A robust monitoring network that provides quantitative information about the status of imperiled species at key life stages and geographic locations over time is fundamental for sustainable management of fisheries resources. For anadromous species, management actions in one geographic domain can substantially affect abundance of subsequent life stages that span broad geographic regions. Quantitative metrics (e.g., abundance, movement, survival, life history diversity, and condition) at multiple life stages are needed to inform how management actions (e.g., hatcheries, harvest, hydrology, and habitat restoration) influence salmon population dynamics. The existing monitoring network for endangered Sacramento River winterrun Chinook Salmon (SRWRC, Oncorhynchus tshawytscha) in California's Central Valley was compared to conceptual models developed for each life stage and geographic region of the life cycle to identify relevant SRWRC metrics. We concluded that the current monitoring network was insufficient to diagnose when (life stage) and where (geographic domain) chronic or episodic reductions in SRWRC cohorts occur, precluding within-and among-year comparisons. The strongest quantitative data exist in the Upper Sacramento River, where abundance estimates are generated for adult spawners and emigrating juveniles. However, once SRWRC leave the upper river, our knowledge of their identity,

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Population diversity is a mechanism for resilience and has been identified as a critical issue for fisheries management, but restoration ecologists lack evidence for specific habitat features or processes that promote phenotypic diversity. Since habitat complexity may affect population diversity, it is important to understand how population diversity is partitioned across landscapes and among populations. In this study, we examined life history diversity based on size distributions of juvenile Central Valley Chinook salmon (Oncorhynchus tshawytscha) within the Yolo Bypass, a remnant transitional habitat from floodplain to tidal sloughs in the upper San Francisco Estuary (SFE). We used a generalized least squares model with an autoregressive (AR1) correlation structure to describe the distribution of variation in fish size from 1998 to 2014, and tested the effect of two possible drivers of the observed variation: (i) environmental/seasonal drivers within the Yolo Bypass, and (ii) the juvenile Chinook source population within the Sacramento River and northern SFE. We found that the duration of floodplain inundation, water temperature variation, season, and sampling effort influenced the observed time-specific size distribution of juvenile Chinook salmon in the Yolo Bypass. Given the lack of seasonally inundated habitat and low thermal heterogeneity in the adjacent Sacramento River, these drivers of juvenile size diversification are primarily available to salmon utilizing the Yolo Bypass. Therefore, enhancement of river floodplain-tidal slough complexes and inundation regimes may support the resilience of imperiled Central Valley Chinook salmon. K E Y W O R D SCalifornia Central Valley Chinook salmon, habitat complexity, hydrologic disturbance, phenotypic diversity, resource management, seasonal floodplain inundation | INTRODUCTIONPopulation diversity has emerged as an important mechanism for resilience in changing environments (Hilborn, Quinn, Schindler, & Rogers, 2003). For Pacific salmon (Oncorhynchus spp.), the link between increased spatial variation in habitat use and decreased interannual variation in production is apparent for both juvenile (Thorson, Scheuerell, Buhle, & Copeland, 2014) and adult life stages.These studies suggest that some aspects of population diversity are dependent upon the maintenance of a range of habitats (Carlson & Satterthwaite, 2011;Jonsson, 1988;Moore, McClure, Rogers, & Schindler, 2010;Schindler et al., 2010). The application of this concept has become increasingly important as we become confronted with potentially irreversible and cascading effects of climate change and other stressors (Battin et al., 2007). Further, hydrology is one of the major disturbance regimes thought to shape habitat conditionsThis is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations a...

Climate and hydrologic variability are defining characteristics of California rivers. Recently, the region experienced an unprecedented drought, and the probability of similarly warm, dry conditions is predicted to increase. In addition to warming air and water temperatures, climate change projections predict increased flooding and sea level rise, likely aggravating the water resource issues that already challenge the western United States. Water managers balance many public interests, including the conservation of native fishes, such as the Chinook Salmon Oncorhynchus tshawytscha. Given projected changes in climate and hydrology, there is an urgent need to understand how salmon respond to these conditions. In this study, we examined how young salmon responded to extreme drought (2012–2015) versus flood (1998–1999) conditions in the Yolo Bypass, a floodplain–tidal slough complex of the Sacramento River, California. We found that the diets of juvenile Chinook Salmon were dominated by aquatic–riparian insects during flooding and were dominated by zooplankton during the drought. Although juvenile salmon that were caught during the drought seemed to have eaten a higher number of prey items on average, they also had higher metabolic costs. Therefore, it is likely that juvenile salmon must augment their foraging behavior to offset higher temperatures and prey shifts. Finally, preferentially consumed, calorically valuable prey (i.e., larger zooplankton and aquatic–riparian insects) have become rare due to habitat degradation and biological invasions, and resource managers must consider re‐establishing productive off‐channel habitats, such as riparian corridors, floodplains, and wetlands.