Glossary of Coral Reef Terminology - P

P-value - in a statistical hypothesis test, the P value is the probability of observing a test statistic at least as extreme as the value actually observed, assuming that the null hypothesis is true. This probability is then compared to the pre-selected significance level of the test. If the P value is smaller than the significance level, the null hypothesis is rejected, and the test result is termed significant; the significance of a statistical test. P-values of less than 0.05 are generally considered to be an indicator that a statistical model is significant; a quantitative estimate of the probability that the observed difference between two groups could have happened by chance alone

Pacific Island Ecosystems Research Center (PIERC) - a U. S. Geological Survey (USGS) Center whose mission is to work with others to provide the scientific understanding and technologies needed to support the sound management and conservation of our Nation's biological resources in the Pacific Basin. PIERC works with federal, state, local and private organizations to provide objective research, baseline information, and technical assistance relating to conservation and restoration of indigenous biological resources occurring within the cultural, sociological and political context of the States and Island Territories of Hawai'i, Guam, truk, the Mariana Islands, American Samoa and others under U.S. jurisdiction in the Pacific Basin

Pacific Islands Marine Protected Area Community (PIMPAC) - a collaboration of MPA managers, non-governmental organizations, federal, state, and territorial agencies, local communities, and other stakeholders working together to collectively enhance the effective use and management of MPAs in the U.S. Pacific Islands and Freely Associated States

Pacific Plate - the largest of the tectonic plates of the earth's crust. The Pacific Plate comprises most of the rock beneath the Pacific Ocean and contains the hot spot that has formed the Hawaiian Islands

PADI ( Professional Association of Diving Instructors ) - the world's largest scuba diving certification agency

paedogenic - sexual reproduction by larval or immature forms

paedomorphosis - phylogenetic retention of juvenile or larval characters in the adult

Cope's giant salamander (Dicamptodon copei) is an example of paedomorphy. The adult retains the juvenile external gills. (Photo: U.S.D.A. Forest Service)

paedomorphy - the retention of juvenile features in an adult organism

paedophagous - larvae or embryo eating; larvivorous

page precedence - in taxonomy, when two names for the same taxon are first published in the same publication, the one which appears on the earlier page has precedence

PAH (polycylic aromatic hydrocarbon) - a class of stable organic molecules made up of only carbon and hydrogen. These molecules are highly carcinogenic, but also very common in the enviropnment. PAHs are formed during the incomplete burning of coal, oil and gas, garbage, and other organic substances, such as tobacco or even charcoal broiled meat. PAHs enter water through discharges from industrial and wastewater treatment plants or through the release of boat engine exhausts. Ultraviolet light (UV) transforms the PAHs into toxic forms that kill crustaceans, polychaetes, and coral larvae

pahutoxin - a marine toxin that has been isolated from the skin secretion of the Hawaiian boxfish, Ostracion lentiginosus

pair bond - the temporary or permanent association formed between a female and male animal during courtship and mating. Pair bonding is characteristic of monogamous species

Note the paired fins on this Townsend angelfish. The pelvic fins (and pelvic girdle) are in the thoracic position. (Photo: Jackie Reid, NOAA)

paired fins - the pectoral and pelvic fins of fishes

Palancar Reef - a Caribbean coral reef located on the southwest side of the Mexican island of Cozumel, off the Yucatan Peninsula. Palancar Reef is part of the Mesoamerican Reef system

palate - roof of the mouth cavity

palatine - a bone in the roof of the mouth of fishes. The palatine is cartilaginous in some primitive bony fishes

paleobiogeography - the distribution of organisms as revealed by the fossil record

paleoclimatology - the study of past climates throughout geological history, and the causes of the variations among them

A paleoecolgical microfossil, this rotifer (Callindina angusticollis) is from the Beringia region of the Arctic. (Photo:Wendy Eisner)

paleoecology - the study of the relationship of extinct organisms or groups of organisms to their environments

paleoenvironmental proxy - an environmental remnant of the past (pollen grains, tree rings, lake sediments, pack rat middens, ice cores, coral skeletons) used to assist researchers in deciphering past climatic conditions

paleopathology - the study of sickness, injuries and other abnormalities in the health of ancient organisms

paleothermometer - a proxy that provides absolute estimates of past temperature. An example is the Sr/Ca ratio found in coral skeletons

Paleozoic - an era of geologic time lasting from 570 to 245 million years ago

paliform crown - a circle of paliform lobes that surround the columella

paliform lobe - an upright skeletal rod or plate at the inner margin of septa formed by upward growth of the septum

pallial - of or pertaining to a mantle, especially to the mantle of mollusks

pallial chamber - the cavity enclosed by the mantle in mollusks

One side of a bivalve shell showing muscle scars, pallial line created by the mantle, hinge and hinge teeth. (Graphic: Biodidac)

pallial line - a linear impression which marks the attachment of the mantle on the inner surface of a bivalve shell

Acropora palmata in a shallow reef zone.

palmata zone - the region of a reef crest of a bank or barrier reef that is closest to the water surface. It is composed almost completely of elkhorn coral (Acropora palmata) in the Caribbean

palmate - hand-shaped

The portion containing the reproductive gametes (the epitoke) of the palolo worm, Palolo viridis, is considered a delicacy in Samoa and other Pacific islands. (Photo: Smithsonian Institution)

palolo - a polychaete worm (Palola viridis) that burrows in the coral reefs of some Pacific Islands. Just before the last quarter of the moon in October and November, they swarm and breed in vast numbers at the sea surface. They are gathered and highly esteemed as food by the islanders. An allied species inhabits the tropical Atlantic and swarms in June or July

palus - one of several upright slender calcareous processes which surround the central part of the calicle of certain corals; vertical radially arranged plates forming one or more cycles between the septa and the central axis in the scleractinian skeleton

Palustrine habitat in the Jobos Bay National Estuarine Research Reserve. (Photo: NOAA)

palustrine - pertaining to swamps or marshy habitats

palynology - the scientific study of pollen, pollen stratigraphy, paleobotany, and paleoclimatology of plants

a soft-bodied hexacoral, Palythoa sp, from American Samoa. The extremely potent toxin, palytoxin, has been isolated from Palythoa sp from Hawaii. (Photo: National park Service/Eva DiDonato)

palytoxin - an extremely powerful neurotoxin naturally found within the bodies of certain soft corals in the genus Palythoa (family Zoanthidae)

pan-tropical - throughout the tropics

pandemic - an epidemic that is geographically widespread; occurring throughout a region or even throughout the world

Pangea - a supercontinent that existed from about 300 to 200 million years ago. It included most of the continental crust of the Earth

panmictic - refers to random-mating populations; one in which all members are equally likely to interbreed

panmixis - random mating in a population

Papahanaumokuakea - Hawaiian name for the Northwestern Hawaiian Islands Marine National Monument. It refers to Hawaiian genealogy and the formation of the Hawaiian archipelago. The name was adopted through consultation with the Native Hawaiian Cultural Working Group, whose members have a longstanding interest and involvement in the region and come from relevant backgrounds including academic scholars, teachers, cultural practitioners, community activists, and resource managers

Papahanaumokuakea Marine National Monument - the Hawaiian name for the Northwestern Hawaiian Islands Marine National Monument

papilla - a raised bump or nipple-like projection on a tissue surface; a cellular outgrowth. Papillae have the appearance of little bumps or fingers on the surface of cells

papilliform - slender, elongate and pointed

papilliform - nipple-shaped

papillose - covered with papillae

Papuan Bird's Head Seascape - a coastal and marine region of 183,000 square kilometers (approximately 70,657 square miles) located in northwest Papua Province of Indonesia, that stretches from Teluk Cenderawasih in its eastern reaches to the Raja Ampat archipelago in the west and the FakFak-Kaimana coastline in the south. It is home to more than 1,200 types of reef fishes and nearly 600 species of hard corals, plus whales, sea turtles, crocodiles, giant clams, manta rays, and dugongs. Bird's Head is perhaps one of Earth's richest seascapes

PAR (Photosynthetically Active Radiation) - those wavelengths of light that can be absorbed by chlorophyll or other light harvesting pigments

para - a prefix meaning "beside"

parabolic reflector - a portable, disk-like device used to gather, magnify, and focus the sounds of birds and other organisms for the purpose of making high-quality, electronic recordings

paradigm - a pattern or model that provides a framework for interpreting observations

paradox - a statement that seems self-contradictory, yet may nevertheless be true

paralectotype - in taxonomy, any one of the original syntypic series remaining after the selection of a lectotype

parallel evolution - the development of similar forms by related but distinct phylogenetic lineages

paralogous genes - two genes or clusters of genes at different chromosomal locations in the same organism that have structural similarities indicating that they derived from a common ancestral gene and have since diverged from the parent copy by mutation and selection or drift. Two genes are said to be paralogous if they diverged after a gene duplication event

paramagnetism - magnetic property in certain iron-bearing minerals that cause them to be weakly attracted to magnetic fields

parameter - a particular physical, chemical, or biological property that is being measured

parapatric - pertains to the ranges of species that are contiguous but not overlapping; adjacent but non-overlapping distributions

parapatric speciation - speciation in which the new species forms from a population contiguous with the ancestral species' geographic range

parapatric speciation - speciation in which the new species forms from a population contiguous with the ancestral species' geographic range. The evolution of reproductive isolating mechanisms occurred when the population entered a new niche or habitat within the range of the parent species

paraphyletic - a group of taxa that includes an ancestral taxon but not all descendants of that taxon

A polychaete worm showing a pair of parapodia per segment. Note the bristle-like chaetae borne by each parapodium. (Photo: Dr. Anthony Picciolo)

parapodium - one of the short unsegmented processes located on each side of most of the body segments in many annelid worms. Parapodia (pl) function in locomotion and often also as tactile or branchial organs. In some marine snails (e.g., sea hares and pteropods) it is a broad lateral expansion of either side of the foot, forming a broad swimming organ

parasite - an organism that lives in or on the living tissue of a host organism. It gives its host nothing beneficial in return, and often is injurious and even lethal to the host

parasitic spawning - fertilization of eggs by a subordinate male while the female and dominant male are spawning

parataxonomist - a field-trained biodiversity collection and inventory specialist recruited from local areas. Parataxonomists are specialists, locally trained by professional biologists, that collect specimens, prepare them, sort them into morphospecies, and organize associated information into a database

paratype - in taxonomy, every specimen in a type series, other than the holotype, which were before the author at the time of preparation of the original description, and were so designated and indicated there

parenchyma - the primary tissue of higher plants composed of thin-walled cells that remain capable of cell division, even when mature. Parenchyma constitutes the greater part of leaves, roots, the pulp of fruits, and the pith of stems. They are fundamental plant tissues as opposed to more highly differentiated tissues. In animals, the parenchyma constitutes the essential functional part of an organ, as contrasted with the organ's connective tissue, nerves, and blood vessels

parenchyme - in cnidarians, mesenchyme with dense cellular components

parenchymula - a sponge larva which appears as a solid ball with exterior flagellated cells (except at the "posterior end")

parent population - any population considered as the source or origin for the population under study or analysis

paresthesia - abnormal neurological sensations which include: numbness, tingling, burning, prickling and hyperesthesia (increased sensitivity); one possible symptom of ciguatera poisoning

parology - homology (similarity of features based on common descent) that arises via gene duplication

Parrotfish are very common inhabitants of coral reef communities (Photo: Keoki and Yuko Stender)

parrotfish - any species of tropical bony fishes in the family Scaridae. Parrotfishes are abundant and common inhabitants of coral reef communities. Their teeth are fused into a sharp "parrot-like" beak strong enough to bite off pieces of stony corals. Some parrotfishes produce an enveloping mucous envelope that surrounds and presumably protects the body at night

parsimony - the principle that the simplest explanation, the one that requires the fewest hypotheses, is the one most likely to be correct; same as Occam's Razor: the simplest of two competing theories is to be preferred

parthenogenesis - reproduction without fertilization; the development of an unfertilized ovum, seed, or spore. It occurs naturally in several species and may also be induced artificially by chemical or mechanical means

partial pressure - the pressure exerted by a single component of a gas within a gas mixture, or dissolved in a liquid

particulate - a very small solid suspended in water

particulate organic matter - particulate material of biological origin that is suspended in water

partim - in part

parts per million (ppm) - number of parts of a substance found in one million parts of a particular gas, liquid, or solid

parts per thousand (ppt) - number of parts of a substance found in one thousand parts of a particular gas, liquid, or solid

parturition - the process of giving birth

passerine - refers to birds in the order Passeriformes, a large order of birds comprising more than half of all bird species. The passerines are the perching birds and songbirds

passive integrated transponder (PIT) - a small microprocessor enclosed in glass which is injected into the shoulder muscle or flipper of sea turtles as a method of identifying individuals. The PIT tag transmits a unique number to a hand held scanner when activated by the scanner

passive search - a feeding strategy where the predator remains more or less stationary and ambushes the prey animal when it comes within range

patch - a nonlinear surface area differing in appearance from its surroundings

patch reef - a coral boulder or clump of corals formed on a shelf, usually of less than 70 m depth, often in the lagoon of a barrier reef or atoll. It is unattached to a major reef structure

patchiness - the condition where organisms occur in aggregations

Elkhorn coral with patchy necrosis in two locations (Photo: Andy Bruckner/NOAA)

patchy necrosis - a disease of corals. Colonies with this condition have small (2-10 cm diameter) circular to irregular patches of denuded skeleton that will increase in diameter an additional 1-10 cm over a period of 5-7 days. The disease typically affects the top surface of elkhorn coral (Acropora palmata) branches. In most cases most of the affected tissue dies rapidly, and subsequent enlargement of the bare skeletal areas slows after a few days and eventually stops. A bacterium has been identified as a causal agent

Pathfinder - a program that focuses on the processing, reprocessing, maintenance, archiving, and distribution of existing Earth science data sets to make them more useful to researchers. NASA, NOAA, and USGS are involved in specific Pathfinder efforts

pathogen - an organism which causes a disease within another organism

pathogenesis - the origin and development of disease

pathogenicity - the quality of producing or having the ability to produce pathologic changes or disease

pathognomonic - a sign or symptom that is so characteristic of a disease, and not found in any other condition, that it makes the diagnosis

patronym - a taxonomic name derived from the name of a person

pavement - rock exposed at the Earth's surface in the form of a more or less horizontal surface, usually with crevices or joints

PCR (polymerase chain reaction) - a method of creating copies of specific fragments of DNA. PCR rapidly amplifies a single DNA molecule into many billions of molecules

pdf (portable document format) - a file format created by Adobe, initially to provide a standard form for storing and editing printed publishable documents. Because documents in .pdf format can easily be seen and printed by users on a variety of computer and platform types, they are very common on the World Wide Web

pectinate - comb-like; in mollusks, it refers to the comb-like lamellae of the ctenidia (gills)

pectiniform - comb-shaped

pectoral - pertaining to the chest area

A flying fish with huge pectoral fins. (Photo: NOAA)

pectoral fin - the farthest forward or uppermost of the paired fins of most fishes, usually located in the thoracic position

An anemone maintains its grip on substrate with its pedal disc. (Photo: Copyright Digital Stock Corp.)

pedal disc - a disc at the aboral end of the body trunk used for attachment. A synonym of basal plate

pedal laceration - a type of asexual reproduction in some sea anemones in which parts of the pedal disc break off and are left behind as the anemone moves

A single pedicellarium from a starfish. (Photo: Rick Gillis, Ph.D., Biology Dept., University of Wisconsin-La Crosse)

pedicellarium - a forceps-like organ which occurs in large numbers on starfishes and sea urchins. Pedicellariae, in general, are multifunctional appendages involved in defense, feeding, and cleaning. They are mainly used to keep small organisms from settling on the aboral surface, to capture small prey, and to discourage predators from feeding on soft tissue. The basic structure of pedicellariae consists of a head, neck, and stalk. The head usually has three jaws and, in some pedicellariae, contains poison glands

pedunculate - having a stem or stalk

peeler crab - a crab that has just recently shed its exoskeleton, i.e., a recently-molted crab

PEET (Partnerships for Enhancing Expertise in Taxonomy) - the National Science Foundation in partnership with academic institutions, botanical gardens, freshwater and marine institutes, and natural history museums, seeks to enhance and stimulate taxonomic research and help prepare future generations of experts. NSF announces a special competition, Partnerships for Enhancing Expertise in Taxonomy (PEET), to support competitively reviewed research projects that target groups of poorly known organisms. This effort is designed to encourage the training of new generations of taxonomists and to translate current expertise into electronic databases and other formats with broad accessibility to the scientific community

An ocean sunfish, Mola mola, is a pelagic species, frequently seen basking at the surface of the water.

pelagic - refers to organisms that inhabit open water, as opposed to benthic

A member of the Pelecypoda, a live scallop (Placopecten magellanicus) in the Stellwagen Bank National Marine Sanctuary. (Photo: Dann Blackwood and Page Valentine, USGS)

Pelecypoda (Bivalvia or Lamellibranchia) - a class of Mollusca that includes clams, oysters and mussels

pellucid - transparent

pelvic fin - the paired fin located ventrally beneath, in front of, or behind, the pectoral fin

penicillate - brush-like; having or resembling a tuft or brush of fine hairs

penis fencing - a type of reproductive behavior found in hermaphroditic flatworms (some have two penises and one or more genital pores for receiving sperm cells delivered during copulation). During penis fencing, each flatworm tries to pierce the skin of the other using one of its penises. The first to succeed becomes the de facto male, delivering its sperm into the other, the de facto female

Pennatulacea - an order of soft corals which includes the sea pens and sea pansies. See "sea pen" and "sea pansy"

penniform - feather-shaped

Bright orange seastar (Pseudarchaster myobrachius) with a typical pentamerous body shape.

pentamerous - divided into five parts; a characteristic of the body plan of echinoderms

penultimate - the one before the last; the second from the end

peppered - used to describe a pigment pattern of dark stippling

peptide - two or more amino acids joined by a peptide bond

peptide bond - the bond between two amino acids formed when a carboxyl (-COOH) group of one amino acid joins an amino (-NH2) group of another amino acid, releasing water in the process

percentile - one of the division points that divides a set of ranked data into one hundred equal points; a value on a scale of zero to one hundred that indicates the percent of a distribution that is equal to or below it. A score in the 95th percentile is a score equal to or better than 95 percent of all other scores

percolation - the movement of water through the openings in rock or soil

perennial - referring to an organism that lives for more than one year

perforate corals - corals which have porous skeletons with connections between the polyps through the skeleton

peri - a prefix meaning "around"

perianal - near or surrounding the anus

periderm - an external layer of secreted cuticular material in many Anthozoa. The term is synonymous with "cuticle." In woody plants, the periderm is a protective secondary tissue produced by the cork cambium

perigee - the point in the orbit of the Moon or man-made satellite nearest to the Earth; the point in the orbit of a satellite nearest to its companion body

Period - in the geologic time scale, a unit of time less than an era and greater than an epoch

Periodic Table - a chart of the known chemical elements, arranged according to their atomic numbers. Elements with similar physical and chemical properties and similar electron arrangements are in the same column

periostracum - the outside layer or covering of a bivalve (Mollusca) shell

peripatric speciation - speciation which occurs when small populations of organisms become isolated in a new environment. This differs from allopatric speciation in that the isolated populations are numerically much smaller than the parental population. In peripatric speciation, the founder effect causes rapid speciation through both rapid genetic drift and natural selection on a small gene pool; a type of speciation in which a founder or sink population is isolated from the parent or metapopulation, usually via colonization of some new region

periphery - the outermost part or region within a precise boundary

perisarc - the chitinous outer coat of common tissue connecting individuals in some colonial hydrozoans

peristome - the region around the mouth in various invertebrates; in cnidarians, it is the portion of the oral disc surrounding the mouth

peritheca - same as the coenosteum, which is the skeleton between corallites within a colony; the living tissue surrounding or between corallites (the coenosarc)

peritoneum - the mesodermally-derived membrane that lines the coelom and covers the coelomic viscera

peritoneum - a membrane lining the body cavity (coelomic cavity) and covering the viscera

permeable - having pores or openings that permit liquids or gasses to pass through

perradial canal - one of four branched ciliated canals that originates directly from the stomach of scyphozoan medusae and moves partially digested food materials from the ring canal to the stomach

Persistent organic pollutant (POP) - an organic chemical that remains intact in the environment for a long period of time

personal communication - unpublished information communicated to the author verbally

perturbation - a disturbance or abnormality

petabyte - a measure of data size. One petabyte is equivalent to 1,000 terabytes

petaloid - describes a form that is similar to a flower petal

petaloid septa - primary septa which have a tapered or curved shape because they are enclosed by other septa

petrel - seabirds in the bird order Procellariiformes. They occur in four families within that group, which also includes the Albatross family, Diomedeidae. The family Procellariidae is the main radiation of medium-sized 'true petrels', characterised by united nostrils with medium septum, and a long outer functional primary. It is dominant in the Southern Oceans, but not so in the Northern Hemisphere

petrochemical - a chemical derived from petroleum or natural gas

petrosaspongiolides M-R - an antiinflammatory drug derived from the marine sponge Petrosaspongia nigra

pH - the logarithm of the reciprocal of hydrogen-ion concentration in gram atoms per liter; provides a measure on a scale from 0 to 14 of the acidity or alkalinity of a solution (where 7 is neutral and <7 is acidic and >7 is basic)

Eusmilia fastigiata is a phaceloid coral with one corallite per branch. (Photo: University of Puerto Rico/Morelock)

phaceloid coral - a coral that has corallites of uniform height which are adjoined toward their base

phage - a virus that infects bacteria; also called a bacteriophage

phagocyte - a cell that engulfs and digests debris and invading microorganisms  

phagocytosis - "cell eating." A process in which phagocytes engulf and digest microorganisms and cellular debris; an important defense against infection

pharmaceutical - refers to man-made and natural drugs used to treat diseases, disorders, and illnesses

pharmaco- - pertaining to drugs

pharyngeal arch - one of several columns of mesenchyme found in the neck region of the developing vertebrate embryo. In lower vertebrates, blood vessels formed here become part of the gills; in higher vertebrates derivatives include portions of the jaw and middle ear; also known as branchial arches, gill arches, or visceral arches

Water entering this sea squirt carries particulate matter which is filtered as water passes through openings in the pharyngeal basket. Food particles are carried to the bottom in mucus and enter the digestive tract. Water that has passed through basket is expelled via the excurrent siphon opening, on right in this illustration. The anus opens at the excurrent siphon so fecal material is carried away. (Photo: Houseman at U. Ottawa; BIODIDAC)

pharyngeal basket - a feeding structure in tunicates (sea squirts) which is a type of pharyngeal gill formed into a mesh-like basket. Cilia on the gill draw water into the mouth, through the basket mesh, and out the excurrent siphon

pharyngeal teeth - in fishes, teeth located on the bones in the pharynx, which is the posterior part of the oral cavity

pharyngeal teeth - in fishes, teeth located behind the gills and before the esophagus, and anchored in bone or gill arches. Fishes may use their pharyngeal teeth for sound production

pharynx - the part of the digestive system of many animals immediately behind the mouth and in front of the esophagus; the throat

phenetic classification - classification based on degree of overall similarity

phenetic species - a concept of species in which a species is a set of organisms that are phenotypically similar to one another

phenetics - classification based on grouping by overall similarity, not recency of common descent

phenocopy - an organism whose phenotype (but not genotype) has been changed by the environment to resemble the phenotype usually associated with a mutant organism

phenology - the science dealing with the relationships between climate and periodic biological phenomena that are related to or caused by climatic conditions, such as the seasonal budding of trees and migration of birds

phenotype - the total characteristics of an individual, i.e., its appearance, resulting from interaction between its genotype (genetic constitution) and its environment

phenotypic plasticity - an alteration of phenotype as an organism adapts from one micro-environment to another and as the local environment changes; when an organism activates different phenotypes in response to its environment. Phenotypic plasticity may cause some organisms to look different from each other even though they are genetically identical

pheromone - a hormone-like substance that is secreted by an organism into the environment as a specific signal to another organism, usually of the same species

philopatry - refers to the drive or tendency of an individual to return to, or stay in, its home area

phoenix coral - regeneration of a coral colony from live deep tissues

Phoenix Islands - a group of eight, mostly uninhabited atolls, and two submerged coral reefs, lying in the central Pacific Ocean east of the Gilbert Islands, west of the Line Islands, and north of Samoa. They are a part of the Republic of Kiribati and total 11 sqare miles (28 sq. km) in land area. The only island of any commercial or historical importance is Kanton (or Abariringa) Island. The other islands include Enderbury, Rawaki (formerly Phoenix), Manra (formerly Sydney), Birnie, McKean, Nikumaroro (formerly Gardner), and Orona (formerly Hull)

Phoenix Islands Protected Area (PIPA) - established in 2006 by the Republic of Kiribati, the PIPA is the largest marine protected area in the Pacific Islands and the third largest in the world. Surpassed in size only by Australia's Great Barrier Reef and the Northwestern Hawaiian Islands, the PIPA represents 8 percent of all marine protected areas on Earth and helps safeguard more than 71,300 square miles of nearly pristine marine wilderness. The PIPA encompasses eight atolls, each with a 60 nautical mile protected perimeter, and two submerged reef systems. More than 120 species of coral and 520 species of reef fishes have been identified in the area

phoretic behavior - the use of one organism by another organism as a means of transportation

phospho-diester bond - a bond in which a phosphate group joins adjacent carbons through ester linkages

phospholipase A2 inhibitor - a drug that acts as an antiinflammatory agent by inhibiting the release of arachidonic acid from cell membrane phospholipids. It prevents the enzyme phospholipase A2 from binding to the membranes. Phospholipase A2 inhibition mode of protection has been recorded from many marine sponges

phosphorylation - the addition of a phosphate group to a compound

photic zone - the vertical zone in the ocean extending from the surface to that depth permitting photosynthetic activity

photo-quadrat - a quadrat that is photographed for purposes of later analysis and permanent record for species monitoring or measurement

photocyte - a light-producing cell

photogenesis - light production

photogrammetry - the process of making surveys and maps using photographs

photometer - an instrument for measuring light intensity

photometric - of or relating to photometry; a more precise measurement of the brightness (intensity) of light, which can be digitized and calibrated

photometry - the quantitative measurement of visible radiation, primarily intensity (brightness), from light sources

photomicrograph - a photograph taken through a microscope

Photomosaic of St. John, U.S. Virgin Islands. Images such as these are valuable in studying and managing coral reefs and other habitats. (Courtesy of NOAA National Ocean Service)

photomosaic - an assemblage of photographs, each of which shows part of a region, and put together in such a way that each point in the region appears once and only once in the assemblage, and scale variation is minimized

photon - a quantum of light energy, or, more generally, of any form of electromagnetic energy having a single wavelength, direction, and polarization

photophile - an organism which grows or thrives in lighted conditions

photophilous - thriving in conditions of strong light

This bright bluish lights are given off by photophores on this black dragonfish (Photo: E. Widder, Harbor Branch Oceanographic Institution)

photophore - a light-producing organ, found especially in marine fishes and cephalopods. Photophores emit light from intrinsic structures, or derive light extrinsically from symbiotic luminescent bacteria

photophosphorylation - the process during photosynthesis in which light energy captured by photosynthetic organisms is transformed into the phosphate bond energy of ATP

photoreceptor - a nerve ending, cell, or group of cells specialized to sense or receive light

photosynthesis - process by which autotrophic chlorophyll-containing organisms manufacture their own energy sources (simple sugars) from the intracellular chemical reaction of carbon dioxide and water in the presence of sunlight and chlorophyll. Oxygen is a photochemical byproduct of photosynthesis

photosynthetic capacity - the maximum photosynthetic rate per unit of biomass

photosynthetic pigment - a pigment that efficiently absorbs light within the 400-700 nm range and is essential for photosynthesis

phototropism - the response of an organism to light, usually expressed as movement of a part of an organism toward or away from the light stimulus, as when plants grow toward sunlight

phototype - in taxonomy, a photograph of the type or a photograph serving as the type

phreatic water - water below the level at which all voids in the rock are completely filled with water

phycocyanin - a blue, water soluble pigment found in red algae and cyanobacteria

phycoerythrin - a red, water soluble pigment found in red algae and cyanobacteria

phycology - the scientific study of algae

phylesis - evolutionary events that modify a taxon without causing speciation, i.e., daughter species are not produced

phyletic extinction - the evolution of an ancestral species into one or more daughter species, none of which resembles the ancestor

phylliform - leaf-shaped

phyllopod - any of various branchiopod crustaceans having swimming and respiratory appendages that resemble leaves

Early stage of a rock lobster phyllosoma larva.(Photo: Russell Bradford/CSIRO)

phyllosoma larva - a larval stage of a spiny lobster. The body is thin, flat, and transparent

PhyloCode - a proposed alternative to the Linnaean system of biological classification. The PhyloCode is based explicitly on phylogeny, the evolutionary history of a species or higher taxon. It would name and organize living things based on common ancestry and the branching of the evolutionary family tree. The Linneaean hierarchical system implies evolutionary relationships, but does not formally incorporate phylogeny. The PhyloCode would abandon Linnaean hierarchical ranks and recognize only species and clades (a group of organisms that share a particular common ancestor)

phylogenetic tree - a branching tree-like diagram (dendrogram) used to represent the evolutionary history of a set of taxa, with the leaves (or terminal branches) representing contemporary taxa and the internal branches representing hypothesized ancestors

phylogenetics - the field of biology that deals with the relationships among organisms

phylogeny - the evolutionary relationships among organisms

phylogeography - the study of the geographic distribution of phylogenetic lineages, usually within species and to reconstruct the origins and diffusion of lineages; the attempt to take into account the geographic distribution of species in establishing their phylogeny, and to understand the geographic patterns that may result from divergence, ultimately leading to the evolution of new species

phylogram - a phylogenetic tree that depicts inferred historical relationships among entities. A phylogram differs from a cladogram in that the branches are drawn proportional to the amount of inferred character change

phylum - a major division of a biological kingdom, consisting of closely- related classes; represents a basic fundamental pattern of organization and, presumably, a common descent

physical change - a change from one state to another, as when water changes from ice to its liquid state

physiology - the branch of biology that is concerned with the study of functions of particular structures or organs of organisms

physoclistous - in fishes having the swim bladder closed, with no connection to the gut

physostomous - in fishes having the swim bladder connected by a tube to the gut

A phytoplankon species of the genus Ceratium.

phytoplankton - microscopic green plant component of the plankton which is responsible for most of the photosynthetic activity in the ocean

Phytoplankton Monitoring Network (PMN) - a NOAA outreach program with the ultimate goal of linking laboratory scientists to the general public. PMN fosters a more informed public while providing qualitative data to scientists. The goals of the PMN are: to create a comprehensive list of harmful algal species inhabiting coastal marine waters; to monitor and maintain an extended survey area along coastal waters throughout the year; to isolate areas prone to harmful algal blooms (HABs) for further study by Marine Biotoxins researchers; to identify general trends, such as time and area, where HABs are more likely to occur; to promote increased awareness and education to the public, particularly students, on HABs; to increase the public's awareness of research conducted by federal and state workers on HABs, and to create a working relationship with open communication between volunteers and researchers through PMN

phytoremediation - the use of plants to clean up pollution

phytotoxin - a substance similar in its properties to an extracellular bacterial toxin

picture element - in a digitized image, this is the area on the ground represented by each digital value. Because the analogue signal from the detector of a scanner may be sampled at any desired interval, the picture element may be smaller that the ground resolution cell of the detector. It is commonly abbreviated as pixel

piebald - with two colors irregularly arranged, usually black and white

piezometer - an instrument for measuring pressure or compressibility

pigment - a wide variety of organic compounds found in organisms which have color (or are colorless in some cases) and perform various functions (e.g., chlorophyll, which aids in the conversion of light energy to chemical enery during photosynthesis; hemoglobin, which carries oxygen in the circulatory system of many animals)

pileated - having a cap or crest

pileiform - umbrella-shaped

piliform - hair-shaped

pinacocyte - a cell type which forms the surface layer (pinacoderm or epidermis) of a sponge. Pinacocytes are capable of synthesising collagen

pinacoderm - the external surface of a sponge, lined with pinacocytes in a single cellular layer

ping - a single output pulse of a sonar system

The presence of an outer ear flap, or pinna, is one characteristic that separates sea lions from seals. The photograph is of a Steller sea lion pup with mother's milk still on it's face. (Photo: Mike Etnier, NMML/ NOAA )

pinna - a small lateral branchlet on a tentacle of an octocorallian (soft coral); the most visible portion of the outer ear of mammals

pinnacle reef - a nearly cylindrical reef with vertical sides; may be up to 200 m diameter and 50 m in height

pinnate - having side branches

pinniped - an aquatic mammal in the order Carnivora, such as seals, sea lions and walruses, whose front limbs have evolved to become "flippers"

pinnule - a side branch structure on the tentacle of soft corals, giving them a feathery appearance

pisciform - having the shape of a fish

pisciform - fish-shaped

piscivore - an animal that feeds on fishes

pit plug - a small cytoplasm connection between cells in many red algae which may help with nutrient exchange

pixel - abbreviation of picture element

placode - a thickened or plate-like region within an epithelium

A drawing of the placozoan, trichoplax adhaerens. These tiny marine animals are cryptic inhabitants of tropical and subtropical seas.(Photo: BIODIDAC )

Placozoa - a phylum of extremely simple and cryptic marine animals, for which only two species have been described, trichoplax adhaerens and treptoplax reptans. These tiny animals were discovered in Europe in the late 1800's living on the glass walls of an aquarium. Since then, most of what has been learned about their biology has come from studying cultures kept in various laboratories around the world. Their bodies are made up of only a few thousand cells of just four types. They also have the smallest amount of DNA measured for any type of animal. They lack tissues, organs and organ systems.They reproduce asexually, but it is not known if they can also reproduce sexually. Practically nothing is known about them in nature. Some scientists believe they emerged early in metazoan evolution, either before or just after the sponges (Porifera). However, recent DNA studies lead others to believe they emerged after the Cnidaria. Of the two species described, treptoplax reptans has never been seen since its description in 1896, causing some to doubt its existence. However trichoplax adhaerens has been reported from the Mediterranean and many tropical and subtropical locations around the world. It may be that trichoplax adhaerens actually consists of more than a single species

White plague disease. (Photo: Dr. A. Bruckner, NOAA)

plague (white plague disease) - a coral disease characterized by a sharp line between apparently healthy coral tissue and freshly exposed coral skeleton.-There is no obvious microbial band present.-The infective pathogen is a bacterium. Plague is currently epidemic throughout the Caribbean, and affects stony corals. For more information and illustrations, see: http://www.coral.noaa.gov/coral_disease/white_plague.shtml

plain - uniformly colored or unadorned with structures or other features

planktivorous - feeding on planktonic organisms

This large copepod (Neocalanus sp.) is part of the Arctic marine plankton community.

plankton - the passively floating or weakly motile aquatic plants (phytoplankton) and animals (zooplankton)

Green plants in a Hawaiian intertidal community.

Plantae - the kingdom of immobile multicellular eukaryotes that obtain energy through photosynthesis, and have cells encased in cell walls composed of cellulose

planula - a ciliated planktonic larval form produced by some anthozoans. It undergoes metamorphosis into the adult stage upon settlement on a suitable substrate

plasmalemma - the cytoplasmic membrane found on the outside of the protoplast adjacent to the cell wall of plant cells; the plasma or cell membrane of plant cells

A super coiled plasmid is the predominant in vivo form in which the plasmid is coiled around histone-like proteins. Supporting proteins are stripped away during extraction from the bacterial cell, causing the plasmid molecule to supercoil around itself in vitro. (Photo: Stanley Maloy, Ph.D., Director, Center for Microbial Sciences, San Diego State University)

plasmid - an autonomous (self-replicating) circular piece of DNA found outside the chromosome in bacteria. Plasmids carry information that give the bacteria resistance to antibiotics. They are often used in genetic engineering as cloning vectors to carry desired genes into organisms

plasmogamy - a process of fusion of the cytoplasm of two sex cells or gametes; the first step in syngamy (fertilization)

plastid - a membrane-bound organelle in plant cells that functions in storage (of food or pigments) or food production. Chloroplasts contain the pigments for photosynthesis

plastron - the ventral (belly) shield or shell of a turtle or tortoise

plate - a rigid part of the Earth's crust and part of the Earth's upper mantle that moves and adjoins another one along a zone of seismic activity

plate like - resembling thin, flat sheets of uniform thickness

plate tectonics - the theory that the Earth's lithosphere consists of large, rigid plates that move horizontally in response to the flow of the asthenosphere beneath them, and that interactions among the plates at their borders cause most major geologic activity, including the creation of oceans, continents, mountains, volcanoes, and earthquakes

platform reef - a large reef of variable shape lacking a lagoon, seaward of a fringing reef and/or a barrier reef, for which the width is more than half its length

platform terminal transmitter (PTT) - a small satellite transmitter attached to a sea turtle, bird, bear, etc in order to monitor its movements and/or behavior. For example, a PTT sends a message to a satellite each time a turtle comes to the surface to breathe. Messages are then received via the satellite regarding the turtle's location

A free-living polyclad flatworm.

Platyhelminthes - an animal phylum containing four classes of flatworms. Three are parasitic (tapeworms, flukes) and one, the Turbellaria, is free-living and contains coral reef inhabiting species

pleiotrophy - in genetics, the condition in which a single gene influences multiple phenotypic traits. Should a new mutation occur in that gene, all traits will be effected simultaneously

Pleistocene epoch - an interval of the Quaternary period, from 1.8 million years before present to 10 thousand years before present

plenary power - in taxonomy, power of the International Commission on Zoological Nomenclature to suspend articles of the Code to settle particular cases

plenary powers - in taxonomy, the International Commission on Zoological Nomenclature (Commission) is empowered by use of its Plenary Powers to prevent the application of a rule of the International Code of Zoological Nomenclature (Code) where such application in a particular case would disturb the stability or universality or cause confusion in zoological nomenclature

pleomorphic - variable in size and shape; polymorphic, occurring in more than one morphological form

pleopod - one of the five paired abdominal appendages used for swimming by shrimps; used for attachment of eggs by female shrimps, lobsters and crabs; also called a swimmeret

plesiomorphy - an ancestral character state

plesiotype - of the same sex as the holotype

pleurite - one of the external lateral processes of a somite (body segment) of a crustacean; also called a 'pleuron'

pleurodont - teeth implanted in the side of a bone, e.g. in parrotfishes and triggerfishes

plexus - a group or network of intersecting nerves and/or blood vessels

plica - a small fold in the skin

plicate - having plicae or a series of folds, grooves or wrinkles in the skin; plaited

plication - a fold

Pliocene epoch - an interval of the late Neogene period, from 5.3 to 1.8 million years before present

Plocoid crust coral, Leptastrea bottae. (Photo: Dave Krupp/Windward) Community College

plocoid colony - a coral colony which has conical corallites with their own walls; a coral growth form in which the coral colony is composed of more or less cylindrical corallites having distinct walls. The coenosteum separates the corallites within a colony

ploidy - refers to the number of sets of chromosomes

plug-in - a small piece of software that adds features to a larger piece of software

plumage - the collective term for all the feathers that cover a bird's body

plume - in hydrodynamics, a plume is a column of one fluid moving through another; a long, feather-shaped cloud of steam or gases; a volume of a substance that moves from its source to places farther away from the source; the fluid formation that is created as hydrothermal vent waters are injected into the ocean from the sea floor; an area of chemicals in a particular medium, such as air or groundwater, moving away from its source in a long band or column; the anterior portion of the body of a vestmentiferan tube worm which extends out of the tube into the water. The plume is comprised of hundreds of branchial filaments which are filled with blood vessels. The red hemoglobin in the blood gives the plumes their bright color

pluripotent - ability of a single stem cell to develop into many different cell types of the body of an organism

Pluteus larva of an Australian sea urchin. (Photo: Ellen Popodi and Rudolf A. Raff)

pluteus larva - a free-swimming, bilaterally symmetrical, ciliated larva of some echinoderms, such as sea urchins and brittlestars

The pneumatocysts are the swellings at the bases of the blades in this kelp. (Photo: Monterey Bay Aquarium Research Institute)

pneumatocyst - one of many gas-filled bladders found in some algae that act as a buoys. In some large brown algae, such as kelp, they act to raise the blades closer to the surface where photosynthesis can occur. Pneumatocysts keep the brown alga, Sargassum, afloat in the Sargasso Sea

Mangrove pneumatophores emerging from the sediments. These structures, also known as rhizophores, have bark rich in lenticels to function in gas exchange for roots that are constantly in water-saturated soil.-(Photo: Copyright Dr. Joseph E. Armstrong, Illinois State University)

pneumatophore - a modified aerial root rising above ground that may function as a respiratory organ in plant species such as mangroves, which are subjected to inundation or soil saturation. Such evolutionary adaptations enable trees to obtain oxygen directly from the air and also helps consolidate swamp sediments. They have special air channels (lenticels) for gas exchange in the atmosphere and there is an internal pathway for getting oxygen into the root and to supply submerged roots. The aerial loop of a mangrove root is sometimes called a "knee" or "peg root"

poacher - a person who hunts or fishes illegally; a family (Agonidae) of small bottom-dwelling cold-water marine fishes

A pod of spinner dolphins in the lagoon of Midway Atoll. (Photo: Ocean Futures Society)

pod - a group of aquatic mammals

point intercept transect - a linear transect protocol where a tape is secured at each end of the transect with the tape draped over the reef in between. Observations are collected on each species and substrate component at specified points along the line

point mutation - a mutation in which a single nucleotide in a DNA sequence is substituted by another nucleotide

point source pollution - origin of a pollutant discharge from a discrete conveyance, such as an effluent from the end of a pipe

PointCount - PointCount for Coral Reefs is a Windows/Win95-based program developed to utilize the random point count method to accurately estimate percent coverage of corals, sponges, and associated substrate from frame grabbed underwater video imagery. See also "Coral Point Count with Excel extensions (CPCe)"

The liver, gonads, intestines, and skin of puffer fish (and other related and unrelated animals) contain high concentrations of tetrodotoxin, a powerful neurotoxin that can cause respiratory paralysis and death, in approximately 60% of persons who ingest it. (Photo: NOAA)

poisonous - an organism that contains poison in its tissues that can be harmful if the organism is ingested

Poisson distribution - a probability distribution of random occurrences in which one occurrence has no influence on any other occurrence. The variance of a poisson distribution is equal to its mean and therefore the standard deviation is equal to the square root of the mean of the distribution

Polar-orbiting satellite data was used to derive this image of Hurricane Erin, September 2001.

polar-orbiting satellite - a satellite traveling in a near-polar orbit around the globe; civilian satellite program managed and operated by NESDIS

polarimeter - an instrument for measuring polarized light

Polaris - see North Star

polariscope - an instrument for detecting polarized light

polarized light - light waves which vibrate in one plane only as opposed to the multi-directional vibrations of normal rays

pollen - the male reproductive cells of flowering plants

poly - a prefix meaning "many"

polyadenylation - the process by which the 3' ends of most eukaryotic mRNAs are formed; the covalent modification of a macromolecule (e.g., mRNA) by the formation of a polyadenyl moiety covalent linked to the macromolecule; post-transcriptional addition of a polyadenylic acid tail to the 3' end of eukaryotic mRNAs; also called 'poly-(A) tailing'

polyadenylic acid - a polymer of adenylic acid that is sometimes attached to eukaryotic mRNA (messenger RNA) and stabilizes the molecule before transport from the nucleus into the cytoplasm

polyandry - a female mating with more than one male

polycarpic - refers to plants that have repeated periods of reproduction; iteroparous

polycentric distribution - the establishment of a population, species or other taxonomic unit in several widely separated geographic places

A marine polychaete worm grazing on the surface of a coral head. (Photo: Dr. Anthony Picciolo)

Polychaeta - a class of the segmented worm phylum Anellida. There are approximately 8,000 species of polychaetes which include errant (free-moving) forms and sedentary ones that live in stabilized burrows, galleries or tubes of various degrees of complexity. Some burrow into coral. Many species are common inhabitants of coral reefs, such as the Christmas tree worms, feather duster worms, fanworms, fireworms, scaleworms, threadworms, and others

polyclad flatworm - a free-living flatworm belonging to the order Polycladida (Class Turbellaria; Phylum Platyhelminthes). Many species are coral reef inhabitants

polyculture - the cultivation of more than one species of organism in an aquaculture system

polygamy - both sexes mating with more than one other individual

polygene - one of many genes of small effect that influence the development of a quantitative trait; results in continuous variation and in quantitative inheritance

polygenic trait - a phenotype controlled by many genes of small effect (polygenes)

polygyny - the mating of a single male with several females

polymer - a compound of high molecular weight consisting of up to millions of repeated linked light and simple molecules

polymerase - a general term for enzymes that carry out the synthesis of nucleic acids

Polymerase chain reaction (PCR) - a technique for quickly making many copies of a specific segment of DNA

polymorphic species - species which have a variety of morphological types

The island of Bora Bora in French Polynesia. (Photo: Anthony R. Picciolo, NOAA)

Polynesia - scattered islands of the central and southern Pacific Ocean roughly between New Zealand in the southwest, Hawaii in the north, and Easter Island in the southeast. The larger islands are volcanic, the smaller ones are generally coral formations

Cnidarian polyp.

polyp - an individual of a solitary cnidarian or one member of a cnidarian colony

polyp bail-out - nonsexual coral reproduction in which a polyp abandons a corallite and reestablishes itself on a new substrate; the dissociation and dispersal of coral polyps from adult colonies

Amino acids in proteins (or polypeptides) are joined together by peptide bonds.

polypeptide - a long chain of amino acids joined by peptide bonds

polyphydont - a type of dentition where the teeth are continuously replaced

polyphyletic group - a group of species that resemble each other but are evolved from different ancestors. A polyphyletic group is composed of members that originated, independently, from more than one evolutionary line

polyploid - cells or organisms having more than twice the haploid number of chromosomes

polypoid - polyp-shaped

polysaccharide - any of a class of carbohydrates whose molecules contain chains of monosaccharide molecules -

polytrophic - pertains to feeding at different levels in the food web; obtaining nutrients from different food sources

polytypic - a taxon including several subordinate taxa, e.g. a polytypic genus is one containing several species

A pony bottle attached to the main size cylinder. (Photo: Aqua Explorers)

pony bottle - a small, but independent alternate air supply for scuba divers, to be used in case of main air failure. It is a small scuba tank with an attached regulator

population - a group of individuals of the same species living in the same area at the same time and sharing a common gene pool; a group of potentially interbreeding organisms in a geographic area

population (statistics) - any entire collection of animals, plants, people, or things from which we may draw a sample and collect data. It is the entire group we are interested in, which we wish to describe or draw conclusions about. In order to make any generalizations about a population, a sample, that is meant to be representative of the population, is often studied. For each population there are many possible samples. A sample statistic gives information about a corresponding population parameter. For example, the sample mean for a set of data would give information about the overall population mean

population crash - sudden decline in the number of individuals found in a population because of a scarcity of required environmental resources

population density - the number of organisms per unit area or volume

population dynamics - the study of the factors that affect the growth, stability, and decline of populations, as well as the interactions of those factors

population explosion - sudden increase in the number of individuals found in a population because of an abundance of useable environmental resources

population genetics - the study of the allele frequency distribution and change in populations under the influence of the four evolutionary forces: (1) natural selection, (2) genetic drift, (3) mutation, and (4) gene flow

population sink - a portion of a species' geographic range where the death rate exceeds the birth rate for a local population

population viability - the probability that a population will persist for a specified period across its range despite normal fluctuations in population and environmental conditions

population viability analysis - an analysis that estimates minimum viable populations

pore space - openings between geologic material found underground; also referred to as void space or interstices

pore water - water between the grains of a sediment; also called interstitial water

A porgy photographed at Bimini (Photo: Mark Rosenstein / Active Window Productions (markrosenstein.com))

porgy - species of bony fishes in the family Sparidae. Porgies are found in temperate and tropical coastal areas of the Atlantic, Indian, and Pacific Oceans. They are especially abundant in the Mediterranean and Red Seas. Porgies have an oval-shaped, deep body with a blunt snout and small, nearly horizontal mouth. They possess strong teeth adapted for crushing their food of hard-shelled benthic invertebrates. Many species are hermaphroditic. Some are simultaneous hermaphrodites, having male and female gonads simultaneously. Others change sex as they get larger. Porgies are important food and game fishes. Other common names of fishes in the family Sparidae are sea breams and sheepsheads

A barrel sponge (Porifera). (Photo: Dr. Anthony Picciolo)

Porifera - an animal phylum that contains the sponges. They are the most primitive of the multicellular animals. Sponges assume many sessile body forms, such as finger, branching, bushy, spherical, tubular, vase and tube-like, encrusting, amorphous and massive. Some bore into coral and mollusk shells. Many of the 5,000 species are colorful and prominent inhabitants of coral reefs

Porites - an important and dominant genus of hermatypic coral. Porites brood or release live young rather than sperm and egg packets like most corals

porocyte - in sponges, a cell surrounding a pore (ostium)

porphyrous - purple color

Porpitidae - a small family of floating, pelagic colonial hydrozoans. They form colonies of hydroids which exhibit a division of labor. Some hydoids are modified to capture prey (microplankton) while others form a central gas-filled disc which keeps the colony afloat. The family Porpitidae was previously classified in a now invalid order, the Chondrophora

port - the left side of a vessel to someone facing the bow or front

portunid crab - any member of the crab family Portunidae (order Decapoda, class Malacostraca). In these crabs, the hindmost pair of legs (5th pair) are flattened into paddles for swimming. The family includes the blue crab (Callinectes sapidus), an edible crab of the Atlantic coast of North America; the velvet crab, Portunus sp of the Atlantic and Pacific oceans and the Mediterranean Sea; and Scylla serrata (mangrove crab) of the Indo-Pacific region; also called swimming crab

POSIDIN (Portal for Oceanographic Services for IOOS Data and information) - an oceanographic observation web portal for the exchange of information for NOAA’s Center for Operational Oceanographic Products and Services and National Data Buoy Center IOOS participants

posit - a proposition that is accepted as true in order to provide a basis for logical reasoning; take as a given; assume as a postulate or axiom

positive allometry - allometric relationship in which the slope of the line comparing two variables is greater than unity

possession - equivalent to 'territory.' Although it still appears in Federal statutes and regulations,  "possession" is no longer current colloquial usage

post-emergent nest - a seaturtle nest in which the majority of hatchlings have emerged through the surface of the sand

The prehensile tail at the posterior end of the seahorse+s body allows it to hold on to aquatic plants

posterior - morphologically, toward the rear or back end of an individual, or distal portion of a bodily part

posting - a single message entered into a network communications system

postlarva - in fishes, a larva following the yolk sac stage; the term is applied only when the post larva's morphology continues to be strikingly different from that of the juvenile

postulate - a statement accepted without proof; a fundamental assumption

potable water - water that is safe for drinking by humans. Specifically, freshwater that generally meets the standards in quality as established in the U.S. Environmental Protection Agency (EPA) Drinking Water Standards

potential coral reef bleaching episode - potential for coral bleaching occurs when the sea surface temperature is at least 1 degree C above the maximum expected summertime temperature

potentiation - the effect of an initial stimulus in evoking a stronger response the next time it is received; the synergistic effect of two drugs given simultaneously; the ability of one chemical to increase the effect of another chemical

PowerPoint: - a program in the Microsoft Office suite which allows users to create presentations and handouts. By creating PowerPoint "slides," users can add color, images, sounds, and movies to their text presentations

practical salinity unit (psu) - a unit of measurement of salinity similar to part per thousand (ppt)

prebiotic - a food substance intended to promote the growth of certain bacteria; also refers to the state of matter before life existed, but was conducive to the origin of life. The prebiotic 'soup' is the mixture of organic molecules in the primeval ocean that are thought to have spontaneous, self-assembly properties for the first formation of an organic complex with self-replicating qualities; Oparin's organic soup

precautionary approach - measures intended to reduce risk to a biological resource and its environment

precious coral - the common name given to the Mediterranean red coral (Corallium rubrum)and several related species of corals found in the Pacific and Atlantic Oceans. The distinguishing characteristic of precious corals is that their skeleton can be polished to a beautiful color and made into jewelry. Precious corals are the red coral (Corallium rubrum), pink coral Corallium sp), black coral (Antipathes grandis), and the Hawaiian gold coral (Gerardia sp)

precipitation - any form of water that falls from the atmosphere to the surface of the earth, i.e., rain, snow, sleet, and hail

precision - the ability of an instrument to measure a variable and to repeatedly obtain the same result

precocial - born or hatched in a fully-developed state; relatively mature and mobile from the moment of birth or hatching; the opposite of altricial

This seahorse keeps its position by anchoring itself with its prehensile tail. (Photo: Dr. Tom Doeppner, Brown University)

prehensile - capable of or adapted for grasping, such as the prehensile tail of a seahorse

preprint - an article printed especially for private distribution in advance of the actual publication

pressure gradient - a graded change in the level of water or air pressure that occurs over distance

prevailing winds - winds that blow consistently from one direction; the typical winds for a particular region and time of year

prevalence - the number of disease cases within a population over a given period of time

prialt - an analgesic drug made from the venom of a species of cone shell snail, Conus magus. The particular anagesic substance in the venom is a conopeptide, one of the first pharmaceuticals that demonstrate the promise of "drugs from the sea"

PRIAs (Pacific Remote Island Areas) - waters of the U.S. exclusive economic zone (U.S. EEZ) around Howland Island, Baker Island, Jarvis Island, Johnston Atoll, Kingman Reef, Palmyra Atoll, Wake Island and Midway Atoll

Primary male or female - a male or female that is genetically determined at birth or hatching and is not the result of sex change

primary polyp - in colonial octocorals, e.g., sea pens, one polyp grows very large and loses its tentacles, forming the central supporting axis. This is the primary polyp. The base of this primary polyp forms a bulb, which anchors it to the substratum. Branching off this primary polyp are various secondary polyps. Some are specialized for feeding (autozoids). Others (siphonozooids) serve as intakes for water, which circulates within the colony and help keep it upright

primary production - a synonym of primary productivity

primary productivity - the rate at which new plant biomass is formed by photosynthesis. Gross primary productivity is the total rate of photosynthetic production of biomass; net primary productivity is gross primary productivity minus the respiration rate

prime meridian - an imaginary line running from north to south through Greenwich, England, used as the reference point for longitude

primer - in genomics, a short pre-existing single-stranded polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase. It anneals to a nucleic acid template and promotes copying of the template starting from the primer site; a single-stranded nucleic acid that can "prime" replication of a template

primeval soup - Soviet biologist, Aleksandr Ivanovich Oparin, in 1924, put forward a theory of life on Earth developing in the oceans through gradual chemical evolution of carbon-based molecules in a rich organic broth or "primeval soup." He hypothesized that the early oceans were rich in organic compounds

primitive character - in evolution, an attribute of taxonomic group which all members of the group possess, i.e., the more common shared characters of a given group of organisms. Primitive characters are also called 'plesiomorphies'

prion (proteinaceous infectious particle -on) - an infectious agent composed only of protein. Prions cause a number of neurological diseases in a variety of animals, and all are currently untreatable and fatal

priority - in taxonomy, the seniority of a taxonomic name fixed by the date of publication; the earliest published name has priority

pristine - an area having its original purity, not contaminated or corrupted by human intervention; the original or pure condition or state of something; unspoiled

probability - a quantitative description of the likely occurrence of a particular event. Probability is conventionally expressed on a scale from 0 to 1; a rare event has a probability close to 0; a very common event has a probability close to 1

probe - in genetics, a DNA or RNA sequence that is labelled or marked with a radioactive isotope. It is used to detect the presence of a complementary sequence by hybridization with a nucleic acid sample

probiotic - a dietary supplement containing potentially beneficial bacteria or yeast

proboscis - an elongated tubular organ of varying use and form, usually associated with the oral region of many invertebrates

prochlorobacteria - a distinct group of Eubacteriophyta which possess both chlorophylls a and b of higher plants. The prochlorobacteria also produce oxygen like the cyanobacteria, but unlike the cyanobacteria, they do not have phycobilin accessary pigments

produced water - water associated with oil and gas reservoirs that is produced along with the oil and gas; also called “brine” (and may contain high mineral or salt content) or “formation water"

producers - the first level in a food pyramid; usually consist of photosynthetic organisms that generate the food used by all other organisms in the ecosystem

progenitor - an ancestor or precursor

Gravid proglottid of the tapeworm Taenia saginata. The dark branched structure is the uterus. Note the mid-lateral genital pore. (Photo: U.S. Center for Disease Control)

proglottid - one of the segments of a tapeworm, containing both male and female reproductive organs

programmed cell death (PCD) - a form of cell death in which a genetically programmed sequence of events leads to the destruction of cells without releasing harmful substances into the surrounding areas. PCD plays an important role in the health of an organism by eliminating aged cells, unnecessary cells, and unhealthy cells; also called "apoptosis" or "cell suicide"

prohibited species - with respect to a foreign (non-U.S.) fishing vessel, any species of fish that that vessel is not specifically allocated or authorized to retain, including fish caught or received in excess of any allocation or authorization (Magnuson-Stevens Fishery Conservation and Management Act)

Project AWARE - a nonprofit organization dedicated to conserving underwater environments through education, advocacy and action. With headquarters in the United States and offices in Australia, Japan, Switzerland and United Kingdom, Project AWARE combats challenges facing aquatic resources in 175 countries and territories with direct support from divers and water enthusiasts worldwide. Project AWARE and dedicated volunteers are committed to conservation initiatives including: underwater cleanups and marine debris prevention; coral reef conservation, monitoring and data collection; shark education, reporting and conservation; improved management policies and marine protection efforts; and environmental training for divers and education programs for kids

Project Seahorse - an international team of biologists, development specialists, and other professionals committed to conserving and managing seahorses, their relatives and habitats, while respecting human needs

prokaryote - an organism whose chromosomes are not enclosed within a nuclear membrane, e.g., a bacterium or cyanobacterium

prokaryotic - descriptive of organisms with cells possessing no distinct nucleus. Prokaryotes include bacteria and cyanobacteria

proliferation - to reproduce or increase rapidly and repeatedly

promiscuous - refers to animals that copulate with several different partners within a short time span

promoter - a DNA sequence that is located in front of a gene and controls gene expression. Promoters are required for binding of RNA polymerase to initiate transcription

The intertidal understory of a mangrove forest shows the muddy soil, the fairly high density of stems, and the tangle of prop and drop roots. (Photo: Copyright Dr. Joseph E. Armstrong, Illinois State University)

prop root - an adventitious root that grows from and supports the trunk above the ground in plants, such as mangroves

Cigar-shaped propagule of the red mangrove, Rhizophora mangle. It may reach 15 cm in length. (Photo: Bill Keogh)

propagule - a structure for mangrove reproduction. After a mangrove is pollinated, it produces a propagule, which grows on a parent plant and requires carbon dioxide and water from the parent, but produces its own sugars from photosynthesis. After a while, it separates from the parent tree and falls into the water where it can be transported great distances. Propagules can resist dessication and survive for long periods of time until they root in a suitable environment.

proprioceptor - a specialized sensory nerve ending that monitors internal changes in the body brought about by movement and muscular activity. Proprioceptors are located in muscles, tendons, and joint capsules and when stimulated, transmit information concerning movements and position of the body; also called "proprioreceptor"

prosopinacocyte - in sponges, an endopinacocyte lining an incurrent canal

prosopinacoderm - in sponges, a surface lined with prosopinacocytes

prosopyle - the opening into the excurrent canal in sponges

prostaglandin - a fatty acid compound that has many effects throughout the body, including activity in inflammation, contraction of smooth muscles, regulation of body temperature, and effects on certain hormones. Sea fans contain high concentrations of prostaglandins

prosthetic group - a specific nonpolypeptide unit in a protein determining and involved in its biological activity

prostomium - the anteriormost, presegmental region of the body of an annelid worm, sometimes bearing eyes and antennae; the portion of the head in annelids that is situated anterior to the mouth

prostrate - lying horizontally or flat on the substrate

prostrate colony - a coral colony which sprawls horizontally over the substrate

protandry - a state in hermaphroditic systems characterized by the development of male reproductive organs, or maturation of their gametes, before the appearance of the corresponding female product, thus insuring against self-fertilization

protease - an enzyme that hydrolyzes proteins, cleaving the peptide bonds that link amino acids in protein molecules

This brilliant sea anemone is from the protected Gulf of the Farallones National Marine Sanctuary.

protected area - a legally established land or water area under either public or private ownership that is regulated and managed to achieve specific conservation objectives

protected species - species which are protected by federal legislation such as the Endangered Species Act, Mammal Protection Act, and Migratory Bird treaty Act

protein - a large complex molecule made up of one or more chains of amino acids. A typical protein contains 200-300 amino acids but some are much smaller and some much larger, e.g., titin, a protein found in skeletal muscle contains approximately 27,000 amino acids in a single chain. Proteins perform a wide variety of essential activities in cells: they largely form the physical structure of cells and cellular matrices; catalysts for all biochemical reactions are enzymes, which contain protein; the transport of materials in body fluids depends of proteins; the receptors for hormones and other signaling molecules are proteins; motion and locomotion of cells and organisms depends on contractile proteins; the transcription factors that turn genes on and off are proteins; proteins are an essential nutrient for heterotrophs; and many more - the activities of cells and organisms are largely reflections of the activities of their proteins

protein kinase C (PKC) inhibitor - an antitumor compound, isolated from marine sponges, which inhibits protein kinase C (PKC). PKC is believed to be the receptor protein of tumor-promoting phorbol esters

protein sequencing - the process of determining the amino acid sequence of a protein, or its component polypeptides

protein synthesis - the creation of proteins from their constituent amino acids, in accordance with the genetic information carried in the DNA of the chromosomes

proteinaceous - any structure composed of proteins

proteolysis - the breaking down by hydrolysis of proteins into peptides and amino acids by cleavage of their peptide bonds

proteolytic enzyme - a term referring to any enzyme which accelerates the breaking down or digestive hydrolysis of proteins into smaller proteins, polypeptides, peptides, or amino acids

proteome - all of the proteins produced from all the genes of a genome

Protista - earliest evolved eukaryotic kingdom. It includes the protozoans, the slime molds, the unicellular algae, and the multicellular algae. However, some consider the multicellular marine algae (seaweeds) as belonging to the kingdom Plantae

protocols - the selections of methods and how they are used to gain data and information at a site

protogynous - pertains to a sequential hermaphrodite in which the organism first functions as a female and later as a male

protogyny - a state in hermaphroditic systems characterized by the development of female reproductive organs, or maturation of their gametes, before the appearance of the corresponding male product, thus insuring against self-fertilization

protonephridium - a simple type of excretory organ of simple invertebrates, such as flatworms and rotifers. It is also called a 'flame bulb.' Protonephridia are primarily concerned with removing excess water from the animal

protoplasm - the complex colloidal substance which constitutes the living matter of cells and performs the life process functions. The protoplasm found between the cell (plasma) membrane and the nuclear membrane is termed the cytoplasm; the protoplasm within the nucleus and separated from the cytoplasm by the nuclear membrane is termed the nucleoplasm

protoplast - a cell from which the entire cell wall has been removed by physical or enzymatic agents. This term is used to describe such plant, bacterial or fungal cells, but not animal cells; More generallythe term refers to that biological unit which is composed of a cell's nucleus and the surrounding protoplasmic materials

protostome - an evolutionary line of coelomates that include mollusks, annelids, and arthropods. They develop their embryo by spiral cleavage, and the blastopore of the gastrula develops into the mouth. The group exhibits bilateral symmetry

prototroch - the main girdle of cilia in larvae of polychaete worms

Protozoa - heterotrophic eukaryotic unicellular organisms that belong to the kingdom Protista

protractile - capable of being protruded or thrust out

The protrusible jaw of a south Florida mojarra (family Gerreidae)

protrusible - capable of being protruded, extended or thrust out, e.g., the tongue or the jaws in some fishes

proximal - the direction towards center of the body; opposite of distal

proximate - immediate or nearest; closest in degree or order (space or time); very close in space or time

proxy - in climate research, a proxy variable is something from which a variable of interest can be obtained. For example, temperature proxies such as tree ring widths and ice core layering are used by paleoclimatologists to create a past temperature record. tree ring widths can also be used to infer precipitation changes. Variations in Beryllium 10 can be used to infer past solar irradiance

proxy signal - paleoclimatic evidence that can be used to indirectly infer or estimate some aspect of the paleoenvironment, such as precipitation or temperature

psammon - organisms growing on, in, or moving through sand; interstitial organisms

pseudocoelom - a closed fluid-filled cavity that acts as a hydrostatic skeleton to maintain body shape, circulate nutrients, and hold the major organs in roundworms, rotifers, spiny-headed worms, and horsehair worms

Spiny-headed worms (Acanthocephala) attached to the intestinal lining of of a fish. This parasitic pseudocoelomate uses a spiny attachment organ to secure itself to the intestine. (Photo: Maine Department of Inland Fisheries and Wildlife)

pseudocoelomate - any of a group of triploblastic invertebrates that has a fluid-filled body cavity, the pseudocoelom, lying between the endoderm and the mesoderm The pseudocoelom is contrasted with the coelom of mollusks, annelid worms, and the more complex animals, including vertebrates, by lacking an endothelial lining. Pseudocoelomates lack a circulatory system, using the pseudocoelom to transport nutrients. The hydrostatic pressure of the pseudocoelom gives the body a supportive framework that acts as a skeleton. Nematodes (roundworms), rotifers, acanthocephalans (spiny-headed worms), kinorhynchs, and nematomorphs (horsehair worms) are pseudocoelomate groups

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

pseudopodium (pseudopod) - a protoplasmic filament or irregular process that can project from any unicellular organism. Formation of pseudopodia (or pseudopods) assist in feeding and locomotion

pseudopterosin - a compound isolated from species of Pseudopterogorgia (soft gorgonacean corals) that may act as a marine pharmaceutical with, inter alia, anti-inflammatory and analgesic properties

psi (pounds per square inch) - a unit of air or water pressure expressed as pounds per square inch (psi)

pterygiophore - in fishes, one of several bones or cartilage with which the base of the rays of the median fins articulate

ptychocyst - a type of cnida used in tube construction by tube anemones (Ceriantharia). Tube anemones build a tube almost entirely from the everted tubules of the ptychocysts

public domain - a work is said to be in the public domain if it is not protected by copyright, or if the copyright for it has expired

published name - in taxonomy, any name which is printed and circulated, i.e., meets the criteria of publication as stated by the International Code of Zoological Nomenclature; it may be available, unavailable, valid or invalid

Puerto Rico Plateau - a shallow-water geological platform comprising the easternmost part of the Greater Antilles in the Caribbean. The emergent portion of the plateau is composed of Puerto Rico, Culebra, Vieques, St. Thomas, St. John, Tortola, Virgin Gorda, Anegada, and assorted smaller islands

A spotted puffer (Arothron meleagris) from Midway Island. When threatened, puffers can inflate their body by swallowing water to increase their body volume as a deterrent to predators.(Photo. Dr. John E. Randall)

puffer - any species of marine bony fishes belonging to the families Tetraodontidae (puffers, blowfishes), or Diodontidae (burrfishes, porcupinefishes, spiny puffers). These fishes are able to inflate their bodies with water or air to form a globe as a protection against predation. The flesh and organs of some blowfishes contain an extremely potent toxin which can be fatal to humans when ingested

Pulley Ridge - the deepest known reef off the continental United States, Pulley Reef is a 100+ km-long series of North-South trending, drowned, barrier islands located in the Southeastern Gulf of Mexico, near the edge of the Florida Continental Shelf. The reef is located approximately 150 miles southwest of Naples Florida and 60 miles northwest of the Dry Tortugas Ecological Reserve. It lies approximately 84 m below the ocean surface. The shallowest parts of the ridge are about 60 m deep. Even at these depths, there are many species of zooxanthellate scleractinian corals, green, red and brown macro algae, and shallow and deep water reef fishes

pulse amplitude modulation (PAM) fluorometer - a portable submersible fluorometer. Fluorometers that use the PAM technique work by rapidly sending brief pulses of light to a plant or other organism  A healthy organism responds to this light very quickly (within microseconds) by re-emitting some of the

pulse fishing - harvesting a stock of fish, then moving on to other stocks or waiting until the original stock recovers

pulse-chase isotope labeling experiment - In this protocol, a cell sample is exposed to a radio-labeled compound for only a brief period of time (the 'pulse'), then it is washed with a buffer solution to remove the isotope, and finally incubated with a non-labeled form of compound (the 'chase').

punctate - describes a surface stippled with tiny pores

punctuated equilibrium - an evolutionary model in which change occurs in relatively rapid bursts, followed by little or no discernible change in a lineage (stasis)

punctule - a minute dot, pit or aperture

pungent - sharp, biting or acrid sensation, especially in taste or smell

pure line - a genetically uniform strain in which all members have descended by self-fertilization or close inbreeding

pure tone - a sound which consists of one single frequency

purine - a nitrogen-containing, double-ring, basic compound that occurs in nucleic acids. The purines in DNA and RNA are adenine and guanine

purse seine - a fishing net used to encircle surface schooling fish. During retrieval the bottom of the net is closed or pursed by drawing a purse line through a series of rings to prevent the fish from escaping. The catch is deposited on the fishing boat. The purse seine is operated by two boats, a large boat that surrounds the catch with the net and a smaller boat which anchors the net. Purse seines may be of up to 1 km length and 300 m depth

pustule - a pimple- or wart-like projection; a bump or raised knob on the outside surface of a mollusk shell

puupehenone - a bioactive marine natural product, obtained from sponges of the genus Hyrtios, which possesses antitubercular, anticancer, and antibacterial properties

The pycnogonid Anoplodactylus evansi is a predator of small marine gastropods as well as other soft bodied invertebrates. (Photo: Dr. Bill Rudman)

pycnogonid - pycnogonids, or sea spiders, are benthic, marine arthropods, with a superficial resemblance to true spiders, to which they are probably only distantly related. They are carnivores and use a muscular pharynx to suck soft food into the gut. The mouth is at the end of a large proboscis. Digestion is intracellular and most feed on sponges, cnidarians, or bryozoans from which they suck fluids. There are no excretory organs, respiratory organs, or body cavity (coelom)

The pygmy goby, Eviota sigillata, has the shortest life span of any known vertebrate on Earth, with a maximum life expectancy of 59 days. (Photo:Dr. John E.Randall)

pygmy goby - the pygmy goby, Eviota sigillata, has the shortest life span of any known vertebrate on Earth, with a maximum life expectancy of 59 days. Eviota sigillata is a small cryptic coral reef fish distributed in the Indo-West Pacific: Seychelles to the Great Barrier Reef and Micronesia, north to the Ogasawara Islands

pyknosis - degeneration of a cell in which the nucleus shrinks in size and the chromatin condenses to a solid, structureless mass

pyknotic - characterized by pyknosis

There are 4-6 intermediate-length pyloric caecae in this specimen (Photo:John Lyons/Wisconsin DNR, the Wisconsin Sea Grant, and the Unviversity of Wisconsin)

pyloric caecum - in fishes, a finger-like pouch connected with the pyloric stomach of the digestive canal. Pyloric caecae may have a digestive and/or absorptive function. They range in number from two or three in some species to thousands in others

pyramid of biomass - in ecology, the total biomass of all organisms at each trophic level in a food chain; typically biomass declines with successively higher trophic levels

pyramid of energy - in ecology, the total energy content of all organisms at each trophic level in a food chain; the energy content declines at successively higher trophic levels

pyramid of numbers - in ecology, the number of organisms supported at each trophic level in a food chain; typically, fewer organisms are supported at successively higher trophic levels

pyranometer - an instrument that measures the amount of radiation.

pyrenoid - pyrenoids are proteinaceous centers of carbon dioxide fixation within the chloroplasts of zooxanthellae, other algae, and some bryophytes. Pyrenoids are not membrane-bound organelles, but specialized areas of the plastid that contain high levels of ribulose-1,5-bisphosphate carboxylase/oxygenase and are associated with the formation or storage of polysaccharide food reserves.

pyriform - pear-shaped

pyrimidine - a nitrogen-containing, double-ring, basic compound that occurs in nucleic acids. The pyrimidines in DNA are cytosine and thymine. The pyrimidines in RNA are cytosine and uracil

pyrolysis - the destruction of a chemical compound by heating or burning

pyrosome - a large barrel-shaped colony of colonial pelagic tunicates belonging to the genus Pyrosoma. The colony propels itself through the water by means of cilia that pump water through the individual tunicates. It responds to mechanical, chemical, and light stimuli by moving and by spectacular blue-green bioluminescent displays