Comparison of Length-at-Date Criteria and Genetic Run Assignments for Juvenile Chinook Salmon Caught at Sacramento and Chipps Island in the Sacramento–San Joaquin Delta of California

There are four distinct runs of Chinook Salmon (Oncorhynchus tshawytscha) in the Central Valley, named after their primary adult return times: fall, late-fall, winter, and spring run. Estimating the run-specific composition of juveniles entering and leaving the Sacramento–San Joaquin Delta is crucial for assessing population status and processes that affect juvenile survival through the Delta. Historically, the run of juvenile Chinook Salmon captured in the field has been determined using a length-at-date criteria (LDC); however, LDC run assignments may be inaccurate if there is high overlap in the run-specific timing and size of juveniles entering and leaving the Delta. In this study, we use genetic run assignments to assess the accuracy of LDC at two trawl locations in the Sacramento River (Delta entry) and at Chipps Island (Delta exit). Fin tissues were collected from approximately 7,500 juvenile Chinook Salmon captured in trawl samples between 2007 and 2011. Tissues were analyzed using 21 microsatellites to determine genetic run assignments for individuals, which we compared with LDC run assignments. Across years, there was extensive overlap among the distributions of run-specific fork lengths of genetically identified juveniles, indicating that run compositions based on LDC assignments would tend to underestimate fall-run and especially late-fall-run compositions at both trawl locations, and greatly overestimate spring-run compositions (both locations) and winter-run compositions (Chipps Island). We therefore strongly support ongoing efforts to include tissue sampling and genetic run identification of juvenile Chinook Salmon at key monitoring locations in the Sacramento–San Joaquin River system.

Shade affects magnitude and tactics of juvenile Chinook salmon antipredator behavior in the migration corridor

Environmental conditions strongly affect antipredator behaviors; however, it is less known how migrating prey adjust antipredator behavior in migration corridors, in part, because active migrants are difficult to observe and study. Migrants are vulnerable and encounter many predators in the corridor, and their propensity to travel towards their destination ties antipredator behavior with movement. We evaluated how environmental risk cues in the migration corridor including in-water habitat structure (present, absent) and overhead shade (sun, shade), and salmon origin (hatchery, wild) affected how juvenile Chinook salmon (Oncorhynchus tshawytscha) reacted to a live predator. We measured how salmon react to predation risk as the difference in time to swim downstream through a 9.1-m long field enclosure with or without a live predatory largemouth bass (Micropterus salmoides). Shade significantly modified the reaction to the predator, and it did so in two ways. First, the magnitude of antipredator behavior was larger in shade compared to direct sun, which suggests salmon perceived shade to be a riskier environment than sun. Second, the escape tactic also varied; salmon slowed down to be cautious in shade and sped up in sun. Structure did not significantly affect behavior and hatchery and wild salmon behaved similarly. Our study suggests that environmental risk cues can shape the magnitude and tactics of how migrants react to predation risk and illustrates how these responses relate to movement with potential to scale up and affect migration patterns.

Juvenile Chinook salmon use of sandbar willows in a large-scale, simulated riparian floodplain: microhabitat and energetics

Outmigrating, juvenile Chinook salmon Oncorhynchus tshawytscha, with access to floodplains (e.g., Yolo Bypass California, USA), grow faster than those restricted to the main channel of the Sacramento River. How these young salmon might use rooted, vegetative structure (e.g., to decrease energy expenditures) while holding positions in flowing water on floodplains and flooded riparian zones is unknown. We conducted daytime experiments in a large (24.4 m long) flume containing a planted area (9.76 m × 1.22 m) of sandbar willows, Salix interior. Flume water was maintained at 1.5 m depth and 16 °C over a 15–90 cm s−1 test velocity range. Fish were videoed using 19 cameras to determine positional behavior, including their depth, use of vegetation, and tail-beat (body-undulation) frequencies (TBFs). These TBFs were replicated with similarly-sized salmon in a calibrated, Brett-type swimming respirometer, where oxygen consumption rates were measured. Using these laboratory measurements, we estimated their swimming velocities and energetic costs associated with occupying sandbar willow habitats in the flume. As flume velocities increased and the leafy canopies of the willows were bent over from the flow, salmon occupied deeper water, among the thick stems of the willows, and maintained their positions. Even at the highest (90 cm s−1) nominal flume velocities, their estimated swimming velocities were only 35.6 cm s−1, within the bottom 15 cm of the water column. This resulted in unchanged energetic costs, compared with those estimated at lower nominal water velocities. The use of vegetated (e.g., with sandbar willow common to the riparian zone) floodplains, rather than non-vegetated ones, can potentially provide energy-saving, growth-promoting daytime habitat for migrating juvenile salmonids during river-flow periods that include floodplain inundation.

Leveraging Delta Smelt Monitoring for Detecting Juvenile Chinook Salmon in the San Francisco Estuary

Monitoring is an essential component in ecosystem management, and leveraging existing data sources for multiple species of interest can be one effective way to enhance information for management agencies. Here, we analyzed juvenile Chinook Salmon (Oncorhynchus tshawytscha) bycatch data that has been collected by the recently established Enhanced Delta Smelt Monitoring program (EDSM), a survey designed to estimate the abundance and distribution of the San Francisco Estuary’s (estuary) endangered Delta Smelt (Hypomesus transpacificus). Two key aspects of the EDSM program distinguish it from other fish surveys in the estuary: a stratified random sampling design and the spatial scale of its sampling effort. We integrated the EDSM data set with other existing surveys in the estuary, and used an occupancy model to assess differences in the probability of detecting Delta Smelt across gear types. We saw no large-scale differences in size selectivity, and while detection probability varied among gear types, cumulative detection probability for EDSM was comparable to other surveys because of the program’s use of replicate tows. Based on our occupancy model and sampling effort in the estuary during spring of 2017 and 2018, we highlighted under-sampled regions that saw improvements in monitoring coverage from EDSM. Our analysis also revealed that each sampling method has its own benefits and constraints. Although the use of random sites with replicates, as conducted by EDSM, can provide more statistically robust abundance estimates relative to traditional methods, the use of fixed stations and simple methods such as beach seining may provide a more cost-effective way to monitor salmon occurrence in certain regions of the estuary. Leveraging the strengths of each survey’s method can enable stronger inferences on salmon abundance and distribution. Careful consideration of these trade-offs is crucial as the management agencies of the estuary continue to adapt and improve their monitoring programs.

Leveraging Delta Smelt Monitoring for Detecting Juvenile Chinook Salmon in the San Francisco Estuary

Monitoring is an essential component in ecosystem management, and leveraging existing data sources for multiple species of interest can be one effective way to enhance information for management agencies. Here, we analyzed juvenile Chinook Salmon (Oncorhynchus tshawytscha) bycatch data that has been collected by the recently established Enhanced Delta Smelt Monitoring program (EDSM), a survey designed to estimate the abundance and distribution of the San Francisco Estuary’s (estuary) endangered Delta Smelt (Hypomesus transpacificus). Two key aspects of the EDSM program distinguish it from other fish surveys in the estuary: a stratified random sampling design and the spatial scale of its sampling effort. We integrated the EDSM data set with other existing surveys in the estuary, and used an occupancy model to assess differences in the probability of detecting Delta Smelt across gear types. We saw no large-scale differences in size selectivity, and while detection probability varied among gear types, cumulative detection probability for EDSM was comparable to other surveys because of the program’s use of replicate tows. Based on our occupancy model and sampling effort in the estuary during spring of 2017 and 2018, we highlighted under-sampled regions that saw improvements in monitoring coverage from EDSM. Our analysis also revealed that each sampling method has its own benefits and constraints. Although the use of random sites with replicates, as conducted by EDSM, can provide more statistically robust abundance estimates relative to traditional methods, the use of fixed stations and simple methods such as beach seining may provide a more cost-effective way to monitor salmon occurrence in certain regions of the estuary. Leveraging the strengths of each survey’s method can enable stronger inferences on salmon abundance and distribution. Careful consideration of these trade-offs is crucial as the management agencies of the estuary continue to adapt and improve their monitoring programs.