No abstract

Recent reductions in the run sizes of Chinook Salmon Oncorhynchus tshawytscha in Southeast Alaska have resulted in social and economic hardships within the region. For Pacific salmon, including Chinook Salmon, brood year (BY) strength may be determined by size‐selective processes that occur during early marine residence. However, the relative importance of freshwater versus marine growth in determining recruitment success is unknown. We conducted a scale‐based retrospective analysis to examine the relative effects of freshwater and marine growth on survival to the age of reproduction for female Chinook Salmon by BY in the Taku (BYs 1979–1985, 1990–1999, 2002–2004) and Unuk (BYs 1981–1983, 1986–1988, 1994–2003, 2005–2006) rivers located in Southeast Alaska. First‐year marine growth of Chinook Salmon was positively related to total return, productivity (returns per spawner), and marine survival for stocks from both systems. In the Taku River, growth during the third year at sea was positively related to marine survival. Annual growth of Taku River Chinook Salmon was correlated with previous growth through the second year at sea; however, no correlations were detected between adjacent growth zones of Unuk River fish. These findings suggest that current declines in Chinook Salmon abundance in Southeast Alaska is attributed to changes in growth conditions during the first year at sea.

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.

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.

Resource managers rely on large‐scale flow and habitat enhancement actions to support sensitive species in the San Francisco Bay–Delta. The effects of these actions on target species and ecosystems are largely unknown. In 2018, we implemented an ecosystem‐scale experiment to reduce salinity and improve access to high‐quality habitat in Suisun Marsh, California, for Endangered Species Act‐listed Delta Smelt Hypomesus transpacificus. The action included a release of approximately 46 million m3 of additional flow in conjunction with the operation of a novel water management facility, the Suisun Marsh Salinity Control Gates. This experimental action resulted in more low‐salinity habitat in Suisun Marsh than would have been present as compared to similar historical low‐flow summer conditions. We evaluated the effect of decreasing salinity on the species assemblage in Suisun Marsh using a combination of ordination analyses and circular statistics. We focused this analysis on long‐term monitoring data collected within Suisun Marsh during July and August and found that the aquatic community changed significantly in small sloughs but not large‐slough habitat in response to the Suisun Marsh action. The assemblage shift from July to August 2018 differed from historical trends in both slough sizes, albeit not significantly in large‐slough habitat. Specifically, we observed (1) a shift in California bay shrimp Crangon franciscorum and Striped Bass Morone saxatilis abundance like that occurring in low‐salinity, wet water year types; and (2) an uncharacteristic seasonal decline in Black Sea jellyfish Maeotias marginata. We posit that the observed community changes were driven by a combination of behavioral responses to lower‐salinity conditions and physical displacement by directional flow resulting from the flow management action.