Use of Linkage Disequilibrium Data to Estimate Effective Size of Hatchery and Natural Fish Populations

A primary parameter in the assessment of the viability of a population is its effective population size ( Ne ). Allozyme analysis of four groups of fishes provided data on linkage disequilibrium, which were then used to estimate Ne . The groups included hatchery samples of juvenile white seabass, Atractoscion nobilis , juvenile rainbow trout, Oncorhynchus mykiss , from the Shasta Hatchery, and juvenile chinook salmon, O. tshawytscha , from the Coleman National Fish Hatchery. The fourth sample consisted of juvenile chinook salmon from the threatened winter run in the upper Sacramento River. The groups of fish were chosen to represent different applications of the methodology to conservation of fishes. For a variety of reasons. Ne may be considerably lower than census counts of fish present in the parental populations. The Ne of the hatchery broodstock that produced the sample of juvenile white seabass was estimated to be approximately 10, although 25 adult white seabass were present in a mass spawning tank. Ne estimates for the parental populations of the Shasta and Coleman Hatchery samples were 35.8 and 132.5, respectively. The actual number of fish spawned at the Shasta Hatchery was approximately 40, whereas nearly 10,000 salmon were spawned at the Coleman Hatchery. The threatened winter run of chinook salmon had an estimated Ne of 85.5 and an approximate run size of 2000 salmon. The method of estimating effective population size from linkage disequilibrium data appears to result in realistic estimates of effective population size when adequate sample size and a sufficient number of polymorphic loci are available.