Association with physical structure or conspecifics can impact the survival and growth of individuals. The necessity and strength of these associations can change with environmental conditions and ontogeny, acting in concert or in opposition to influence an individual’s behavior and ultimate success. To test the hypotheses that affinity for physical structure and aggregating behavior changes along a dynamic river gradient and with development of a migratory fish, I conducted a field experiment on the San Joaquin River, California with juvenile Chinook salmon (Onchorynchus tschawyscha). I created orthogonal combinations of turbidity, fish size, and structural cover by manipulating the presence of artificial structure within net pens at three locations along the river continuum. I recorded the affinity of juvenile Chinook salmon to physical structure and propensity to aggregate with conspecifics with video cameras. I used generalized linear models and model selection to evaluate the effects of turbidity, size (fork length), density, and structure level on proximity of individuals to structure and conspecifics. First, I found there was no difference in the total number of salmon in structure or no-structure levels. Second, I found the number of aggregating observations increases with increasing density and fork length. When structure was present, aggregating behavior was low across turbidities. In contrast, when structure was absent, aggregating behavior increased in low turbidities. Ultimately, I found both ontogeny and a changing environmental gradient influenced the number of aggregating observations. These results indicate how environmental conditions (turbidity and availability of physical structure), size, and density interact to determine fish behavior and increase understanding of the complicated interactions surrounding fish habitat use.

The introduced yellowfin goby (YFG) is now common throughout the tidal portion of the Sacramento-San Joaquin River system. We investigated its habitat use, size and diet in the Mokelumne River, an eastern tributary to the system. Catch per unit effort (CPUE) by boat electrofishing was significantly higher in the fall than all other seasons sampled over four years. Habitat type, turbidity and dissolved oxygen were not significantly related to CPUE between years and seasons. Temperatures were negatively related to CPUE in fall sampling only. Delta outflow and CPUE showed a significant negative relationship. Fish captured ranged from 27 mm SL (standard length) (33 mm TL (total length)) to 155 mm SL (196 mm TL) (mean 113 mm SL (138 mm TL)), with largest fish captured during the fall. Seasonal and annual analysis showed a diet composed of a variety of macroinvertebrates, including chironomids, gammarids, aquatic isopods and ephemeropterans with no difference in composition among seasons or years. The YFG’s generalist diet gives it an advantage as a successful invader, but salinity requirements appear to limit its expansion potential.

A primary goal of the Central Valley Project Improvement Act is to at least double natural production of Chinook salmon (Oncorhynchus tshawytscha), in California Central Valley (CV) streams on a sustainable basis. Achievement relies on restoration actions that involve both discharge (e.g., dam releases) and non-discharge (e.g., gravel augmentation, screening) components. Annual adult and juvenile abundance estimates for individual watersheds must be tracked to assess effectiveness of individual actions. However, to date, no substantial efforts have been taken to demonstrate success or deficiencies of their implementations. A major challenge in interpreting time series of counts at any one life stage is that they reflect the cumulative effects of both freshwater and marine factors over the full life cycle. To address this issue, we developed a conceptual framework based on ratios of the abundance of consecutive CV fall-run Chinook salmon life stages and how variation in these ratios tracks key independent variables during the freshwater portion of the life cycle. Model validation with several case studies shows that estimates of previous stage class production correlate well with estimated individuals produced in the next class, indicating that transition rates tend to vary within a constrained range, and that monitoring programs generate abundance estimates whose errors are small enough not to swamp out the underlying signal. When selected environmental parameters were added to demonstration models, abundance estimates were more closely modeled and several tested relationships between environmental drivers and life-stage transition rates proved consistent across watersheds where data were available. Results from this generalized life-stage conceptual model suggest a potential framework for tracking the success of actions meant to improve survival for a given life stage within an individual stream and for determining how successive stages respond to these changes. Though examples are provided for CV Chinook salmon, these concepts can be applied wherever migratory salmonid populations and associated environmental data are being adequately monitored.