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Objective: Long‐term standardized monitoring programs are fundamental to assessing how fish populations respond to anthropogenic stressors. Standardized monitoring programs may need to adopt new methods to adapt to rapid environmental changes that are associated with a changing climate. In the upper Yellowstone River, Montana, biologists have used a standardized, mark–recapture monitoring protocol to annually estimate the abundance of trout since 1978 to assess population status and trends. However, within the past two decades, climate change has caused changes in discharge timing that have prevented standardized monitoring from occurring annually. Methods: We investigated the feasibility of using two analytical methods, N‐mixture models and mean capture probability, for estimating the abundance of three trout species in the upper Yellowstone River using the historical long‐term data set; these methods allow abundance to be estimated when a mark–recapture estimate cannot be obtained due to hydrologic conditions. Result: When compared with abundance estimates from mark–recapture methods, N‐mixture models most often resulted in negatively biased abundance estimates, whereas mean capture probability analyses resulted in positively biased abundance estimates. Additionally, N‐mixture models produced negatively biased estimates when tested against true abundance values from simulated data sets. The bias in the N‐mixture model estimates was caused by poor model fit and variation in capture probability. The bias in the mean capture probability estimates was caused by heterogeneity in capture probability, likely caused by variable environmental conditions, which were not accounted for in the models. Conclusion: N‐mixture models and mean capture probability are not viable alternatives for estimating abundance in the upper Yellowstone River. Thus, exploring additional adaptations to sampling methodologies and analytical approaches, including models that require individually marked fish, will be valuable for this system. Climate change will undoubtedly necessitate changes to standardized sampling methods throughout the world; thus, developing alternative sampling and analytical methods will be important for maintaining the utility of long‐term data sets. Impact StatementClimate change is causing conditions that prevent mark–recapture trout monitoring in the Yellowstone River. Two alternative analysis methods, N‐mixture models and mean catchability, showed limited utility; thus, other alternate sampling and analytical methods could be explored. [ABSTRACT FROM AUTHOR]

Understanding how invasive species affect the stability and function of ecosystems is critical for conservation. Here, we quantified the effect of an actively suppressed invasive species on the Yellowstone Lake ecosystem using a food web energetics approach. We compared energy flux, functional state, and stability of four food web states: a pre‐invasion network and three post‐invasion networks undergoing active invasive species suppression, namely, initial invasion, expansion, and decline. Invasion caused ≥ 25% change (±) in energy flux for most consumers, and total flux increased twofold post‐invasion. Flux to the species of conservation concern, Yellowstone cutthroat trout (Oncorhynchus virginalis bouvieri), was 2.8 times less post‐invasion versus pre‐invasion, whereas invasive lake trout (Salvelinus namaycush) flux was up to 17.3 times higher compared to the initial invasion network. The dominant functional state and food web stability did not change post‐invasion, likely due to introduction of a generalist predator and the stabilizing effect of suppression. Lake trout invasion in Yellowstone Lake caused large changes to energy flux, shifting dominant fluxes away from the species of conservation concern, despite not changing functional state or stability. We demonstrate that changes in energy flux may signal invasions in ecosystems, but functional state or stability may not necessarily reflect the magnitude of invasion influences. For invaded fish communities, a better understanding of how the invasive species control the food web beyond just the direct influence on prey can be achieved by investigating energy flux, functional state, and food web stability. Furthermore, evaluating the effect of suppression beyond the invasive species can demonstrate the far‐reaching value of suppression management actions for conservation. [ABSTRACT FROM AUTHOR]

In Yellowstone Lake, Wyoming, the largest inland population of nonhybridized Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri, hereafter Cutthroat Trout, declined throughout the 2000s because of predation from invasive Lake Trout Salvelinus namaycush, drought, and whirling disease Myxobolus cerebralis. To maintain ecosystem function and conserve Cutthroat Trout, a Lake Trout gill netting suppression program was established in 1995, decreasing Lake Trout abundance and biomass. Yet, the response of Cutthroat Trout to varying Lake Trout suppression levels, collectively with the influence of disease and climate, is unknown. We developed an ecosystem model (calibrated to historical data) to forecast (2020–2050) whether Cutthroat Trout would achieve recovery benchmarks given disease, varying suppression effort, and climate change. Lake Trout suppression influenced Cutthroat Trout recovery; current suppression effort levels resulted in Cutthroat Trout recovering from historical lows in the early 2000s. However, Cutthroat Trout did not achieve conservation benchmarks when incorporating the influence of disease and climate. Therefore, the National Park Service intends to incorporate age‐specific abundance, spawner biomass, or both in conservation benchmarks to provide better indication of how management actions and environmental conditions influence Cutthroat Trout. Our results illustrate how complex interactions within an ecosystem must be simultaneously considered to establish and achieve realistic benchmarks for species of conservation concern. [ABSTRACT FROM AUTHOR]