Evaluation of genetic effects on wild salmon populations from stock enhancement

Many salmonid populations are of conservation concern, and the release of hatchery-produced juveniles is a frequently used measure to alleviate declines and increase harvest opportunities. While such releases may be of conservation value for some populations, stocking may also decrease the effective population size and subsequently impose additional strain on already threatened populations. In this study, we assessed how the cohort-wise effective number of breeders in five populations of Atlantic salmon (Salmo salar) were affected by supplementation. Altogether, 19 cohorts were studied (2–7 cohorts per population) by estimating the proportion hatchery-released individuals and the effective number of wild and captive breeders in each cohort of the respective populations. We show that the effect of releasing captive-bred individuals varies both between populations and between years within the same population. A Ryman–Laikre effect—where the effective number of breeders has decreased as a consequence of supplementation—was observed for 11 cohorts. We discuss how supplementation can be adapted to optimize the effective population size, demonstrate that evaluation of supplementation can be reliably achieved, and show that supplementation programmes that lead to high proportions of hatchery-origin fish on spawning grounds are more likely to induce a Ryman–Laikre effect.

Mating systems and predictors of relative reproductive success in a cutthroat trout subspecies of conservation concern

Mating systems and patterns in reproductive success of fishes play an important role in ecology and evolution. While information on the reproductive ecology of many anadromous salmonids (Oncorhynchus spp.) is well-detailed, there is less information for non-anadromous species including the Yellowstone Cutthroat Trout (O. clarkii bouvieri), a species of recreational angling importance and conservation concern. Here, we used data from a parentage-based tagging study to describe the mating system of Yellowstone Cutthroat Trout from a spawning tributary of the South Fork Snake River, Idaho, and identify predictors of relative reproductive success. We detected evidence of monogamy, polygyny, and polyandry and showed that reproductive success was best explained by arrival time at the spawning ground and total length. Specifically, the largest adults arrived earliest in the season and produced a disproportionate number of offspring. Lastly, we estimated the effective number of breeders (N) and effective population size (N) and showed that while Nb was lower than Ne, both are sufficiently high to suggest Yellowstone Cutthroat Trout in Burns Creek represent a genetically stable and diverse population.

AgeStrucNb: Software for Simulating and Detecting Changes in the Effective Number of Breeders (Nb)

Estimation of the effective number of breeders per reproductive event (Nb) using single sample DNA-marker-based methods has rapidly grown in recent years. However, estimating Nb is difficult in age-structured populations because the performance of estimators is influenced by the Nb / Ne ratio, which varies among species with different life histories. We provide a computer program, AgeStrucNb, to simulate age-structured populations (including life history) and also estimate Nb. The AgeStrucNb program is composed of 4 major components to simulate, subsample, estimate, and then visualize Nb time series data. AgeStrucNb allows users to also quantify the precision and accuracy of any set of loci or sample size to estimate Nb for many species and populations. AgeStrucNb allows users to conduct power analysis to evaluate sensitivity to detect changes in Nb or the power to detect a correlation between trends in Nb and environmental variables (e.g., temperature, habitat quality, predator or pathogen abundance) that could be driving changes in Nb. The software provides Nb estimates for empirical data sets using the LDNe (linkage disequilibrium) method, includes publication-quality output graphs, and outputs genotype files in Genepop format for use in other programs. AgeStrucNb will help advance the application of genetic markers for monitoring Nb, which will help biologists to detect population declines and growth, which is crucial for research and conservation of natural and managed populations.