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

Brian Mahardja,Cory Graham,Catherine Johnston,Bryan Matthias,Pascale Goertler,Michael Beakes,Lara Mitchell,Gonzalo Castillo,Denise Barnard

doi:10.15447/sfews.2021v19iss1art2

Abstract

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.

Highlights

Estuaries are among the most important, heavily affected, and degraded ecosystems on Earth
Beach seine monitoring programs consistently captured a large percentage of the monthly catch (Table 2), with Delta Juvenile Fish Monitoring Program (DJFMP) and Yolo Bypass sampling accounting for approximately 16.1% and 7.2% of the total salmon catch, respectively
Results from our model indicate that certain methods are more cost-effective at detecting juvenile Chinook Salmon if the species is present in some areas

Summary

Introduction

Estuaries are among the most important, heavily affected, and degraded ecosystems on Earth. The majority of the human population lives in coastal areas around estuaries, in part because estuaries are some of the most biologically productive areas in the world (Kennish 2002) and provide valuable ecosystem services (Lotze et al 2006; Borja et al 2010). The majority of the estuary’s historical wetlands have been drained, tidal rivers have been channelized, and many reservoirs have been constructed on rivers that flow into the estuary. These system alterations have profoundly affected a number of endemic aquatic species and their habitats in the estuary (Stevens and Miller 1983; Nichols et al 1986; Cloern et al 2016)

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Discussion

Conclusion