Publications

# APPENDIX 2

## GLOSSARY

AgeingA fish that is less than 1 year old (counted from time of spawning by its parents) is considered a subyearling, or zero-age. A yearling fish is more than 1 year and less than 2 years old. Adult ages are also reckoned from time of egg deposition and are typically based on counts of annual rings on scales or otoliths (a calcareous "earstone" found in the internal ear of fishes). The age of an adult is sometimes estimated by length.

Adult Fish CountsA fish-viewing window is at the upstream end of most fish ladders. Observers count the number of fish, by species and size, passing the window for 50 minutes of every hour for 16 hours per day. Extrapolations are made for the hours and minutes not counted to provide an estimate of daily adult fish passage for each dam. In general, separate counts are made for adults and jacks (precocious males that can be identified by their smaller size).

Adult Fish LaddersThe main-stem hydroelectric dams on the Columbia and lower Snake Rivers have fish ladders that allow adults to pass the dams on their upstream spawning migration. Entrances for fish ladders are placed on shorelines. For fish attracted to turbine discharge flows, a collection channel built across the downstream face of the dams provides a conduit to move fish toward the fish ladders. Fish ladders that are in compliance with established performance guidelines effectively pass most fish that enter them; however, a small percentage of fish at each dam may not find the entrances to the ladders.

BatholithA large mass of igneous rock bounded by irregular, cross-cutting surfaces or planes, believed to have crystallized at a considerable depth below the earth's surface.

Bypass SystemsJuvenile salmonid bypass systems consist of moving screens lowered into turbine intakes to divert fish away from turbines at hydroelectric dams. Fish move into a channel that transports them safely around the dam. Bypassed fish are then typically returned directly to the river below the dam, although some Columbia River Basin dams have facilities to load bypassed fish into barges or trucks for transport to a release site downstream from all the dams.PIT-tag detectors (see below) interrogate all PIT-tagged fish passing through the bypass system. In addition, the systems are equipped with subsampling capabilities that allow hands-on enumeration and examination of a portion of the collection for coded-wire tags (CWT), brands, species composition, injuries, etc. Recovery information at bypass systems is used to develop survival estimates, travel time estimates, and run timing; to identify problem areas within the bypass system; and as the basis for flow management decisions during the juvenile migrations.

Coded-Wire TagsCoded-wire tags (CWT) are tiny pieces of wire which are implanted in the cartilage in snouts of juvenile salmon. Each tag is notched with a binary code that identifies the fish with a particular release group. CWTs are inserted into the snout using a tagging machine. A head mold, which is sized for the fish being tagged, ensures proper placement of the tag to avoid injury to the fish. Large groups of fish can be coded-wire tagged quickly and inexpensively without altering the behavior of the fish.Fish that have been coded-wire tagged are identified by an external mark (generally, removal of the adipose fin). This enables fish samplers to later identify tagged fish for recovery of the tag. Coded-wire tags are usually retrieved from dead fish by using a core sampler and a magnetic detector; the code is then read under a microscope. 

ElectrophoresisElectrophoresis 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 2 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. Utter et al. (1987) provide a review of the method using examples from Pacific salmon, and the laboratory manual of Aebersold et al. (1987) provides detailed descriptions of analytical procedures. Genetic techniques that focus directly on variation in DNA also routinely use electrophoresis to separate fragments of DNA of different lengths.Other genetic terms used in this document include allele (an alternate form of a gene); dendrogram (a branching diagram, sometimes resembling a tree, that provides one way of visualizing similarities between different groups or samples); gene (the basic unit of heredity passed from parent to offspring); gene locus (pl. loci; the site on a chromosome where a gene is found); genetic distance (a quantitative measure of genetic differences between a pair of samples); and introgression (introduction of genes from one population or species into another).

FecundityFecundity is the reproductive potential of an individual and is equal to its capacity to produce eggs and sperm. In salmon, it generally refers to the number of eggs produced by a female.

HatcherySalmon hatcheries use artificial procedures to spawn adults and raise the resulting progeny in fresh water for release into the natural environment, either directly from the hatchery or by transfer into another area. In some cases, fertilized eggs are outplanted, 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 brood stock of some hatcheries is based on the 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.

PIT TagsPassive integrated transponder (PIT) tags have been developed to monitor the movements of anadromous salmonids primarily through juvenile bypass systems or adult fish ladders at dams. In contrast to radio tags, which have a battery that eventually will cease to function, PIT tags contain a small computer chip that transmits its code only when induced by an external energy source. Using current technology, the PIT tag can only be detected at a distance of up to 18 cm in water. Although this limits some applications of PIT tags, bypass facilities at hydroelectric dams provide excellent opportunities for monitoring movements of juvenile and adult fish.Each PIT tag is 12.0 mm long by 2.1 mm in diameter and is coded with one of 34 billion unique codes. Tags are inserted into the body cavity with nearly 100% tag retention and high fish survival. The tag is interrogated at 400 kHz and transmits a return signal at 40 to 50 kHz. In specially designed facilities at hydroelectric dams, computerized systems automatically detect, decode, and record individual PIT tag codes, thereby providing time, date, and location of detection and eliminating the need to anesthetize, handle, or restrain fish during data retrieval. The information collected daily at each dam is automatically transferred from the monitor system to a central data base for storage and processing. Although only developed in the mid-1980s by NMFS scientists, PIT tags have already provided a wealth of information about the distributions, migration timing, migration rates, and survival of juvenile salmonids.

PhenotypeThe phenotype is the appearance of an organism resulting from the interaction of the genotype and the environment.

Population viability analysis (PVA)PVA provides a means of quantifying future risks faced by a population due to demographic, environmental, and genetic factors. PVA methods can be used to identify the minimum viable population size (MVP)--that is, the smallest number of individuals that will allow the population to persist for a specified amount of time (t) with a specified degree of certainty (P). There is no purely scientific way of choosing optimal values for t and P, but combinations most commonly suggested in the literature are t = 100 years and P = 95% probability or, more conservatively, t = 1,000 years and P = 99% probability.Some detailed PVA models have been described in the literature, but they generally require types of data [e.g., means and variances (over a number of years) of sex ratio, fecundity, and age-specific survival rates] not typically available for Pacific salmon. In the current ESA evaluations, the BRT used the stochastic extinction model of Dennis et al. (1991) to provide some idea of the likely status of the population in the future. A major advantage of the Dennis model is its simplicity, requiring as input only a time series of abundance data. Predictions are obtained by taking the current state of the population and projecting it into the future, based on the assumption that future fluctuations in population abundance are determined by parameters of the population measured in the recent past. However, the simplicity of the model also means that it may fail to capture some important aspects of population dynamics. In particular, it does not take density-dependent factors into consideration. Nevertheless, the model is useful for identifying outcomes that are likely if no protective measures are taken.The Dennis model can be used to identify "extinction" and "threatened" thresholds to compare with the current abundance of a population. In this evaluation, the BRT identified an "endangered" threshold as the abundance at which the population was estimated to have a P = 95% chance of surviving for t = 100 years. Populations whose current abundance was above the "endangered" threshold were evaluated with respect to a "threatened" threshold, which was defined as the abundance at which the population was estimated to have a 50% chance of falling below the "endangered" threshold within 10 years.

Redd CountsA spawning female salmon prepares a series of nests, called a redd, in suitable areas of streams by turning onto her side and beating her caudal fin up and down. Primary factors affecting suitability of spawning habitat include the size of rocks in the substrate and stream flow (high enough to provide adequate aeration for the eggs; low enough to prevent erosion of the nest). A completed redd is a shallow depression in the stream bottom with a rim extending to the downstream end. During spawning, the female continuously digs upstream, covering previously deposited eggs with gravel. Most redds occur in predictable areas and are easily identified by an experienced observer by their shape, size, and color (lighter than surrounding areas because silt has been cleaned away).Redd counts are conducted annually in certain heavy use areas of streams called index streams, which are usually surveyed repeatedly through the spawning season. Colored flags are sometimes placed on nearby trees to identify redds so that they will not be counted repetitively. Annual redd counts are used to compare the relative magnitude of spawning activity between years.

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