GLOSSARY

An alternative form of a gene that can occur at the same location (locus) on homologous (paired) chromosomes. A population can have many alleles for a particular locus, but an individual can carry no more than two alleles at a diploid locus.

Alternative forms of an enzyme that have the same function, are produced by different alleles, and are often detected by protein electrophoresis.

Caused or produced by human action.

A statistical test whereby an individual of unknown origin is assigned into a source population. The probability of an unknown individual’s membership into each putative source population is calculated, and the unknown is assigned to the population of highest probability.

A polycyclic aromatic hydrocarbon produced by combustion of gasoline, garbage, or any animal or plant materials that burns. Found in soot and smoke, including cigarette smoke, and in coal tar and creosote. The U.S. Department of Health and Human Services has determined that B[a]P may reasonably be anticipated to be a carcinogen. It may also be associated with reproductive problems and birth defects. In the body, B[a]P is changed to related chemical substances (metabolites) that can bind with DNA, the genetic material of the body.

Bile

Fluid produced by the liver and stored in the gall bladder, and secreted into the stomach to aid in digestion. Toxic substances broken down and detoxified by the liver are often excreted into the bile.

Uptake and retention of chemical contaminants in tissues of animals. Usually involves lipid-soluble compounds that accumulate in body fat.

The team of scientists who evaluated a scientific information considered in the National Marine Fisheries Service status review.

Virgin population size or the expected population level in the absence of fishing.

A population size equal to 40% of B₀ (Original Biomass).

The population size that results when a stock is fished at a fishing mortality rate that produces maximum sustainable yield (MSY).

Concentration of a contaminant that accumulates in the body.

A manufactured chemical that was used as a pesticide in the United States from 1948 to 1988. Banned for all uses by EPA in 1988 because of concern about possible effects on wildlife and human health. Persistent in soils and sediment, and bioaccumulates in animal tissues.

Pesticides containing chlorine. Examples include DDTs, chlordane, aldrin, and dieldrin.

Federal, state, and tribal agencies that cooperatively manage groundfish in the Pacific Northwest.

Catch_per_unit effort

Dichlorodiphenyltrichloroethane (DDT) and closely related compounds DDE (1,1-dichloro-2,2-bis(chlorophenyl) ethylene) and DDD (1,1-dichloro-2,2-bis(p-chlorophenyl) ethane). Was a commonly-used insecticide until it was banned in the United States in 1972 because of its effects on development and reproduction in wildlife. Persistent in soils and sediment, and bioaccumulates in animal tissues.

Disease conditions or abnormalities that involve death and degeneration of cells.

Insecticides with similar structures. Aldrin quickly breaks down to dieldrin in the body and in the environment. Popular pesticides for agricultural crops from 1950-1970. Banned for all uses by EPA in 1987 because of concerns possible effects about wildlife and human health. Persistent in soils and sediment, and bioaccumulates in animal tissues.

Chlorinated dibenzo-p-dioxins (75 chemicals) occurs mainly from eating food that contains the chemicals. Dioxins are not intentionally manufactured, but may be formed during the chlorine bleaching process at pulp and paper mills, during chlorination by waste and drinking water treatment plants, and as contaminants in the manufacture of certain organic chemicals. They are also released into the air in emissions from municipal solid waste and industrial incinerators. Exposure in humans is associated with skin diseases such as chloracne, liver damage, alterations in glucose metabolism and hormone levels, and possibly increased risk of cancer. In animals, exposure has been linked to weight loss, liver damage, disruption of the endocrine system, weakening of the immune system, reproductive damage, and birth defects.

The amount of gaseous oxygen held in solution.

A population, or group of populations of a vertebrate organism that is "discrete" from other populations and "significant" to the biological species as a whole.

DNA is a complex molecule that carries an organism's heritable information. DNA consists of a polysugar_phosphate backbone from which the bases (nucleotides) project. DNA forms a double helix that is held together by hydrogen bonds between specific base pairs (thymine to adenine, guanine to cytosine). Each strand in the double helix is complementary to its partner strand in terms of its base sequence. The two types of DNA commonly used to examine genetic variation are mitochondrial DNA (mtDNA), a circular molecule that is maternally inherited, and nuclear DNA, which is organized into a set of chromosomes (see also allele and electrophoresis).

Weight of a substance after the normal water content has been removed e.g., weight of tissue or sediment before water is removed.

Exclusive Economic Zone; the extended 200 mile jurisdictional zone that surrounds the USA coastline.

Level, e.g., level of exposure for chemical contaminants, associated with the onset of a biological effect.

Electrophoresis is the movement of charged particles in an electric field. This process has been developed as an analytical tool to detect genetic variation revealed by charge differences on proteins or molecular weight in DNA. Data obtained by electrophoresis can provide insight into levels of genetic variability within populations and the extent of genetic differentiation between them.

A species in danger of extinction throughout all or a significant portion of its range.

Protein that serves as a catalyst (facilitates) a biochemical reaction within a living organism, e.g., proteins that catalyze the breakdown of toxic chemicals taken up by an animal.

Increased activity of enzymes in response to some stimulus; e.g., increased activity of enzymes involved in toxicant metabolism in response to exposure to a chemical.

U.S. Environmental Protection Agency.

  U.S. Endangered Species Act, of 1973, as amended.

Organisms that tolerate a wide range of salinities.

An ESU represents a distinct population segment of Pacific salmon under the Endangered Species Act that: 1) is substantially reproductively isolated from nonspecific populations, and 2) represents component an important component of the evolutionary legacy of the species.

A series of coefficients used to quantify the distribution of genetic variation within and among populations and groups of populations. Most often used is Fst, which describes overall differentiation among a group of populations, or more specifically, the correlation of genes among individuals in each population.

Breakdown products (metabolites) of aromatic compounds which have fluorescent properties because of their chemical structure. These compounds can be detected in bile to provide evidence of exposure to PAHs.

Fishery Management Plan.

The fishing mortality that produces maximum sustainable yield (MSY).

When the original founders of a new population contain only a part of the genetic variability of their parental population.

Chlorinated dibenzofurans are a family of chemicals that contain one to eight chlorine atoms attached to the carbon atoms of the parent chemical, dibenzofuran. There are 135 different types with varying harmful health and environmental effects. Other than for research purposes, they are not deliberately produced by industry. Most are produced in small amounts as undesirable by-products of certain processes, such as manufacturing other chemicals or bleaching at paper and pulp mills. They can also be released from incinerators. Their biological effects are similar to those of dioxins.

A quantitative measure of genetic difference between a pair of samples.

The occurrence of random changes in the gene frequencies of populations.

The semi_enclosed marine basin comprised of the Strait of Georgia, Puget Sound proper, North Puget Sound together with the lands that drain into these marine waters.

The amount of gonadal tissue divided by the amount of gonadal and somatic tissue.

Greater Puget Sound

Greater Puget Sound refers to the area of North Puget Sound and Puget Sound proper combined.

The collective genotype of a number of closely linked loci; the constellation of alleles present at a particular region of genomic or mitochondrial DNA.

The proportions of genotypic frequencies predicted on the basis of the allele frequencies in the population. These proportions depend on the assumption that mating occurs randomly in the population.

A measure of allelic diversity at a locus (or averaged over several loci) whereby alternate alleles at a locus are different.

The condition of having two different alleles at a given locus of a chromosome pair.

Any kind of abnormality in a tissue or organ.

Any of numerous fats and fat-like materials.

The level of lipid in a substance, usually a body tissue. Most often expressed as a percentage of total weight.

Locus (pl. loci)

The site on a chromosome where a gene is found; often used more or less synonymously with gene (cf. polymorphic locus, allozymes, isozymes).

The survey collects and disseminates information regarding recreational fisheries in maritime states.

A discretely varying and countable trait (e.g., number of fin rays or basibranchial teeth); cf. traits with continuous variation (e.g., weight, length) or discrete variation (e.g., male, female, mature, immature).

The functioning of any specific substance within the body; for toxicants, the chemical processes involved in the breakdown and elimination of the substance.

Any of various organic compounds produced by metabolism; for toxicants, breakdown products of the toxic substance that is metabolized.

Magnuson-Stevens Fishery Conservation and Management Act.

A class of repetitive DNA. Microsatellites are simple sequence repeats one to eight nucleotides in length. For example, the repeat unit can be simply "CA", and might exist in a tandem array (CACACACACA...) 50 or more repeat units in length. The number of repeats in an array can be highly polymorphic.

Minor Statistical Area (MSA)

Geographical subdivisions of the marine waters of the Strait of Juan de Fuca and Strait of Georgia used by the Canadian Department of Fisheries and Oceans for marine fish management purposes.

The DNA genome contained within mitochondria and encoding a small subset of mitochondrial functions; mtDNA is typically circular and 15_20 kilobases in size, containing little noncoding information between genes.

A discretely varying trait related to the size and shape of landmarks from whole organs or organisms analyzed by appropriately invariant biometric methods in order to answer biological questions.

Maximum sustainable yield; the largest constant annual catch that can be obtained from a stock of fish on a continuing basis.

A polycyclic aromatic hydrocarbon found in fuel oils and other petroleum products and used in the manufacture of dyes, resins, and mothballs. It evaporates easily and does not bind strongly to sediments. Exposure to naphthalene has been associated with the development of hemolytic anemia, nausea, vomiting, diarrhea, kidney damage, jaundice, liver damage, and cataracts. It does not appear to be carcinogenic.

National Marine Mammal Laboratory.

North Puget Sound is defined by the United States-Canadian border on the north, a line due north of Cape Flattery on the west, the mainland on the east and a line drawn between Point Wilson and Partridge Point on Whidbey Island on the south. Washington Department of Fish and Wildlife (WDFW) defines their North Puget Sound sampling area at a line drawn due north of the Sekiu River, however, the petitioner included the area between the Sekiu River and Cape Flattery in the petition for listing.

Nuclear DNA (nDNA)

The DNA contained in the chromosomes within the nucleus of eukaryotic cells. The nuclear genome in Pacific salmon is approximately 4.6 billion base pairs in size.

Northwest Fisheries Science Center.

Crystalline calcium_carbonate structures within the inner ear of fish. These structures have distinctive shapes, sizes, and internal and surface features that can be used for age determination and species identification.

Whenever population size falls below 50% of B_msy (by the national standard) or 25% of B₀ (Pacific Fishery Management Council standard).

Whenever the fishing rate exceeds a rate equivalent to F_msy.

Polycyclic aromatic hydrocarbons (PAHs) are a group of over 100 different chemicals that are formed during the incomplete burning of coal, oil and gas, garbage, or other organic substances like tobacco or char broiled meat; some PAHs are also manufactured. PAHs are found in coal tar, crude oil, creosote, and roofing tar, and a few are used in medicines or to make dyes, plastics, and pesticides. Exposure to PAHs has been associated with cancer, reproductive problems, birth defects, and immune dysfunction in animals. The Department of Health and Human Services has determined that some PAHs are reasonably expected to be human carcinogens.

Polychlorinated biphenyls (PCBs) are a group of manufactured organic chemicals that contain 209 individual chlorinated chemicals (known as congeners). Some commercial mixtures are known by the trade name Aroclor. PCBs have been used widely as coolants and lubricants in transformers, capacitors, and other electrical equipment. The manufacture of PCBs stopped in the United States in 1977 because of evidence that they build up in the environment and cause harmful effects. A subset of PCB congeners, known as dioxin-like congeners, are similar in structure and have toxic effects much like those of dioxins, although their toxicity is not as great. Exposure to PCBs in animals has been associated with liver and kidney damage, stomach, and thyroid gland injuries, anemia, acne, reproductive problems, and increased cancer risk. Humans exposed to PCBs may develop skin irritations such as acne and rashes, and there may be some increased risk of birth defect, reproductive problems, and cancer, although this has not been established conclusively.

The appearance (or other measurable characteristic) of an organism that results from interaction of the genotype and environment.

Having more than one form (e.g., polymorphic gene loci have more than one allele).

A locus characterized by more than one allele in a sample. If different alleles can be detected at a gene locus, the locus is considered polymorphic. If all alleles are of the same type, the locus is considered monomorphic. Many population genetic analyses are based on the frequency of different alleles at polymorphic loci.

A group of individuals of a species living in a certain area that maintain some degree of reproductive isolation.

Principal component analysis (PCA)

An ordination technique for analyzing data from several variables, such as allelic frequencies or morphological data. The method finds linear trends (principal components) through the clouds of sample points in multidimensional space. These principal components account for the greatest amount of variation present in the data. The residual variance is removed from the data with the calculation of each successive principal component.

An allelle found at a single location only.

Disease condition or abnormalities that involve abnormal growth or proliferation of cells.

An analytical laboratory technique that measures differences in the amino acid composition of proteins from different individuals. Because the amino acid sequence of proteins is coded for by DNA, data provided by protein electrophoresis provide insight into levels of genetic variability within populations and the extent of genetic differentiation between them. See electrophoresis.

Puget Sound Ambient Monitoring Program, a multi-year environmental monitoring program conducted by the State of Washington to assess trend in environmental quality in Puget Sound. As part of this program, concentrations of toxic contaminants in sediments, water, and biota of Puget Sound are measured.

Puget Sound Water Quality Action Team. This Washington State sponsored team works with tribal and local governments, community groups, citizens and businesses, and state and federal agencies to develop and carry out two-year work plans that guide protection of water quality and biological resources in the Sound. This group oversees the Puget Sound Ambient Monitoring Program.

A coastal fjord-like estuarine inlet of the Pacific Ocean located in northwest Washington State between the Cascade and Olympic mountains and covering an area of over 9,000 km² including 3,700 km of coastline.

Puget Sound proper is defined as the marine waters south of Admiralty Inlet and east of Deception Pass.

(restriction fragment length polymorphism) variations occurring within a species in the length of DNA fragments generated by a specific restriction endonuclease. Such variation is generated either by base substitutions that cause gain or loss of sites, or by insertion/deletion mutations that change the length of fragments independent of restriction site changes.

Sustainable Fisheries Act.

Standard Length, defined as the length from the tip of the head to the tip of the caudal peduncle.

Biological - A small group of organisms formally recognized by the scientific community as distinct from other groups. Legal - refers to joint policy of the USFWS and NMFS that considers a species as defined by the ESA to include biological species, subspecies, and DPSs.

The body of water separating the southern portion of Vancouver Island and the British Columbia mainland. The strait extends from Cortes Island and Desolation Sound in the north to the San Juan Islands in the south.

The body of water separating the southern portion of Vancouver Island and the Olympic Peninsula in Washington. The strait extends from the Pacific Ocean east to the San Juan and Whidbey Islands. In this document, generally referred to as a portion of North Puget Sound.

Not resulting in death (e.g., a disease condition not resulting in death).

Causing birth defects or developmental abnormalities.

A species not presently in danger of extinction but likely to become so in the foreseeable future.

A poison or poisonous agent; does not include poisonous substances secreted by organisms (e.g., venoms), which are known as toxins.

The enzyme involved in the breakdown of toxicants.

A disease condition caused by toxic chemicals.

Pertaining to nutrition. A trophic migration would be a movement of fish to a feeding area.

An excess of homozygote individuals in a population that suggests that the population is not freely interbreeding and in Hardy-Weinberg equilibrium. An example might be two recently united populations that were previously separated and have not had time to return to Hardy-Weinberg equilibrium.

Washington Department of Fish and Wildlife, which co_manages groundfish fisheries in Washington State with WWTIT and other fisheries groups. The agency was formed in the early-1990s by combining the Washington Department of Fisheries and Washington Department of Wildlife.

The weight of a substance including the weight of its normal water content of a substance, e.g., weight of tissue or sediment before water is removed.

Western Washington Treaty Indian Tribes, an organization of Native American tribes with treaty fishing rights recognized by the United States. WWTIT co_manages groundfish fisheries in western Washington in cooperation with WDFW and other fisheries groups.

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