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Scientists from WFRC are creating new tools and techniques to help natural resource managers explore data and ecosystem scenarios, making it easier to use complex modeling and data for water and fish management decisions.

Effective fish population management requires an understanding of how their numbers change on an ongoing basis. However, obtaining good abundance and survival estimates in dynamic river systems, with fish migrating and responding to man-made structures, habitat alterations, and varying environmental conditions can be challenging.

One well-known technique for making population estimates – mark-recapture – is being used and further developed by WFRC scientists to help manage migrating salmon populations. In mark-recapture studies, scientists capture and mark (or tag) a sample of individuals from the population, release them back into their original environment, then periodically attempt to recapture (or detect) those same individuals. The proportion of fish recaptured over time combined with the amount of effort put forth to capture them can be used to make inferences about the status of the larger population.

Map showing location of acoustic telemetry receiving stations
Map of the Sacramento River and Sacramento–San Joaquin Delta showing the location of acoustic telemetry receiving stations (black circles) used to detect migrating acoustic tagged juvenile salmon from 2014 through 2018 as described in Hance et al. (2022). These telemetry stations divide the Delta into seventeen discrete reaches, shown as shaded regions labeled by sampling occasions in each migration route (01–10, A–E). Yolo Bypass (reaches 03B and 08B) is only accessible when the Fremont weir overtops, which only occurred in 2016, 2017, and 2018.

Originally developed to estimate population size, mark-recapture methods can also be used to approximate mortality, immigration, and emigration within populations. At WFRC, we have extended mark-recapture models to investigate fish survival, behavior, migration routes, and responses to environmental variables such as temperature, flow, and man-made structures.

Recent studies by WFRC’s Quantitative Ecology team have been using mark-recapture methods and advancing modeling techniques to learn about salmon behavior and survival in complex, altered river systems. In California’s Sacramento River and Delta (Delta), novel mark-recapture models that integrate telemetry data from acoustic-tagged juveniles with a suite of partner-provided environmental data are being used to link the effect of daily flow and temperature on survival, routing, and travel time (Plumb et al. 2015, Perry et al. 2018, Pope et al. 2021, Dodrill et al. 2022). A specific example by Hance et al. 2022 related the daily survival and migration dynamics of an endangered anadromous salmon to river flow and water temperature during both extreme drought and severe flooding. This study is timely as weather extremes appear to be increasingly frequent with climate change. The Quantitative Ecology team has also applied similar approaches in other basins including the Snake River (Hance et al. 2019) and Yakima River (Perry et al. 2016). This information helps to understand how water management actions such as flow releases from upstream storage reservoirs affects migration, routing, and survival (Perry et al. 2019).

Mark-recapture strategies are a critical tool for species management. But how do you take layers of data and intensive statistic models and make them accessible to the people who need it? Tools! Specifically, decision support tools. Leveraging new mark-recapture models and a wealth of data, WFRC is working with partners to develop interactive tools that can explore information in real time and see how changes in the environment impacts fish populations.

Screenshot of Central Valley Enhanced Acoustic Tagging Project website (Central Valley Enhanced Acoustic Tagging Project ( showing a map (left) of the locations of routes and survival probabilities (right) for Chinook salmon released from Livingston Stone Hatchery in 2022.

One such tool is the San Francisco Bay Delta Survival, Travel time, and Routing Simulation (STARS). Made publicly available, this tool allows anyone to explore survival, travel times, and routes of juvenile salmon as the migrate through the Delta. This tool is part of a larger CalFish Track Central Valley Enhanced Acoustic Tagging Project website, supported together with California Fish and Wildlife, U.S. Fish and Wildlife, National Oceanic and Atmospheric Administration, University of Washington, and U.S. Bureau of Reclamation. The outputs of STARS are being used by U.S. Bureau of Reclamation for in-season monitoring and water management planning, and by the National Marine Fisheries Service in support of salmon life-cycle modelling.

Here at WFRC, we’re committed to innovation in science and modeling, developing tools that are accessible and easy to use, and tailoring our work to meet the decision-making needs of resource managers. For more information contact:  Russell Perry, head of the Quantitative Ecology Team. Team members include Adam Pope, Dalton Hance, John Plumb, Jake Kelley, and Michael Dodrill.

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