Temporal Changes of Allele Frequency in Pacific Salmon: Implications for Mixed-Stock Fishery Analysis

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Abstract
The effects of temporal variation in allele frequency on mixed-stock fishery analysis of Pacific salmon (Oncorhynchus spp.) are examined. The concept of effective sample size (Se), which equates the precision obtained from a sample from a finite population with that from one with no temporal variability, is used to evaluate the magnitude of the problems introduced by genetic drift. Results from simulations modeling the overlapping year-class pattern typical of chinook salmon (O. tshawytscha) indicate that the ratio of effective to actual sample size (Se/S) is determined primarily by the ratio of sample size to the effective number of breeders per year (S/Nb). Unless Nb is large relative to S, effective sample size can be considerably less than the actual number of individuals sampled. Sampling in more than 1 yr results in a higher Se than does taking the same total number of individuals in 1 yr; furthermore, the advantages to multiple sampling are greatest in small populations, in which the effects of genetic drift are most pronounced. By choosing an appropriate sampling strategy, the sources of uncertainty in the analysis attributable to genetic drift can be reduced below any arbitrary level.

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