior bioacoustics hydrocaulus the main stem of a colonial hydrozoan which consists of a cylindrical tube of living tissue (coenosarc) covered by a thin outer membrane (perisarc) hydrocaulus disulfide bond disulfide bond a chemical bond between the sulfur atoms of two different amino acids in a protein gill tuft gill tuft a fluffy cluster of gill filaments key stimulus in ethology or animal behavior, the stimulus which releases a fixed action pattern key stimulus polymerase a general term for enzymes that carry out the synthesis of nucleic acids polymerase a learning process where an animal learns by copying the behavior of other animals observational learning observational learning a sac that stores spermatophores in cephalopods Needham's sac Needham's sac a reef with very little calcium carbonate accretion. A non-reef coral community veneer reef veneer reef denaturation denaturation the inducing of structural alterations that disrupt the biological activity of a molecule. It often refers to breaking hydrogen bonds between base pairs (by heat) in double-stranded nucleic acid molecules to produce single-stranded polynucleotides, or altering the secondary and tertiary structure of a protein, destroying its activity enzyme enzyme an organic catalyst satellite mapping satellite mapping digital maps derived from satellite images chlorophyll b the chlorophyll generally characteristic of higher plants and green algae .It is absent in other types of algae chlorophyll b ecotourism travel undertaken to experience sites or regions of unique natural or ecological quality, or the provision of services to facilitate such travel ecotourism zoophyte an invertebrate which resembles a plant in appearance or mode of growth, as for example, hard corals, sea fans, and other soft corals, sea anemones, hydroids, bryozoans, sponges, etc., especially any of those that form compound colonies having a tree-like form zoophyte thorax the central region of a crustacean body thorax a facility containing a series of tanks, screens, filters and other processes by which pollutants are removed from water wastewater treatment plant wastewater treatment plant basal basal of, at or forming a base dry weight dry weight the moisture-free weight of a biological sample obtained by drying at high (oven-drying) or low (freeze-drying) temperatures for an time sufficient to remove all water the epithelial lining of the gastrovascular (digestive) cavity of cnidarians and ctenophores (comb jellies) gastrodermis gastrodermis atmospheric pressure atmospheric pressure the pressure of the atmosphere at any given altitude or location; it is synonymous with barometric pressure cell body the enlarged portion of a neuron which contains most of the organelles cell body binomen a two-part name given to a species in which the first part is the name of the genus and the second is the specific name binomen t. t. according to; on the evidence of (teste) eutrophic eutrophic a situation in which the increased availability of nutrients such as nitrate and phosphate stimulates the growth of plants such that the oxygen content is depleted and carbon sequestered secretion secretion the passage of a molecule from the inside of a cell through the cell membrane into the periplasmic or interstitial space, or the extracellular medium; the organic process of synthesizing and releasing some substance from the body of an organism ectodermis the outer cellular covering of a polyp ectodermis species which have a variety of morphological types polymorphic species polymorphic species calcareous rock which is removed from the vicinity of a coral reef with some of the life forms on it still living. These may include bacteria, coralline algae, sponges, worms, crustaceans and other invertebrates. Live rock is commonly used in reef aquaria because it contains bacteria that can help filter the water through nitrification live rock live rock truncate having the end squared off truncate a charged lepton about 200 times more massive than an electron; an elementary particle with a negative charge and a half-life of 2 microsecond; decays to electron and neutrino, and antineutrino muon muon a relative time scale based upon fossil content. Geological time is divided into eons, eras, periods, and epochs geologic time scale geologic time scale advanced advanced new, unlike the evolutionary ancestral or primitive condition expected value in statistics, the mean value calculated for a statistic over an infinite number of samples expected value a ship's striking a shoal or reef grounding grounding pallial pallial of or pertaining to a mantle, especially to the mantle of mollusks oceanic island oceanic island an island in the ocean formed by breaking away from a continental landmass, volcanic action, coral formation, or a combination of sources penicillate penicillate brush-like; having or resembling a tuft or brush of fine hairs an asexual, spore-like reproductive unit in sponges, capable of overwintering and developing into an adult sponge the following summer gemmule gemmule a scanning radiometer with six spectral channels centered at 0.443, 0.520, 0.550, 0.670, 0.750 and 11.5 micrometers and selected to allow measurement of ocean color and temperature, suspended sediment and chlorophyll concentrations, and ocean pollutants CZCS (Coastal Zone Color Scanner) CZCS (Coastal Zone Color Scanner) the point in the orbit of the Moon or man-made satellite farthest from the Earth; the point in the orbit of a satellite farthest from its companion body apogee apogee anomaly anomaly the deviation of a particular variable (e.g., temperature) from the mean or normal over a specified time genome genome all the DNA contained in an organism or a cell, which includes both the chromosomes within the nucleus and the DNA in mitochondria qualitative analysis qualitative analysis the analysis of a phenomenon to determine its qualitative characteristics versus its quantitative characteristics, i.e., characteristics for which precise numerical characterization is not appropriate a planktonic larval form produced by some anthozoans planula planula feather stars are echinoderms in the class Crinoidea. The juveniles attach to the substrate by a stalk with rootlike branches. The mouth side faces upward. In the adult stage they break away from the stalk and move about freely.They possess appendages, known as cirri, attached to the underside of the body with which they cling to to sponges or corals. Some can swim by undulating movements of the arms. Some have five arms, others up to 200 feather star feather star a floating platform for navigational purposes or supporting scientific instruments that measure environmental conditions buoy buoy alecithal alecithal a type of egg that does not contain yolk pinacocyte pinacocyte a cell type which forms the surface layer (pinacoderm or epidermis) of a sponge. Pinacocytes are capable of synthesising collagen the time of the year during which mating occurs breeding season breeding season diverticulum diverticulum a blind sac branching off a cavity or canal Cheliceramorpha an order of arthropods that includes horseshoe crabs, daddy-longlegs, and extinct "sea-scorpions, spiders and scorpions, mites and ticks, " Most of its marine representatives are extinct, but were prominent in the Paleozoic Cheliceramorpha index based on the strength and duration of local HotSpots to monitor bleaching events bleaching index bleaching index corallum corallum a complete coral colony; a coral head automated bleaching early warning system automated bleaching early warning system automated bleaching alerts/warnings directly from satellite and/or in situ derived indices a structure that lacks reef characteristics, such as diversification and domination stages reef mound reef mound climate-induced bleaching coral bleaching as a result of changing climate patterns, e.g., temperature climate-induced bleaching chaeta chaeta a stiff hair or bristle, made of chitin, characteristic of annelid worms. In the earthworm they occur in small groups projecting from the skin in each segment and function in locomotion. The chaetae of marine polychaete worms are borne in larger groups on paddle-like appendages called parapodia the largest complex barrier coral reef in the world, approximately 2,000 km (1,250 mi) long, in the Coral Sea, forming a natural breakwater for the northeastern coast of Australia. It is separated from the mainland by a shallow lagoon from 16-161 km (10 to 100 mi) wide. It is It is composed of more than 2,800 individual reefs and in some places it is more than 122 m (400 ft) thick. The Great Barrier Reef Marine Park, more than 340,000 km2 (130,000 mi2), encompasses most of the reefs and interreef areas as well as the neighboring lagoon and a large section of the continental shelf. It is the largest UNESCO World Heritage Area Great Barrier Reef Great Barrier Reef the process by which the genetic information encoded in a linear sequence of nucleotides in one strand of DNA is copied into an exactly complementary sequence of mRNA (messenger RNA). The mRNA then carries this information to the cytoplasm of the cell, where it serves as the blueprint for the manufacture of a specific protein transcription transcription notopodium notopodium a lobe of the parapodium closer to the dorsal side in polychaete worms a form of protective mimicry in which noxious species evolve through convergent evolution to resemble each other Mullerian mimicry Mullerian mimicry spiny lobster spiny lobster a crustacean of the Family Palinuridae; it lacks large claws and has a flexible, leathery tail fan acrosphere acrosphere the knobbed tentacle tip of an anthozoan, usually bearing numerous nematocysts NOS is a scientific and technical organization of NOAA whose mission is to preserve and enhance the nation's coastal resources and ecosystems along 95,000 miles of shoreline and 3.5 million square miles of coastal ocean. At the same time, it works to support economic growth for the long-term benefit of the nation. This theme is central to the sustainable development agenda of both NOAA and the U. S. Department of Commerce (DOC). For detailed information, see: http://www.oceanservice.noaa.gov/about/welcome.html NOAA's National Ocean Service (NOS) NOAA's National Ocean Service (NOS) neuston planktonic organisms associated with the air-water interface neuston the point of the celestial sphere which is directly overhead zenith zenith a slender, flexible appendage or part of an organism, usually having a tactile function cirrus cirrus operculum a lid or flap covering an aperture, such as the gill cover in most bony fishes; the gill cover; also the horny lid closing the aperture of various species of mollusks operculum a class of the segmented worm phylum Anellida. There are approximately 8,000 species of polychaetes which include errant (free-moving) forms and sedentary ones that live in stabilized burrows, galleries or tubes of various degrees of complexity. Some burrow into coral. Many species are common inhabitants of coral reefs, such as the Christmas tree worms, feather duster worms, fanworms, fireworms, scaleworms, threadworms, and others Polychaeta Polychaeta the living tissue of a cnidarian polyp, consisting of the outer, nonciliated epidermis and the inner, ciliated gastrodermis with the thin, acellular meoglea in between. The coenosarc connects the coral polyps of a coral colony. It spreads along the surface of the calcareous exoskeleton coenosarc coenosarc mixed zone the populous region of most bank/barrier reefs seaward of the lower palmata zone. It begins at a depth of 6-8 m mixed zone viable having the capacity to live, grow, germinate or develop; capable of life or normal growth and development viable in hospite in hospite within the host native to a particular country or area indigenous indigenous cloudy water, usually caused by the suspension of fine particles in the water column. The particles may be inorganic, such as silt, or organic, such as high densities of single-celled organisms turbidity turbidity interstitial fauna animals that live in the spaces within sediment particles (interstitial spaces) interstitial fauna a group of organic compounds, including the fats, oils, waxes, steroids, and triglycerides, that are insoluble in water but soluble in common organic solvents, and are oily to the touch. Together with carbohydrates and proteins, lipids constitute the principal structural materials of cells lipid lipid drop root drop root an adventitious root in mangroves that originates from the branches, and roots in the surface-sediments a ciliated, free-swimming pelagic larva of a hemichordate tornaria larva tornaria larva Holocene epoch an epoch of the Quaternary period dating from the end of the Pleistocene approximately 8,000 years ago until the present Holocene epoch allorecognition the ability of an individual organism to distinguish its own tissues from those of another; the recognition of antigens, expressed on the surface of cells of non-self origin. Allorecognition has been described in nearly all multicellular phyla allorecognition pedal disc a disc at the aboral end of the body trunk used for attachment. A synonym of basal plate pedal disc controlled environment controlled environment the environment in which parameters, such as light, temperature, salinity, etc., are fully controlled isotonic contraction a muscular contraction in which tension is constant while the length of the muscle changes isotonic contraction the strand of chromosomal DNA that is transcribed; a DNA sequence that is complementary to all or part of an mRNA molecule antisense DNA antisense DNA the enormous wedge of sediment deposited at the base of the continental slope continental rise continental rise a branch of biology that studies the biology of a cell at the molecular level. Molecular biological studies are directed at studying the structure and function of biological macromolecules and the relationship of their functioning to the structure of a cell and its internal components. Great attention is given to genetic aspects such as replication, transcription and translation molecular biology molecular biology a scraping organ for mastication in certain mollusks, such as snails. In many gastropods the radula consists of a variable number of chitinous teeth, of different shape and size, located in the anterior portion of the pharynx. In the cone shell family it has been reduced to a sharp and grooved tooth, fit to harpoon and inject prey with a powerful venom, which is also potentially fatal to humans radula radula type locality type locality in taxonomy, the geographical (and, where relevant, stratigraphical) location of the occurrence of the population from which the type specimen (i.e. holotype, lectotype or neotype) was taken spermatophore a packet containing sperm cells which is produced by the male genital system for transfer to the female. This method of sperm transfer is found in some vertebrates (salamanders) as well as invertebrates spermatophore senior synonym senior synonym in taxonomy, the older name of two synonyms the total amount of chemical energy fixed by the processes of photosynthesis minus the chemical energy lost through respiration; same as 'net photosynthetic rate' net primary productivity net primary productivity channel channel a deep and relatively narrow body of water (as in a river, harbor, or a strait linking two larger bodies) that allows the best passage for vessels; an open conduit either naturally or artificially created which periodically or continuously contains moving water, or which forms a connecting link between two bodies of water. River, creek, run, branch, and tributary are some of the terms used to describe natural channels. Canal and floodway are some of the terms used to describe artificial channels. the brood chamber of a bryozoan (Ectoprocta), usually located at the distal end of the maternal zooid. Embryos are brooded until they develop into non-feeding larvae, which swim briefly, then settle and metamorphose to found a new colony ovicell ovicell independent variable a variable controlled by the experimenter independent variable a non-food species that is produced and maintained solely for exhibit purposes in home or public aquaria, or in ornamental garden ponds ornamental ornamental a thermometric scale in which 0 degrees C (Celsius) marks the freezing point of water and 100 degrees C indicates the boiling point of water at sea level Centigrade Temperature Scale Centigrade Temperature Scale open sea open sea that part of the ocean that extends outward from the continental shelf diploid phase in the life cycle of red algae which produces haploid tetraspores.The tetrasporophyte is the site of meiosis, more specifically, the tetrasporangia where haploid tetraspores are produced. These tetraspores are released, settle, and grow into the gametophyte, completing the basic red algal life history tetrasporophyte tetrasporophyte a tissue layer of cells which lines body cavities and tubules, or covers surfaces. The cells may be ciliated or non-ciliated, and may be squamous (flat, scale-shaped), cuboidal (cube-shaped), or columnar (column-shaped) in shape. The cells may occur in a single layer, or may be multi-layered (stratified) epithelium epithelium a non-motile diploid spore formed on the carposporophyte stage of the red algae life cycle which germinates to form the tetrasporophyte stage carpospore carpospore a corallite of some species which is located at the base of a funnel-shaped depression foveolate corallite foveolate corallite reproduction that does not involve the union of sex cells (gametes) to produce a zygote. Examples in corals are budding and fragmentation asexual reproduction asexual reproduction anchialine pool anchialine pool a land-locked brackish body of water that displays tidal fluctuations but has no surface connection to the sea. Anchialine pools are restricted to highly porous substrates, such as recently solidified molten rock or limestone adjacent to the sea variant variant any individual or group that deviates form the typical anatomy or behavior; in genetics, an organism that is genetically different from the wild type organism red tide red tide discoloration of surface waters, most frequently in coastal areas, caused by large concentrations of microorganisms, such as algae or cyanobacteria a physical, chemical or biological factor that adversely affects organisms; an agent, condition or similar stimulus that causes stress to an organism stressor stressor phreatic water water below the level at which all voids in the rock are completely filled with water phreatic water mass extinction a catastrophic, widespread perturbation where major groups of species become extinct in a relatively short time mass extinction a fishing vessel that tows an open-mouthed fishing net drawn along the sea bottom or in the water column trawler trawler monoecious having combined sexes. Individuals of monoecious species contain the reproductive systems of both males and females monoecious an artificial, single or multilaminar vesicle, made from a lipid, that is used for the delivery of a variety of biological molecules or molecular complexes to cells, e.g., drug delivery and gene transfer. Liposomes are also used to study membranes and membrane proteins liposome liposome the depth at which a Secchi disk disappears from view as it is lowered in water Secchi disk a white disk 20-30 cm in diameter, used as a qualitative way of measuring water clarity. It is lowered from a vessel and viewed from above the surface in full solar illumination to estimate the light attenuation in the water column. This is done empirically by relating the depth at which the disk disappears to the attenuation of light Secchi depth Secchi depth a molecule that is capable of reacting with free radicals and neutralizing them; a compound that slows the rate of oxidation reactions antioxidant antioxidant binding binding the ability of molecules to stick to each other because of the exact shape and chemical nature of parts of their surfaces embayment embayment an indentation in the shoreline that forms a bay pleopod pleopod one of the five paired abdominal appendages used for swimming by shrimps; used for attachment of eggs by female shrimps, lobsters and crabs; also called a swimmeret a behavior that occurs when an animal immediately mimics the actions of another animal while they are in each other's presence imitation imitation Gastropoda Gastropoda a class of the phylum Mollusca that includes snails, sea slugs, nudibranchs, limpets, and cone shells. There are approximately 30,000 living species described. Many species are inhabitants of coral reefs and nearby seagrass beds a mound-like layered structure built by and predominantly composed of organic remains such as shells and skeletons of sedentary organisms biogenic reef biogenic reef sonar signals arriving at a target, or the towfish, from a single source but along different paths. The multibeam sonar system consist of a transducer, motion sensor, gyrocompass, and navigation system. When collected in slightly overlapping swaths (fanlike coverages from sonar scans), multibeam sonars can produce a sonar data set that represents nearly 100 percent acoustic coverage of the seafloor multibeam sonar multibeam sonar a body shape which is flattened laterally, bringing the right and left sides closer together, e.g., a butterfly fish or a flounder compressed compressed the protein coat of a virus particle capsid capsid tautonymy in taxonomy, the use of the same word for the name of a genus-group taxon and for one of its included species or subspecies tautonymy marine snow dense concentrations of particulate organic detritus and living organisms whose downward drift appears similar to a snowfall marine snow an informal taxonomic unit that includes coleomatic metazoans which possess a specialized filter-feeding organ, the lophophore. Almost all lophophorates are marine organisms and all are suspension feeders. Lophophorates are deutersotomes and are typically considered relatively closely related to chordates and echinoderms. There are three lophophorate phyla: Phoronida, Bryozoa and Brachiopoda lophophorate lophophorate CARICOMP (Caribbean Coastal Marine Productivity) CARICOMP (Caribbean Coastal Marine Productivity) a regional coral reef, seagrass and mangrove monitoring program and network involving a number of Caribbean laboratories, parks and reserves to study land-sea interaction processes in the wider Caribbean region. Twenty-seven institutions in 17 countries participate in CARICOMP suborbital an area below the eye suborbital mean high tide the level to which the water rose on an average day over a previous period of time (years or decades); the average of all the high tides as calculated over a long period of time mean high tide Law of Conservation of Energy energy can be transferred from one system to another in many forms, however, it can not be created nor destroyed. Thus, the total amount of energy available in the universe is constant Law of Conservation of Energy phospho-diester bond phospho-diester bond a bond in which a phosphate group joins adjacent carbons through ester linkages in, near, or toward the stern (rear) of a vessel aft aft start codon start codon the set of three nucleotides in an mRNA molecule with which the ribosome starts the process of translation. The start codon sets the reading frame for translation. The most commonly used start codon is AUG, which is decoded as methionine in eukaryotes, and as N-formylmethionine in prokaryotes; also called 'initiator codon' dissociation dissociation the temporary or reversible chemical process in which a molecule or ion is broken down into smaller molecules or ions tidelands the zone between the mean high water and mean low water lines. It is identical with intertidal zone (technical definition) when the type of tide is semi-diurnal or diurnal tidelands referring to water with a salinity higher than that of natural seawater hypersaline hypersaline triglyceride triglyceride a complex molecule which is the main component of dietary and body fat. It is made up of a combination of glycerol and three fatty acids sac-like saccate saccate a situation in which the best-fitting regression line is a straight line linear relationship linear relationship the spread of a species to a new location. In many organisms, this happens at a particular stage in the life cycle, and is often critical for the species' survival. Organisms may disperse as spores, seeds, eggs, larvae, juveniles, or adults dispersal dispersal DNA (deoxyribosenucleic acid) DNA (deoxyribosenucleic acid) also termed deoxyribonucleic acid. The molecule that encodes genetic information in the cells. It resembles a double helix held together by weak bonds of four nucleotides (adenine, guanine, cytosine, and thymine) that are repeated ad infinitum in various sequences. These sequences combine into genes that govern the production of proteins. The DNA located within the nuclear membrane of eukaryotic cells is sometimes referred to as nDNA sink sink a process or place that acts to absorb or remove energy or a substance from a system. The ocean, for example, is a sink for carbon dioxide a molecule that serves as the pattern for synthesizing another molecule ; in the process of replication or transcription, the strand of DNA that serves as the source of information template template in taxonomy, power of the International Commission on Zoological Nomenclature to suspend articles of the Code to settle particular cases plenary power plenary power SCUBA (Self-Contained Underwater Breathing Apparatus) SCUBA (Self-Contained Underwater Breathing Apparatus) a diving mode independent of surface air supply in which the diver uses open circuit self-contained underwater breathing apparatus which supplies air or breathing gases at ambient pressure a life cycle stage in certain algae that produces male and female reproductive organs gametophyte gametophyte an agent that causes a permanent genetic change in a cell other than that which occurs during normal genetic recombination mutagen mutagen in biology, the division of the body into a series of more or less similar segments (metameres), as in an annelid worm or a lobster metamerism metamerism metagenesis an alternation of sexual and asexual generations. When metagenesis occurs in cnidarians, the polyp is the asexual generation and the medusa is the sexual generation. A generalized life cycle occurs as follows: medusae produce gametes which unite to form zygotes. Each zygote divides repeatedly and develops into a free-swimming planula larva, which eventually settles and develops into a polyp. Each polyp then asexually produces medusae to complete the life cycle metagenesis dead ahead dead ahead a position directly in front of a vessel FRA (Fish Replenishment Area) a designated area, within a Fisheries Management Area (FMA), where certain specified fish harvesting activities are prohibited FRA (Fish Replenishment Area) biogenesis biogenesis a central concept of biology that all living organisms are descended from predecessor living organisms genetic marker genetic marker a DNA sequence used to "mark" or track a particular location (locus) on a particular chromosome exothermic reaction a reaction that gives off heat exothermic reaction Halimeda Halimeda an important genus of calcareous green algae in coral reef environments a process for separating molecules by forcing them to migrate through a gel under the influence of an electric field gel electrophoresis gel electrophoresis a "user-driven" integrated system of observations, data management and communications, and data analysis and modeling that provides data and information required to achieve seven societal goals: 1) Improve predictions of climate change and variability (weather) and their effects on coastal communities and the nation; 2) Improve the safety and efficiency of marine operations; 3) More effectively mitigate the effects of natural hazards; 4) Improve national and homeland security; 5) Reduce public health risks; 6) More effectively protect and restore healthy coastal marine ecosystems; and 7) Enable the sustained use of marine resources IOOS (Integrated Ocean Observing System) IOOS (Integrated Ocean Observing System) not forming an essential part of a thing; arising or originating from the outside extrinsic extrinsic laws that predict how gases will behave with changes in temperature, pressure, and volume gas laws gas laws refers to a climatic process that re-occurs every three to ten years. El Nino is an example of a climatic process that re-occurs every 4-6 years interannual interannual alloantigen an antigen that occurs in some but not other members of the same species alloantigen oogamy oogamy the union of a large nonmotile egg with a small motile or nonmotile male sperm cell intraspecific intraspecific among members of the same species a sensory structure in some jellyfish (Scyphozoa), associated with a rhopalium, which responds to touch (pressure); a fleshy lobe lappet lappet allopatric speciation the evolution of a new species because of the isolation of a small group of individuals from the other members of a population allopatric speciation a modified aerial root rising above ground that may function as a respiratory organ in plant species such as mangroves, which are subjected to inundation or soil saturation. Such evolutionary adaptations enable trees to obtain oxygen directly from the air and also helps consolidate swamp sediments. They have special air channels (lenticels) for gas exchange in the atmosphere and there is an internal pathway for getting oxygen into the root and to supply submerged roots. The aerial loop of a mangrove root is sometimes called a "knee" or "peg root" pneumatophore pneumatophore having an internal body temperature that is dependent on the surrounding temperature. Most aquatic animals are ectotherms; also caled poikilothermal or "cold blooded" ectothermic ectothermic chela chela a pinching claw of a decapod crustacean, composed of a moveable finger, the dactylus, and a fixed finger, a distal extension of the propodus ovulation ovulation the release of an egg from the ovary outrigger outrigger a floatation device attached to one or both sides of the hull of a boat to help prevent a capsize planktivorous feeding on planktonic organisms planktivorous clavate club-shaped clavate the technique of selectively removing, modifying, or adding genes to a DNA molecule by use of recombinant DNA or other specific molecular gene transfer or exchange techniques. These techniques produce endogenous proteins with properties different from those of the normal, or to produce entirely different proteins altogether. Organisms modified by genetic engineering are sometimes referred to as transgenic, bioengineered, or genetically modified genetic engineering genetic engineering the selections of methods and how they are used to gain data and information at a site protocols protocols an undesirable substance not normally present, or an usually high concentration of a naturally occurring substance in the environment; a substance in water that might adversely affect the health and welfare of the biota contaminant contaminant receiving waters water bodies that receive treated or untreated waste waters receiving waters in coral sexual reproduction, the polyps of many species release bundles of eggs and sperm cells, called gamete bundles, that float to the sea surface. The layers surrounding the egg and sperm bundles soon rupture, releasing the gametes at the surface, where fertilization occurs gamete bundle gamete bundle survey (biology) the systematic and usually standardized collection or inventorying, processing, and analysis of representative portions of a biological community or defined site with its habitats, to determine the community structure and function survey (biology) gorgonin gorgonin a fibrous protein in the mesoglea which provides skeletal support for sea fans and other members of the Order Gorgonacea gill net gill net a net primarily designed to catch fish by entanglement in a mesh that consists of a single sheet of webbing which hangs between cork line and lead line, and which is fished from the surface of the wate