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.

American Fisheries Society

Caused or produced by human action.

An aromatic hydrocarbon with five benzene rings that is representative of HAHs.

The depletion of oxygen associated with eutrophication from excess nutrient inputs or with of discharge organic matter.

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

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

Catch-per-unit effort

1,1,1-trichloro-2,2-bis-(p-chlorophenyl)ethane (DDTs)

Persistent contaminants of aquatic sediments and biota. Commercial formulations of DDTs are mixtures of individual chlorinated biphenyls. Prior to the 1975 congressional ban on DDT manufacture, DDTs were commonly used as pesticides

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).

Refers to unit of chemical concentration for a sample in which all water has been removed.

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.

U.S. Environmental Protection Agency

U.S. Endangered Species Act

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.

Organisms that tolerate a wide range of salinities.

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.

Fish possess a significant capability, primarily in the liver, to readily metabolize PAHs and related aromatic compounds to more polar products (metabolites) that pass into the bile for excretion. These compounds are not detectable in customary PAH analytical procedures, but are determined by their fluorescence, most of which is retained during the metabolic transformations.

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, and the Juan de Fuca Strait together with the lands that drain into these marine waters.

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

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.

In contrast to the LAHs, the HAHs are less water soluble and generally more tightly sorbed to sediment. HAHs are present in crude oil, fossil fuels and in combustion residue (e.g., soot) from all incomplete combustion processes, including natural processes such as forest fires. The HAHs have four to six aromatic rings, and are known more for their chronic toxicity than acute toxicity.

International Union for the Conservation of Nature.

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

Relative to the HAHs, the LAHs are more volatile and water-soluble. The LAHs have two to three aromatic rings, and are generally known for their acute toxicity. Sources of LAHs include all fossil fuels and discharges of products of their incomplete combustion, as well as crude oil.

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).

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

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.

An aromatic hydrocarbon with two benzene rings that is representative of LAHs.

National Marine Mammal Laboratory

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.

A unit of chemical concentration.

Phenanthrene (PHN)

An aromatic hydrocarbon with two benzene rings that is a significant component of crude oil.

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

Persistent contaminants of aquatic sediments and biota that are very widespread. Commercial formulations of PCBs are mixtures of individual chlorinated biphenyls (congeners) varying according to the numbers of chlorines and their ring positions on the biphenyl. Prior to the 1975 congressional ban on PCB manufacture, various mixtures of some 209 individual PCBs were used extensively in electrical transformers, capacitors, paints, waxes, inks, dust control agents, paper and pesticides.

The PAHs are widely distributed throughout the marine environment and commonly occur in sediments in urban coastal and estuarine areas. Sources include crude oil, petroleum products and residues from combustion of fossil fuels. They are composed of fused benzene rings, with or without alkyl substituents (e.g., methyl groups).

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.

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 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.

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.

(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.

Self-contained underwater breathing apparatus.

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.

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

The summed total of all the individual PAHs detected in a sample.

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

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.

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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