Early Life History of Fishes in the San Francisco Estuary and Watershed

2004 ◽  
Keyword(s):  
San Francisco ◽  
Chinook Salmon ◽  
Reference Group ◽  
Central Valley ◽  
Study Groups ◽  
San Francisco Estuary ◽  
Study Group ◽  
First Feeding ◽  
Back Calculation ◽  
Juvenile Chinook

<em>Abstract.</em>—We compared two approaches to back-calculation with otolith microstructure to develop a method for accurately estimating growth rates of juvenile fall-run Chinook salmon <em>Oncorhynchus tshawytscha </em>in California’s Central Valley. Total otolith width was a strong determinant of fork length (FL) in linear regressions used to determine the <em>y</em>-intercept in the fish size–otolith size relationship in two study groups of Chinook salmon. The Fraser-Lee back-calculation model estimated FL at first feeding in both study groups that did not differ significantly from lengths of first-feeding Chinook salmon in a reference group. In comparison, the biological-intercept method produced back-calculated lengths that were significantly greater in one study group than lengths of first-feeding Chinook salmon in the reference group. Chinook salmon emergence dates, estimated from counts of daily growth increments beyond the first-feeding check, corresponded with observed emergence periods in the river and hatchery populations from which the study groups were sampled. Size-at-age relationships were well described by a power function in both study groups, where mean FL over time approached an apparent asymptote at approximately 80 mm after 90 d postemergence. Growth rate estimates, using back-calculated size from the Fraser-Lee model, averaged 0.50 mm/d in one study group and 0.43 mm/d in the other study group. These estimates fell within the range of previous growth rate estimates for juvenile Chinook salmon in Central Valley riverine, floodplain, and delta environments and were about 2.5 times higher on average than an estimate for the San Francisco Estuary and about 2.3 times lower on average than estimates from the Strait of Georgia. We discuss the utility of otolith microstructure to not only estimate growth rates, but also to reconstruct emergence-date distributions in cohorts of emigrating juvenile Chinook salmon for stock identification purposes.

scholarly journals Managed Wetlands Can Benefit Juvenile Chinook Salmon in a Tidal Marsh

2021 ◽  
Author(s):  
Nicole M. Aha ◽  
Peter B. Moyle ◽  
Nann A. Fangue ◽  
Andrew L. Rypel ◽  
John R. Durand
Keyword(s):  
San Francisco ◽  
Growth Rates ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Nursery Habitat ◽  
San Francisco Estuary ◽  
Rice Fields ◽  
Fish Growth ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook

AbstractLoss of estuarine and coastal habitats worldwide has reduced nursery habitat and function for diverse fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Underutilized off-channel habitats such as flooded rice fields and managed ponds present opportunities for improving rearing conditions and increasing habitat diversity along migratory corridors. While experiments in rice fields have shown enhanced growth rates of juvenile fishes, managed ponds are less studied. To evaluate the potential of these ponds as a nursery habitat, juvenile Chinook salmon (~ 2.8 g, 63 mm FL) were reared in cages in four contrasting locations within Suisun Marsh, a large wetland in the San Francisco Estuary. The locations included a natural tidal slough, a leveed tidal slough, and the inlet and outlet of a tidally muted managed pond established for waterfowl hunting. Fish growth rates differed significantly among locations, with the fastest growth occurring near the outlet in the managed pond. High zooplankton biomass at the managed pond outlet was the best correlate of salmon growth. Water temperatures in the managed pond were also cooler and less variable compared to sloughs, reducing thermal stress. The stress of low dissolved oxygen concentrations within the managed pond was likely mediated by high concentrations of zooplankton and favorable temperatures. Our findings suggest that muted tidal habitats in the San Francisco Estuary and elsewhere could be managed to promote growth and survival of juvenile salmon and other native fishes.

scholarly journals Leveraging Delta Smelt Data for Juvenile Chinook Salmon Monitoring in the San Francisco Estuary

2020 ◽  
Author(s):  
Brian Mahardja ◽  
Lara Mitchell ◽  
Michael Beakes ◽  
Catherine Johnston ◽  
Cory Graham ◽  
...  
Keyword(s):  
San Francisco ◽  
Chinook Salmon ◽  
Detection Probability ◽  
San Francisco Estuary ◽  
Sampling Effort ◽  
Occupancy Model ◽  
Delta Smelt ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook ◽  
Abundance And Distribution

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 when making management decisions. 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&rsquo;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 dataset with other existing surveys in the estuary and used an occupancy model to assess detection probability differences 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 due to the program&rsquo;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 due to 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 seine may provide a more cost-effective way of monitoring salmon occurrence in certain regions of the estuary. Stronger inference on salmon abundance and distribution can be made by leveraging the strengths of each survey&rsquo;s method. Careful consideration of these trade-offs is crucial as the management agencies of the estuary continue to adapt and improve their monitoring programs.

scholarly journals Leveraging Delta Smelt Data for Juvenile Chinook Salmon Monitoring in the San Francisco Estuary

2020 ◽  
Author(s):  
Brian Mahardja ◽  
Lara Mitchell ◽  
Michael Beakes ◽  
Catherine Johnston ◽  
Cory Graham ◽  
...  
Keyword(s):  
San Francisco ◽  
Chinook Salmon ◽  
Detection Probability ◽  
San Francisco Estuary ◽  
Sampling Effort ◽  
Occupancy Model ◽  
Delta Smelt ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook ◽  
Abundance And Distribution

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 when making management decisions. 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 (estuary) endemic and 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 dataset with other existing surveys in the estuary and used an occupancy model to assess detection probability differences 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 due to the program&rsquo;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 due to 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 seine may provide a more cost-effective way of monitoring salmon occurrence at certain regions of the estuary. Stronger inference on salmon abundance and distribution can be made by leveraging the strengths of each survey&rsquo;s method. Careful consideration of these trade-offs and key monitoring objectives is crucial as the management agencies of the estuary continue to adapt and improve their monitoring programs.

scholarly journals Reconsidering the Estimation of Salmon Mortality Caused by the State and Federal Water Export Facilities in the Sacramento–San Joaquin Delta, San Francisco Estuary

2020 ◽  
Vol 18 (3) ◽  
Author(s):  
Andrew Jahn ◽  
William Kier
Keyword(s):  
San Francisco ◽  
Chinook Salmon ◽  
Near Field ◽  
San Francisco Estuary ◽  
The State ◽  
Juvenile Salmon ◽  
Small Fish ◽  
Accuracy And Precision ◽  
Behavioral Barriers ◽  
Existing Data

Combined water exports from Old River in the south end of California’s San Francisco Estuary (estuary) by state and federal pumping facilities entrain small fishes, including out-migrating juvenile salmon. Both export projects have fish salvage facilities that use behavioral barriers (louvers) in combination with screens to guide fish into collection areas from which they are trucked to release points in the western Delta. Sacramento River-origin Chinook Salmon are regularly taken in the projects’ fish salvage operations. Survival has been estimated within the boundaries of both intake structures, but not in Old River. Prevailing methods for estimating fish losses are based on studies of louver efficiency, near-field survival at the state facility, and assumed survival at the federal facility. The efficiency of the fish salvage operations is affected by several factors, including intake velocity, debris build-up on the louvers and trash racks, and by the omnipresence of predators in front of and within the fish guidance structures. Analysis of existing data suggests that under average conditions, juvenile salmon survive entrainment into the forebay of the state facility at a rate of less than 10%. There is no evidence for better survival at the federal facility. We found no data on predation outside of either the state’s forebay or the federal trash boom, structures which are separated by an approximately 2-km reach of Old River where predation on small fish is thought to be intense. We suggest an improvement to the existing loss estimation, and discuss some features of the studies needed to increase its accuracy and precision.

Energy dynamics and growth of Chinook salmon (Oncorhynchus tshawytscha) from the Central Valley of California during the estuarine phase and first ocean year

2010 ◽  
Vol 67 (10) ◽  
pp. 1549-1565 ◽  
Author(s):  
R. Bruce MacFarlane
Keyword(s):  
San Francisco ◽  
Chinook Salmon ◽  
Climate Models ◽  
Oncorhynchus Tshawytscha ◽  
Energy Content ◽  
Central Valley ◽  
Energy Dynamics ◽  
Period Data ◽  
Energy Gains ◽  
Engraulis Mordax

The greatest rates of energy accumulation and growth in subyearling Chinook salmon ( Oncorhynchus tshawytscha ) occurred during the first month following ocean entry, supporting the importance of this critical period. Data from an 11-year study in the coastal ocean off California and the San Francisco Estuary revealed that juvenile salmon gained 3.2 kJ·day–1 and 0.8 g·day–1, representing 4.3%·day–1 and 5.2% day–1, respectively, relative to estuary exit values. Little gain in energy (0.28 kJ·day–1) or size (0.07 g·day–1) occurred in the estuary, indicating that the nursery function typically ascribed to estuaries can be deferred to initial ocean residence. Calculated northern anchovies ( Engraulis mordax ) equivalents to meet energy gains were one anchovy per day in the estuary (8% body weight·day–1) and about three per day immediately following ocean entry (15% body weight·day–1). Energy content in the estuary was positively related to higher salinity and lower freshwater outflow, whereas in the ocean, cooler temperatures, lower sea level, and greater upwelling resulted in greater gains. These results suggest that greater freshwater flows, warmer sea temperatures, and reduced or delayed upwelling, all of which are indicated by some (but not all) climate models, will likely decrease growth of juvenile Chinook salmon, leading to reduced survival.

Can behavioral fish-guidance devices protect juvenile Chinook salmon (Oncorhynchus tshawytscha) from entrainment into unscreened water-diversion pipes?

2014 ◽  
Vol 71 (8) ◽  
pp. 1209-1219 ◽  
Author(s):  
Timothy D. Mussen ◽  
Oliver Patton ◽  
Dennis Cocherell ◽  
Ali Ercan ◽  
Hossein Bandeh ◽  
...  
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Central Valley ◽  
Large River ◽  
Water Diversion ◽  
Small Scale ◽  
Fish School ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook ◽  
And Behavior

Entrainment through water-diversion structures is a major passage challenge for fishes in watersheds worldwide. Behavioral guidance devices may be effective in passing fish by diversion inlets, thereby decreasing entrainment without reducing water-diversion rates, but data on their effectiveness is limited. In California’s central valley, out-migrating Chinook salmon (Oncorhynchus tshawytscha) are a species at risk for entrainment through unscreened, small-scale water-diversion pipes. Therefore, we tested entrainment susceptibility and behavior of juvenile Chinook salmon in a large-river-simulation flume at a “river” velocity of 0.15 m·s–1 with a 0.46 m diameter pipe diverting water at 0.57 m3·s–1, during the day and night. Compared with control conditions (no fish deterrent devices present), mean fish entrainment increased by 61% (day) and 43% (night) when underwater strobe lights were active, decreased by 30% when using a metal vibrating (12 Hz) ring during the night, and was unaffected by velocity cap attachments. Fish entrainments started at water velocities of 0.8 m·s–1 and decreased by 54% from spring to summer, possibly resulting from decreased pipe-passage frequency and smaller fish-school sizes. Our findings suggest that substantial entrainment can occur if fish repeatedly pass within 1.5 m of active unscreened diversions, with an estimated 50% of fish lost after encountering 18 pipes in spring and 50 pipes in summer.

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

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Brian Mahardja ◽  
Lara Mitchell ◽  
Michael Beakes ◽  
Catherine Johnston ◽  
Cory Graham ◽  
...  
Keyword(s):  
San Francisco ◽  
Chinook Salmon ◽  
Detection Probability ◽  
Sampling Effort ◽  
Data Set ◽  
Occupancy Model ◽  
Delta Smelt ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook ◽  
Abundance And Distribution

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.

Differences in the onset of salinity tolerance between juvenile chinook salmon from two coastal Oregon river systems

1995 ◽  
Vol 52 (3) ◽  
pp. 623-630 ◽  
Author(s):  
Karen Young Kreeger
Keyword(s):  
Salinity Tolerance ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Sodium Concentration ◽  
Minimum Size ◽  
Plasma Sodium ◽  
Juvenile Chinook Salmon ◽  
First Feeding ◽  
Juvenile Chinook ◽  
Interpopulational Differences

Trask River juvenile chinook salmon (Oncorhynchus tshawytscha) rear in an estuarine environment, whereas Rogue River juveniles rear in a riverine environment, suggesting these populations differ in the ontogeny of smolting physiology. To study differences in the onset of salinity tolerance between these populations, I reared individuals from the Trask and Rogue rivers (Oregon) in a common environment and monitored changes in their physiology throughout their first 5–6 months. Trask fish were able to tolerate oceanic salinities at a smaller size and younger age than Rogue juveniles. Fifty days post-first feeding and at < 2 g 65% of Trask juveniles survived in 32 ppt compared with 40% of Rogue juveniles. Trask juveniles also maintained their water balance in 32 ppt seawater relative to freshwater at 50 days post-first feeding compared with 80 days for Rogue juveniles. Plasma sodium concentration indicated that both populations did not competently osmoregulate until approximately 108 days post-first feeding. Although the minimum size and age of salinity tolerance depended on which indicator of tolerance was chosen for study, physiological parameters suggested interpopulational differences in the timing of the onset of salinity tolerance.

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