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.

Genetic stock assignment is not routinely used when describing the dynamics and demographics of individual stocks supporting mixed‐stock fisheries, and capture location and timing are often used as alternative assignment methods. However, variation in stock demographics and dynamics may not be accounted for if stock assignments based on capture location or timing do not accurately reflect genetic assignments. We used Lake Whitefish Coregonus clupeaformis in Lake Michigan as a model fishery to determine whether stock mixing could undermine efforts to describe stock status when using October capture location as a proxy for genetic stock assignment. Accuracy of stock assignments based on October capture location ranged from 54% to 100% among management zones. Metrics describing length and age distributions, weight at length, fecundity, and growth varied among genetic stocks. Stock‐specific metrics were typically similar between stock assignment methods (capture location versus genetics) because only one or two genetic stocks were collected in most locations and the majority of those fish were from spatially proximal stocks with similar metrics. However, more extensive mixing of Lake Whitefish stocks has been documented; thus, using capture location for stock assignment could result in incorrect conclusions regarding stock status and harvest management depending on stock composition. Ambiguity in genetic stock assignments was a problem in two management zones, where between 23% and 42% of Lake Whitefish did not assign to a specific stock with a probability of at least 0.70. In the future, using genomic techniques rather than microsatellites may provide different conclusions regarding genetic stock structure; these differences could affect the accuracy of using capture location for stock assignment. Use of capture location as a proxy for genetic stock assignment may not be warranted for all mixed‐stock fisheries but may be appropriate when stock mixing is limited or is restricted to stocks with consistently similar characteristics.

The Columbia River basin is home to a run of spring–summer Chinook Salmon Oncorhynchus tshawytscha that returns to the Snake River drainage of Idaho, Oregon, and Washington in the Pacific Northwest. Historically, the run was one of the more productive throughout the Columbia River basin. However, Snake River spring–summer Chinook Salmon have experienced declines in abundance due to overfishing, habitat degradation, and dams. Several stocks are listed as threatened under the U.S. Endangered Species Act and are supported by mitigation hatcheries funded by Idaho Power Company, the Lower Snake River Compensation Plan, and the Bonneville Power Administration. To maximize tribal and state harvest of returning hatchery adults, minimize impacts on wild fish, and ensure that enough hatchery fish return to meet broodstock needs, careful fisheries management is required. Since 2008, managers have used hatchery adults, PIT‐tagged as juveniles and detected at Lower Granite Dam, to generate adult abundance estimates. In season, these estimates inform state and tribal harvest shares and ensure that broodstock needs are met. Postseason, they provide smolt‐to‐adult survival and return rates. Since 2012, parentage‐based tagging (PBT) has provided an alternative method to estimate stock‐ and age‐specific returns at Lower Granite Dam, since returning hatchery adults sampled at Lower Granite Dam can be assigned to their parents. We compared stock‐specific abundance estimates between PIT‐ and PBT‐derived methodologies for return years 2016–2019. Across all years, PIT tag estimates accounted for 65% of the PBT‐based estimates at Lower Granite Dam across all age‐groups and release sites combined. This underrepresentation across all groups equated to 49,833 fish that were not accounted for in PIT tag abundance estimates. It is clear that PBT‐based estimates should aide in‐season harvest management and postseason run reconstruction to avoid the known bias of estimates from PIT tags, especially during years of low returns when increased accuracy is critical.