A

Abundance: The number of fish in a population.
Active channel width: The distance across a stream or channel as measured from bank to bank at bankful flow.
Akaike Information Criterion: A statistical criterion for selecting among models of different complexity, based on the difference between the number of parameters in the model and the goodness of fit to a particular data set.
Allelle: Any one of a number of alternative forms of a gene that can occur at the same location (locus) on a chromosome. A population can have many alleles for a particular locus, but an individual can carry no more than two alleles at a diploid locus.
Allozymes: Alternative forms of an enzyme that have the same function, are produced by different alleles, and are often detected by protein electrophoresis.
Anthropogenic: A circumstance or influence caused or produced by human action.
Anthropogenic factor: A circumstance or influence caused or produced by human action.
Arithmetic mean: The average of a set of values, calculated as the sum of the values divided by the number of values in the set.
Artificial propagation: Hatchery spawning and rearing of salmon, usually to the smolt stage. AUC (Area Under the Curve); A statistical technique for estimating an annual total number of spawners from periodic spawner counts.
Autocorrelation: "The correlation between paired values of a function of a statistical variable taken at usually constant intervals that indicates the degree of periodicity of the function" (Merriam Webster Dictionary).

B

Barrier: A blockage such as a waterfall, culvert, or rapid that impedes the movement of fish in a stream system.
Bayesian analysis (or Bayesian estimation): A branch of statistics concerned with estimating parameters for models from multiple sources of information. Bayesian analysis divides information into two classes: "prior" information that is known before considering a new set of observations, and "posterior" information that incorporates both the prior information and the new information contained in the new observations.
Best Professional Judgment (BPJ): A process of analyzing a problem by utilizing an expert or expert panel to use collective experience in relation to the problem.
Biogeographical Strata: Groups of populations with genetic, ecological, and geographical similarities.
Biological Review Team (BRT): The team of scientists who evaluate scientific information for the National Marine Fisheries Service (NMFS) status reviews.
Boolean logic: A system of logic that allows organizing things in sets using AND, OR, UNION, and other operators. Any item is either fully a member of a particular set or not at all a member of that set. In this type of logic, statements are typically described as true or false.
Bootstrapping: A statistical method for estimating the variability of a parameter for a population where a small sample is repeatedly resampled and analyzed. This allows for statistical analysis using a relatively small sample compared to analysis on a traditional single sample from the population.

C

Carrying capacity: The number of individuals that the resources of a habitat can support.
Catastrophic events: Sudden events that disastrously alter large areas of landscape. These can include floods, landslides, forest fires, and volcanic eruptions.
Channel gradient: The slope of a stream reach.
Coefficient of Variation: In describing variation in a population, the standard deviation is expressed as a fraction of the mean.
Coded-wire tag (CWT): A small piece (0.25 x 0.5 or 1.0 mm) of stainless steel wire that is injected into the snouts of juvenile salmon and steelhead. Each tag is etched with a binary code that identifies its release group.
Co-managers: Federal, state, and tribal agencies that cooperatively manage salmon in the Pacific Northwest.
Compensation: A decrease in productivity with increasing abundance, which results in an approach to some maximum level of production.
Compensatory smolt production curve: A decrease in smolt productivity with increasing abundance, which results in an approach to some maximum level of production.

D

Decision Support System (DSS): A computer application that assists users in using data and models to solve problems (Scott Morton 1971). Typically, decision support systems are computer programs that analyze many pieces of data or models, producing results that aid in decision-making rather than replacing human judgment (Turban and Aronson 2001).
Delisting (or narrow-sense recovery): A process resulting in the ESU being removed from the formal protections of the ESA as a consequence of no longer being endangered nor likely to become endangered within the foreseeable future in a significant portion of its range. DEM (Digital Elevation Model); A digital data set representing a topographic map that can be used for computer analysis.
Demographic: Pertaining to the processes of birth, development, growth, and mortality that control the dynamics of populations.
Demographic stochasticity: "Chance events in the survival and reproductive success of a finite number of individuals" (Shaffer 1981).
Density effects: Survival of juvenile salmon may be influenced by their density. Survival is usually higher when density is low.
Dendrogram: A branching diagram, sometimes resembling a tree, that provides one way of visualizing similarities between different groups or samples.
Dependent Populations: Populations that rely upon immigration from surrounding populations to persist. Without these inputs, Dependent Populations would have a lower likelihood of persisting over 100 years (Lawson et al. 2007).
Depensation: The effect where a decrease in spawning stock leads to reduced survival or production of eggs through either 1) increased predation per egg given constant predator pressure, or 2) the "Allee effect" (the positive relationship between population density and the reproduction and survival of individuals) with reduced likelihood of finding a mate. Diploid; Having two complete chromosome pairs in a nucleus.
DNA (deoxyribonucleic acid): 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 and electrophoresis).
Distinct population segment (DPS): A population, or group of populations of a vertebrate species that is "discrete" from other populations and significant to the biological species as a whole.
Donor populations: These are Functionally Independent or Potentially Independent populations that are large enough to "donate" migrant adults to Dependent populations.

E

Ecoregion: An integration of physical and biological factors such as geologic history, climate, and vegetation.
Effective migration rate: The proportion of successfully spawning adults that migrate to a new population. (Excludes migrants that do not successfully reproduce.) (See also Migration rate.)
Effective population size: The size of an idealized (panmictic) population that would have the same rate of loss of heterozygosity as the real (nonpanmictic) population.
Electrophoresis: 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.
Endangered species: A species in danger of extinction throughout all or a significant portion of its range.
ESA: U.S. Endangered Species Act.
Escapement: Usually refers to adult fish that "escape" from both fisheries and natural mortality to reach the spawning grounds.
Estuarine habitat: Areas available for feeding, rearing, and smolting in tidally influenced lower reaches of rivers. These include marshes, sloughs and other backwater areas, tidal swamps, and tide channels.
Evaporation potential: The maximum depth of water that could evaporate in a year. Evaporation potential is principally determined by temperature and relative humidity. It is a measure of how much moisture "stress" plants are under due to dry conditions.
Evolutionarily Significant Unit (ESU): An ESU represents a distinct population segment of Pacific salmon under the Endangered Species Act that 1) is substantially reproductively isolated from conspecific populations and 2) represents an important component of the evolutionary legacy of the species. See also Distinct population segment.
Exploitation rate: The proportion of adult fish from a population that die as a result of fisheries.
Extinction: The loss of a species, or ESU. May also be used for the extirpation of local populations.
Extinction risk: The probability of a species going extinct within a particular time period.

F

Factors for decline: These are factors identified that caused a species to decrease in abundance and distribution and become threatened or endangered.
Fecundity: The number of offspring produced per female.
Fishery mortality rate: The number of fish that die when intercepted by a fishery in relation to the number of fish as a whole.
Foreseeable future: Lying within the range of when forecasts are possible (Merriam Webster Dictionary).
Fourth-Field and Fifth-Field Hydrologic Units: In the United States Geological Survey (USGS), hydrologic units have been divided at different scales. The area of a fourth-field hydrologic unit is 440,000 acres and a fifth-field hydrologic unit is between 40,000 and 250,000 acres.
Freshwater habitat: Areas available for spawning, feeding, and rearing in freshwater.
Fry: Young salmon that have emerged from the gravel and no longer have an egg sack.
Fully Seeded: Having enough spawners to fully occupy available juvenile habitat with offspring.
Functionally Independent population: A high-persistence population whose dynamics or extinction risk over a 100-year time frame is not substantially altered by exchanges of individuals with other populations (migration). Functionally independent populations are net "donor" populations that may provide migrants for other types of populations. This category is analogous to the "independent populations" of McElhaney et al. (2000).

G

Gamma distribution: A continuous probability distribution usually used to describe the amount of time until the nth occurrence of a process with a Poisson distribution.
Genetic drift: Random changes in gene frequencies of populations.
Genetic distance: A quantitative measure of the genetic difference between a pair of samples, based on allele frequencies at multiple loci.
Genetic stochasticity: Random changes in the genetic make-up of populations.
Geometric mean: A measure of central tendency similar to the arithmetic mean, except that the computation uses multiplication instead of addition to summarize data values. It is a useful statistic for summarizing highly skewed data values. For two numbers the geometric mean equals the square root of the product of the two numbers, i.e. (x1x2)-0.5.
Gradient: The slope of a stream system.

H

Habitat quality: The suitability of physical and biological features of an aquatic system to support salmon in the freshwater and estuarine system.
Harmonic mean: The harmonic mean is another way of calculating an average. It is the reciprocal of the arithmetic mean of reciprocals of the data. For n numbers x1, x2, ... , xn, the harmonic mean equals n/(1/x1 + 1/x2 + ... + 1/xn).
Hatchery: A facility where artificial propagation of fish takes place. Salmon hatcheries typically spawn adults in captivity and raise the resulting progeny in fresh water for release into the natural environment.
Hatchery Fish: Fish incubated or reared under artificial conditions for at least a portion of their life cycle (ODFW 2003).
Heterozygosity: The variation in alleles at the same locus on a chromosome. Loss of heterozygosity in populations could be damaging to the ability of a population to adapt to changes in the environment.
Historical abundance: The number of fish that were produced before the influence of European settlement.
Homing fidelity: The propensity of an adult salmon to return to its natal stream.
Hydrologic Units (HUCs): "The United States is divided and sub-divided into successively smaller hydrologic units which are classified into four levels: regions, sub-regions, accounting units, and cataloging units. The hydrologic units are arranged within each other, from the smallest (cataloging units) to the largest (regions). Each hydrologic unit is identified by a unique hydrologic unit code (HUC) consisting of two to eight digits based on the four levels of classification in the hydrologic unit system" (http://water.usgs.gov/GIS/huc.html).
Hydrology: The distribution and flow of water in an aquatic system.

I

Immigration: The movement of individuals into a population that they were not born into.
Inbreeding depression: Reduced survival rates of individuals in a population suffering from the effects of harmful recessive genes through matings between close relatives. Inbreeding depression may become a problem when populations get very small.
Independence: Reflects the interaction between isolation and persistence. A persistent population that is highly isolated is highly independent.
Independent Population: A population that historically would have had a high likelihood of persisting in isolation from neighboring populations for 100 years (Lawson et al. 2007).
Intrinsic growth rate: The growth rate of a population in the absence of compensation.
Intrinsic potential: A modeled attribute of streams that includes the channel gradient, valley constraint and mean annual discharge of water. Intrinsic potential in this report refers to a measure of potential coho salmon habitat quality (Burnett et al. 2003).
Intrinsic productivity: Productivity of a population in the absence of compensation, estimated as the mathematical limit of population productivity as abundance approaches zero.
Introgression: Introduction of genes from one population or species into another.
Isolating mechanisms: Things that reduce the ability of populations to interbreed. These could include physical mechanisms such as distance, and behavioral mechanisms such as run timing.
Isolation: The degree to which a population is unaffected by migration to and from other populations. As the influence of migration decreases, a population�s isolation increases.

J

Jack: A coho salmon that matures at age 2 and returns from the ocean to spawn a year earlier than normal. Jacks are all male fish.
Jacking rate: The proportion of adult coho salmon from a brood that return as jacks.
Juvenile: A fish that has not matured sexually.
Juvenile capacity: The capacity of habitat to provide conditions for rearing for nonadult fish that have not smolted and subsequently migrated to sea.

L

Latitudinal cline (also known as a latitudinal diversity gradient): A change in a biological trait that occurs across latitudes. For example, jacking rate generally increases from north to south.
Life history: The specific life cycle of a fish from egg to adult.
Limiting factors: Factors that limit survival or abundance. They are usually related to habitat quantity or quality at different stages of the life cycle. Harvest and predation may also be limiting factors.
Listed species: Species included on the "List of Endangered and Threatened Species" authorized under the Endangered Species Act and maintained by the U.S. Fish and Wildlife Service and NOAA Fisheries.
Littoral zone: In lakes, the area of lake bottom that receives enough light for rooted plants to grow. In the ocean, the marine ecological realm that experiences the effects of tidal and longshore currents and breaking waves to a depth of 5 to 10 m (16 to 33 feet) below the low-tide level, depending on the intensity of storm waves. (Encyclop�dia Britannica 2004).
Locus: Location on a chromosome that holds a specific gene. Plural is loci.
Lowland habitat: Low-gradient stream habitat with slow currents, pools, and backwaters used by fish. This habitat is often converted to agricultural or urban use.

M

Marine survival rate: The proportion of smolts entering the ocean that survive to be harvested or return to freshwater.
Mean: One of several methods of calculating an average, usually referring to an arithmetic mean.
Mean annual discharge of water: A single value or average that summarizes or represents the annual discharge amount, typically expressed in cubic meters per second.
Metric: A clearly defined measurement of some quantity or quality.
Microsatellite: A class of repetitive DNA used for estimating genetic distances.
Migrant: A fish that is born in one population but returns to another population to spawn.
Migration: Movement of fish from one population to another.
Migration rate: The proportion of spawners that migrate from one population to another. See also Effective migration rate.
Mitochondrial DNA (mtDNA): The DNA genome contained within mitochondria and encoding a small subset of mitochondrial functions. Only female mtDNA is transmitted to the next generation.
Monte Carlo Simulation: A method for solving a statistical problem by generating suitable pseudorandom numbers and observing that fraction of the numbers obeying some property or properties.
Mortality: Death, or the death rate for individuals in a population.
Mutation: A change in an allele at a locus. This can happen through random events or exposure to chemicals and radiation.

N

Natural return ratio (NRR): The ratio N/T, where N is naturally produced spawners in one generation and T is total (hatchery produced + naturally produced) spawners in the previous generation.
Naturally produced fish: Fish that were spawned and reared in natural habitats, regardless of parental origin (see also Wild fish).
NMFS: National Marine Fisheries Service, also known as NOAA Fisheries Service.
NOAA: National Oceanic and Atmospheric Administration.
NOAA Fisheries Service: The fisheries branch of NOAA, also known as NMFS.
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. NWFSC; NOAA Fisheries Northwest Fisheries Science Center.

O

Oregon Plan: "In 1997, with the support and participation of a wide spectrum of stakeholders from all sectors and regions of the state, the Oregon Legislature and Governor established the Oregon Plan for Salmon and Watersheds. Motivated at first by the conviction that Oregon must devise its own homegrown response to listings of coho salmon and other salmon species under the federal Endangered Species Act, the plan quickly evolved and expanded into an unprecedented statewide program to preserve and profit from Oregon�s natural legacy" (http://www.oregon-plan.org).
Oregon Production Index (OPI): An estimate of coho salmon adult abundance for the marine area extending from Leadbetter Point, Washington, to the U.S./Mexico border.
OWEB: Oregon Watershed Enhancement Board.

P

Parr: The life stage of salmonids that occurs after fry and is generally recognizable by dark vertical bars (parr marks) on the sides of the fish.
Persistence.: A population�s relative ability to sustain itself without input from neighboring populations.
Persistent population (or ESU): One that is able to persist (i.e., not go extinct) over a 100-year period without artificial support. This includes an ability to survive prolonged periods of adverse environmental conditions, which may be expected to occur at least once in the 100-year time frame.
Phenotypic diversity: Variation in the set of observable characteristics of an individual or group as determined by the genotype and the environment.
Phenotypic plasticity: The ability to vary the set of observable characteristics of an individual or group as determined by the genotype and the environment generally in response to environmental change.
Phylogenetic tree: The genetic distances and relationships among populations, frequently represented with a branching or tree-like diagram.
Poisson distribution: A discrete statistical probability distribution, expressing the probability of a number of independent events occurring in a fixed interval of time or region of space.
Population: A group of fish of the same species that spawns in a particular locality at a particular season and does not interbreed substantially with fish from any other group.
Population classification: The grouping of populations into Functionally Independent, Potentially Independent, and Dependent classes.
Population dynamics: Changes in the number, age, and sex of individuals in a population over time, and the factors that influence those changes. Five components of populations that are the basis of population dynamics are birth, death, sex ratio, age structure, and dispersal.
Population identification: Delineating the boundaries of historical populations.
Population structure: The distribution of characteristics (such as age, size, or physiological state) of individuals within a population.
Potentially Independent populations: High-persistence populations whose population dynamics are substantially influenced by periodic immigration from other populations. In the event of the decline or disappearance of migrants from other populations, a Potentially Independent population could become a Functionally Independent population.
Population viability analysis (PVA): "[A] set of analytical and modeling approaches for assessing the risk of extinction. Life history, demography, and genetics of a species are integrated with environmental variability to project the future course of populations" (Beissinger and McCullough 2002, p. xiv).
Posterior distribution: The statistical distribution of a parameter (or set of parameters) that is obtained by combining the prior distribution with information resulting from a new set of observations (see Bayesian analysis).
Prior distribution: The statistical distribution of a parameter (or set of parameters) that is known before incorporating a new set of observations (see Bayesian analysis).
Production: The number of fish produced by a population in a year.
Productive capacity: Maximum possible production from a given area.
Productivity: The rate at which a population is able to produce reproductive offspring.
Protein electrophoresis: An analytical laboratory technique that measures differences in the amino acid composition of proteins from different individuals. See also Electrophoresis.
PVA: See Population Viability Analysis.

Q

Quasi-extinction threshold (QET): A threshold representing the minimum allowable population abundance in population viability modeling, below which the population is assumed to be essentially extinct. It is defined primarily for convenience and may be based on a number of considerations including Allee effects and uncertainties in population functional response at very low abundance.

R

Reach: A segment of a stream with uniform physical characteristics.
Recovery: A general term for the reestablishment or restoration of populations at risk. In this report, it is used in two senses: in a "narrow sense" as it is defined in the ESA (see delisting), and in a "broad sense" to include efforts that extend beyond the requirements of the ESA (see restoration).
Recovery domain: The geographic area for which a Technical Recovery Team is responsible.
Recovery plan: Under the ESA, a document identifying actions needed to improve the status of a species or ESU to the point that it no longer requires protection.
Recovery scenarios: Various sequences of events expected to lead to recovery of Oregon Coast Coho Salmon.
Recruit: A pre-harvest maturing adult salmon, i.e., an adult in the ocean that would be expected to return to spawn in freshwater if it is not harvested.
Recruitment: (1) The number of recruits a given year or generation. Typically estimated as the number of adults that return to spawn divided by the total fishery escapement rate (one minus the total harvest rate). (2) The number of recruits in one generation per spawner in the previous generation (also "recruitment rate").
Restoration (or broad-sense recovery): A process leading to conditions such that the populations of naturally produced fish that make up the Oregon Coast Coho Salmon ESU are sufficiently abundant, productive, and diverse (in terms of life histories and biogeographic distribution) that the ESU as a whole (a) will be self-sustaining, and (b) will provide environmental, cultural, and economic benefits (modified from Oregon SRTF, Anonymous 2002b).
RSRP: Recovery Science Review Panel.
Run timing: The time of year (usually identified by week) when spawning salmon return to the spawning beds.

S

Salmonid: Any of the species of fish in the family Salmonidae, including salmon, trout, and char.
Selection: An evolutionary process that drives adaptation to environmental change through differential reproductive success of organisms that have variability in their genetic makeup.
Significant: Biological significance refers to an effect that has a noteworthy impact on health or survival.
Smolt: A life stage of salmon that occurs just before the fish leaves freshwater. Smolting is the physiological process that allows salmon to make the transition from fresh to salt water. Smolt capacity; The maximum number of smolts a basin can produce. Smolt capacity is related to habitat quantity and quality.
Spawner: A reproductive adult fish.
Spawner surveys: Efforts to estimate the number of adult fish on spawning grounds. 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.
Spawner-to-spawner ratio: A measure of the productivity of salmon populations, based on the ratio of the number of spawners (those fish that reproduced or were expected to reproduce) in one generation to the number of spawners in the previous generation. A spawner-to-spawner ratio of 1.0 indicates that, on average, each spawner produced one offspring that survived to spawn.
Species: In the ESA, either a recognized biological species, or any recognized subspecies, or (for vertebrate fish or wildlife) any distinct population segment which interbreeds when mature. By NOAA policy, the last definition includes Evolutionarily Significant Units (ESUs) of salmon. STEP; ODFW�s Salmon and Trout Enhancement Program.
Stochastic: Influenced by random variation.
Stock transfer: The practice of moving fish between basins or populations.
Stratified Random Survey (SRS): A statistical design used to sample subgroups more effectively with fewer samples needed than if the entire population was randomly sampled.
Stray rate: As used in this document, the stray rate refers to the number of spawning adults that return to a stream other than their natal stream within a basin. (See also Migration rate.)
Stream-estuary ecotone: This is the area where the physical characteristics of a stream change to the physical characteristics of an estuary. This is where water becomes brackish, there is mixing of stream and estuary nutrients, and the physical attributes are affected by tides and ocean water influences. This tends to be a very productive area due to phosphorus and nitrogen inputs from both oceanic and upland influences.
Student�s t test: A statistical test for the significance of the difference between a sample mean and a specified criterion.
Sustainability: An attribute of a population that persists over a long period of time and is able to maintain its genetic legacy and long-term adaptive potential for the foreseeable future.
Sustainable population (or ESU): One that, in addition to being persistent, is also able to maintain its genetic legacy and long-term adaptive potential for the foreseeable future. "Sustainable" implies stability of habitat availability and other conditions necessary for the full expression of the population�s (or ESU�s) life history diversity into the foreseeable future.
SWFSC: NOAA Southwest Fisheries Science Center.

T

Threatened species: Under the ESA, any species which is likely to become an endangered species within the foreseeable future throughout all or a significant portion of its range.
Time series: A sequence of observations over a period of time.
TRT: Technical Recovery Team.

U

Upwelling: The upward transport of cold, nutrient-rich water to the surface; conditions that favor the survival and growth of salmon and other fish species. Upwelling along the Oregon Coast occurs in Spring and Summer, driven by winds from the Northwest.
USFS: United States Forest Service.
USGS: United States Geologic Survey.

V

Variance: A statistical measure of how spread out a distribution is. For example, a small variance would mean that the observations were similar to each other, while a large variance would mean that observations were less similar to each other.
Valley constraint: The valley width available for a stream or river to move between valley slopes.
Viability: The likelihood that a population will sustain itself over a 100-year time frame.
Viability criteria: A prescription of the biological conditions for populations, biogeographic strata, and ESUs that together imply that the ESU will have a negligible risk of extinction over a 100-year time frame.
VSP: Viable Salmonid Population.

W

Warmwater fish: Spiny-rayed fish such as sculpins, minnows, darters, bass, walleye, crappie, and bluegill that generally tolerate or thrive in warm water.
Wild fish: Fish whose ancestors have always lived in natural habitats, i.e. those with no hatchery heritage (see also Naturally produced fish).

Source of definitions:

Lawson, P. W., E. Bjorkstedt, M. Chilcote, C. Huntington, J. Mills, K. Moore, T. E. Nickelson, G. H. Reeves, H. A. Stout, and T. C. Wainwright. 2004. Identification of Historical Populations of Coho Salmon (Onchorhynchus kisutch) in the Oregon Coast Evolutionarily Significant Unit. Review Draft. Oregon Northern California Coast Technical Recovery Team. NOAA/NMFS/NWFSC. 129 p.

Wainwright, T. C., M. W. Chilcote, P. W. Lawson, T. E. Nickelson, C. W. Huntington, J. S. Mills, K. M. S. Moore, G. H. Reeves, H. A. Stout, and L. A. Weitkamp. In review. Biological Recovery Criteria for the Oregon Coast Coho Salmon Evolutionarily Significant Unit. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC.