Anadromous Salmonids in the Delta: New Science 2006-2016

Abstract

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.

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

“…provided valuable information on the timing and movements of acoustically-tagged SRWRC from the conservation hatchery (Klimley et al 2017), and information on the potential vulnerability of the hatchery-origin SRWRC to the opening of the DCC during the drought, which could route fish into the interior Delta, a route with lower survival, as reviewed in Perry et al 2016. In-season survival estimates associated with testing experimental pulse flows from tributaries can be of significant value to scientists and managers.…”

“…• Current and previous Central Valley AT tagging programs have provided important new insights into migration rates, reach-specific survival estimates, behaviors at junctions, and survival related to environmental co-variates (reviewed in Perry et al 2016) • Extensively used in Columbia River Basin to estimate survival of juvenile salmon through dams (McMichael et al 2010) • Real-time receivers can provide in-season detections and fish distribution and movement data, and with modeling support can be used to monitor in-season survival standards 18 VOLUME 15, ISSUE 3, ARTICLE 1 long-term viability, especially given their recent population bottlenecks and low genetic diversity (Banks et al 2000;Lindley et al 2007). Monitoring within-population genetic diversity, effective population size, relative reproductive success of individuals as a function of origin (hatchery versus wild), and spawning behavior (timing and location) provide important insights into how management actions (e.g., hatchery broodstock management) and water project operations (e.g., water temperature, flow timing, and the magnitude of flow releases) may influence the population's long-term genetic integrity.…”

The State of Bay-Delta Science 2016: An Introduction

“…Only about 3% of the original marsh remains (Whipple et al 2012). Before levee construction, the aquatic and terrestrial ecosystems of the Delta interacted strongly, and this interaction was critical to the ecology of native species (Wiens et al 2016;Brown et al, forthcoming;Perry et al 2016). The levees have isolated the aquatic and terrestrial ecosystems, contributing to the problem of native species conservation.…”

“…Four races of Chinook Salmon (Oncorhynchus tshawytscha) and Steelhead Trout (Oncorhynchus mykiss) move through the Delta on their seaward and spawning migrations. Acoustic tagging of smolts is revealing important details of where and when young salmon suffer mortality in the Delta (Perry et al 2016). Yet these species continue to decline.…”

Recent Advances in Understanding Flow Dynamics and Transport of Water-Quality Constituents in the Sacramento–San Joaquin River Delta

“…Movement of fish in the Delta is affected by water flows and is a key management concern. Fish movement is presented elsewhere in this volume (Moyle et al 2016;Perry et al 2016).…”