Glossary of Coral Reef Terminology - A

Sea otters are in direct competition with humans for abalone. (Photo: Ron McPeak)

The ventral surface of the abdomen of an American lobster. Prominent are the swimmerettes, uropods, and telson.

Spines protect the aboral surface of a sea urchin. (Photo: NOAA)

A parasitic tapeworm is an absorptive feeder. The narrowest point is the "head" or scolex which attaches the parasite to the intestinal lining by means of suckers and/or little hooks. Predigested nutrients are absorbed through the wall of each of the progressively larger segments. These animals have no digestive canal. (Photo: HHS/Centers for Disease Control and Prevention)

Crown-of-Thorns starfish (Acanthaster sp.), a voracious predator of corals.

The phylum Acanthocephala contains about 1,000 species of spiny-headed worms. All are endoparasites in the intestinal tract of vertebrates, especially fishes. (Image: Dr. Rick Gillis, Biol. Dept., Univ. of Wisconsin)

Acoelomate flatworms such as this Pseudoceros sp. lack a coelom (body cavity). (Photo: Adam Petrusek)

Radio tag (anterior) and acoustic tag (posterior) attached to a loggerhead turtle. (Photo: ALan Rees/ARCHELON)

Staghorn coral (Acropora sp.).

Longitudinal section of A. alicemartinae (azocarmine triple staining). Ac: acrorhagus; Bm: basilar muscle; Co: column; Me: mesenteries; Od: oral disc; Pd: pedal disc; T: tentacles (Photo:V.Häussermann & G.Försterra/U.Frankfort)

This squirrel fish is a member of the class Actinopterygii, the ray-finned fishes. Note the hard and soft rays in its fins.

Actinula larval stage of the hydrozoan, Tubularia. (photo: BIODIDAC)

The fierasfer, Carapus bermudensis, possess an acuminate shape. The tapered end allows the fish to retreat tail first, for protection, into the digestive canal of a sea cucumber when threatened. (Photo: D. Flescher, NOAA/National Marine Fisheries Service)

Diagram of the chemical structure of adenine, one of the four nitrogenous bases in DNA.

The dorsal fin of the remora (also called shark sucker or pilotfish) is modified to function as an adhesive disc (Photo: NOAA)

Adipose tissue. The large empty looking structures are adipocytes (fat cells). (Photo: University of Saskatuwan Biology Dept.)

The adipose fin of this chum salmon lies between the dorsal and caudal fins. (Image: U.S. Fish and Wildlife Service)

An adult Nassau grouper. It is sexually mature and capable of reproducing.

Aeolid nudibranchs lack gills and utilize their dorsal cerata for respiration and defense. (Photo: Dr Bill Rudman)

Three antennular segments with pairs of aesthetasc sensilla on their ventral surfaces. (Photo: Deforest Mellon, Ph.D./University of Virginia)

Sunrise as viewed from the aft deck of the NOAA Ship Albatross IV. (Photo:NOAA)

The mouth of a jawless agnathan, the sea lamprey. Adults feed by attaching themselves to their prey, rasping a hole in the skin, and consuming blood and body fluids. (Photo: Minnesota Sea Grant)

AIMS field operations jetty at Cape Ferguson.  (Photo: AIMS)

An albino catfish. The fish's skin cells contain no dark melanin granules.

Alcyonarians are colonial soft corals that lack the CaCO3 exoskeleton of the hard or stony corals. An endoskeleton of calcareous spicules provide support for the body, which is studded with polyps.

Green algae are found in all aquatic environments, including marine, fresh and brackish water. (Photo: David Burdick)

algaestat - a chemical agent which retards and prevents the reproduction and growth of algae

algal bloom - a sudden spurt of algal growth that can indicate potentially hazardous changes in local water chemistry

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.

A helmet conch feeding on an algal mat in sand (Photo: James Stuby)

algal mat - a dense layer of algae, usually filamentous, which blankets the bottom in a shallow water environment. An algal mat can also be a ‘mat’ of microscopic species, usually diatoms, covering soft bottoms, or a mat of floating algae

Coralline algae makes up part of an algal reef.

algal reef - a reef, usually exposed to wave action, composed of coralline algae and vermatid gastropods. The coralline algae occur in forms of cups or funnels

algal ridge - a low ridge at the seaward margin of a reef flat, largely composed of skeletons of calcareous algae. A synonym of Lithothamnion ridge

algal turf - densely packed algae, usually filamentous, which rise less than one centimeter above the substratum upon which they are growing. A synonym of turf algae

algicolous - pertaining to an organism that lives on or around seaweed

algin - a polysaccharide derived from brown algae. Algins are used for many industrial processes

algophagous - refers to an organism that feeds upon algae

algorithm - A computer program (or set of programs) which is designed to systematically solve a certain kind of problem

alien species - a species which does not naturally occur within an area and which has usually arrived as a result of deliberate or accidental human intervention. Alien species often have adverse effects on native species as a result of competition

alima - a larval stage of a mantis shrimp

alimentary canal - the canal, including the stomach and intestines, leading from the mouth to the anus

aliquot - a portion of a sample; a subsample

A Dover sole, cleared and stained with alizarin red S, to highlight the bony structures (Photo: Natural History Museum, london)

alizarin - a red dye made from the roots of the madder plant, Rubia tinctorum, or produced synthetically from coal tar. A bone specific stain, alizarin red S is commonly used to stain the skeletal elements of a fish specimen. In this procedure, the muscles are rendered transparent by emersing the specimen in a caustic agent, such as potassium hydroxide

alkaline - having a pH of more than 7. Alkaline solutions are also said to be basic

All Islands Coral Reef Committee (AIC) - the U.S. All Islands Committee (AIC) was established in 1994 by the governor-appointed Points of Contact (POCs) from the U.S. states, territories and commonwealths of American Samoa, the Commonwealth of the Northern Marianas, Guam, Hawai`i, Puerto Rico, and the U.S. Virgin Islands. The AIC was recognized as a key element of the overall U.S. Coral Reef Initiative in Presidential Executive Order 13089 which established the U.S. Coral Reef Task Force (USCRTF) in 1998. The State of Florida joined the Committee as an Associate member in 2000 and became a full member in early 2007. Affiliate Members of the AIC are the Federated States of Micronesia, the Republic of the Marshall Islands, and the Republic of Palau

All Islands Coral Reef Initiative - a cooperative effort among Hawaii, American Samoa, Guam, the Commonwealth of the Northern Mariana Islands, Puerto Rico, and the U.S. Virgin Islands to improve the management of coral reefs in island areas

ALL Species Foundation - a non-profit organization dedicated to the complete inventory of all species of life on Earth within the next 25 years - a human generation (http://www.all-species.org/)

all-or-none law - an action that occurs either completely or not at all, such as the generation of an action potential by a neuron, or the contraction of a muscle cell

allantois - 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

Allee's Principle - there is a positive relationship between individual fitness and either the numbers or density of conspecifics. In other words, as the number of individuals in a population increases, or as population density increases, survival and reproduction also increase

allele - one of the variant forms of a gene at a particular locus, or location, on a chromosome. Different alleles produce variation in inherited characteristics. In an individual, one form of the allele (the dominant one) may be expressed more than another form (the recessive one)

allelochemical - a chemical substance produced by one organism that is toxic or inhibitory to the growth or well being of another

Schooling fish exhibit allelomimetic behavior. (Photo: Paige Gill, Florida Keys NMS)

allelomimetic behavior - behavioral activities that have strong components of social facilitation, imitation, and group coordination; imitation of behavioral habits of another animal, usually of the same species; behavior in social animals in which each animal does the same thing as those nearby. It is developed to a high degree in schools of fishes, flocks of birds, and and herds or pods of mammals

allelopathic substance - a substance produced by one organism that adversely affects another organism

allelopathy - 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

allergen - an antigen that provokes an immune response

allo - - a prefix meaning other, or differing from the normal or usual

alloantigen - an antigen that occurs in some but not other members of the same species

allochoric - occurring in two or more communities within a given geographical region

allochronic speciation - speciation without geographical separation through the acquisition of different breeding seasons or behavior patterns

allochthonous population - an organism or a population of organisms foreign to a given ecosystem; they have arrived from elsewhere

allocryptic - pertaining to organisms that conceal themselves with coverings of other organisms or with inanimate materials

allogenic - resulting from factors acting from outside a system or material transported into an area from the outside which alters the system's habitat; genetically different individuals belonging to the same species; when describing transplantation biology, the donating individual is of the same species, but not one's self

allogenic succession - a kind of ecological succession in which one kind of community replaces another because of a change in the environment which was external to and independent of that produced by the community itself

allograft - a piece of tissue or an organ transferred from one individual to another individual of the same species

allometric equation - the general form of the allometric equation is y = bxa where y = measure/process in question, x is size, a is the allometric exponent (which tells you the relationship between x & y), and b = a constant (the allometric coefficient)

allometric growth - type of differential growth in which parts of the same organism grow at different rates. For example, in humans, the head and body grow at different rates, resulting in a human adult with completely different proportions from those of an infant

allometry - study of the relative growth relationships between different parts of an organism; mathematically expressed by the allometric equation y = mx + b, where y = predicted size of body part; x = observed body weight; m = slope acquired; and b = the value of y where it intercepts the vertical axis. Allometry is studied during the growth of a single organism, as a comparison between different organisms of the same species, and between organisms in different species. The allometric equation is graphed on an XY axis, with the body size on the x-axis and the part size on the y-axis. The scatter produced by the different measurements being compared can then be analyzed for useful data

allomone - a chemical substance that induces a response in an individual of another species that is beneficial to the emitting organism. Many allomones are essentially chemical deterrents. For example, a chemical substance that is produced by a prey species to repel a predator species

allomorphosis - allometry based on the comparison of related individuals, rather than upon ontogeny. Systematic change of shape among successive adults of a phyletic sequence, for example, is allomorphosis; the rapid development of specialized organs or increase of specialization in an organism

alloparent - an animal which exhibits parental behavior towards another animal's offspring

allopatric speciation - speciation which occurs in populations initially isolated geographically, such as by habitat fragmentation or migration. As natural selection and genetic drift act independently in isolated populations, separation will eventually produce organisms that cannot interbreed

allopatric species - species occupying mutually exclusive geographical areas

allopolyploid - a type of polyploid species resulting from two different species interbreeding and combining their chromosomes

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

alloresponse - allorecognition, followed by the immune effector mechanisms generated by the recognition process

allosome - a chromosome which deviates in size, form or behavior from other chromosomes. An allosome is usually a sex chromosome

allotopic - refers to species with overlapping ranges but do not occupy the same space. They do not "live together"

allotype - in taxonomy, a paratype of the opposite sex to the holotype

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

alluvial - relating to mud and/or sand deposited by flowing water

alluvium - sediments deposited by erosional processes, usually by streams

almost atoll - an atoll whose rim is less than 75 percent complete as a circle at low tide

Along track Reef Imaging System (AtrIS) - a boat-mounted instrument that acquires continuous digital still EXIF-format images of shallow-marine substrates. Images are acquired via a digital still camera mounted in a waterproof housing that is deployed on a pole attached to a survey vessel. Images are instantaneously transferred to a shipboard computer and stored. AtrIS acquires high resolution, color digital images that are accurately geo-located in real-time. For a typical mission, 1,000 AtrIS images are captured per hour at a survey speed of 1 knot. AtrIS was developed by the U.S. Geological Survey

alpha animal - in animal behavior, the individual that takes a lead role and occupies the dominant position in a group

alpha particle - a particle emitted from the nucleus of an atom, containing two protons and two neutrons, identical to the nucleus (without the electrons) of a helium atom

alpha taxonomy - descriptive taxonomy concerned primarily with the discovery, description, and naming of species, usually on the basis of morphological characters

alternation of generations - a life cycle in which a multicellular diploid stage is followed by a haploid stage, and so on; found in land plants and many algae and fungi

alternative hypothesis - in statistics, the hypothesis that is adopted when the null hypothesis is rejected

altimeter - an instrument for measuring altitude

Artist's rendition of a satellite measuring altimetry.

altimetry - a technique to measure the height of the sea surface from radar pulses transmitted from a satellite

altricial - born or hatched undeveloped; requiring maternal care after birth; as opposed to precocial

altruism - a form of behavior in which an individual risks lowering its fitness for the benefit of another; in evolutionary biology, an organism is said to behave altruistically when its behavior benefits other organisms, at a cost to itself. The costs and benefits are measured in terms of reproductive fitness, or expected number of offspring

alveolus - one of thousands of tiny air sacs at the end of the bronchioles in lungs. Alveoli are the sites of gaseous exchange between the atmosphere and the blood. Oxygen passes into the lung capillaries and CO2 passes from the capillaries into the lungs and is exhaled

The sounds produced by the spotted boxfish, Ostracion meleagris, contribute to the ambient noise on Pacific reefs. (Photo: Hawai'i Coral Reef network)

ambient noise - acoustic signals originating from a variety of underwater sources, such as propeller cavitation, engine noises, animal sounds, wind, waves, and rain

ambient pressure - 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

ambit - the geographic range or extent in which an organism normally lives or grows

The ray of a starfish revealing the ambulacral groove and tube feet.

ambulacrum - a row of tube feet of an echinoderm

ambush predator - a predator that hides and waits for prey to pass in close proximity rather than actively hunting for it

amensalism - a type of symbiosis where two (or more) organisms from different species live in close proximity to one another, and where one of the members suffers as a result of the relationship while the other is unaffected by it

amino acid - 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 sequence - the order of amino acids as they occur in a polypeptide chain. This is referred to as the 'primary structure' of proteins

amino group - a nitrogen atom single-bonded to two hydrogen atoms (_NH2); imparts basic properties to an amino acid

amitosis - an unusual form of cell division in which the nucleus cleaves without change in its component structure (such as the formation of chromosomes), followed by the division of the cytoplasm. Amitosis may occur chiefly in highly specialized cells which are incapable of long-continued multiplication, in transitory structures, and in early stages of degeneration

ammonotelic - having ammonia as the chief excretory product of nitrogen metabolism

amnion - a non-vascular extra-embryonic membrane of amniote embryos that forms a fluid-filled cavity surrounding the embryo. It protects the embryo by functioning as a shock absorber

amniote - a vertebrate whose embryo is surrounded by a fluid-filled sac, the amnion; characteristic of reptiles, birds, and mammals

An amoeba thrusting out pseudopodia (false feet). (Photo: NASA)

amoeba - a-naked freshwater or marine protozoan protist that forms temporary pseudopodia for food and water capture, and locomotion -

amoebocyte - 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

amoeboid - amoeba-like

amoeboid movement - a type of motility of a cell in which cytoplasmic streaming (directional flow of cytoplasm) extrudes outward of the cell to form pseudopodia (false feet) so that the cell can change its location

amorphous - lacking a distinct form or shape

The African Bullfrog, Pyxicephalus adspersus. This amphibian is an inhabitant of Namibia. (Photo: Copyright Miguel Vences and Frank Glaw, 1998)

Amphibia - 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

Amphiblastula larva of a sponge. (Photo: Copyright BIODIDAC)

amphiblastula - a sponge larva that appears as a hollow ball with anterior flagellated cells and posterior larger and nonflagellated cells (megascleres)

amphidiploid - an allopolyploid; an organism produced by hybridization of two species followed by chromosome doubling

amphidromous - refers to the migratory behavior of fishes moving from fresh water to the ocean and vice versa, not for reproductive purposes but occurring regularly at some stage of the life cycle

amphimixis - sexual reproduction involving the fusion of male and female gametes and the formation of a zygote

amphipathic - refers to molecules with both hydrophobic and hydrophilic regions. Proteins and lipids may be amphipathic

amphophilic - having an affinity for both basic and acidic dyes

amplicon - the DNA product of a polymerase chain reaction (PCR), usually an amplified segment of a gene or DNA sequence

amplification - in genomics, the process of increasing the number of copies of a particular gene or chromosomal sequence

amplified ribosomal DNA restriction analysis (ARDRA) - DNA fingerprinting based on restriction patterns of ribosomal DNA. The method consists of amplification of the 16S rRNA gene (rDNA) and subsequent restriction digestion of the amplicon

ampulla - a membranous vesicle

The ampullae of Lorenzini are small vesicles and pores that form part of a subcutaneous sensory network of sharks. These vesicles and pores are found around the head of the shark and are visible to the naked eye. They appear as dark spots in this photograph of a porbeagle shark head. (Photo: Dr. Steven Campana, Bedford Institute of Oceanography)

ampullae of Lorenzini - 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

amural form - a coral growth form in which the corallite walls are partially or wholly lost; the septa stay unreduced

amylopectin - a highly branched polymer of glucose found in plants

amylose - a linear polymer of glucose

anabolism - the metabolic processes that consumes energy and involve the synthesis of larger, complex molecules from simpler ones

The chinook salmon is an anadromous fish which spends most of its life in the ocean, but returns to fresh water streams for spawning

anadromous species - a species that spends its adult life in the ocean but swims upriver to freshwater spawning grounds in order to reproduce, e.g., Pacific salmon

anaerobe - an organism that can live in the absence of oxygen

anaerobic - deriving energy from a process that does not require free oxygen

anagenesis - the evolutionary process whereby one species evolves into another without any splitting of the phylogenetic tree

anaglyph - a stereoscopic picture consisting of two images of the same object, taken from slightly different angles, in two complementary colors. When viewed through colored spectacles, the images merge to produce a stereoscopic sensation, i.e., that appears three-dimensional when superimposed; anything carved in low relief

Anal fin of a bony fish. (Photo: John Lyons, University of Wisconsin)

anal fin - the single fin situated on the ventral midline of a fish, behind the anus, and anterior to the caudal fin

analgesia - the absence of pain in response to stimulation that would normally be painful

analgesic - any drug intended to alleviate pain. Analgesics increase a patient's pain threshold, thereby decreasing the sensation of pain. Analgesics range from aspirin and acetaminophen to narcotics

analogous behavior - behavior exhibited by different species that is similar in function, but does not originate from a common ancestry

analogous structure - a body part that serves the same function in different organisms, but differs in structure and embryological development, e.g., the wing of an insect and a bird

analysis of covariance - an analysis of variance in which the data are adjusted or controlled for the presence of one or more other variables

analysis of variance - a statistical technique for testing for differences in the means of several data populations

Fish eggs and larvae. These aquatic vertebrates do not possess an amnion during embryonic development. (Photo: NOAA/National Marine Fisheries Service)

anamniote - an aquatic vertebrate whose embryonic stage is not surrounded by an amnion. Fishes and amphibians are anamniotes

anaphylaxis - a severe, potentially life-threatening, allergic reaction, which can occur after an animal sting or as a reaction to an injected drug. Less commonly, the reaction occurs after a particular food or drug has been taken by mouth. Symptoms may include vascular collapse, shock and respiratory distress; also called "anaphylactic shock"

anastomose - a term that refers to coral branches which grow back together after the initial division

anastomosis - the union or connecting of branches forming a meshwork or a network

anatomy - the science of internal morphology as revealed by dissection

ancestor - any organism, population, or species from which some other organism, population, or species is descended

ancestral - in evolution, a trait that has been inherited unchanged from an ancestor

ancestral polyp - an anthozoan polyp which develops from a sexually produced larva and gives rise to a colony by asexual budding

ancestral trait - a trait shared by a group of organisms as a result of descent from a common ancestor

ancestrula - the first (parental) zooid of a bryozoan colony, formed from a settled and metamorphosed larva. It is often smaller and morphologically distinct from the zooids that bud from it

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

An anchialine pool, Halua Pond, located in the Ühihi-Kïna'u Reserve, Maui (Photo: Hawai'i's Natural Area Reserves System (NARS))

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

Andavadoaka - a small fishing village located on the southwestern coast of Madagascar. It lies on the edge of a shallow lagoon protected from the open ocean by a series of fringing and submerged barrier reefs The coral reefs, including patch reefs, in the region are in generally pristine shape, ranging from moderate to excellent. The reefs are not directly threatened by terrigenous sedimentation, as elsewhere in the country, due to the absence of major rivers. However, they are at risk from over fishing from a still small but rapidly increasing population of Vezo fishermen. Conservation efforts are currently underway to maintain the present status of these coral reefs, including the establishment of a marine protected area network encompassing parts of the barrier and patch reef systems

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

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

anemochory - the dispersal of seeds, fruits, or other plant parts by wind

anemometer - an instrument for measuring wind velocity

A sea anemone of the Phylum Cnidaria, Class Anthozoa. The tentacles bear stinging cells which are used for food capture and defense.

anemone - a cnidarian of the class Anthozoa that possesses a flexible cylindrical body and a central mouth surrounded by tentacles

aneuploidy - the condition of having an abnormal number of chromosomes; a chromosome number that is not an exact multiple of the haploid number

The yellowmask angelfish (Pomacanthus xanthometopon) photographed on a reef in Papua New Guinea (Photo: Tom Doeppner/Brown University)

angelfish - any species of colorful deep-bodied, laterally compressed, spiny-rayed fishes in the family Pomacanthidae. They resemble the closely related butterfly fishes, but generally possess a more robust body and a sharp preopercular spine. There are other kinds of unrelated fresh water angelfishes, belonging to the family Cichlidae, which are common home aquarium fishes

angiogenesis - the growth and proliferation of new blood vessels. Angiogenesis is a normal biological process that occurs in both healthy and disease states. It is essential for the growth of tumors. Tumor cells release chemicals to encourage blood vessel growth for their nourishment

A skiff, a guide, and an angler fishing for bonefish in Florida. (Photo: Bonefish and Tarpon Unlimited)

angler - a person catching fish or shell fish with no intent to sell; includes people releasing the catch

angstrom - a unit of length equal to one ten-thousandth of a micron (10-4 micron) or 10-10 of a meter

The oyster toadfish, Opsanus tau, produces sounds during the reproductive season.These sounds facilitate mating. (Photo: NOAA)

animal communication - animals use several ways to communicate with one another. These include the visual, auditory, and tactile senses, as well as certain chemicals involved in taste and smell. Other possibilities are magnetic fields and electrical discharges. Communication among animals helps them to recognize each other, cause reproductive behavior, and to organize social behaviors

animal hemisphere - the half of an oocyte or egg which contains less yolk, or the corresponding half of an early embryo with the more actively dividing cells

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

Animalia - the kingdom of multicellular heterotrophic eukaryotes that are capable of motility during some stage of their life history

animated GIF (Graphics Interchange Format) file - a graphic image on a Web page that moves

anisogamous - characterized by reproducing by the fusion of gametes that differ only in size, as opposed to gametes that are produced by oogamous species. Gametes of oogamous species, such as egg and sperm cells, are highly differentiated

ankylose - to fuse together

anneal - the pairing of complementary DNA or RNA sequences, via hydrogen bonding, to form a double-stranded polynucleotide. It is most often used to describe the binding of a short primer or probe

A marine segmented worm of the phylum Annelida.

Annelida - an animal phylum that comprises the segmented worms, and includes earthworms, leeches, and a number of marine and freshwater species

Annual Composite HotSpot map - a map that composites all of the average monthly HotSpot (see HotSpot) images for a given year

annular - ring-shaped

annulation - a circular or ring-like formation

annulus - a mark or ring that forms annually on the otoliths, scales, and bones of fishes that correspond to the annual period of growth. Annuli can be use to determine age and growth rates of fishes

anomaly - the deviation of a particular variable (e.g., temperature) from the mean or normal over a specified time

anonymous work - according to the International Code of Zoological Nomenclature, a published work that does not state the name of the author(s)

anoxic - the absence of free oxygen

antagonistic pleiotropy - in genetics, a situation in which a single gene creates multiple competing effects, such that beneficial effects of a trait created by the gene are offset by "losses" in other traits

A spiny lobster displaying its paired uniramous antennae and biramous antennules. (Photo: Copyright Corel Corporation)

antenna - one of the paired, flexible, and jointed sensory appendages on the head of a crustacean, an insect, or a myriapod (e.g., a centipede)

antennal gland - the main organ in crustaceans used for excretion and osmoregulation; the green gland

antennular fosette - in crustaceans, a depression, pit or socket containing the basal portion of the antennule

antennule - a small antenna, especially the first pair of antennae in crustaceans

Close up of the anterior end of a spotlight parrotfish supermale.

anterior - morphologically, toward the head or front end of an individual, or proximal portion of a bodily part

anteromesal - in the front and along the midline of a body

anteroposterior axis - the longitudinal axis of an animal, from head to tail

anthoblast - in stony corals, a young sessile polyp producing an anthocyathus, the disklike crown that separates from the stalk (anthocaulus)

anthocaulus - a polyp that develops asexually on the skeletons of some coral species

anthocodium - the free oral end of an anthozoan polyp, the basal portion of which is united with other zooids in a common mass; the upper tentacular part of the polyp that can be retracted into the calyx; It is a site of bioluminescence in some anthozoans

anthocyathus - the disklike crown portion of solitary stony corals that separates from the stalk (anthocaulus)

anthostele - 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

A deep-sea anemone photographed by the Alvin 2001 during a survey of Blake Ridge off the U.S. Georgia coast (Deep East expedition).

Anthozoa - a class of Cnidaria that includes the stony corals, soft corals, sea anemones, gorgonians, and corallimorpharians

anthozooid - any of the individual zooids of a compound anthozoan

anthropogenic - made by people or resulting from human activities

anthropomorphism - attributing a human characteristic to an inanimate object or a non-human species

anti-codon - 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

antibiosis - an antagonistic association between two organisms in which one of the organisms is adversely affected; an association between organisms that is harmful to one of them or between organisms and a metabolic product of another; the inhibition of growth of a microorganism by a substance produced by another microorganism

antibiotic - a chemical substance, e.g., penicillin, that kills or inhibits the growth of bacteria

antibody - a protein produced by higher animals in response to the presence of a specific antigen

This stonefish possesses anticryptic coloration, allowing it to blend in with the surrounding environment. (Photo: David Burdick)

anticryptic coloration - a color or color pattern used for concealment by a predator

anticyclone - an area of high pressure. Circulation is clockwise around the high in the Northern Hemisphere and counterclockwise in the Southern Hemisphere

antigen - a foreign macromolecule introduced into a host organism that elicits an immune response

antigenicity - the ability of an antigen to induce an immune response and combine with specific antibodies or T-cell receptors

antihelmintic - a chemical agent used to combat parasitic worms, such as roundworms and tape worms

Antillean z trap - a common type of fish trap used widely in the Caribbean and elsewhere. It takes the form of a double chevron or "Z" with two down-curving "horse-neck" entrance funnels. Typically, these measure between 180 and 230 cm in length and are 60 cm high

Antilles Current - one of the currents of the North Atlantic subtropical gyre flowing along the northern side of the Greater Antilles. Its water is supplied from the northern branch of the North Equatorial Current, drawn mainly from the Gulf Stream recirculation. The Antilles Current merges with the Florida Current east of the Straits of Florida

antinutrient - a compounds that inhibits the normal uptake of nutrients

antioxidant - a molecule that is capable of reacting with free radicals and neutralizing them; a compound that slows the rate of oxidation reactions

antioxidant - a substance that prevents cellular damage caused by free radicals, which are are highly reactive chemicals that often contain oxygen. They are produced when molecules are split to yield products that have unpaired electrons (oxidation). Antioxidants counteract the damaging effects of oxidation in body tissues

Black coral in the order Antipatharia.

Antipatharia - an order of corals which contains the black and horny corals

antipathin - a proteinaceous and chitinous material that forms the axis in an antipatharian coral

antipodal - diametrically opposite; located on the opposite side

antisense DNA - the strand of chromosomal DNA that is transcribed; a DNA sequence that is complementary to all or part of an mRNA molecule

antisymmetry - a pattern of deviation without a side bias. A side difference occurs for a given trait, but the larger side varies at random among individuals

antitoxin - a substance that neutralizes a toxin

antivenom (or antivenin, or antivenene) - a biological product (antitoxin) used in the treatment of venomous bites and stings

antrum - a hollow space or cavity

anus - the posterior opening of the digestive tract, through which waste products of digestion are released

aperture - an opening in some structure. For example, the opening in a snail's shell through which the snail emerges

apex - the tip, top, point, or angular summit of anything

This large blue shark is an apex predator in the ocean. (Photo: Greg Skomal, NOAA/NOS National Marine Sanctuaries)

apex predator - a predator which is not itself preyed upon as a species. These animals are often at the end of food chains, where they have a crucial role in maintaining and determining the health of ecosystems

aphorism - a concise statement of a general truth; a short pithy instructive saying

aphotic zone - that portion of the ocean where light is insufficient for plants to carry on photosynthesis

aphrioid form - a coral growth form in which the septa are reduced at their outer ends so neighbouring corallites are united by a zone of dissepiments (horizontal partitions within or outside of a corallite)

apical - relating to or located at the tip (an apex), or opposite to the base

apiculate - ending in a short, sharp point

Aplacophora - a class of Mollusca. They are a small group (less than 300 species) of wormlike mollusks that lack a shell. Some are associated with soft corals. Creeping species feed on cnidarians. Burrowing species are deposit feeders and carnivores

apobiosis - the local death of a part of an organism

Apode fishes, such as the American and European eel (Anguilla sp), lack pelvic (ventral) fins (Photo: NOAA Photo Library collection)

apode fish - a fish which lacks pelvic (ventral) fins, such as the American or European eel

apogee - 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

apomixis - the asexual production of diploid offspring without the fusion of gametes. The embryo develops by mitotic division of the maternal or paternal gamete, or in the case of plants, by mitotic division of a diploid cell of the ovule

apomixis - in flowering plants, asexual reproduction through seed

apomorph - a derived character differing from the ancestral condition

apomorphy - a relatively derived or advanced or unique character state

apopinacocyte - in sponges, an endopinacocyte lining the excurrent canal

apopinacoderm - in sponges, a surface lined with apopinacocytes

apoptosis - a normal cellular process involving a genetically programmed series of events leading to the death of a cell; also called "programmed cell death (PCD)" or "cell suicide"

apopyle - the opening of a choanocyte chamber of a sponge into an excurrent canal

aporrhysa - the exhalent canals in sponges

A venemous lionfish (Pterois volitans) with conspicuous coloration. (Photo: Copyright Corel Corporation)

aposematism - conspicuous warning coloration

aposymbiosis - loss of a symbiont, such as zooxanthellae in hard corals

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

appeasement behavior - any conciliatory behavioral display. Appeasement cues often are exhibited toward threatening conspecifics when flight is either difficult or impossible; conciliation directed toward an aggressor or potential aggressor

appendage - any body part that extends from the main axis or trunk or cephalized portion of an organism

appendicular - relating to the appendages, as opposed to axial, which refers to the trunk and head of an organism

applet - a small Java program that can be embedded in a web page to create special effects. Applets differ from full-fledged Java code. They are not allowed to access certain resources on the local computer such as files and serial devices, and are prohibited from communicating with most other computers across a network

apprehensive behavior - any behavior that indicates an organism' s anticipation of an adverse or noxious experience. Some behaviors include high level of alertness, defensive postures, and threat displays

approximate - in morphlogy, placed close together

apron reef - the initial stage of a fringing reef. It is discontinuous and covers a small area

Aquaculture tanks located in in green houses. (Photo: Eileen McVey, NOAA)

aquaculture - 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

aquarist - a hobbiest or professional that keeps organisms in an aquarium

The Aquarius, an underwater ocean laboratory located in the NOAA Florida Keys National Marine Sanctuary. (Photo: NOAA/OAR National Undersea Research Program)

Aquarius - 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

aqueous solution - a solution in which water is the solvent

Diagram of an aquifer system. (Diagram: Texas A&M Univ.)

aquifer - a subterranean layer of porous water-bearing rock, gravel, or sand capable of storing and conveying water to wells and streams

aquiferous system - water circulatory system in sponges composed of choanoderm, pores and chambers

Ara-A - an antiviral drug developed from the discovery of particular nucleosides (the basis of synthesis of Ara-A) in the marine sponge Cryptotethia crypta

Ara-C - an anticancer drug developed from the discovery of particular nucleosides (the basis of synthesis of Ara-C) in the marine sponge Cryptotethia crypta

arachnactis - a planktonic larva of tube anemones (Ceriantharia)

Arachnida - a class of chiefly terrestrial arthropods, which includes spiders, ticks, mites, whipscorpions, pseudoscorpions, and harvestmen. Some species inhabit fresh waters and marine waters

aragonite - a mineral species of calcium carbonate (CaCO3) with a crystal structure different from the other two forms of CaCO3 (vaterite and calcite). It is precipitated from ocean surface waters mainly by organisms (e.g., coral) that use it to make their shells and skeletons

aragonite saturation horizon - a natural boundary in the oceans below which organisms such as stony corals cannot maintain calcium carbonate structures. As carbon dioxide levels increase, the aragonite saturation horizon becomes shallower, severely limiting the distribution of stony corals in certain parts of the deep ocean; the limit between undersaturation and supersaturation of aragonite

aragonite skeleton - skeletons primarily composed of the aragonite form of calcium carbonate

arborescent - having a large tree-like appearance

arborescent colony - a coral colony with a tree-like growth structure

arc - in a geographical information system (GIS), an arc is a line that begin and end with a node. Intersections of arcs are always connected with a node. Arcs also make up part of a polygon

Arc/INFO - geographical information system (GIS) software developed by ESRI that is used to do more robust GIS operations

ArcCatalog - similar to Windows Explorer, ArcCatalog was designed by ESRI to transfer ESRI and other database documents without corrupting their file structure. This program was specifically designed to recognize all the relevant files that must be transferred with shapefiles, coverages, and all of the other types of map documents

ArcEditor - the midlevel software suite designed for advanced editing of spatial data published in the proprietary ESRI format. It provides tools for the creation of map and spatial data used in geographic information systems (GIS)

ArcGIS - a group of geographic Information System (GIS) software product lines produced by the Environmental Systems Research Institute (ESRI)

arch- - a prefix meaning 'ultimate beginning'

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

Archaebacteria - an ancient group of prokaryotes, over 3.5 billion years old; sometimes this group is placed into a separate kingdom, the Archaea. Most biologists currently place it within the Kingdom Monera. Archaebacteria inhabit extreme environments

archaeocyte - in sponges, an amoeboid cell capable of phagocytosis. Archaeocytes are totipotent, having the capability of differentiating into other types of sponge cells

archenteron - 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

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

archi- - a prefix meaning primitive, original, or ancestral

archipelago - a cluster of islands usually in the open ocean. Archipelagos are often volcanic, forming along ocean ridges or hotspots. Examples of archipelagos are the Japanese islands, the Hawaiian Islands, the Philippines, and the Malay archipelago,which includes all of the islands of Indonesia

arciform - bow-shaped

ArcIMS - ESRI software that allows for centrally hosting and serving GIS maps, data, and applications for use on the Internet

ArcMap - a component of ESRI's ArcGIS developed as client software specifically for the Microsoft Windows environment to enable more intuitive processing and presentation of ArcGIS data

ArcScene - a 3D visualization application designed by ESRI that allows one to view GIS data in three dimensions

arcuate - crescent-shaped

ArcView - desktop geographical information system (GIS) software developed by ESRI used to do some basic GIS operations and print maps

area cladogram - a dendrogram that displays historical relationships among geographic areas, rather than phylogenetic relationships among taxa

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

arenicolous - living in sand

a grouper with an areolate pattern of pigment (Photo: Agriculture, Fisheries and Conservation Department, Hong Kong)

areolate - appearance of a surface characterized by circular spots of tissue or areolae

argent - silvery color

A vessel preparing to recover an ARGO float. (Photo: Japan Coast Guard)

ARGO Project - Argo is a global array of 3,000 free-drifting profiling floats that measures the temperature and salinity of the upper 2000 m of the ocean. This allows continuous monitoring of the temperature, salinity, and velocity of the upper ocean, with all data being relayed and made publicly available within hours after collection

Aristotle's lantern - a highly developed chewing apparatus used for feeding in some sea urchins

ARKive - a not-for-profit, UK-based organization whose mission is ‘to promote the conservation of nature and public appreciation of biodiversity, through the power of wildlife imagery.' by finding, sorting, cataloging and copying the key audio-visual records of the world’s animals, plants and fungi, and building them into comprehensive and enduring multi-media digital profiles (http://www.arkive.org/coral/Coral/coral.html)

ARMDES (AIMS Reef Monitoring Data Entry System) adapted database) - a data entry and analysis program running on Microsoft Access, which enables users to input data from line transects, manta tows, and fish visual censuses into a standard access database and to carry out basic analysis of the data. It was created by AIMS and is distributed free of charge

aromatic - a type of hydrocarbon, such as benzene or toluene, with a specific type of ring structure

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

arrhenotoky, arrhenotokous - parthenogenetic production of haploid males from unfertilized eggs. Fertilized eggs produce viable diploid females

arribada - a large aggregation of female sea turtles coming to shore to nest at the same place and at the same time

ARS (autonomous replicating sequence) - any eukaryotic DNA sequence that initiates and supports chromosomal replication; also called autonomous(ly) replicating segment

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

artesian pressure - hydrostatic pressure of artesian water, often expressed in terms of pounds per square inch; or the height, in feet above the land surface, of a column of water that would be supported by the pressure

artesian water - groundwater confined in an aquifer and under pressure great enough to cause the water to rise above the top of the aquifer when it is tapped by a well

artesian well - a well tapping a confined aquifer.  Water in the well rises above the top of the aquifer under artesian pressure, but does not necessarily reach the land surface; a flowing artesian well is a well in which the water level is above the land surface

A spiny lobster (phylum Arthropoda).

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

articular - pertaining to a joint

articulated - jointed, as in for example, the soft fin rays of fishes

articulating - united by means of a moveable joint

artifact - an object made by human workmanship, usually for some practical purpose

artificial classification - in taxonomy, classification based on convenient or conspicuous diagnostic characters without attention to characters which indicate phylogenetic relationship; often a classification based on a single arbitrarily chosen character, rather than an evaluation of the totality of characters

These concrete blocks were the first artificial structures deployed to provide a substrate for reestablishing colonies of Oculina coral (Oculina varicosa) and simulating fish habitat on Oculina Bank (central Florida Atlantic coast), which were destroyed by bottom trawling in the 1990s.

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

artificial selection - the practice of choosing individuals from a population for reproduction (selective breeding), usually because these individuals possess one or more desirable traits

artificial selection - a process in which humans select desireable genetic characteristics in plants and animals and selectively breed those animals and cultivate those plants to ensure that future generations of descendents have those specific desireable traits

artisanal fishing - fishing which is typically a small-scale operation that uses simple fishing methods; fishing for subsistence by coastal or ethnic island groups using traditional methods; fishing with the purpose of catching/collecting aquatic products for sale

These adult ascideans (sea squirts) resemble invertebrates, but they are closely related to vertebrates and other members of the phylum Chordata.

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

ASCII (American Standard Code for Information Interchange) - a set of codes for representing alphanumeric information (e.g., a byte with a value of 77 represents a capital M). Text files, such as those created with the text editor of a computer system, are often referred to as ASCII files

asco - a prefix meaning "sack"

Asconoid sponges have the simplest organization. Flagellated choanocytes line the spongocoel, drawing water through small ostia and expelling it through the osculum. (Illustration: BIODIDAC)

asconoid - simplest body form of sponges, with canals leading directly from the surrounding water to the interior spongocoel

ase - a suffix used for the name of an enzyme, e.g., polymerase, lipase, cellulase

asexual embryogenesis - the sequence of events whereby embryos develop from somatic cells

asexual reproduction - reproduction that does not involve the union of sex cells (gametes) to produce a zygote. Examples in corals are budding and fragmentation

Asia-Pacific-Network for Global Change Research (APN) - an inter-governmental network for the promotion of global change research and links between science and policy making in the Asia-Pacific Region

aspergilliform - brush-shaped

A Caribbean sea fan infected with the fungus Aspergillus. (Photo: NOAA Coral Health and Monitoring Program)

aspergillosis - a widespread fungal infection of Caribbean soft corals. It affects six species of sea fans and sea whips. The pathogen is Aspergillus sydowii, a terrestrial fungus which infects gorgonia after germination of spores on the coral surface. This is followed by penetration and spread of hyphae in coral tissue, resulting in highly visible lesions which may be associated with complete loss of tissue and skeleton. Lesions often occur at multiple sites across an infected colony.-Purple galls may be produced by the coral host to encapsulate fungal hyphae.

asperity - a peak or projection from a surface; pertains to roughness of a surface

assay - in general, the qualitative or quantitative analysis of a substance to determine its constituents and the relative proportion of each, or to determine the biological, chemical, or pharmacological potency of a drug

assemblage - a group or association of interacting populations of organisms in a given area or volume

assimilation - the biological process of absorbing nutrients into an organism's body after digestion

assimilation efficiency - the fraction of ingested food that is absorbed and used in metabolism

association - a group of species living in the same place at the same time

Association of Marine Laboratories of the Caribbean (AMLC) - AMLC is a confederation of more than 30 marine research, education, and resource management institutions endeavoring to encourage the production and exchange of research and resource management information, advance the cause of marine and environmental education in the region, and facilitate cooperation and mutual assistance among its membership. It was founded in 1956 by marine researchers with interests in the marine science of the tropical Atlantic and the Caribbean. The strength of AMLC lies in the diversity of its member laboratories and the extensive expertise of its membership

astaxanthin - a carotenoid pigment found in crustaceans. Astaxanthins may give a green color to the musculature of fishes which feed on crustaceans

astern - behind the vessel; toward the rear of the vessel

asthenosphere - a layer of soft but solid, mobile rock comprising the lower part of the upper mantle from about 100 to 350 km beneath the Earth's surface

asymmetric competition - competition between two organisms (or species) in which one is much more adversely affected than the other

asymmetry - the lack or absence of balanced proportions between parts of a thing; without symmetry

ata (atmosphere absolute) - one (1) ata is the atmospheric pressure at sea level

atavism - the reapperance of an ancestral character after an interval of generations

atmosphere - a unit of pressure, abbreviated as atm; "one atmosphere" is the pressure of the atmosphere at sea level, i.e., 760 mm Hg. Two atmospheres is twice this pressure, 1520 mm Hg, etc.; the air surrounding the earth, from sea level to outer space

atmospheric pressure - the pressure of the atmosphere at any given altitude or location; it is synonymous with barometric pressure

atoke - the anterior, nonreproductive part of a marine polychaete worm, as distinct from the posterior, reproductive part (epitoke) during the reproductive season

A small Pacific atoll. Note the coral reef encircling the calm and shallow lagoon.

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

atom - the smallest component of an element, made up of neutrons, protons, and electrons

ATPase - an enzyme that functions in producing or using adenosine triphosphate (ATP)

atresia - an abnormal condition in which a normal opening or tube in the body is closed or absent

atrial siphon - in tunicates, the opening that carries water, wastes, and gametes from the organism. Also called the excurrent or exhalent siphon/canal

atrichous - in Cnidaria, lacking spines or barbs

atrichous isorhiza - in hydrozoans, a small cnidocyst (nematocyst) with a smooth tubule.These are only type of cnidocysts found in all the classes of Hydrozoa. they are never very common, but all the classes have some species with them .This type of cnidocyst occurs also in the Anthozoa, Cubozoa and Scyphozoa

atrium - a cavity or passageway; a heart chamber which receives blood

atrophy - a wasting or decrease in size of a tissue or organ because of a reduction in the size or number of its cells. Atrophy may result from cellular death, reduced cellular division, pressure, ischemia, malnutrition, decreased activity or hormonal changes

atrous - jet black color

attachment stage - a stage in an animal's life cycle when it ceases being free swimming or motile, and becomes attached to a substrate

attendant male - a male fish which is not a member of a spawning pair, but hovers close by; often a sneaky male

attitude - in animal behavior, the posture or expression assumed by an organism

attribute - a measurable component of a biological system; a particular feature or character possessed by an organism

auditory ossicle - one of a series of bones conducting sound in some fishes

aulostomatous - having a tubular-shaped mouth, such as a cornetfish

aureate - golden yellow in color

Late-stage auricularia of Stichopus californicus - ca. 17-18 days old, raised in culture by T.H.J. Gilmour. (Photo: University of Saskatchewan Archives)

auricularia larva - larva of a sea cucumber; an early bipennaria larva of a starfish

austral - relating to or coming from the south; of the south temperate region, between the antarctic and tropical regions

Australian Centre of Excellence for Innovative science for sustainable management of coral reef biodiversity - the primary goal of this Australian Research Council Centre of Excellence is to undertake research programs of international significance (through the establishment of new collaborative teams of Australia’s leading coral reef researchers) that transcend traditional disciplinary, institutional and geographic boundaries. The Centre of Excellence cements Australia’s leading contribution to coral reef sciences, and fosters stronger collaborative links between James Cook University, The Australian National University, University of Queensland, and 28 other leading institutions in nine countries. Collectively, the JCU-led Centre creates the world’s largest concentration of coral reef scientists. The aim is to add focus, scale and scope to build an enduring program of innovative research development, leading to world leadership in coral reef science. A key outcome of the Centre of Excellence is to actively transfer scientific knowledge to industry partners and end-users, to increase their capacity and effectiveness, and provide benefits to all Australians

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

autecology - the ecology of a single species

author - in taxonomy, the person(s) to whom a work, a scientific name, or a nomenclatural act is attributed

authority - in taxonomy, the name of the author of a taxonomic name, cited after the name

autochory - the process of seeds and fruits dispersal by means of some kind of explosive physical expulsion.The fruit "explodes", propelling its seeds some distance to the ground surrounding the parent plant; also called "discharge dispersal"

autochthonous - native; indigenous; originating or occurring naturally in the place specified

autoepizooism - settlement and growth of hydrozoan colonies on older animals of the same species

autoevisceration - ejection of intestines and associated organs, in animals such as sea cucumbers, caused by adverse environmental conditions. Regeneration of the organs may occur within weeks

autoimmune disease - a disease in which the organism produces antibodies against its own tissues

autoimmunity - 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

autologous cells - cells that are taken from an individual, cultured, and possibly genetically manipulated before being infused back into the original donor

autolysis - the spontaneous disintegration of cells or tissues by the organism's proteolytic enzymes and macrophage activity, as occurs after death and in some pathologic conditions

automated bleaching early warning system - automated bleaching alerts/warnings directly from satellite and/or in situ derived indices

automyxis - obligatory self-fertilization

autonomous underwater vehicle (AUV) - an unmanned, battery or fuel cell-operated underwater robot or vehicle which can operate at depths greater than 6000 meters. Autonomous underwater vehicles carry sensors to navigate autonomously and map features of the ocean floor. They should not be confused with remotely operated vehicles (ROV) that are controlled and powered from the surface by an operator/pilot via an umbilical; AUVs are also known as Unmanned Undersea Vehicles (UUV)

autopolyploid - a polyploid formed from the doubling of a single genome

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

autoskeleton - the endoskeleton of sponges, comprised of spicules or spongin fibers

autosome - any chromosome that is not a sex chromosome; distinguished from a sex chromosome

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

autotrophic - relating to organisms that have a type of nutrition in which organic compounds used in metabolism are obtained by synthesis from inorganic compounds

autozooecium - a tube that encloses a bryozoan autozooid

autozooid - a feeding polyp of a bryozoan (Ectoprocta). Autozooids compose the majority of a bryozoan colony

autumnal equinox - the equinox at which the sun approaches the Southern Hemisphere and passes directly over the equator. It occurs around September 23

auxesis - to grow; growth resulting from increase in cell size without cell division

auxotroph - a polyploid formed from the doubling of a single genome

auxotroph - 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

available name - in taxonomy, any name which conforms to all mandatory provisions of the Code. There are general requirements of publication and date, language, name formation etc. An available name is not necessarily a valid name, as an available name may be in synonymy. Conversely a valid name must always be an available one

aversive stimulus - a noxious stimulus in its immmediate environment that an organism tends to remove or avoid

Aves - the name of the class of vertebrates that consists exclusively of birds; the Latin word for "bird"

Artist's rendition of POES satellite.

AVHRR (Advanced Very High Resolution Radiometer) - a broad-band, four or five channel (depending on the model) scanner, sensing in the visible, near-infrared, and thermal infrared portions of the electromagnetic spectrum. This sensor is carried on NOAA's Polar Orbiting Environmental Satellites (POES). AVHRR is used for studying and monitoring vegetation conditions. Applications include agricultural assessment, land cover mapping, producing image maps of large areas and tracking regional and continental snow cover. AVHRR data are also used to retrieve various geophysical parameters such as sea surface temperatures (SST) and energy budget data

avian - of, relating to, or characteristic of birds

A magnified view of an avicularium from the marine colonial bryozoan Bugula sp. (Photo: Dr. Rick Gillis, Biol. Dept., Univ. of Wisconsin)

avicularium - a small bryozoan heterozooid in which the zooecium and operculum form a beak-like, snapping structure that deters small predators

avifauna - the birds of a specific region or period

avirulent - unable to cause disease

Avogadro's number - a large constant used in chemistry and physics. It is the number of molecules (6.02214 × 10 23 )in one mole of substance; also called "Avogadro's Constant"

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 Access¼ 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

axenic - a culture containing only one type of microorganism; not contaminated by or completely free of the presence of other organisms; a pure culture

axial - refers to the head and trunk of an individual

axial corallite - a corallite which forms the tip of a branch

axial cortex - the layer around the central core of the axis of an octocoral

axial polyp - the longest polyp of a group of polyps which produces secondary polyps by budding

axial sheath - the coenenchyme which surrouds the axis on the Gorgonacea and Pennatulacea

axial skeleton - in a vertebrate skeleton, the skull, vertebral column, ribs, and sternum

axial swimming - the predominant swimming mode of fishes. This swimming movement involves lateral bending of the body caused by contractions of the lateral body musculature and oscillating movements of the caudal fin

axis - the internal, usually calcium carbonate skeletal rod of sea fans (Gorgonacea) and sea pens (Pennatulacea)

axis epithelium - the layer of ectodermally-derived cells which consists of corticocytes, which produce the axis, and desmocytes, which attach tissues to the axis

axocoel - the most anterior of three coelomic spaces that appear during larval development of echinoderms

axon - the single motor branch of a neuron that passes the nervous impulse away from the cell body to another neuron or effector organ

axoneme - a bundle of microtubules and other proteins forming the core of each cilium or flagellum

azooxanthellate coral - a coral which does not have symbiotic zooxanthellae in its tissues

azure - light or sky blue color