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Glossary of Terminology: A

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Number of records found : 430


Image of an abalone

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


abalone - a univalve mollusk (class Gastropoda) of the genus Haliotis. Abalones are harvested commercially for food consumption. The shell is lined with mother-of-pearl and used for commercial (ornamental) purposes

abatement - reducing the degree or intensity of, or eliminating

abaxial - away from, or distant from the axis

abbreviate - shortened

Image of lobster abdomen

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


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    

abdominal fin - a term used to describe the location of the pelvic (ventral) fins when they are inserted far behind pectorals. This is the more primitive condition. More recently evolved conditions have the pelvic fins in the thoracic or jugular positions. A salmon, for example, has its pelvic fins in the abdominal position. An angelfish has the pelvic fins in the thoracic position, and blennies have the pelvic fins in the jugular position, anterior to the pelvic girdle

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

abiogenic - refers to things not involved with or produced by living organisms

abiotic - refers to nonliving objects, substances or processes

ablation - the experimental removal or killing of some part of an organism

abnormal - not normal; contrary to the usual structure, position, behavior or rule

Image of sea urchins

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


aboral - situated opposite to, or away from the mouth; normally used to describe radially symmetrical animals, such as starfishes, sea urchins, and jellyfishes

abraded - worn or frayed

abranchiate - lacking gills

abrasion - the mechanical process of gradually breaking down a hard layer

absolute tautonymy - in taxonomy, the identical spelling of a generic-group name and one of its included specific-group names, such as the fish, Badis badis, or the western lowland gorilla, Gorilla gorilla gorilla

absolute zero - the temperature at which all motion will cease (0 degrees Kelvin or -273.15 degrees C)

absorption - the biological process that follows digestion, by which the products of digestion are transferred into the organism's internal environment, enabling them to reach the cells

Image of a tapeworm

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)


absorptive feeder - an animal, such as a parasitic tapeworm, that absorbs digested food products through the body wall

abundance - the number or amount of something, e.g., the number of organisms per unit of habitat space or number of individuals in a stock or a population

Image of Crown-of-Thorns starfish

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


Acanthaster - the Crown-of-Thorns starfish genus. Acanthaster planci is a voracious Indo-Pacific predator of corals

Image of an Acanthocephala

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)


acantho- - a prefix meaning "with spines"

acanthocaulus - a juvenile coral of some species that is attached to the substrate either directly or on a stalk

acanthoid - thorny, spiny, sharp

acanthotrich (acanthotrichium) - in fishes, a spiny dorsal or anal fin ray

acaudal - lacking a tail

acaudal - lacking a tail

accepted name - in taxonomy, a name adopted by an author as the correct name for a taxon

accessory pigment - a photosynthetic pigment which absorbs light and transfers energy to chlorophylls during photosynthesis

accessory respiratory organ - in fishes, a superficial or internal organ which complements the gills in respiration when the fish is in poorly oxygenated water or in air

acclimation (acclimatization) - a change that occurs in an organism to allow it to tolerate a new environment

accretion - growth by virtue of an increase in intercellular material

accuracy - the closeness by which a set of measurements approaches the true value

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

aciculate - needle-like or having needle-like parts

acid - a substance that increases the hydrogen ion concentration in a solution

acid rain - the precipitation of sulfuric acid and other acids as rain. The acids form when sulfur dioxide and nitrogen oxides released during the combustion of fossil fuels combine with water and oxygen in the atmosphere

acidic - having a pH of less than 7

acidophilia - an abnormal increase in the number of eosinophils in the blood which is characteristic of allergic states and various parasitic infections; also called "eosinophilia"

acidophilous - having an affinity for or thriving in acidic conditions, e.g., in a bog or marsh

Image of acoelomate flatworm

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


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)

acolonial coral - a solitary coral that does not form a colony

acontium - a thread-like part of a coral polyp's or anemone's digestive system and employed as defensive or aggressive structures when extruded

acoustic scattering - the irregular reflection, refraction, or diffraction of a sound in many directions

Image of a loggerhead turtle

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


acoustic tag - a sound transmittor attached to an aquatic animal to track its movements

acquired - developed in response to the environment, not inherited, such as a character trait resulting from environmental effects (acquired characteristic)

acquired character - a non-inherited character, of function or structure, developed in an organism as a result of environmental influences during the individual's life

Image of staghorn coral

Staghorn coral (Acropora sp.).


Acropora - a genus of hard (stony) corals that contain the elkhorn and staghorn corals

acrorhagus - a sac, covered with nematocysts, that protrudes from below the sweeper tentacles or on the column of certain anthozoans

acrosome - a protrusion on the anterior end of a sperm cell that contains digestive enzymes that enables the sperm cell to penetrate the layers around the oocyte (ovum)

acrosphere - the knobbed tentacle tip of an anthozoan, usually bearing numerous nematocysts

actic - pertains to littoral rocky shores as a habitat

actin - a contractile protein found in muscle cells. Together with myosin, actin provides the mechanism for muscle contraction

actinometer - an instrument for measuring incident radiation

actinopharynx - the tubular throat of an anthozoan polyp that lies between the mouth and the gastric cavity; the stomodaeum

actinophore - a pterygiophore and its associated fin ray

Image of ray-finned fish

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


Actinopterygii - 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

actinotroch - a larval form found in the Phoronida (horseshoe worms)

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

activated charcoal - activated charcoal is generally called the "universal antidote" by toxicologists, since it is active in adsorbing most toxicants except inorganic salts and heavy metals

activator - a substance or physical agent that stimulates transcription of a specific gene or operon

active search - search behavior in which a herbivore or predator moves around its environment looking for food

active site - a specific region of an enzyme where a substrate binds and catalysis takes place

active transport - the pumping of molecules or ions through a membrane against their concentration gradient.This action requires the expenditure of energy through ATP hydrolysis

aculeate - bearing a sharp point

aculeiform - having a sharp point; needle-shaped

Image of acuminate fish

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)


acuminate - a shape which gradually tapers to a point

acute - sudden or brief

adaptation - changes in gene frequencies resulting from selective pressures being placed upon a population by environmental factors. This results in a greater fitness of the population to its ecological niche

adaptive behavior - any behavior that enables an organism to adjust to a particular situation or environment

adaptive bleaching hypothesis (ABH) - a coral bleaching hypothesis wherein under changing environmental conditions, the loss of one or more kinds of zooxanthellae is rapidly followed by the formation of new symbiotic cnidarian-algal relationships with different zooxanthellae that are more suited to the new conditions in the host's habitat. Fundamental assumptions of the ABH include (1) different types of zooxanthellae respond differently to environmental conditions, specifically temperature, and (2) bleached adults can secondarily acquire zooxanthellae from the environment

adaptive radiation - the evolution of a single evolutionary stock into a number of different species

adaptive value - the degree to which a characteristic helps an organism to survive and reproduce, or affords greater fitness in its environment

adducent - leading or conducting toward

adductor - a type of muscle whose function is to pull an appendage or body part inwards, towards the body of an animal

ADELIE software - a post-processing tool-set which has been developed to visualize, handle, and enhance images, videos and data recorded during IFREMER underwater vehicle dives

Diagram of adenine

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


adenine - one of the four nitrogenous bases in DNA that make up the letters ATGC. Adenine is the "A". The others are guanine, cytosine, and thymine. Adenine always pairs with thymine

adenosine triphosphate (ATP) - a nucleoside triphosphate, ATP is the predominant supplier of metabolic energy in living cells. ATP supplies the chemical energy to drive endergonic reactions (requiring work or the expenditure of energy), perform mechanical work, provide heat and even produce bioluminescence

adenovirus - a group of DNA-containing viruses which cause diseases in animals. In humans, they produce acute respiratory tract infections with symptoms resembling the common cold. They are used in gene cloning, as vectors for expressing large amounts of recombinant proteins in animal cells. They are also used to make live-virus vaccines against more dangerous pathogens

adhesion - the molecular force of attraction between two unlike materials that acts to hold them together

adhesive disc - in fishes, a sucker-like organ for clinging to various surfaces, e.g. the modified pelvic fins in clingfishes and snailfishes, and the dorsal fin in remoras (shark suckers)

adhesive egg - an egg which adheres on contact to a substrate or to other eggs

Adiabatic process - a process in which no heat is gained or lost by the system

Image of adipose tissue

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


adipocyte - a fat cell

Image of a salmon

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


adipose fin - in fishes, a small fleshy fin which lacks fin rays. It is found in fishes such as salmon, and most catfishes

adjacently sympatric - pertains to those aspects of a parapatric speciation event whereby the daughter species are minimally isolated geographically

adnate - joined together

Adobe acrobat - Acrobat Reader is a software product from Adobe, designed to view .pdf (portable document format) documents downloaded from the World Wide Web

adpressed - pressed close to or lying flat against something; apressed

adradial canal - one of eight non-branched ciliated canals which originates from the gastric pouches of scyphozoan medusae. The flow of digested food materials is toward the ring canal

Image of a Nassau grouper

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


adult - a fully developed and sexually mature animal, physically capable of reproducing under appropriate physiological, ecological and sociobiological conditions

advanced - new, unlike the evolutionary ancestral or primitive condition

Image of POES satellite

Artist's rendition of POES satellite.


Advanced Very High Resolution Radiometer (AVHRR) - 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

adventitious root - a root that originates from any part of the plant other than the root system

aeolid nudibranch - a type of nudibranch (order Nudibranchia) in which the mantle is extended into long finger-like projections, the cerata (sing: ceras), rather than a feather-like external gill on the dorsal surface. The cerata contain branches of the digestive gland. The tips of the cerata contain cnidosacs which usually store nematocysts that are obtained from ingested cnidarian prey, such as hydroids, sea anemones and soft corals. If threatened, the nudibranch is capable of discharging these stinging cells through a terminal pore in the ceras. This action is an effective deterrent to predators

aerenchyma - a specialized parenchymous tissue in seagrass leaves that has regularly arranged air spaces or lacunae. These internal air spaces serve for flotation and exchange of gasses

aerial photography - photographs taken from an aircraft or satellite utilized to interpret environmental conditions and geographic features

aerobic - deriving energy from a process requiring free oxygen

aerobic respiration - a form of respiration in which molecular oxygen is consumed and carbon dioxide and water are produced

aesthete - unique to chitons (Polyplacophora -Mollusca), aesthetes are photosensitive mantle cells, present in very high densities. Although they are involved in light responses, their exact function is unknown

affinity index - a measure of the relative similarity of the composition of two samples. Reciprocal affinity is a measure of distance

aft - in, near, or toward the stern (rear) of a vessel

agamospecies - species which replicate asexually

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

agarose - a polysaccharide, which together with another class of polysaccharide, agaropectin, is a component of agar. Agarose is the preferred matrix for work with proteins and nucleic acids because of its neutral charge and lower degree of chemical complexity.

agarose gel electrophoresis - a method used to separate a mixed population of nucleic acid (DNA and RNA) fragments by length of the molecule. Nucleic acid molecules are separated by applying an electrical field to move the negatively charged molecules through an agarose (a component of agar) matrix. Shorter molecules move faster and migrate farther than longer ones because shorter molecules migrate more easily through the pores of the gel

age class - a group of individuals of a species all of the same age

age distribution - the frequency of different ages or age groups in a given population

age structure - the relative proportion of individuals in each age group in a population

aggregate - 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 - a collection of units or particles forming a body or mass (noun); to form such a body or mass (verb)

aggressive mimicry - 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

Image of sea lamprey mouth

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)


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

agonistic behavior - aggressive, negative behaviors, such as fighting, threatening, and fleeing

agricultural pollution - the liquid and solid wastes from all types of farming, including runoff from pesticides, fertilizers and feedlots; erosion and dust from plowing, animal manure, carcasses, crop residues and debris

Agulhas ring - large pulses of warm and salty water of Indian Ocean origin which enter the Atlantic Ocean directly south of the Cape of Good Hope in the form of anticyclonic eddies. The process of ring detachment is associated with perturbations of the Agulhas Current that retroflects south of Africa

ahead - in front of, or forward of the vessel

ahermatypic coral - a coral that lacks zooxanthellae and does not build reefs

AIMS Reef Monitoring Data Entry System (ARMDES) 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

AIMS Video Transect Analysis System (AVTAS) - 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

air bladder - an air sac located in the coelomic cavity of many fishes. In some fishes it may retain a tubular connection with the pharynx or esophagus; also known as a gas bladder or swim bladder, it functions variously as a hydrostatic organ, a sound conductor, a sound production organ, and in respiration. It is absent in sharks and rays, and some bony fishes

air compressor - an apparatus that compresses or pressurizes air for scuba tanks. Air is compressed from the atmospheric level (14.7 psi at sea level) to the capacity of the tank, which is generally between 2500-3000 psi

aktological - pertaining to shallow inshore environments and communities

alate - winged

albatross - any of large web-footed birds belonging to the family Diomedeidae, chiefly distributed throughout the oceans of the southern hemisphere. Albatrosses have a hooked beak and long, narrow wings

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)

albicant - whitish color

Image of albino catfish

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


albinism - hereditary absence of pigment in an organism. Albino animals have no color in their skin, scales, hairs and eyes. The term is also used for absence of chlorophyll in plants. Some organisms exhibit partial albinism. White tigers, for example, possess black stripes on a white background

albugineous - white colored

alcohol - any of a class of organic compounds in which one or more hydroxyl groups are attached to a carbon compound

Image of an alcyonarian (soft coral)

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.


alcyonarian - a soft coral of the order Alcyonacea, class Anthozoa, phylum Cnidaria. They consist of a firm body, throughout which calcareous spicules are dispersed. The surface is studded with polyps. They are closely related to the scleractinian (hard or stony) corals but lack the rigid, stony exoskeleton

alecithal - a type of egg that does not contain yolk

Alee effect - the social dysfunction and failure to mate successfully when population density falls below a certain threshold

algae - unicellular, multicellular, solitary, or colonial organisms that contain chlorophyll. They lack roots, stems, leaves, flowers, and seeds. Algae are in the Kingdom Protista

algaecide - a chemical agent specifically designed and used to kill or inhibit the growth of algae; also called 'algicide'

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. For more information and illustrations, see: http://www.coral.noaa.gov/coral_disease/algal_galls.shtml

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

Image of coralline 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

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

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

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

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

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-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

all-purpose tool (APT) - a tool used in the performance of visual fish censuses. An APT is a T-shaped, meter-long reference device used by scientific divers for measuring habitat vertical relief, estimating fish lengths, and the location of the center and outer edge of the sample cylinder. The shaft is a PVC t-stick marked at 10cm intervals with a 30cm cross-piece marked at 1cm intervals

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

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

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 pefix 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

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

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

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

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

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 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

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, developed by the U.S. Geological Survey, that acquires continuous digital still images of shallow-marine substrates

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

Image of satellite

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

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

Image of a spotted boxfish

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

ambilateral - occurring on both sides

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

Image of a starfish ambulacral groove with tube feet

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

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

Image of amoeba

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

Image of bullfrog

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

Graphic of amphiblastula

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

amphidromic point - a point within a tidal system where the tidal range is almost zero

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

amphophylic - having an affinity for both acidic and basic dyes

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

ampulla - a membranous vesicle

Image of shark head

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

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

Image of a chinook salmon

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

Image of anal fin

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 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

Image of fish eggs and larvae

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

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

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

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

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

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

anemometer - an instrument for measuring wind velocity

Image of sea anemone

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

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

Image of anglers

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

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

Image of marine worm (Annelida)

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

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

Image of spiny lobster

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

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

Image of spotlight parrotfish (anterior end)

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

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. It is a site of bioluminescence in some anthozoans

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

Image of blue deep-sea anemone

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

anthropogenic - made by people or resulting from human activities

anthropogenic climate change - climate change due to 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 - 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

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

antienzyme - a substance that neutralizes an enzyme

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

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

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

Image of black coral

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 of a black coral (Antipatharia)

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

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

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

Image of blue shark

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


apex predator - an organism at the top of the food chain, relying on smaller organisms for food

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

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

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

Apo Reef - the second largest contiguous coral reef in the world, after Australia's Great Barrier Reef. Apo Reef is located around 33 kilometers west of the mid-western coast of the Philippine island of Mindoro. The reef and its surrounding waters are administered as a National Park as part of the Apo Reef Natural Park project

apobiosis - the local death of a part of an organism

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

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

Image of lionfish

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


aposematism - conspicuous warning coloration

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

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

approximate - in morphology, placed close together

approximate - in morphlogy, placed close together

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

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

Image of the underwater laboratory Aquarius

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

Aquarius Reef Base - NOAA's Aquarius Reef Base is composed of the undersea laboratory, a separate ocean observing station with real-time results available via the Internet and limited plug-in capability for additional sensors, and a shore base. Together,these assets provide a state-of-the-art diving facility for coral reef science along with synchronous ocean observing, a test bed for technology development, and advanced communications that allow for telepresence research, education, and outreach; see also "Aquarius"

aqueous solution - a solution in which water is the solvent

Diagram of aquifer

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

arachnactis - a planktonic larva of tube anemones (Ceriantharia)

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 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

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

arciform - bow-shaped

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

arcuate - crescent-shaped

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

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

argent - silvery color

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

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

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

Image of spiny lobster

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

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

Image of an artificial reef

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

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

Image of ascideans (sea squirts)

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

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

aspergilliform - brush-shaped

aspergillosis - a widespread fungal infection of Caribbean soft corals. It affects six species of sea fans and sea whips. The pathogen is Aspergillosis 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. For more information and illustrations, see: http://www.coral.noaa.gov/coral_disease/aspergillosis.shtml

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

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

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

Atlantic and Gulf Rapid Reef Assessment (AGRRA) - an international collaboration of scientists and managers aimed at determining the regional condition of reefs in the Western Atlantic and Gulf of Mexico

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

Image of a Pacific atoll

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

atomic force microscopy (AFM) - a very high-resolution type of scanning microscopy with resolution of fractions of a nanometer (one nanometer = one billionth of a meter); also called "scanning force microscopy (SFM)"

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

atramentous necrosis (AtN) - a coral disease characterized by spreading black lesions, often covered by a white film

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

atrium - a body cavity; 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

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

attenuated - the gradual loss in intensity of any kind of flux through a medium; a gradual diminishing in the strength of something; long and tapering

attribute - a measurable component of a biological system

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

Image of auricularia (starfish larva)

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

Image of AIMS field operations

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


Australian Institue of Marine Science (AIMS) - 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

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"

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

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 destruction (lysis) of a cell through the digestive action of its own enzymes

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

Autonomous Reef Monitoring Structures (ARMS) - Structures designed to mimic the complex coral reef environment and attract colonizing coral reef organisms in order to assess invertebrate biodiversity by measuring/monitoring diversity of cryptic organisms globally over time. ARMS provide standard methods for taxonomic and molecular analyses to assess invertebrate biodiversity. Information from the ARMS will provide managers with a tool to assess this diversity along with the affects of climate change and ocean acidification, globally. More than 500 ARMS have been deployed throughout the Pacific, Indian, and Atlantic Oceans

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

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

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

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

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

avian - of, relating to, or characteristic of birds

Image of avicularium

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

avirulent - unable to cause disease

axial - refers to the head and trunk of an individual

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

axial polyp - the longest and terminal polyp of a group of polyps, from which secondary (daughter) polyps are produced by budding

axial sheath - the part of the coenenchyme immediately surrounding the axis of octocorals (gorgonians and pennatulaceans)

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 cortex - the layer surrounding the central core of the axis (inner supporting structure), secreted by the axis epithelium

axis epithelium - a layer of ectodermal cells that produce the axis of octocorals and cells that attach the soft 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