Native Fish Society Glossary & Acronyms

Scientific Glossary

Abundance. The number of individuals in a population. For anadromous populations, this number is most often expressed in terms of adult spawners and is compiled by monitoring and evaluation of fish populations over time.

Adfluvial. Fish that spawn in tributary streams where young rear from 1 to 4 years before

migrating to a lake, where they grow to maturity.

Allee Effect. Reduced per capita growth rates in low-density populations. This can be a concern in salmon populations when low densities reduce the likelihood of finding a mate.

Anadromous. A fish that is born in freshwater, spends its life at sea and then returns to freshwater in order to spawn.

Aquatic Macroinvertebrates. These are invertebrates that live in freshwater for all, or a significant portion of their lives and are large enough to be seen without magnification. Included in this category are mussels, clams, mites, and insects such as caddisflies, mayflies, and stoneflies. These animals serve as an important food source for juvenile and resident salmonids, and are also indicative of stream water and habitat quality.

Asynchronous. Populations of salmonids that do not have peaks and declines in abundance at the same time.

Before-After-Control-Impact. Common ecological experimental design in which measurements of variables of interest are measured before and after an intervention is implemented in both the target watershed or population and in control watersheds or populations.

Biological Diversity. The variability among living organisms and the ecological complexes of which they are part; including genetic and ecological diversity within species, between species and of ecosystems.

Broken Links. The interruption of habitat connections across the full range of a species’ life history. When one of section of the watershed is impaired (from headwater tributaries to the estuary and ocean) the productivity of the species will be impacted and reduce its success.

Carrying Capacity. The number of individuals of a specific species that a given habitat can support. Conservation Hatchery Program. The use of artificial propagation to conserve genetic resources of a fish population at extremely low population abundance, and decrease the potential for extinction, using methods such as captive propagation and cryopreservation.

Density Dependent Mortality. Increased competition among individuals at high densities resulting in lower survival..

Depressed. Below an established goal, such as fish production or escapement, shown in a management plan or below the level of production or escapement that managers determine to be an optimal level.

Distribution. The spatial arrangement of a species. Distribution of salmon includes their freshwater spawning, rearing, and migration areas as well as their marine foraging areas. Domestication. The genetic, physiological, and behavioral adaptation of salmonids when they are spawned and reared in an artificial environment. Hatchery fish perform better in the hatchery environment than wild fish, but have poor performance in the natural environment compared to wild fish. Hybrids between hatchery and wild fish have an intermediate performance in both environments. Domestication selection in a fish hatchery can cause a 20% reduction in fitness in the first generation.

Equilibrium Abundance. Average maximum number of spawners a population can sustain given the habitat capacity and natural mortality.

Escapement. A numerical threshold for the portion of a stock or group of stocks that is protected from harvest and allowed to spawn to meet management objectives and perpetuate the stock.

Fitness. Measure of an individual’s genetic contribution to future generations.

Flow Regime. Includes the magnitude, frequency, duration, timing, and predictability of high and low flow events in river ecosystems. Fish such as salmon and steelhead rely on a natural flow regime to provide accurate cues for them to migrate and spawn. The construction of dams and climate change have altered natural flow regimes so that flow is no longer a reliable cue for key life history events.

Fluvial. Fish that spawn in tributary streams where young rear from 1 to 4 years before migrating to a larger river, where they grow to maturity.

Genotype. The set of genes an organism has. Sometimes, genotype refers to the entire genome of an organism and sometimes it refers to the alleles at a particular gene.

Hatchery-origin. Fish that have been incubated, hatched or reared in a hatchery or other artificial production facility regardless of parentage.

Hatchery-Origin Recruits (HOR). The sum of hatchery-origin spawners, hatchery-origin broodstock, and hatchery-origin fish intercepted in fisheries.

Heterozygous. Possessing two different alleles at a specific gene locus.

Heterozygosity. Genetic variation. Can refer to the fraction of individuals in a given population that are heterozygous at a given locus, or the fraction of loci that are heterozygous in an individual.

Home Stream Theory. It was originally believed that salmon returned to streams to spawn randomly. In the 1930s, Dr. Willis Rich tagged individual salmon, demonstrating that they return to their natal streams to spawn. Based on his research, Rich advocated for watershed-level management to avoid depletion of salmonids.

Inbreeding Depression. The reduction in a population’s ability to survive and reproduce as a result of inbreeding, or breeding of related individuals. Generally only a problem in small populations.

Integrated Hatchery Program. A hatchery program in which a high proportion of wild individuals are incorporated in the hatchery broodstock each generation, maintaining the genetic similarity of wild and hatchery stocks. IHPs potentially result in greater reproductive interactions between wild and hatchery stocks and decreased reproductive success in wild fish.

Integrated Hatchery Strategy. A broodstock management strategy where the intent is for returning adults of wild- and hatchery-origin fish to be reproductively integrated to form a single, composite stock. This requires wild-origin adults in the hatchery broodstock, and hatchery-origin adults may spawn naturally with wild salmonids.

Introgression. In salmonid conservation, this refers to the transfer of genetic material from hatchery to wild fish.

Iteroparous. Organisms that reproduce multiple times (e.g., steelhead). Contrast with semelparous.

Lamba. Finite rate of increase in a population at one time step (often 1 year).

Life history. The age-specific schedule of reproduction and mortality of a population of individuals. Migration timing, growth rates, and spawn timing are all components of a salmon’s life history, among others.

Limiting Factors. In biology, limiting factors are resources or environmental conditions that limit the growth, abundance, or distribution of an organism or population of organisms. Examples of biological and physical limiting factors for wild fish include, but are not limited to, water temperature or availability, habitat degradation, predation, harvest, competition, and access to spawning grounds.

Local Adaptation. The evolution of a population to be more well-suited to its local environment.

Natural-Origin. Fish that are produced by spawning and rearing in the natural habitat, regardless of parentage.

Natural-origin Broodstock. These are natural-origin fish that are used in a controlled environment for hatchery production.

Optimum. The desired fish production level as stated in management plans or set by specific Commission action.

Out of basin stock. These are a stock of fish that are not indigenous to the watershed they are being released and are often used to provide harvest-oriented fisheries in segregated hatchery programs. Also called Stock Transfer, a management program that moves fish among watersheds for harvest fisheries.

Outbreeding Depression. Occurs when offspring from crosses between individuals from different populations have lower fitness than progeny from crosses between individuals from the same population.

Phenology. The relationship between external abiotic triggers (e.g., temperature, streamflow) and the timing of periodic ecological events, such as migration and spawning.

Phenotype. Any observable trait of an organism that is determined by the interaction between its genes and environment.

Philopatry. The tendency of an organism to stay in, or return to, its home area. The causes of philopatry are numerous, but natal philopatry, where animals return to their birthplace to breed, is probably the most common form. The term “philopatry” derives from the Greek ‘home-loving’, and migratory species that demonstrate site fidelity: reusing stopovers, staging points, and wintering grounds.

Production. The number or pounds of fish raised in a hatchery or resulting from natural spawning and rearing in freshwater, estuarine, or ocean habitats; also used in reference to harvest.

Productivity. In fish is often measured through biological indices such as fish density or biomass, and is used to measure habitat quality and capacity.

Poikilotherm. An organism whose body temperature fluctuates with that of its surroundings. The vast majority of fish, including all salmonids, are poikilothermic.

Population. A group of interacting individuals of the same species..

Quasi Extinction Threshold. Threshold of adult abundance that indicates functional extinction of a population. This is set at 50 spawners per year and is based on loss of genetic diversity and demographic stochasticity.

Recruitment. The number of fish born within a given time period that survive to the juvenile stage. It is typically described in terms of ‘annual recruitment’, the number of survivors in each year, also known as a ‘cohort’ or ‘year-class’.

Reproductive success. The number of juvenile offspring (less than a year old) produced by a adult. Relative reproductive success is typically used to compare hatchery-origin fish relative to wild-origin fish when both groups are allowed to spawn in the wild.

Residualism. The failure of some juvenile salmonids to out-migrate as smolts with the rest of their cohort. Residualism does occasionally occur in natural populations, but is much more frequent in hatchery salmon and steelhead. Residualized hatchery fish may adversely affect natural fish populations through predation, predator attraction, and competition.

River Specific Management. Management of adult spawner abundance designed for each river with egg deposition objectives.

Rough Fish. These fish are generally native, non-game fish that are not specifically managed by state fish and game departments. Examples include sculpin, suckers, and chub. Rough fish may prey on, compete with, or even provide food for juvenile and resident salmonids. Also known as “coarse fish” or “trash fish,” rough fish are often under-researched and so their interactions with salmonids are generally not well-known or appreciated, though many play important roles in Indigenous culture.

Segregated Hatchery Program. A hatchery program in which only hatchery individuals are used in hatchery broodstocks and greater domestication selection may occur, including intentional selection to alter spawn timing of hatchery stocks to reduce expense of hatchery production by producing smolts in a year or less.

Segregated Hatchery Strategy. A broodstock management strategy where the intent is for the hatchery stock to have no reproductive interactions with wild stocks. Also referred to as an Isolated Hatchery Strategy. Challenges: Recent research has provided strong evidence that both segregated and integrated hatcheries have productivity, genetic, ecological, and mixed stock fishery impacts that are harmful to wild stocks in a one-year program, and this prevents their use for recovery.

Semelparous. Reproducing only once in a lifetime, a common life history trait in anadromous salmon. Contrast with iteroparous.

Smolt-to-Adult Returns (SAR). Refers to the number of returning adults as a percentage of smolts released, and is an indicator of relative reproductive success for a given population.

Stock. A group of fish within a species substantially reproductively isolated from other groups of the same species. NMFS regards “stock” and “population” to be interchangeable.

Stray Rate. The rate at which salmon from a specific population return to spawn in a watershed different from the one in which they originated. Natural stray rates are <1% to 3%. For hatchery fish, stray rate refers to the proportion of straying adults into the natal habitats of native fish. Transporting juveniles by barge or trucks downstream of dams increases stray rates, especially for steelhead.

Straying. A natural phenomenon in anadromous salmonids that is important for colonizing habitats such as rivers where dams have been removed. It is also important to the genetic health of locally adapting populations.

Supplementation. The release of hatchery fish to augment the numbers of naturally occurring fish. Often, the goal of supplementation programs is to increase the abundance of a wild population rather than only producing fish for harvest.

Viable Population. A self-supporting population with sufficient numbers and genetic variety among healthy individuals and breeding pairs that are well enough distributed to ensure a high probability of survival despite the foreseeable effects of demographic, environmental and genetic events, and of natural catastrophes. Also frequently referred to as “Minimum Viable Population.”

Watershed. Area above a point in a stream that catches the water that flows down to that point; also called a “catchment.” No matter where you are on land, you are in a watershed.

Common Acronyms




Brood Year


Clean Water Act


Coded Wire Tag


Distinct Population Segment (refers to steelhead populations)


Environmental Monitoring Assessment Program


Endangered Species Act


Evolutionarily Significant Unit




Hatchery Genetic Management Plan


Hatchery Scientific Review Group


Minimum Viable Population


Effective population size over a reproductive cycle


Effective population size (the number of successful spawners) in a generation


National Marine Fisheries Service


Percentage of hatchery-origin fish used as hatchery broodstock.


Percentage of hatchery-origin recruits.


Percentage of hatchery-origin fish spawning naturally.


Proportion of natural influence in a breeding population.


Percentage of natural origin fish used as hatchery broodstock.


Percentage of natural origin fish spawning naturally.


Population Viability Analysis


Quasi Extinction Threshold


Relative Reproductive Success


Adult recruits per spawner.


Smolt to Adult Return (sometimes Smolt to Adult Survival)


Smolt to Adult Survival


Viable Salmonid Population

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