Survival Of Juvenile Chinook Salmon Research Articles

Juvenile Chinook Salmon Survival, Travel Time, and Floodplain Use Relative to Riverine Channels in the Sacramento–San Joaquin River Delta

AbstractFloodplains provide multiple benefits to both resident and migratory fish species, including juvenile Chinook Salmon Oncorhynchus tshawytscha, but direct comparisons of survival during migration through a floodplain versus riverine routes are scarce. The Yolo Bypass is a broad floodplain of the Sacramento River that floods in about 30% of years in response to large, uncontrolled runoff events. We analyzed data from an acoustic telemetry study conducted in winter 2016 to estimate the proportion of tagged juvenile Chinook Salmon entrained from the Sacramento River into the Yolo Bypass and their spatial distribution within the Yolo Bypass. In addition, we compared survival and travel time of Chinook Salmon that migrated through the Yolo Bypass to those migrating via alternative non‐floodplain migration routes at varying stages of a flood event that activated the Yolo Bypass. We found that entrainment into the Yolo Bypass ranged from 1% to 80% among different release groups, with the highest entrainment coinciding with the peak of the March 2016 flooding event. Survival for Chinook Salmon migrating through the Yolo Bypass was similar to survival of those migrating through main‐stem migration routes. At the relatively high flows necessary to enable flooding of the Yolo Bypass, survival estimates varied little among release groups and migration routes. Furthermore, mean daily survival rates for Chinook Salmon migrating through the flooded Yolo Bypass were comparable to those of fish migrating through the other non‐floodplain routes. Median travel times remained relatively constant during various stages of flooding in the Yolo Bypass. This research should help managers to better understand the potential costs and benefits to floodplain restoration and routing of migrating Chinook Salmon into off‐channel habitat.

Experimental Quantification of Piscivore Density and Habitat Effects on Survival of Juvenile Chinook Salmon in a Tidal Freshwater Estuary

Introduction of non-native piscivores has been implicated in the decline of native Chinook Salmon Oncorhynchus tshawytscha via predation during juvenile life stages. However, isolating effects of predation on Chinook Salmon survival is complicated by changes in physical habitat that are often concomitant with non-native piscivore establishment. We performed two field experiments with enclosures deployed in tidal freshwater habitat to quantify effects of non-native Largemouth Bass Micropterus salmoides density and habitat type on the survival and movement behavior of juvenile Chinook Salmon. In experiment one, bass densities were doubled and quadrupled across treatment levels with a baseline value of field-observed densities. In experiment two, three habitat types (dock, submerged aquatic vegetation (SAV), and open water) were tested while bass density was held at the medium (doubled) value. Juvenile Chinook Salmon implanted with passive integrated transponders were released into the enclosures to assess their survival and movement through the treatments over multiple trials. Mark-recapture models indicated that the survival of juvenile Chinook Salmon was reduced in the medium bass density, but not the high-density treatment, when compared to the lowest density value suggesting relationships may be non-linear. The SAV treatment had a well-supported negative effect on juvenile Chinook Salmon survival relative to a dock or open water. Residence time was positively related to bass density. Relationships with a habitat were not consistently different. These results suggest that restoration strategies targeting non-native SAV control could reduce predation on juvenile Chinook Salmon by Largemouth Bass. However, piscivore density manipulation may only be effective over a narrow range of densities.

Low-Lipid Diets Fed at Reduced Ration: Effects on Growth, Body Composition, and Survival of Juvenile Chinook Salmon

Abstract There is a growing demand within research and conservation hatcheries to rear fish that more closely approximate the smaller size and leaner body composition of their wild counterparts. Low-lipid diets may help achieve this goal as they can provide all the nutritional needs of young fish and can lead to slower growth and leaner bodies. We compared growth of Chinook Salmon Oncorhynchus tshawytscha fed three experimental low-lipid diets (11–12, 8–9, 4–6% lipid) at the onset of feeding with a commercially available high-lipid diet (18–20%) and an experimentally formulated high-lipid control (13.9% lipid). After 5 mo on their respective treatments, the size, growth rate, and daily growth index of fish on the commercial diet were significantly higher than those on the three low-lipid diets. We also compared whole-body lipid content across our five diet treatments. Whole-body lipid content was significantly different across the five diets, with fish fed the commercial diet having, on average, an almost twofold higher lipid content over fish fed the lowest lipid diet formulation. We present comparable data from a limited sample of wild juvenile conspecifics as observations. We suggest that low-lipid starter diets can be used to produce healthy fish that more likely emulate some of the variations in size and body composition of wild fish.

Survival of Juvenile Chinook Salmon in the Yolo Bypass and the Lower Sacramento River, California

Author(s): Johnston, Myfanwy E.; Steel, Anna E.; Espe, Matthew; Sommer, Ted; Klimley, A. Peter; Sandstrom, Philip; Smith, David | Abstract: While our knowledge of the range of survival that outmigrating juvenile Chinook Salmon experience in different routes of the Sacramento–San Joaquin Delta has increased in recent years, few studies have focused on their survival during outmigration in the Yolo Bypass, the Delta’s primary floodplain. The Yolo Bypass floodplain provides valuable rearing habitat and growth benefits to juvenile fish in flood years, and efforts are underway to improve access to the Yolo Bypass and the Toe Drain, its perennial navigation channel, under a broader range of flows and river stages than is currently possible. We compared variation in transit time, and estimated survival between different release groups of fish outmigrating through the Yolo Bypass or through migratory routes in the lower Sacramento River. Tagged late-fall-run juvenile Chinook Salmon were released in both systems in 2012 and 2013. There was no significant difference between the estimated cumulative probability of survival in the Yolo Bypass system and combined routes of the lower Sacramento River in either year (0.312–0.629 vs. 0.342–0.599, 95% credible interval in 2012; and 0.111–0.408 vs. 0.240–0.407, 95% credible interval in 2013, respectively). The Yolo Bypass had a higher coefficient of variation (CV) in travel time relative to the lower Sacramento River routes in both years (0.34 vs. 0.29 in 2012, and 0.44 vs. 0.34 in 2013). This work suggests that in relatively low water years, the estimated survival of outmigrating juvenile Chinook Salmon in the Toe Drain is directly comparable to routes in the lower Sacramento River, and that metrics of behavioral diversity in movement behavior can and should be incorporated into future telemetry studies.

Juvenile Chinook Salmon Survival When Exposed to Simulated Dam Passage after Being Implanted with a New Microacoustic Transmitter

AbstractThe current minimum size for tagging Chinook Salmon Oncorhynchus tshawytscha in the Columbia River basin with acoustic transmitters is ≥95 mm FL. Using a newly developed cylindrical microacoustic transmitter (AT; weight in air, 0.22 g), our objective was to evaluate the minimum size of Chinook Salmon for tagging. We measured Chinook Salmon survival and the retention of transmitters and viscera after their exposure to rapid decompression (n = 399) or shear forces (n = 308) that simulated dam passage. Fish (69–107 mm FL) were implanted with an AT (AT‐only) or an AT and a PIT tag (weight in air = 0.10 g; AT+PIT) through a 3‐mm incision with no sutures, or did not receive an incision or tag (untagged control fish). Tag burden averaged 2.9% (range, 1.4–6.2%) in the AT‐only group and 4.2% (range, 2.0–7.9%) in the AT+PIT group. Proportional survival and the retention of transmitters and viscera was significantly lower for AT‐only (0.70) and AT+PIT (0.54) fish than for untagged fish (0.85) after their exposure to pressure change scenarios. No transmitters were fully expelled, but 9% of AT‐only and 22% of AT+PIT salmon had protruding viscera or transmitters. Following shear exposure, the proportional survival and retention of transmitters and viscera was significantly lower for AT‐only (0.70) and AT+PIT (0.61) fish than for untagged fish (0.98). Visceral expulsion was attributed to 90% and 93% of mortal injuries in AT‐only and AT+PIT fish, respectively. In both tests the tagged fish suffered more mortal injuries and death than did untagged fish over the range of tag burdens tested, and no tag burden threshold below which tagged and untagged fish performed similarly was found. As such, a generalized linear model that included tag burden as a predictor variable provided the best fit to the survival data. Without a significant tag burden threshold, we recommend the minimum size for tagging Chinook Salmon using the transmitters and PIT tags evaluated, applied with a 3‐mm incision and no sutures, should remain at 95 mm FL.

Flow-mediated effects on travel time, routing, and survival of juvenile Chinook salmon in a spatially complex, tidally forced river delta

We evaluated the interacting influences of river flows and tides on travel time, routing, and survival of juvenile late-fall Chinook salmon (Oncorhynchus tshawytscha) migrating through the Sacramento–San Joaquin River Delta. To quantify these effects, we jointly modeled the travel time, survival, and migration routing in relation to individual time-varying covariates of acoustic-tagged salmon within a Bayesian framework. We used observed arrival times for detected individuals and imputed arrival times for undetected individuals to assign covariate values in each reach. We found travel time was inversely related to river inflow in all reaches, yet survival was positively related to inflow only in reaches that transitioned from bidirectional tidal flows to unidirectional flow with increasing inflows. We also found that the probability of fish entering the interior Delta, a low-survival reach, declined as inflow increased. Our study illustrates how river inflows interact with tides to influence fish survival during the critical transition between freshwater and ocean environments. Furthermore, our analytical framework introduces new techniques to integrate formally over missing covariate values to quantify effects of time-varying covariates.

Dam Operations Affect Route-specific Passage and Survival of Juvenile Chinook Salmon at a Main-stem Diversion dam

Dam Operations Affect Route-specific Passage and Survival of Juvenile Chinook Salmon at a Main-stem Diversion dam

Influence of multiple dam passage on survival of juvenile Chinook salmon in the Columbia River estuary and coastal ocean

Multiple dam passage during seaward migration is thought to reduce the subsequent survival of Snake River Chinook salmon. This hypothesis developed because juvenile Chinook salmon from the Snake River, the Columbia River's largest tributary, migrate >700 km through eight hydropower dams and have lower adult return rates than downstream populations that migrate through only 3 or 4 dams. Using a large-scale telemetry array, we tested whether survival of hatchery-reared juvenile Snake River spring Chinook salmon is reduced in the estuary and coastal ocean relative to a downstream, hatchery-reared population from the Yakima River. During the initial 750-km, 1-mo-long migration through the estuary and coastal ocean, we found no evidence of differential survival; therefore, poorer adult returns of Snake River Chinook may develop far from the Columbia River. Thus, hydrosystem mitigation efforts may be ineffective if differential mortality rates develop in the North Pacific Ocean for reasons unrelated to dam passage.

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

AbstractThe 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 2010) was low (0.05); again, survival was higher through the Old River. Most fish in the Old River that survived to the end of the Delta had been salvaged from the federal water export facility on the Old River and trucked around the remainder of the Delta. The very low survival estimates reported here are considerably lower than observed salmon survival through comparable reaches of other large West Coast river systems and are unlikely to be sustainable for this salmon population. More research into mortality factors in the Delta and new management actions will be necessary to recover this population.Received March 28, 2012; accepted September 5, 2012

Survival of Juvenile Chinook Salmon during Barge Transport

AbstractTo estimate survival during barge transport over a distance of 470 km from Lower Granite Dam on the Snake River to a release area downstream of Bonneville Dam (the lowermost dam on the Columbia River), we used a novel adaptation of a release–recapture model with 1,494 acoustic‐tagged yearling Chinook salmon Oncorhynchus tshawytscha smolts. Smolts were collected at Lower Granite Dam, received surgically implanted acoustic transmitters, and were divided into three groups: (1) a barge group (RB) that was released into the raceway with fish that were later loaded into transportation barges (general barge population); (2) a control group (RA) that was held in a net‐pen suspended within the barge hold containing the general barge population until 5–6 h prior to barge evacuation (i.e., fish release into the river), at which time they were confirmed to be alive and then released into the barge hold; and (3) a dead group (RD) that was euthanized and then released into the barge hold 5–6 h prior to barge evacuation in order to validate a model assumption. Six replicates of each group were loaded onto fish transport barges that departed from Lower Granite Dam between 29 April and 13 May 2010. Detections on acoustic receiver arrays between 70 and 220 km downstream of the barge evacuation site served as the basis for estimation of survival within the barge. The ratio of RB: RA survival from release to river kilometer 153 provided the estimate of within‐barge survival. The replicate survival estimates ranged from 0.9503 ( = 0.0253) to 1.0003 ( = 0.0155). The weighted average of the replicate estimates of survival during the barge transportation experience was 0.9833 ( = 0.0062). This study provides the first active telemetry documentation that the assumed survival rate of 98% during the barge transportation experience appears to be justified for yearling Chinook salmon smolts.Received March 4, 2011; accepted August 30, 2011

Survey of Pathogens in Hatchery Chinook Salmon with Different Out‐Migration Histories through the Snake and Columbia Rivers

The operation of the Federal Columbia River Power System (FCRPS) has negatively affected threatened and endangered salmonid populations in the Pacific Northwest. Barging Snake River spring Chinook salmon Oncorhynchus tshawytscha through the FCRPS is one effort to mitigate the effect of the hydrosystem on juvenile salmon out-migration. However, little is known about the occurrence and transmission of infectious agents in barged juvenile salmon relative to juvenile salmon that remain in-river to navigate to the ocean. We conducted a survey of hatchery-reared spring Chinook salmon at various points along their out-migration path as they left their natal hatcheries and either migrated in-river or were barged through the FCRPS. Salmon kidneys were screened by polymerase chain reaction for nine pathogens and one family of water molds. Eight pathogens were detected; the most prevalent were Renibacterium salmoninarum and infectious hematopoietic necrosis virus. Species in the family Saprolegniaceae were also commonly detected. Pathogen prevalence was significantly greater in fish that were barged through the FCRPS than in fish left to out-migrate in-river. These results suggest that the transmission of infectious agents to susceptible juvenile salmon occurs during the barging process. Therefore, management activities that reduce pathogen exposure during barging may increase the survival of juvenile Chinook salmon after they are released.

An Evaluation of the Influence of Stock Origin and Out‐migration History on the Disease Susceptibility and Survival of Juvenile Chinook Salmon

Various methods have been developed to mitigate the adverse effects of the Federal Columbia River Power System on juvenile Pacific salmon out-migrating through the Columbia River basin. In this study, we found that hatchery-reared spring Chinook salmon Oncorhynchus tshawytscha in the river are in varying degrees of health, which may affect delayed mortality and the assessment of the effectiveness of management actions to recover listed stocks (e.g., barging fish downstream versus leaving fish in the river). A laboratory disease challenge with Listonella anguillarum was completed on fish from Rapid River Hatchery and Dworshak National Fish Hatchery (NFH) with different out-migration histories: (1) transported by barge, (2) removed from the river before barging, or (3) left to travel in-river. Barged fish from Rapid River Hatchery experienced less mortality than fish from Dworshak NFH. No statistical differences were found between the hatcheries with fish that had in-river out-migration histories. We suggest that the stressors and low survival associated with out-migration through the hydropower system eliminated any differences that could have been present. However, 18-25% of the fish that were barged or collected before barging died in the laboratory before the disease challenge, compared with less than 2% of those that traveled in-river. Owing to disproportionate prechallenge mortality, the disease-challenged populations may have been biased; thus, they were also considered together with the prechallenge mortalities. The synthesis of prechallenge and disease-challenged mortalities and health characteristics evaluated during out-migration indicated that the benefit of barging was not consistent between the hatcheries. This finding agrees with adult survival and delayed mortality estimates for the individual hatcheries determined from adult returns. The results suggest that the health status of fish and their history before entering the hydropower system (hatchery of origin and out-migration path) are critical variables affecting the conclusions drawn from studies that evaluate mitigation strategies.

Contrasting Early Marine Ecology of Chinook Salmon and Coho Salmon in Southeast Alaska: Insight into Factors Affecting Marine Survival

AbstractTo identify processes potentially contributing to the differential marine survival rates of Chinook salmon Oncorhynchus tshawytscha and coho salmon O. kisutch originating from Southeast Alaska, we compared the early marine ecology of the two species during the critical first summer in marine waters. We predicted that the higher survival rates for coho salmon relative to Chinook salmon were related to the larger size, faster growth, or different habitat or species associations of coho salmon. Our size and growth expectations were largely substantiated: juvenile coho salmon were larger than juvenile Chinook salmon and had faster length‐based growth, although weight‐based growth rates were similar. The most obvious difference was in their distributions. Juvenile coho salmon overlapped spatially and temporally with abundant juvenile pink salmon O. gorbuscha and chum salmon O. keta, whereas juvenile Chinook salmon were geographically separated from other salmonids. This suggests that coho salmon benefited from a predation buffer that did not extend to Chinook salmon. Our results indicate that factors influencing marine survival of juvenile Chinook salmon and coho salmon in Southeast Alaska are attributable to species‐specific differences in their early marine distribution patterns and species interactions.

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

AbstractA 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 delta releases was considerably lower than that of main‐steam releases (mean ratio of survival probabilities, 0.35). The ratio of survival probabilities was negatively associated with water export levels, but various model selection criteria gave more (or nearly equal) weight to simpler models that excluded exports. However, the signal‐to‐noise ratio, defined in terms of the export effect relative to environmental variation, was very low, and this could explain the indeterminacy in the results of the model selection procedures. Many more years of data would be needed to more precisely estimate the export effect. Whatever the factors that adversely affect survival through the interior delta, the fraction of out‐migrants that enter the interior delta needs to be estimated in order to determine the overall effect of water exports on out‐migrating Sacramento river Chinook salmon.

Mean free-path length theory of predator–prey interactions: Application to juvenile salmon migration

Ecological theory traditionally describes predator–prey interactions in terms of a law of mass action in which the prey mortality rate depends on the density of predators and prey. This simplifying assumption makes population-based models more tractable but ignores potentially important behaviors that characterize predator–prey dynamics. Here, we expand traditional predator–prey models by incorporating directed and random movements of both predators and prey. The model is based on theory originally developed to predict collision rates of molecules. The temporal and spatial dimensions of predators–prey encounters are determined by defining movement rules and the predator's field of vision. These biologically meaningful parameters can accommodate a broad range of behaviors within an analytically tractable framework suitable for population-based models. We apply the model to prey (juvenile salmon) migrating through a field of predators (piscivores) and find that traditional predator–prey models were not adequate to describe observations. Model parameters estimated from the survival of juvenile chinook salmon migrating through the Snake River in the northwestern United States are similar to estimates derived from independent approaches and data. For this system, we conclude that survival depends more on travel distance than travel time or migration velocity.

Statistical Relationship between Parr-to-Smolt Survival of Snake River Spring–Summer Chinook Salmon and Indices of Land Use

We used simple regression models to demonstrate an association between land use and parr survival of chinook salmon Oncorhynchus tshawytscha from overwintering areas in the Snake River drainage of Idaho and Oregon to the first main-stem dam encountered during emigration to the Pacific Ocean. We used data on tagged (passive integrated transponder tags) releases of naturally produced Snake River spring–summer chinook parr and subsequent tag detections, as well as indices of land use, vegetation, and road density. We spot-checked the land-use and vegetation indices in a field survey of spawning and rearing areas in the summer of 1999, and we believe that they are reliable indicators of land-use patterns. The models also employed month of release, length of parr at release, and a drought index as independent variables. The models were developed and tested using parr tagged from 1992 through 1998. Age-0 parr that reared in wilderness areas (a land-use category; not necessarily federally designated Wilderness Areas) had the highest survival during their last 6–9 months of freshwater residence. In contrast, parr that reared in young, dry forests (typically, intensively managed timber lands) had the lowest survival. Similarly, parr that reared in areas of low road density had substantially higher survival than those in areas of high road density. We concluded that in the area studied there is a close association between land-use indices and survival of chinook salmon parr during their last 6–9 months of freshwater residence. This analysis suggests that road-building and associated land-use activities in the region may have a detrimental effect on the survival of juvenile chinook salmon and that mitigative changes in these activities could be warranted because Snake River spring–summer chinook salmon are listed as threatened under the Endangered Species Act.

A Review and Assessment of Transportation Studies for Juvenile Chinook Salmon in the Snake River

Abstract We reviewed research conducted by the U.S. National Marine Fisheries Service from 1968 through 1989 on the benefits of using trucks and barges to transport migrating juvenile Chinook salmon Onchorhynchus tsawytscha from the Snake River around dams and reservoirs in the lower Snake and Columbia rivers. Early results from studies that used trucks indicated that Chinook salmon benefited from transportation: therefore, transportation was adopted as a management strategy by the late 1970s. Our review shows that large-scale transportation by truck was unlikely to benefit survival of juvenile Chinook salmon. Our results from reviewing more recent studies indicate that the use of barges to transport juvenile Chinook salmon may result in improved survival. Benefits may be lower than previously reported because results may have been biased by experimental design: however, even after we adjusted for those potential violations, results from four of six studies on the use of barges indicated that survival of ...

Survival of Juvenile Chinook Salmon Challenged withRenibacterium salmoninarumand Administered Oral Doses of Erythromycin Thiocyanate for Different Durations

Abstract Erythromycin thiocyanate was administered orally at three daily dosages (50, 100, and 200 mg/kg body weight) for 7, 14, or 21 d to duplicate groups of yearling chinook salmon Oncorhynchus tshawytscha challenged with an intraperitoneal inoculation of kidney disease bacterium, Renibacterium salmoninarum. Two experiments were conducted sequentially to test the effects of the drug and bacterium challenge at 12 and 8°C. In each experiment, the number offish surviving at the end of the trial was significantly higher in tanks offish administered erythromycin, and survival was highest in tanks of fish administered the highest dosage of erythromycin for 21 d. In tests conducted at 12°C, mortality from bacterial kidney disease began much sooner than in tests conducted at 8°C. How long the drug was administered was a significant factor in tests conducted at both temperatures; survival increased in drug treatments of longer duration. Palatability of feed may be a complicating factor in determining the most a...