Parentage-based tagging improves escapement estimates for ESA-listed adult Chinook Salmon and Steelhead in the Snake River basin

Parentage-based tagging (PBT) is a non-lethal, genetic tagging method that has been successfully applied in hatchery supplemented populations to manage hatchery broodstock and monitor hatchery harvest and straying rates. We show that PBT can also improve the accuracy of escapement estimates by significantly reducing the number of hatchery-origin fish falsely classified as natural-origin. Unlike conventional abundance estimates, which use physical marks and tags to distinguish hatchery individuals from their wild counterparts, PBT identifies origin independent of physical form. We applied PBT to populations of Chinook Salmon (Oncorhynchus tshawytscha) and Steelhead (O. mykiss) which are classified as threatened under the Endangered Species Act and subject to extensive hatchery supplementation efforts. For spawn years 2014-2018, 16,511 adipose-intact Chinook Salmon and 21,953 adipose-intact Steelhead were sampled, and PBT identified 19.6% of returning Chinook Salmon and 8.3% of Steelhead were of hatchery-origin, despite having no physical or mechanical marks. The 90% confidence intervals for escapement estimates of natural-origin Chinook Salmon and Steelhead made with and without corrections using PBT were non-overlapping for nine of ten comparisons indicating that failing to account for unmarked, untagged hatchery-origin fish would result in a significant overestimation of natural abundance.

Evaluating benefits of stocking on sockeye recovery projections in a nutrient-enhanced mixed life history population

Dam construction often blocks migration of anadromous sockeye salmon (Oncorhynchus nerka), resulting in a residualized population that is often managed as landlocked kokanee. Anadromy resumes when a reconnection to the ocean is established; however, there may be selective pressure acting on threshold trait(s) affecting smolt timing and probability. While there may be interest in predicting persistence of anadromous and residual sockeye forms, this is difficult because the heritability of smolting in these populations is poorly known. We develop a fully density-dependent age-structured model to project abundances for both anadromous and resident sockeye. The model considers trophic interactions due to nutrient variation and the density-dependent consequences for smolting and adult returns. Moreover, it asks how each life history type will persist if a hatchery were used to promote anadromous sockeye through artificial selection. We show hatchery supplementation is unlikely to impact anadromous or resident sockeye significantly, although there is substantial prediction uncertainty suggested in projections. Our study suggests that providing passage for previous land-locked anadromous populations will lead to the return of anadromous fish in the short term, but long-term prospects are far from certain.

Effects of hatchery supplementation on abundance and productivity of natural-origin Chinook salmon: two decades of evaluation and implications for conservation programs

Hatchery supplementation has been developed to conserve salmonid populations and provide fisheries. We evaluated supplemented and reference Chinook salmon (Oncorhynchus tshawytscha) populations prior to, during, and after supplementation ceased for 22 years in two major drainages in Idaho, USA. Basin-level analyses showed supplementation increased abundance at some life stages, but effects did not persist into the postsupplementation phase and had no apparent influence on productivity. Natural-origin juvenile abundance increased during supplementation but results for adults were ambiguous. After supplementation ceased, abundance and productivity in supplemented and reference populations returned to their presupplementation relationships. Intensive analyses of supplemented populations with weirs showed abundance increased at some life stages with the addition of female spawners. However, the rate of increase varied with female origin (natural > supplementation ≥ nontreatment hatchery), and effects diminished through the life cycle. Based on these findings, we provide guidance for conservation programs. Supplementation alone is not a panacea because it does not correct limiting factors, which must be addressed to achieve population levels capable of sustaining ecological function and harvest.