Predicting species responses to climate change is a central challenge in ecology. These predictions are often based on lab-derived phenomenological relationships between temperature and fitness metrics. We tested one of these relationships using the embryonic stage of a Chinook salmon population. We parameterised the model with laboratory data, applied it to predict survival in the field, and found that it significantly underestimated field-derived estimates of thermal mortality. We used a biophysical model based on mass transfer theory to show that the discrepancy was due to the differences in water flow velocities between the lab and the field. This mechanistic approach provides testable predictions for how the thermal tolerance of embryos depends on egg size and flow velocity of the surrounding water. We found support for these predictions across more than 180 fish species, suggesting that flow and temperature mediated oxygen limitation is a general mechanism underlying the thermal tolerance of embryos.

Migratory species are particularly vulnerable to climate change because habitat throughout their entire migration cycle must be suitable for the species to persist. For migratory species in rivers, predicting climate change impacts is especially difficult because there is a lack of spatially continuous and seasonally varying stream temperature data, habitat conditions can vary for an individual throughout its life cycle, and vulnerability can vary by life stage and season. To predict thermal impacts on migratory riverine populations, we first expanded a spatial stream network model to predict mean monthly temperature for 465,775 river km in the western U.S., and then applied simple yet plausible future stream temperature change scenarios. We then joined stream temperature predictions to 44,396 spatial observations and life‐stage‐specific phenology (timing) for 26 ecotypes (i.e., geographically distinct population groups expressing one of the four distinct seasonal migration patterns) of Chinook salmon (Oncorhynchus tshawytscha), a phenotypically diverse anadromous salmonid that is ecologically and economically important but declining throughout its range. Thermal stress, assessed for each life stage and ecotype based on federal criteria, was influenced by migration timing rather than latitude, elevation, or migration distance such that sympatric ecotypes often showed differential thermal exposure. Early‐migration phenotypes were especially vulnerable due to prolonged residency in inland streams during the summer. We evaluated the thermal suitability of 31,699 stream km which are currently blocked by dams to explore reintroduction above dams as an option to mitigate the negative effects of our warmer stream temperature scenarios. Our results showed that negative impacts of stream temperature warming can be offset for almost all ecotypes if formerly occupied habitat above dams is made available. Our approach of combining spatial distribution and phenology data with spatially explicit and temporally explicit temperature predictions enables researchers to examine thermal exposure of migrating populations that use seasonally varying habitats.

Among four extant and declining runs of Chinook Salmon Oncorhynchus tshawytscha in California's Central Valley, none has declined as precipitously as the Sacramento River winter run. Migratory winter-run Chinook Salmon employ a life history strategy to reside and feed in stopover habitats on their way from freshwaters to the ocean. Migratory winter run, on their way from freshwaters to the ocean, employ a life history strategy to reside and feed in stopover habitats that have been affected by anthropogenic disturbance. Using acoustic telemetry, we examined conditions that influenced reach-specific movement and survival of out-migrating juveniles during a prolonged, multi-year drought from 2013 to 2016, followed by one of the wettest years on record (2017). We modeled how time-varying individual riverine covariates and reach-specific habitat features influenced smolt survival. Model selection favored a model with mean annual flow, intra-annual deviations from the mean flow at the reach scale, reach-specific channel characteristics, and travel time. Mean annual flow had the strongest positive effect on survival. A negative interaction between mean annual flow and intra-annual reach flow indicated that within-year deviations at the reach scale from annual mean flow had larger effects on survival in low-flow years. These factors resulted in higher survival during years with pulse flows or high flows. Changes in movement behavior in response to small-scale changes in velocity were negatively associated with survival. Covariates of revetment and wooded bank habitat were positively associated with survival, but the effect of these fixed habitat features changed depending on whether they were situated in the upper or lower part of the river. Fish exhibited density-dependent stopover behavior, with slowed downstream migration in the upper river in the wet years and extending to the lower river in the most critically dry year. This paper contributes two key findings for natural resource managers interested in flow management and targeted habitat

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Recovery of anadromous salmonid populations is complicated by their complex life-histories. We examined the spatiotemporal interplay of stream temperature, geomorphic features, and a species’ thermal sensitivity mediated by biological interactions in a case study of steelhead trout (Oncorhynchus mykiss) and Chinook salmon (O. tshawytscha) in California’s Eel River watershed. We estimated habitat suitability and fish capacity for each salmonid run and freshwater life stage during average, cool, and warm years in each of the watershed’s subbasins, including a historically-occupied high-elevation subbasin upstream of an impassable dam. Our estimates varied depending on whether we accounted for exposure to the Sacramento pikeminnow (Ptychocheilus grandis), an introduced predator/competitor. Our results indicate that the dammed subbasin has substantial salmonid capacity relative to the rest of the watershed and could provide an important cool-water refuge during warm years and from pikeminnow, potentially improving the productivity and resilience of multiple anadromous salmonid populations. Our approach can be applied in any setting where spatially explicit habitat metrics can be estimated and population specific and life-stage specific habitat criteria can be specified.

In North America, impassable, man-made barriers block access to salmonid spawning habitat and require costly restoration efforts in the remaining habitats. Evaluating restored spawning habitat quality requires information on salmon water velocity and depth preferences, which may vary in relation to other variables (e.g. water temperature). We demonstrate a generalizable, low cost method to gather and analyze this data by combining aerial redd surveys of winter-run Chinook salmon (Oncorhynchus tshawytscha), 2D hydraulic modeling, and generalized linear models to calculate spawning resource selection functions (RSFs). Our method permits the examination of interactions between environmental variables on habitat selection, which are frequently treated as independent. Our methods resulted in a RSF that shows interactions between both velocity and depth preference with changing temperature. Preferred depth increased and preferred velocity decreased with increasing temperature. Spawning RSFs for environmental variables may change as other environmental conditions (i.e. water temperature) change, thus it is importance to account for potential interactions when using or producing RSFs.

Historically, anadromous steelhead Oncorhynchus mykiss and spring‐run Chinook Salmon O. tshawytscha used high‐elevation rivers in the Sierra Nevada of California but were extirpated in the 20th century by construction of impassable dams. Plans to reintroduce the fish by opening migratory passage across the dams and reservoirs can only succeed if upstream habitats have the capacity to support viable populations of each species. To estimate capacity in the Tuolumne and Merced rivers of the central Sierra Nevada, we used a high‐resolution approach based on remote sensing and dynamic habitat modeling. Our results suggested that for both species in both systems, sediment grain sizes would support widespread spawning and the water temperatures, depths, and velocities would generate ample capacity for fry and juveniles. However, the unregulated Merced River was consistently too warm for adult Chinook Salmon to hold in the dry season prior to spawning, while the regulated Tuolumne River maintained a cooler, more stable thermal regime with a capacity for thousands of holding adults. In our high‐resolution approach, we also discovered several specific physical controls on life history expression, including thermal constraints on the timing of spawning, hydraulic prompts for downstream migration of fry, divergence of the hydraulic niches of steelhead and Chinook Salmon, and a key but uncertain role for thermal tolerance in adult Chinook Salmon. Our results suggested that steelhead reintroduction could succeed in either system and Chinook Salmon could succeed in the Tuolumne River if passage strategies account for large numbers of migrant fry and juveniles driven downstream by winter storms and snowmelt. The Merced River appeared too warm for adult Chinook Salmon, which raises questions about the current limited understanding of thermal tolerance in holding adults. Our study shows how a high‐resolution approach can provide valuable insights on specific limiting factors that must be addressed for reintroduction to succeed.

In North America, impassable, man-made barriers block access to salmonid spawning habitat and require costly restoration efforts in the remaining habitats. Evaluating restored spawning habitat quality requires information on salmon water velocity and depth preferences, which may vary in relation to other variables (e.g. water temperature). We demonstrate a generalizable, low cost method to gather and analyze this data by combining aerial redd surveys of winter-run Chinook salmon ( Oncorhynchus tshawytscha), 2D hydraulic modeling, and generalized linear models to calculate spawning resource selection functions (RSFs). Our method permits the examination of interactions between environmental variables on habitat selection, which are frequently treated as independent. Our methods resulted in a RSF that shows interactions between both velocity and depth preference with changing temperature. Preferred depth increased and preferred velocity decreased with increasing temperature. Spawning RSFs for environmental variables may change as other environmental conditions (i.e. water temperature) change, thus it is importance to account for potential interactions when using or producing RSFs.