U.S. Dept Commerce/NOAA/NMFS/NWFSC/Publications

NOAA-NWFSC Tech Memo-24: Status Review of Coho Salmon

Appendix A



An allele is an alternate form of a gene (the basic unit of heredity passed from parent to offspring). By convention, the "100 allele" is the most common allele in a population and is the reference for the electrophoretic mobility of other alleles of the same gene. Other genetic terms used in this document include allozymes (alternate forms of an enzyme produced by different alleles and often detected by protein electrophoresis); dendrogram (a branching diagram, sometimes resembling a tree, that provides one way of visualizing similarities between different groups or samples); gene locus (pl. loci; the site on a chromosome where a gene is found); genetic distance (D) (a quantitative measure of genetic differences between a pair of samples); and introgression (introduction of genes from one population or species into another). See also DNA, electrophoresis, and transferrin.

artificial propagation

See hatchery.

Biological Review Team (BRT)

The team of scientists from National Marine Fisheries Service formed to conduct the status review.

Cape Blanco

A geographic feature on the Oregon coast at 4350 N.

Cape Mendocino

A geographic feature on the California coast at 4025 N.

Ceratomyxa shasta

A freshwater myxosporean parasite of salmonids that causes high mortalities in susceptible strains of fish. Other common diseases of Pacific salmon include vibriosus, cold water disease, bacterial kidney disease, and furunculosis.

coded-wire tag (CWT)

A small piece of wire, marked with a binary code, that is normally inserted into the nasal cartilage of juvenile fish. Because the tag is not externally visible, the adipose fin of coded wire- tagged fish is removed to indicate the presence of the tag. Groups of thousands to hundreds of thousands of fish are marked with the same code number to indicate stock, place of origin, or other distinguishing traits for production releases and experimental groups.

DNA (deoxyribonucleic acid)

DNA is a complex molecule that carries an organism s heritable information. 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, electrophoresis, and transferrin.


Electrophoresis refers to the movement of charged particles in an electric field. It has proven to be a very useful analytical tool for biochemical characters because molecules can be separated on the basis of differences in size or net charge. Protein electrophoresis, which measures differences in the amino acid composition of proteins from different individuals, has been used for over two decades to study natural populations, including all species of anadromous Pacific salmonids. 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. Genetic techniques that focus directly on variation in DNA also routinely use electrophoresis to separate fragments formed by cutting DNA with special enzymes (restriction endonucleases). See also allele, DNA, and transferrin.


The U.S. Endangered Species Act.


The number of fish that survive to reach the spawning grounds or hatcheries. The escapement plus the number of fish removed by harvest form the total run size.

evolutionarily significant unit (ESU)

A "distinct" population of Pacific salmon, and hence a species, under the Endangered Species Act.


Salmon hatcheries typically spawn adults in captivity and raise the resulting progeny in fresh water for release into the natural environment. In some cases, fertilized eggs are outplanted (usually in "hatch-boxes"), but it is more common to release fry (young juveniles) or smolts (juveniles that are physiologically prepared to undergo the migration into salt water). The fish are released either at the hatchery (on-station release) or away from the hatchery (off-station release). Releases may also be classified as within basin (occurring within the river basin in which the hatchery is located or the stock originated from) or out-of-basin (occurring in a river basin other than that in which the hatchery is located or the stock originated from).

The broodstock of some hatcheries is based on adults that return to the hatchery each year; others rely on fish or eggs from other hatcheries, or capture adults in the wild each year.


Male salmon that return from the ocean to spawn one or more years before full-sized adults return. For coho salmon in California, Oregon, Washington, and southern British Columbia, jacks are 2 years old, having spent only 6 months in the ocean, in contrast to adults, which are 3 years old after spending 1 years in the ocean.

Point Grenville

A geographic feature of the Washington coast located at 47o17 N.


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

principal component analysis (PCA)

A statistical technique that attempts to explain variation among several (n) variables in terms of a smaller number of composite independent factors called principal components. These principal components are represented byeigenvectors, or the perpendicular axes of central trend that pass through the clouds of points represented in n-dimensional space. The matrix of eigenvectors and the matrix of correlations of independent variables are used with linear algebra to calculate the equations describing the principal components that account for the greatest amount of the variation expressed in the original variables. Principal component one (PC1) is defined as a linear combination of the n variables that accounts for more of the variance in the data than any other linear combination of variables. Second (PC2) and subsequent components are defined as linear combinations that account for residual variance after the effect of the first (and subsequent) component(s) is removed from the data. PC values or "scores" are calculated for each individual and subjected to statistical analysis.

Punta Gorda A geographic feature of the California coast at 40o15 N.

Queen Charlotte Strait

The body of water separating the northern portion of Vancouver Island and the British Columbia mainland. The strait extends south from the Pacific Ocean at the north tip of Vancouver Island to approximately Gilford Island and the Broughton Island Archipelago.

river kilometer (RKm)

Distance, in kilometers, from the mouth of the indicated river. Usually used to identify the location of a physical feature, such as a confluence, dam, waterfall, or spawning area.

Salt Creek

A small creek on the south shore of the Strait of Juan de Fuca that flows into Crescent Bay. Salt Creek is adjacent and to the west of the Elwha River.


verb- The physiological process that prepares a juvenile anadromous fish to survive the transition from fresh water to salt water.

noun- A juvenile anadromous fish that has smolted.

spawner surveys

Spawner surveys utilize counts of redds (nests dug by females in which they deposit their eggs) and fish carcasses to estimate spawner escapement and identify habitat being used by spawning fish. Annual surveys can be used to compare the relative magnitude of spawning activity between years. Surveys are conducted on a regular basis on standard stream segments, groups of which form a spawner index, and are occasionally conducted on supplemental stream segments (those that are not part of the standard surveying plan).

Several methodologies have been used to estimate trends in spawner abundance based on the results of redd counts or spawner surveys. The peak count (PC) methodology simply uses the largest number of fish observed during the peak of spawning activity. The area under the curve (AUC) approach estimates the number of fish days (one fish day is equal to one fish (spawner) present on the spawning ground for one day) for a given stream segment; AUC is calculated from the total number of spawners observed over the course of the season, divided by the average residence time of spawners on the spawning ground. Stratified random sampling (SRS) provides an estimate of the number of spawners in a given area based on spawner counts in both standard and supplemental surveys.

spawner-to-spawner ratio

Several measures are employed to estimate the productivity of salmon populations. The spawner-to-spawner ratio estimates the number of spawners (those fish that reproduced or were expected to reproduce) in one generation produced by the previous generation s spawners. A spawner-to-spawner ratio of 1.0 indicates that, on average, each spawner produced one offspring that survived to spawn. The recruit-to-spawner ratio estimates the number of recruits (fish that are available for harvest in addition to those that bypass the fishery to spawn) produced by the previous generation s spawners.

Strait of Georgia

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.

Strait of Juan de Fuca

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.


Transferrin is a serum protein that is characterized by its specific ability to reversibly bind iron and other metal ions and exhibits a high degree of polymorphism.

west coast coho salmon

For the purposes of this document, west coast coho salmon are defined as coho salmon originating from fresh waters of British Columbia, Washington, Oregon, and California.

Table of Contents