Predicting juvenile Chinook Salmon routing in riverine and tidal channels of a freshwater estuary

As juvenile salmon enter the Sacramento-San Joaquin River Delta ("the Delta") they disperse among its complex channel network where they are subject to channel-specific processes that affect their rate of migration, vulnerability to predation, feeding success, growth rates, and ultimately, survival. In the decades before 2006, tools available to quantify growth, dispersal, and survival of juvenile salmon in this complex channel network were limited. Fortunately, thanks to technological advances such as acoustic telemetry and chemical and structural otolith analysis, much has been learned over the past decade about the role of the Delta in the life cycle of juvenile salmon. Here, we review new science between 2006 and 2016 that sheds light on how different life stages and runs of juvenile salmon grow, move, and survive in the complex channel network of the Delta. One of the most important advances during the past decade has been the widespread adoption of acoustic telemetry techniques. Use of telemetry has shed light on how survival varies among alternative migration routes and the proportion of fish that use each migration route. Chemical and structural analysis of otoliths has provided insights about when juveniles left their natal river, and provided evidence of extended rearing in the brackish or saltwater regions of the Delta. New advancements in genetics now allow individuals captured by trawls to be assigned to specific runs. Detailed information about movement and survival in the Delta has spurred development of agent-based models of juvenile salmon that are coupled to hydrodynamic models. Although much has been learned, knowledge gaps remain about how very small juvenile salmon (fry and parr) use the Delta. Understanding how all life stages of juvenile salmon grow, rear, and survive in the Delta is critical for devising management strategies that support a diversity of life history strategies.

Section: Migration Routingmentioning

confidence: 63%

Anadromous Salmonids in the Delta: New Science 2006-2016

Perry¹,

Buchanan²,

Brandes³

et al. 2016

“…Results of acoustic tagging studies in the Sacramento and San Joaquin rivers have generated important insights into overall low survival, effects of flows and turbidity on survival, diversity in migration behaviors among races of Chinook Salmon, and variability in survival rates among different regions of the river, Delta, and bays (Buchanan et al 2013;Singer et al 2013;Cavallo et al 2015;Michel et al 2015;reviewed in Perry et al 2016). However, most of these studies were conducted on hatcheryorigin salmon from different runs, highlighting the need to expand this approach to gathering comparable information on salmon originating and migrating from Central Valley rivers.…”

Section: Introductionmentioning

confidence: 99%

Science Advancements Key to Increasing Management Value of Life Stage Monitoring Networks for Endangered Sacramento River Winter-Run Chinook Salmon in California

Johnson¹,

Windell²,

Brandes³

et al. 2017

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,

“…The development of spatially explicit mechanistic fish movement models in response to environmental conditions was identified as an important step in improving water resource management in the Sacramento−San Joaquin Delta (Rose et al 2011;Delta ISB 2015). Yet statistical models that summarize the relationship between migration routing and hydrodynamics have been instrumental in understanding how individual fish behavior gives rise to emergent patterns that water management actions ultimately influence (Cavallo et al 2015;Perry et al 2015Perry et al , 2018. We view our model as a bridge between a purely mechanistic or purely statistical model because it provides a quantitative description of a conceptual model that is rooted in physical and biological principles.…”

Section: Discussionmentioning

confidence: 99%

Combining Models of the Critical Streakline and the Cross-Sectional Distribution of Juvenile Salmon to Predict Fish Routing at River Junctions

Hance¹,

Perry²,

Burau³

et al. 2020

Because fish that enter the interior Delta have poorer survival than those emigrating via the Sacramento River, understanding the mechanisms that drive entrainment rates at side channel junctions is critically important for the management of imperiled juvenile salmon. Here, we implement a previously proposed process-based conceptual model to study entrainment rates based on three linked elements: the entrainment zone, critical streakline, and cross-sectional distribution of fish. The critical streakline is the location along a channel cross-section immediately upstream of a junction that forms the spatial divide between parcels of water that enter a side channel or remain in the main channel. The critical streakline therefore divides the main channel into entrainment zones within which fish would likely