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A Genetics Perspective to Fitness

of Snake River Spring/Summer Chinook Salmon
Idaho Fish & Game Report to the Director 5/1/98


Snake River spring/summer chinook salmon persisted through an apparent bottleneck (period of low abundance) in the 1980s and again in the 1990s. Genetic analysis of samples collected from 1989 through 1994 revealed no changes in within or between population variability that could have resulted from the bottlenecks. Thus there is no evidence of genetic change occurring that would impact growth, survival, and reproduction in the population and preclude the population from rebounding should conditions change.

Introductory Concepts

Fitness of fishes can be quantified at either the individual level or the population level. Fitness of an individual fish is typically described as its ability to successfully reproduce, and is influenced by fitness-related traits such as growth and survival rates (Kapuscinski and Jacobsen 1987). The fitness of a population is a function of the fitness of individuals within the population.

The fitness of fish populations has been linked to the genetic variation measured in individuals or populations. Genetic variation is necessary for adaptation to changing environments and the ability to persist through environmental changes. Conversely, loss of genetic variation increases the chance of extinction in the long-term. At one extreme end of the spectrum, a population with no genetic variation possesses no adaptive or evolutionary potential, and in the long-term is not likely to persist. If individuals are unable to adapt to new environmental conditions, their survival and growth would tend to be reduced, hence a reduction in fitness.

Mechanisms owing to the loss population genetic variation are inbreeding, genetic drift, migration (gene flow), and selection (Kapuscinski and Jacobsen 1987). The greatest concern to managers at this time is the decade-long low abundance of Snake River spring/summer chinook salmon and the potential loss of genetic variation at these low abundances. At low population sizes (population bottlenecks) inbreeding and genetic drift are the primary causes of loss of genetic variation. The rate of loss of genetic variation due to inbreeding is inversely related to the population size, and is often expressed as F (the per generation rate of loss) = 1/2Ne, where = Ne is the effective size of the breeding population (e.g. Crow and Kimura 1970, Nunney 1992, Ryman and Laikre 1991). Robertson (1955) noted that inbreeding had its greatest effect on "fitness characters" related to reproduction. Genetic drift is a random process that leads to loss of genetic variation; its effects are also more pronounced at low population sizes.

Also of concern form many stocks of Pacific Salmon are genetic interactions between wild and hatchery stocks that may have negative genetic impacts on the wild populations (Waples 1991). The hybridization of wild and hatchery stocks may result in reduced interpopulation genetic diversity. If non-native stocks are allowed to interbreed with wild endemic stocks, a reduction in fitness may occur through outbreeding depression. Research is currently being conducted in the Snake River basin to measure the effects of hatchery outplanting on wild populations' genetic characteristics (Waples 1991, 1993)

Measuring Genetic Variation

The most commonly used technique in fisheries literature for measuring genetic variation is allele frequency data of selectively neutral alleles. Because selectively neutral alleles are examined, different genotypes that are revealed have no adaptive or fitness differences (Currens et al. 1986). This allele frequency information is used primarily to discern genetic differences between or among populations. Typically the geneticist is interested in identifying a unique species or distinct population segment(s) within a species. Metrics commonly reported in the literature to express the amount of genetic variation are proportion of all loci examined that are polymorphic (genetically variable) and the total amount of genetic variation (heterozygosity) observed in the samples. The total heterozygosity can be partitioned into the proportion due to variation within populations and the proportion due to variation between populations.

Fishery managers must be cautious in trying to infer future fitness information about populations from such genetic data. Currens et al. (1996) noted that there is both empirical and theoretical evidence that genetic variation is important for adaptation and long-term persistence, but neither of these can be predicted from allozyme [allele frequency] data. It is important to remember that although fitness levels cannot be predicted from genetic data, numerous studies have demonstrated reduce fitness owing to mechanisms that can reduce genetic variation (e.g. Kincaid 1976, Leary et al. 1985, Young 1995).

Snake River Spring/Summer Chinook Salmon

The recovery potential of Snake River spring / summer chinook salmon is dependent on the fitness of the population. We can not predict the future fitness (or adaptive or recovery potential) of Snake River Spring/summer chinook salmon. However, we can infer from genetic data whether recent reductions in population abundance (or fishery management actions such as hatchery releases) may have resulted in reduced population genetic variation that may lead to reduced fitness. If a temporal reduction in genetic variation can be demonstrated, we should conclude that some adaptive potential in the population has been lost. This does not proscribe the population to extinction or preclude the ability of the population to increase (e.g. Caro and Laurenson 1994).

Genetic analysis of Snake River chinook salmon populations has been conducted by Waples et al. (1993) beginning with collections made in 1989 and 1990. Marshall (1992, 1993, 1996) analyzed samples collected in Idaho from 1991 through 1994.

The findings of Waples et al. (1993) are summarized below.

Snake River spring/summer chinook salmon are a genetically diverse group, and that more than 96% of the variation in allozyme loci surveyed exits as individual heterozygosity. (The authors further noted that Gyllensten (1985) noted a similar pattern of individual variation for other anadromous species.)

". . . population structure of in Snake River spring/summer chinook salmon occurs primarily at the level of differences between individual populations or groups of geographically proximate populations."

". . . it also seems unlikely that these populations are currently experiencing serious short-term problems associated with inbreeding." (The authors conditioned this statement on the assumption that their estimates of the effective numbers of breeders per year are accurate.)

Results of tests comparing heterozygosity and indices of asymmetry "provide little evidence for a relationship between heterozygosity and asymmetry in any population."

". . . the greatly reduced abundance of Snake River spring/summer chinook salmon has not been severe enough or protracted enough to substantially reduce levels of genetic variability in local populations."

Marshall (1996) provided a combined analysis of four years of Snake River spring/summer chinook salmon samples. Her conclusion was that despite the recent declining abundance of fish, genetic variation and diversity had persisted in the populations examined.


Some of the within population variability may have been maintained over time by the age structured nature of spawning population, where several age classes contribute to spawning in any one year. Marshall (1996) noted that between year variation in allele frequency was high in samples that could be temporally compared, and that this temporal variation was greater that that detected in large wild and hatchery populations in Washington. When multiple age classes spawn together, between year genetic variation is converted to within population variation. Although loss of genetic variation in Snake River spring/summer chinook salmon can not be demonstrated, the future potential sizes are cumulative over time if a population bottleneck persists over two or more generations. Snake River spring/summer chinook salmon are at risk of loss of genetic variation and adaptive potential because of current low population sizes that may persist over several years.

Their Status and Recovery Options
Report to the Director Idaho Fish & Game 5/1/98
Issue Paper: A Genetics Perspective to Fitness of Snake River Spring/Summer Chinook Salmon

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