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.

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 Ancient DNA Analysis of Archaeological Specimens Extends Chinook Salmon’s Known Historic Range to San Francisco Bay and Its Southernmost Watershed

2020 ◽  
Author(s):  
Richard B. Lanman ◽  
Linda Hylkema ◽  
Cristie M. Boone ◽  
Brian Alleé ◽  
Roger O. Castillo ◽  
...  
Keyword(s):  
Native American ◽  
San Francisco ◽  
Ancient Dna ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Dna Analysis ◽  
Oncorhynchus Tshawytscha ◽  
San Francisco Bay ◽  
Bay Area ◽  
Guadalupe River

Understanding a species’ historic range guides contemporary management and habitat restoration. Chinook salmon ( Oncorhynchus tshawytscha ) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropomorphic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Using ichthyofaunal analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara circa 1781-1834 CE, 86 salmonid vertebrae were identified. Ancient DNA sequencing identified three of these as from Chinook salmon and the remainder from steelhead trout. These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their historic range to include San Francisco Bay’s southernmost watershed.

Analysis of microsatellite DNA resolves genetic structure and diversity of chinook salmon (Oncorhynchus tshawytscha) in California’s Central Valley

2000 ◽  
Vol 57 (5) ◽  
pp. 915-927 ◽  
Author(s):  
Michael A Banks ◽  
Vanessa K Rashbrook ◽  
Marco J Calavetta ◽  
Cheryl A Dean ◽  
Dennis Hedgecock
Keyword(s):  
Genetic Structure ◽  
Chinook Salmon ◽  
Microsatellite Dna ◽  
Life Histories ◽  
Oncorhynchus Tshawytscha ◽  
Random Mating ◽  
Central Valley ◽  
Microsatellite Dna Markers ◽  
Maximum Likelihood Methods ◽  
Genetic Structure And Diversity

We use 10 microsatellite DNA markers to assess genetic diversity within and among the four runs (winter, spring, fall, and late fall) of chinook salmon (Oncorhynchus tshawytscha) in California's Central Valley. Forty-one population samples are studied, comprising naturally spawning and hatchery stocks collected from 1991 through 1997. Maximum likelihood methods are used to correct for kinship in juvenile samples and run admixture in adult samples. Through simulation, we determine the relationship between sample size and number of alleles observed at polymorphic microsatellite markers. Most samples have random-mating equilibrium proportions of single and multilocus genotypes. Temporal and spatial genetic heterogeneity is minimal among samples within subpopulations. An FST of 0.082 among subpopulations, however, indicates substantial divergence among runs. Thus, with the exception of our discovery of two distinct lineages of spring run, genetic structure accords with the diverse chinook life histories seen in the Central Valley and provides a means for discrimination of protected populations.

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 Spatial and temporal covariability in early ocean survival of Chinook salmon (Oncorhynchus tshawytscha) along the west coast of North America

2014 ◽  
Vol 71 (7) ◽  
pp. 1671-1682 ◽  
Author(s):  
D. Patrick Kilduff ◽  
Louis W. Botsford ◽  
Steven L. H. Teo
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Survival Rates ◽  
Central Valley ◽  
Vancouver Island ◽  
Regional Patterns ◽  
Migration Patterns ◽  
The Pacific ◽  
Spatial Coverage ◽  
Correlation Scale

Abstract Knowledge of the spatial and temporal extent of covariation in survival during the critical ocean entry stage will improve our understanding of how changing ocean conditions influence salmon productivity and management. We used data from the Pacific coastwide coded-wire tagging program to investigate local and regional patterns of ocean survival of Chinook salmon (Oncorhynchus tshawytscha) from the Central Valley of California to southeastern Alaska from 1980–2006. Ocean survival of fish migrating as subyearlings covaried strongly from Vancouver Island to California. Short-term correlations between adjacent regions indicated this covariability increased, beginning in the early 1990s. Chinook salmon survivals exhibited a larger spatial scale of variability (50% correlation scale: 706 km) than those reported for other northeast Pacific Ocean salmon. This scale is similar to that of environmental variables related to ecosystem productivity, such as summer upwelling (50% correlation scale: 746 km) and sea surface temperature (50% correlation scale: 500–600 km). Chinook salmon ocean survival rates from southeastern Alaska and south of Vancouver Island were not inversely correlated, in contrast to earlier observations based on catch data, but note that our data differ in temporal and spatial coverage from those studies. The increased covariability in Chinook salmon ocean survival suggests that the marine phase contributes little to the reduction in risk across populations attributable to the portfolio effect. In addition, survival of fish migrating as yearlings from the Columbia River covaried with Chinook salmon survival from the northernmost regions, consistent with our understanding of their migration patterns.

Separable Virtual Population Analysis of Pacific Salmon with Application to Marked Chinook Salmon, Oncorhynchus tshawytscha, from California's Central Valley

1987 ◽  
Vol 44 (6) ◽  
pp. 1213-1220 ◽  
Author(s):  
Robert G. Kope
Keyword(s):  
Chinook Salmon ◽  
Goodness Of Fit ◽  
Oncorhynchus Tshawytscha ◽  
Pacific Salmon ◽  
Population Analysis ◽  
Central Valley ◽  
Virtual Population Analysis ◽  
Virtual Population ◽  
California's Central Valley ◽  
California’S Central Valley

A separable virtual population analysis model is developed for Pacific salmon which utilizes aged catch and spawning escapement data. This model is applied to marked chinook salmon, Oncorhynchus tshawytscha, from California's Central Valley hatcheries using weighted least squares criteria for goodness of fit. Structural inadequacies of the model apparently produce discrepancies between predicted values and observed data that are of about the same magnitude as the observational errors in estimating the recoveries of marked fish. Some of the inadequacy of the model may be due to environmentally induced variability in population parameters, but for the marked fish used in this analysis, some of the variability is probably due to year-to-year variability in hatchery practices. From this analysis it appears that although nominal fishing effort has been relatively stable or even declining in recent years, fishing mortality has been increasing with the exception of 1983 and 1984.

scholarly journals Survival of a threatened salmon is linked to spatial variability in river conditions

2021 ◽  
Author(s):  
Colby L. Hause ◽  
Gabriel P. Singer ◽  
Rebecca A. Buchanan ◽  
Dennis E. Cocherell ◽  
Nann A. Fangue ◽  
...  
Keyword(s):  
Pacific Northwest ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Oncorhynchus Tshawytscha ◽  
Central Valley ◽  
Data Generation ◽  
Habitat Variability ◽  
River Habitat ◽  
San Joaquin River ◽  
The Pacific

AbstractExtirpation of the Central Valley spring-run Chinook Salmon ESU (Oncorhynchus tshawytscha) from the San Joaquin River is emblematic of salmonid declines across the Pacific Northwest. Habitat restoration and fish reintroduction efforts are ongoing, but recent telemetry studies have revealed low outmigration survival of juveniles to the ocean. Previous investigations have focused on modeling survival relative to river discharge and geographic regions, but have largely overlooked the effects of habitat variability. To evaluate the link between environmental conditions and survival of juvenile spring-run Chinook Salmon, we combined high spatial resolution habitat mapping approaches with acoustic telemetry along a 150 km section of the San Joaquin River during the spring of 2019. While overall outmigration survival was low (5%), our habitat-based classification scheme described variation in survival of acoustic-tagged smolts better than other candidate models based on geography or distance. There were two regional mortality sinks evident along the longitudinal profile of the river, revealing poor survival in areas that shared warmer temperatures but that diverged in chlorophyll-α, fDOM, turbidity and dissolved oxygen levels. These findings demonstrate the value of integrating river habitat classification frameworks to improve our understanding of survival dynamics of imperiled fish populations. Importantly, our data generation and modeling methods can be applied to a wide variety of fish species that transit heterogeneous and diverse habitat types.

scholarly journals Evaluation of Long-Term Mark-Recapture Data for Estimating Abundance of Juvenile Fall-Run Chinook Salmon on the Stanislaus River from 1996 to 2017

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Tyler Pilger ◽  
Matthew Peterson ◽  
Dana Lee ◽  
Andrea Fuller ◽  
Doug Demko
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Estimation Method ◽  
Central Valley ◽  
Mark Recapture ◽  
Important Species ◽  
Trap Efficiency ◽  
Monitoring Programs ◽  
Abundance Estimates

Conservation and management of culturally and economically important species rely on monitoring programs to provide accurate and robust estimates of population size. Rotary screw traps (RSTs) are often used to monitor populations of anadromous fish, including fall-run Chinook Salmon (Oncorhynchus tshawytscha) in California’s Central Valley. Abundance estimates from RST data depend on estimating a trap's efficiency via mark-recapture releases. Because efficiency estimates are highly variable and influenced by many factors, abundance estimates can be highly uncertain. An additional complication is the multiple accepted methods for how to apply a limited number of trap efficiency estimates, each from discrete time-periods, to a population’s downstream migration, which can span months. Yet, few studies have evaluated these different methods, particularly with long-term monitoring programs. We used 21 years of mark-recapture data and RST catch of juvenile fall-run Chinook Salmon on the Stanislaus River, California, to investigate factors associated with trap efficiency variability across years and mark-recapture releases. We compared annual abundance estimates across five methods that differed in treatment of trap efficiency (stratified versus modeled) and statistical approach (frequentist versus Bayesian) to assess the variability of estimates across methods, and to evaluate whether method affected trends in estimated abundance. Consistent with short-term studies, we observed negative associations between estimated trap efficiency and river discharge as well as fish size. Abundance estimates were robust across all methods, frequently having overlapping confidence intervals. Abundance trends, for the number of increases and decreases from year to year, did not differ across methods. Estimated juvenile abundances were significantly related to adult escapement counts, and the relationship did not depend on estimation method. Understanding the sources of uncertainty related to abundance estimates is necessary to ensure that high-quality estimates are used in life cycle and stock-recruitment modeling.

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 Optimizing an eDNA protocol for monitoring endangered Chinook Salmon in the San Francisco Estuary: balancing sensitivity, cost and time

2019 ◽  
Author(s):  
Thiago M. Sanches ◽  
Andrea M. Schreier
Keyword(s):  
Dna Extraction ◽  
San Francisco ◽  
Chinook Salmon ◽  
Magnetic Beads ◽  
Oncorhynchus Tshawytscha ◽  
Environmental Dna ◽  
San Francisco Estuary ◽  
Time Cost ◽  
Dna Yield ◽  
Pcr Inhibitor

AbstractEnvironmental DNA (eDNA) analysis has gained traction as a precise and cost effective method for species and waterways management. To date, publications on eDNA protocol optimization have focused primarily on DNA yield. Therefore, it has not been possible to evaluate the cost and speed of specific components of the eDNA protocol, such as water filtration and DNA extraction method when designing or choosing an eDNA pipeline. At the same time, these two parameters are essential for the experimental design of a project. Here we evaluate and rank different eDNA protocols in the context of Chinook salmon (Oncorhynchus tshawytscha) eDNA detection in an aquatic environment, the San Francisco Estuary. We present a comprehensive evaluation of multiple eDNA protocol parameters, balancing time, cost and DNA yield. For estuarine waters, which are challenging for eDNA studies due to high turbidity, variable salinity, and the presence of PCR inhibitors, we find that a protocol combining glass filters and magnetic beads, along with an extra step for PCR inhibitor removal, is the method that best balances time, cost, and yield. In addition, we provide a generalized decision tree for determining the optimal eDNA protocol for other studies on aquatic systems. Our findings should be applicable to most aquatic environments and provide a clear guide for determining which eDNA pipeline should be used for a given environmental condition.Author SummaryThe use of environmental DNA (eDNA) analysis for monitoring wildlife has steadily grown in recent years. Though, due to differences in the ecology of the environment studied and the novelty of the technique, eDNA currently shows a lack of standards compared to other fields. Here we take a deep look into each step of an eDNA assay, looking at common protocols and comparing their efficiencies in terms of time to process the samples, cost and how much DNA is recovered. We then analyze the data to provide a concise interpretation of best practices given different project constraints. For the conditions of the San Francisco Estuary we suggest the use of glass fiber filtration, the use of paramagnetic beads for DNA extraction and the use of a secondary inhibitor removal. We expect our findings to provide better support for managers to decide their standards ahead of project submission not only for estuarine conditions but for other waterine conditions alike.

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