Patricia L. Brandes

Estimating Survival and Migration Route Probabilities of Juvenile Chinook Salmon in the Sacramento–San Joaquin River Delta

Abstract Juvenile Chinook salmon Oncorhynchus tshawytscha emigrating from natal tributaries of the Sacramento River must negotiate the Sacramento–San Joaquin River Delta, a complex network of natural and man-made channels linking the Sacramento River with San Francisco Bay. Natural processes and water management actions affect the fractions of the population using the different migration routes through the delta and survival within those routes. However, estimating these demographic parameters is difficult using traditional mark–recapture techniques, which depend on the physical recapture of fish (e.g., coded wire tags). Thus, our goals were to (1) develop a mark–recapture model to explicitly estimate the survival and migration route probabilities for each of four migration routes through the delta, (2) link these route-specific probabilities to population-level survival, and (3) apply this model to the first available acoustic telemetry data of smolt migration through the delta. The point estimate of sur...

Hierarchical Modeling of Juvenile Chinook Salmon Survival as a Function of Sacramento–San Joaquin Delta Water Exports

Abstract A multiyear study was carried out in the Sacramento–San Joaquin Delta system to examine the relationship between the survival of out-migrating Chinook salmon Oncorhynchus tshawytscha and the amount of water exported from the system by the two major pumping stations in the southern portion of the delta. Paired releases of groups of coded-wire-tagged juvenile late-fall-run Chinook salmon were made at two locations in the delta, one in the main-stem Sacramento River and one in the interior portion of the delta where they were more likely to be directly affected by the pumping stations. Shortly after release, the fish were recovered downstream by a midwater trawl, and over a 2–4-year period the fish were recovered in ocean fishery catches and spawning ground surveys. A Bayesian hierarchical model for the recoveries was fit that explicitly accounted for the between-release variation in survival and capture probabilities as well as the sampling variation in the recoveries. The survival of the interior ...

Route Use and Survival of Juvenile Chinook Salmon through the San Joaquin River Delta

Abstract The survival of juvenile Chinook Salmon through the lower San Joaquin River and Sacramento–San Joaquin River Delta in California was estimated using acoustic tags in the spring of 2009 and 2010. The focus was on route use and survival within two major routes through the Delta: the San Joaquin River, which skirts most of the interior Delta to the east, and the Old River, a distributary of the San Joaquin River leading to federal and state water export facilities that pump water out of the Delta. The estimated probability of using the Old River route was 0.47 in both 2009 and 2010. Survival through the southern (i.e., upstream) portion of the Delta was very low in 2009, estimated at 0.06, and there was no significant difference between the Old River and San Joaquin River routes. Estimated survival through the Southern Delta was considerably higher in 2010 (0.56), being higher in the Old River route than in the San Joaquin route. Total estimated survival through the entire Delta (estimated only in 2...

Sensitivity of survival to migration routes used by juvenile Chinook salmon to negotiate the Sacramento-San Joaquin River Delta

Populations of juvenile salmon emigrating from natal rivers to the ocean must often traverse different migratory pathways that may influence survival. In regulated rivers, migration routes may consist of a network of channels such as in the Sacramento-San Joaquin River Delta, or of different passage structures at hydroelectric dams (e.g., turbines or spillways). To increase overall survival, management actions in such systems often focus on altering the migration routing of fish to divert them away from low-survival routes and towards high-survival routes. Here, we use a 3-year data set of route-specific survival and movement of juvenile Chinook salmon in the Sacramento-San Joaquin Delta to quantify the sensitivity of survival to changes in migration routing at two major river junctions in the Sacramento River. Our analysis revealed that changes in overall survival in response to migration routing at one river junction depended not only differences in survival among alternative routes, but also on migration routing at the other river junction. Diverting fish away from a low-survival route at the downstream river junction increased population survival by less than expected, given the difference in survival among routes, because part of the population used an alternative migration route at the upstream river junction. We also show that management actions that influence only migration routing will likely increase survival by less than actions that alter both migration routing and route-specific survival. Our analysis provides an analytical framework to help fisheries managers quantify the suite of management actions likely to maximize increases in population level survival.

Migration route selection of juvenile Chinook salmon at the Delta Cross Channel, and the role of water velocity and individual movement patterns

We examined movement tracks of ultrasonic-tagged juvenile Chinook salmon (Oncorhynchus tshawyscha) smolts at the juncture of two migratory pathways. This migratory juncture occurs where the Delta Cross Channel splits from the Sacramento River in California’s Sacramento–San Joaquin Delta. Smolt tracks were analyzed to compare the importance of river flow and individual parameters in migratory route selection. The two routes differ significantly in smolt survival probabilities (Perry et al. N Am J Fish Manag 30:142–156, 2010), thus a clearer understanding of the variables contributing to route selection will be valuable for management of this declining species. A comparison of the two migratory groups showed that fish remaining within the Sacramento River: 1) Encountered the migratory juncture when river water velocities were much higher than those in the Delta Cross Channel (p < 0.0001), 2) showed more direct swimming paths (p = 0.03) and 3) migrated at higher speeds (p = 0.04). Logistic regression models showed that the ratio of mean water velocity between the two routes was a much stronger predictor of ultimate route selection than any other variable tested. However, parameters for both the lateral position of smolts within the river and smolt size added predictive power to the final model. Our results suggest that river flow remains the most important variable for predicting smolt migration route, but note that knowledge of individual smolt attributes and movement patterns can increase our predictive ability.

Effect of Tides, River Flow, and Gate Operations on Entrainment of Juvenile Salmon into the Interior Sacramento–San Joaquin River Delta

AbstractJuvenile Chinook Salmon Oncorhynchus tshawytscha emigrating from natal tributaries of the Sacramento River, California, must negotiate the Sacramento–San Joaquin River Delta (hereafter, the Delta), a complex network of natural and man-made channels linking the Sacramento River with San Francisco Bay. Fish that enter the interior and southern Delta—the region to the south of the Sacramento River where water pumping stations are located—survive at a lower rate than fish that use alternative migration routes. Consequently, total survival decreases as the fraction of the population entering the interior Delta increases, thus spurring management actions to reduce the proportion of fish that are entrained into the interior Delta. To better inform management actions, we modeled entrainment probability as a function of hydrodynamic variables. We fitted alternative entrainment models to telemetry data that identified when tagged fish in the Sacramento River entered two river channels leading to the interio...

Adjusting survival estimates for premature transmitter failure: a case study from the Sacramento-San Joaquin Delta

In telemetry studies, premature tag failure causes negative bias in fish survival estimates because tag failure is interpreted as fish mortality. We used mark-recapture modeling to adjust estimates of fish survival for a previous study where premature tag failure was documented. High rates of tag failure occurred during the Vernalis Adaptive Management Plan’s (VAMP) 2008 study to estimate survival of fall-run Chinook salmon (Oncorhynchus tshawytscha) during migration through the San Joaquin River and Sacramento-San Joaquin Delta, California. Due to a high rate of tag failure, the observed travel time distribution was likely negatively biased, resulting in an underestimate of tag survival probability in this study. Consequently, the bias-adjustment method resulted in only a small increase in estimated fish survival when the observed travel time distribution was used to estimate the probability of tag survival. Since the bias-adjustment failed to remove bias, we used historical travel time data and conducted a sensitivity analysis to examine how fish survival might have varied across a range of tag survival probabilities. Our analysis suggested that fish survival estimates were low (95% confidence bounds range from 0.052 to 0.227) over a wide range of plausible tag survival probabilities (0.48–1.00), and this finding is consistent with other studies in this system. When tags fail at a high rate, available methods to adjust for the bias may perform poorly. Our example highlights the importance of evaluating the tag life assumption during survival studies, and presents a simple framework for evaluating adjusted survival estimates when auxiliary travel time data are available.