Juvenile Chinook Salmon Research Articles

Experiments on the hydraulics and swimming responses of juvenile Chinook Salmon encountering a floating guidance structure

AbstractFloating guidance structures are intended to promote safe passage for juvenile salmon migrating downstream through reservoirs. However, the ability of an engineered structure to guide fish to safe passage has been primarily tested through large‐scale implementation in reservoirs or in laboratory studies and computer simulations without live fish. Research is needed that integrates fluid mechanics with fish behaviour to study how hydraulic conditions around a guidance structure trigger swimming behaviours. In this study, an outdoor experimental channel was used to identify: (a) the hydraulic signature of a floating guidance structure and (b) changes in fish swim behaviour in relation to channel hydraulics. The flow field surrounding a guidance structure at two deployment angles was characterized using acoustic Doppler velocimeters. Swimming behaviours of juvenile Chinook salmon were recorded using underwater videogrammetry. A statistical method for behaviour change detection identified the most likely locations of swimming behaviour changes in fish as they first encountered the guidance structure. Finally, the locations of behaviour changes were compared to the hydraulics surrounding each guidance structure. Taken together, results indicated the fish did respond to the guide wall with behaviour changes, but did not distinguish between the two guide wall angles. While the two guide wall angles did produce statistically different distributions of hydraulic variables, the differences were small, potentially too small for the fish to produce a behavioural response. To inform the design of guidance structures, further work may clarify if swim responses vary with more aggressive wall angles and/or higher approach velocities, or if any contraction of flow and/or visual cue will produce similar behaviour responses.

English

This study investigated the effects of coloured structures on the growth of juvenile landlocked fall Chinook salmon (Oncorhynchus tshawytscha, Walbaum) during hatchery rearing. Structures consisted of an array of four aluminum angles painted one of four colours: Silver, red, black and green, which were vertically suspended in circular tanks. After 25 days, mean total lengths and weights of individual salmon reared in tanks with the green arrays were significantly (P 0.05) among the colour treatments. Final total tank biomass and gain were also not significantly different (P > 0.05) among the colour treatments. The results of this study indicate that structural colours could be considered to maximize juvenile Chinook salmon growth during hatchery rearing. Key words: Chinook salmon, colour, Oncorhynchus tshawytscha, hatchery rearing.

Metabolomic profiling for juvenile Chinook salmon exposed to contaminants of emerging concern

Both targeted and non-targeted metabolomic analyses were conducted on juvenile ocean-type fall Chinook salmon (Oncorhynchus tshawytscha) residing in two estuaries receiving wastewater treatment plant (WWTP) effluent and one reference estuary. The data show that the metabolome patterns for fish from the two WWTP-receiving estuaries were more similar to each other compared to that for the reference site fish. Also, a comparison of the metabolome for fish from the reference site and fish from a hatchery upstream of one of the effluent-receiving estuaries indicated no differences, implying that residency for fish in the contaminated estuary resulted in major changes to the metabolome. Based on general health parameters including whole-body lipid content and condition factor, plus the availability of prey for these fish, we conclude that juvenile Chinook salmon in these contaminated estuaries may have been experiencing metabolic disruption without any overt signs of impairment. Additionally, a non-targeted analysis was performed on hatchery summer Chinook salmon from a laboratory study where fish were dosed for 32 days with feed containing 16 of the most common contaminants of emerging concern (CECs) detected in wild fish. In the laboratory experiment a relationship was observed between dose and the number of liver metabolites that were different between control and treatment fish. Laboratory fish were exposed to only 16 CECs, but are generally exposed to hundreds of these compounds in contaminated aquatic environments. These results have implications for the health of juvenile Chinook salmon and the likelihood of a successful life cycle when exposed to effluent-related chemicals.

Some like it slow: a bioenergetic evaluation of habitat quality for juvenile Chinook salmon in the Lemhi River, Idaho

Management and conservation of freshwater habitat requires fine spatial resolution and watershed-scale and life-stage-specific methods due to complex linkages among land, climate, water uses, and aquatic organism necessities. In this study, we present a valley-scale microhabitat resolution, process-based bioenergetics approach that combines high-resolution topobathymetric LiDAR survey with two-dimensional hydrodynamic and bioenergetics modeling. We applied the model to investigate the role of lateral habitat, stream morphological complexity, water use, and temperature regimes on aquatic habitat quality distribution of juvenile Chinook salmon (Oncorhynchus tshawytscha) within the Lemhi River (eastern Idaho, USA). Modeling results showed two key aspects: (i) a reduction in diverted flows is not sufficient to improve habitat quality potentially because of a legacy of morphological simplification (directly due to straightening and wood removal and indirectly due to low in-channel flows) and (ii) morphological complexity and connectivity with side channels and margin areas, which are key and vital elements to support suitable habitats that meet or exceed energetic needs to sustain or promote growth of individuals and populations.

Effects of Hatchery Rearing Density, Handling, and Nutrition on Renibacterium salmoninarum Infection Prevalence in Juvenile Chinook Salmon.

Bacterial kidney disease, caused by Renibacterium salmoninarum (RS), is a chronic and often fatal disease of salmonid species, and can be particularly harmful to hatchery-reared Chinook Salmon Oncorhynchus tshawytscha. A considerable amount of research has focused on the prevention of vertical and horizontal transmission; however, a comparatively little amount has investigated factors that increase the prevalence of RS infection in captive environments. We evaluated the effects of three common hatchery conditions (handling, nutrition level, and rearing density) on RS infection prevalence. Fish were sampled at 30-d and 60-d postexposure to RS. Of 577 juveniles examined, 65 (11.27%) had anterior kidneys infected with RS. Using a logistic mixed model analysis, we found effects of nutrition level (P=0.018), handling (P=0.010), and sampling period (P=0.003) on the prevalence of RS. The interactions of nutrition and handling (P=0.008) and nutrition and time (P<0.001) were also significant. When fed a standard-nutrition diet, proportionately fewer fish were infected with RS when not handled (7.16% versus 0.04%; P=0.003). Fish in the standard-nutrition group also had a lower prevalence of RS during the second sampling period (4.08% versus 0.08%, respectively; P<0.001). When not handled, rearing with standard nutrition (11.50% versus 0.04%; P=0.004) resulted in a reduction in prevalence of RS infection. Additionally, nonhandled fish had a much lower prevalence of RS infection during the second sampling period (2.66% versus 0.21%; P=0.009). While density did not affect the prevalence of RS infection (P=0.145), fish reared at a higher density had lower RS infection when not handled (16.48% versus 0.84%, P=0.004). For fish at a higher density, the RS prevalence was lower during the second sampling period (10.57% versus 1.40%; P=0.002). Our results suggest that hatchery managers can reduce RS infection prevalence by maintaining an adequate nutritional regime as recommended by the manufacturer. Additionally, the prevalence of RS may be reduced if managers decrease handling of hatchery-reared Chinook Salmon if exposed to RS.

Evidence for rapid gut clearance of microplastic polyester fibers fed to Chinook salmon: A tank study

Marine and freshwater plastic pollution is a challenging issue receiving large amounts of research and media attention. Yet, few studies have documented the impact of microplastic ingestion to aquatic organisms. In the Pacific Northwest, Chinook salmon are a culturally and commercially significant fish species. The presence of marine and freshwater microplastic pollution is well documented in Chinook salmon habitat, yet no research has investigated the impacts to salmon from microplastic ingestion. The majority of the marine microplastics found in the Salish Sea are microfibers, synthetic extruded polymers that come from commonly worn clothing. To understand the potential impacts of microfiber ingestion to fish, we ran a feeding experiment with juvenile Chinook salmon to determine if ingested fibers are retained or digestion rates altered over a 10 day digestion period. The experiment was completed in two trials, each consisted of 20 control and 20 treatment fish. Treatment fish were each fed an amended ration of 12 food pellets spiked with 20 polyester microfibers and control fish were fed the same ration without added microfibers. Fish were sampled at day 0, 3, 5, 7, and 10 to assess if fibers were retained in their gastrointestinal tract and to determine the rate of digestion. Fibers for the experiment came from washing a red polyester fleece jacket in a microfiber retention bag. Fibers had a mean length of 4.98 mm. Results showed fish were able to clear up to 94% of fed fibers over 10 days. Differences in mean gastrointestinal mass were not statistically significant at any sampled time between treatment and controls, suggesting that the ingestion of microfibers did not alter digestion rates. Further work is needed to understand if repeated exposures, expected in the environment, alter digestion or food assimilation for growth.

Biotransport of persistent organic pollutants in the southern Hemisphere by invasive Chinook salmon (Oncorhynchus tshawytscha) in the rivers of northern Chilean Patagonia, a UNESCO biosphere reserve

Biotransport is often associated with migration patterns of species, including large, anadromous salmonids. Several studies have reported biotransport of persistent organic pollutants in the Northern Hemisphere, but there is no published information on biotransport ocurring south of the equator. Chile’s Patagonia is one of the last largely intact natural areas in the world. The objective of this study was to determine whether persistent organic pollutants are transported by the invasive Pacific Chinook salmon (O. tshawytscha) from the Pacific Ocean to Chilean Patagonia. Samples of juvenile and adult Chinook salmon were analyzed for polychlorinated biphenyls, pesticides and polybrominated diphenyl ethers. The results revealed that concentrations of POPs in adults migrating into Patagonian rivers were significantly higher than those found in juveniles migrating seaward. A mass balance analysis indicates that Chinook salmon are a source of persistent organic pollutants to Chilean Patagonia inland waters.Capsule: Biotransport of Persistent Organic Pollutants (POPs) by Chinook salmon (O. tshawytscha) from the Pacific Ocean to Chilean Patagonia has been confirmed by mass balance of POPs.

Effects of Tidally Varying River Flow on Entrainment of Juvenile Salmon into Sutter and Steamboat Sloughs

Survival of juvenile salmonids in the Sacramento–San Joaquin Delta (Delta) varies by migration route, and thus the proportion of fish that use each route affects overall survival through the Delta. Understanding factors that drive routing at channel junctions along the Sacramento River is therefore critical to devising management strategies that maximize survival. Here, we examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs from the Sacramento River. Because these sloughs divert fish away from the downstream entrances of the Delta Cross Channel and Georgiana Slough (where fish access the low-survival region of the interior Delta), management actions to increase fish entrainment into Sutter and Steamboat sloughs are being investigated to increase through-Delta survival. Previous studies suggest that fish generally “go with the flow”—as net flow into a divergence increases, the proportion of fish that enter that divergence correspondingly increases. However, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. Therefore, we modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data, which was collected using temporary gaging stations deployed between March and May of 2014. Our results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of an individual’s probability of being entrained. In addition, interactions between discharge and the proportion of flow revealed a non-linear relationship between flow and entrainment probability. We found that the highest proportions of fish are likely to be entrained into Steamboat Slough and Sutter Slough on the ascending and descending limbs of the tidal cycle, when flow changes from positive to negative. Our findings characterize how patterns of entrainment vary with tidal flow fluctuations, providing information critical for understanding the potential effect of management actions (e.g., fish guidance structures) to modify routing probabilities at this location.

Consequences of Piscine orthoreovirus genotype 1 (PRV-1) infections in Chinook salmon (Oncorhynchus tshawytscha), coho salmon (O.kisutch) and rainbow trout (O.mykiss).

Piscine orthoreovirus genotype 1 (PRV‐1) is the causative agent of heart and skeletal muscle inflammation (HSMI) in farmed Atlantic salmon (Salmo salar L.). The virus has also been found in Pacific salmonids in western North America, raising concerns about the risk to native salmon and trout. Here, we report the results of laboratory challenges using juvenile Chinook salmon, coho salmon and rainbow trout injected with tissue homogenates from Atlantic salmon testing positive for PRV‐1 or with control material. Fish were sampled at intervals to assess viral RNA transcript levels, haematocrit, erythrocytic inclusions and histopathology. While PRV‐1 replicated in all species, there was negligible mortality in any group. We observed a few erythrocytic inclusion bodies in fish from the PRV‐1‐infected groups. At a few time points, haematocrits were significantly lower in the PRV‐1‐infected groups relative to controls, but in no case was anaemia noted. The most common histopathological finding was mild, focal myocarditis in both the non‐infected controls and PRV‐1‐infected fish. All cardiac lesions were judged mild, and none were consistent with those of HSMI. Together, these results suggest all three species are susceptible to PRV‐1 infection, but in no case did infection cause notable disease in these experiments.

Temporal trends in aluminum smelter-derived polycyclic aromatic hydrocarbons in outmigrant juvenile Chinook salmon from Kitimat, British Columbia, Canada

Aluminum smelter-derived polycyclic aromatic hydrocarbons (PAHs) in outmigrant juvenile Chinook salmon were evaluated in Kitimat Arm, British Columbia, Canada from 2000 to 2004, and in 2015. Decades of continual smelter operations by Rio Tinto resulted in PAH contamination of marine sediments at levels associated with adverse effects in juvenile salmon. Recently, smelter operations have undergone process changes to reduce PAH input to the environment. The PAH concentrations in juvenile Chinook salmon observed in 2000 to 2004, at sites nearest the smelter were comparable to salmon in other urban areas where reduced disease resistance was observed; the levels were lower in 2015 than 2000–2004 suggesting that the recent process changes were effective. Further, these data establish a benchmark for assessing any future changes affecting PAH input and the potential risks to the receiving environment.

The use of non-targeted metabolomics to assess the toxicity of bifenthrin to juvenile Chinook salmon (Oncorhynchus tshawytscha)

An increase in urban and agricultural application of pyrethroid insecticides in the San Francisco Bay Estuary and Sacramento San Joaquin Delta has raised concern for the populations of several salmonids, including Chinook salmon (Oncorhynchus tshawytscha). Bifenthrin, a type I pyrethroid, is among the most frequently detected pyrethroids in the Bay-Delta watershed, with surface water concentrations often exceeding chronic toxicity thresholds for several invertebrate and fish species. To better understand the mechanisms of bifenthrin-induced neurotoxicity, juvenile Chinook salmon were exposed to concentrations of bifenthrin previously measured in the Delta. Non-targeted metabolomic profiles were used to identify transcriptomic changes in the brains of bifenthrin-exposed fish. Pathway analysis software predicted increased apoptotic, inflammatory, and reactive oxygen species (ROS) responses in Chinook following exposure to 0.15 and 1.50 μg/L bifenthrin for 96 h. These responses were largely driven by reduced levels of inosine, hypoxanthine, and guanosine. Subsequently, in the brain, the expression of caspase 3, a predominant effector for apoptosis, was significantly upregulated following exposure to 1.50 μg/L bifenthrin. This data suggests that metabolites involved in inflammatory and apoptotic responses, as well as those involved in maintaining proper neuronal function may be disrupted following sublethal exposure to bifenthrin and further suggests that additional population studies should focus on behavioral responses associated with impaired brain function.

Optimizing an eDNA protocol for estuarine environments: Balancing sensitivity, cost and time

Environmental 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 protocol. At the same time, these two parameters are essential for the experimental design of a project. Here we evaluate and rank 27 different eDNA protocols in the context of Chinook salmon (Oncorhynchus tshawytscha) eDNA detection in an estuarine environment. We present a comprehensive evaluation of multiple eDNA protocol parameters, balancing time, cost and DNA yield. We collected samples composed of 500 mL estuarine water from Deverton Slough (38°11'16.7"N 121°58'34.5"W) and 500 mL from tank water containing 1.3 juvenile Chinook Salmon per liter. Then, we compared extraction methods, filter types, use of inhibitor removal kit for DNA yield, processing time, and protocol cost. Lastly, we used an MCMC algorithm together with machine learning to understand the DNA yield of each step of the protocol as well as the interactions between those steps. Glass fiber filtration was to be the most resilient to high turbidites, filtering the samples in 2.32 ± 0.08 min instead of 14.16 ± 1.86 min and 6.72 ± 1.99 min for nitrocellulose and paper filter N1, respectively. The filtration DNA yield percentages for paper filter N1, glass fiber, and nitrocellulose were 0.00045 ± 0.00013, 0.00107 ± 0.00013, 0.00172 ± 0.00013. The DNA extraction yield percentage for QIagen, dipstick, NaOH, magnetic beads, and direct dipstick ranged from 0.047 ± 0.0388 to 0.475 ± 0.0357. For estuarine waters, which are challenging for eDNA studies due to high turbidity, variable salinity, and the presence of PCR inhibitors, we found that a protocol combining glass filters, magnetic beads, and 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 in aquatic systems. Our findings should be applicable to most aquatic environments and provide a clear guide for determining which eDNA protocol should be used under different study constraints.

Identifying Under‐Ice Overwintering Locations of Juvenile Chinook Salmon by Using Environmental DNA

AbstractThe detection of fish by using environmental DNA (eDNA) analysis has been shown to be more cost‐effective than traditional sampling methods are in certain situations, but this method has not been assessed under extreme winter conditions. We conducted a multiyear pilot study to test the effectiveness of eDNA for detecting fish under ice. In the spring of 2016, 2017, and 2018, we sampled for juvenile Chinook Salmon Oncorhynchus tshawytscha in the Tanana Flats (Alaska, USA) by using minnow traps and by using eDNA in the spring of 2017 and 2018. We used traps at 97 sites and analyzed eDNA that was isolated from water samples at 36 sites, using an established, species‐specific quantitative polymerase chain reaction (qPCR) assay for Chinook Salmon. We detected Chinook Salmon by using eDNA at 12 of the 36 eDNA‐sampled sites but did not capture any live juveniles in the minnow traps. Assuming that positive eDNA detections are reliable indicators of recent fish presence, we found that eDNA can be a more efficient and cost‐effective alternative for monitoring aquatic communities under extreme winter conditions. Based on our experience, including eDNA‐based screening of target sampling sites could prove to be a significant boost to the effectiveness of fish monitoring in remote and challenging habitats.

Carcass Additions Influence Food Webs Through Bottom-Up and Direct Consumption Pathways Along a Fish Species Assemblage Gradient

The loss of subsidies delivered by anadromous fish to inland stream ecosystems may have profound influences on stream food webs. However, studies have focused on food web responses in ecosystems where the fish assemblage is dominated by salmonids. We evaluated food web responses to carcass additions in three locations of an interior Columbia River Basin stream with varying native fish assemblages. Periphyton biomass responses were mixed with increases in treatment compared to control reaches of the middle and downstream pairs, but not in the upstream pair where scavenging by bears removed the majority of carcasses. Stable isotope analysis revealed marine-derived nutrient (MDN) enrichment of periphyton and invertebrate functional feeding groups in the middle and downstream pairs (up to 12% MDN derived), but not in the upstream pair. Non-salmonid fish exhibited limited MDN assimilation (~ 5 and 10% MDN derived), with isotopic enrichment patterns similar to lower trophic levels and little evidence of eggs and carcass material consumption, suggesting bottom-up transfer of MDN to non-salmonid fishes. In contrast, across the three study pairs, juvenile Chinook Salmon (Oncorhynchus tshawytscha) and steelhead trout (O. mykiss) assimilated MDN rapidly, obtaining up to 25% and 57% of their nitrogen from carcasses, respectively. Diet analysis and isotopic enrichment patterns indicated that juvenile salmonid assimilation occurred primarily through direct consumption of eggs and carcass tissue. Our findings suggest that salmonids in this region may experience more benefit from carcass additions containing eggs, while non-salmonids are likely to experience minimal MDN incorporation whether or not eggs are present.

Threats to Rearing Juvenile Chinook Salmon from Nonnative Smallmouth Bass Inferred from Stable Isotope and Fatty Acid Biomarkers

AbstractNonnative Smallmouth BassMicropterus dolomieuare increasingly sympatric with juvenile spring Chinook SalmonOncorhynchus tshawytschain the rivers of western North America. Understanding the potential effects of introduced Smallmouth Bass is essential to efficiently direct salmon management efforts, especially given the potential for upstream range expansion of Smallmouth Bass in response to the climate‐induced warming that many rivers may experience. However, the predatory and competitive threats of Smallmouth Bass to juvenile salmonids remain largely unexamined, particularly in salmon rearing areas. To address this knowledge gap, we collected stable isotope (δ13C and δ15N) and fatty acid data to assess the trophic role of Smallmouth Bass in the upstream reaches of the North Fork John Day River, a tributary of the Columbia River where the upstream invasion extent of Smallmouth Bass co‐occurs with the native predator Northern Pikeminnow and river‐rearing juvenile Chinook Salmon. We found that Smallmouth Bass and Northern Pikeminnow occupy divergent dietary niches, and there was little evidence of a strong predation or competition threat to juvenile Chinook Salmon from either predator. In addition, we found a disproportionate reliance on autochthonous resources across the entire community and low isotopic uniqueness, suggesting potential competition among the broader fish community given the scarcity of resources. Importantly, this study focused on the overlap between the upstream‐most habitats of encroaching Smallmouth Bass and downstream‐most habitats of juvenile Chinook Salmon. Therefore, the relative scarcity of rearing salmon in comparison with other available prey in this zone may limit current predation threats. The results from this study help guide resource‐limited managers that are tasked with conserving and restoring native salmonid populations.

Environmental and behavioral controls on juvenile Chinook salmon migration pathways in the Columbia River estuary

Juvenile Chinook salmon population dynamics in the Columbia River estuary are influenced by physical processes, hatchery practices, and behavioral decision-making. To better understand how environmental forcing and swimming behavior influence estuarine migration and travel times, we developed an individual-based model (IBM) that uses 3-D outputs from a hydrodynamic model to simulate Lagrangian transport as well as swimming and bioenergetics sub-models to simulate active swimming and growth. Simulations were run in 2010 during the migration seasons for yearling and subyearling Chinook salmon. For both life history types, alternative behaviors were simulated, from random walks to behaviors that optimized efficient system migration for yearling Chinook salmon and growth for subyearling Chinook salmon. Simulation results compared well against observed data on travel times and common migration pathways; the simulated travel times for both yearling and subyearling Chinook salmon were within several hours of the observed travel times. In general, residence times and pathways were largely driven by river discharge and the phase of the tide. During periods of greater river discharge, simulated estuarine residence times were reduced and variability across individuals was minimal. The timing of estuarine exit was closely tied to the phase of the tide, with most simulated individuals exiting the system during the ebb phase. While travel times were largely driven by flow velocities, swimming behavior was likewise important. Simulated yearling Chinook salmon behaviors that optimized movement with surrounding flows resulted in reduced estuarine residence times when compared to passive and random walk behaviors. Similarly, simulated subyearling Chinook salmon behaviors that optimized growth directed individuals to shallow peripheral habitats, resulting in longer residence times and higher growth rates. Even if potentially important factors such as predator avoidance were not included, this IBM provides an informative tool to model migration pathways, growth, and residence times of juvenile salmon in an estuarine environment and could be used to inform management decisions by evaluating various scenarios.

An escape theory model for directionally moving prey and an experimental test in juvenile Chinook salmon.

Prey evaluate risk and make decisions based on the balance between the costs of predation and those of engaging in antipredator behaviour. Economic escape theory has been valuable in understanding the responses of stationary prey under predation risk; however, current models are not applicable for directionally moving prey.Here we present an extension of existing escape theory that predicts how much predation risk is perceived by directionally moving prey. Perceived risk is measured by the extent antipredator behaviour causes a change in travel speed (the distance to a destination divided by the total time to reach that destination). Cryptic or cautious antipredator behaviour slows travel speed, while prey may also speed up to reduce predator–prey overlap. Next, we applied the sensitization hypothesis to our model, which predicts that prey with more predator experience should engage in more antipredator behaviour, which leads to a larger change in travel speed under predation risk. We then compared the qualitative predictions of our model to the results of a behavioural assay with juvenile Chinook salmon Oncorhynchus tshawytscha that varied in their past predator experience.We timed salmon swimming downstream through a mesh enclosure in the river with and without predator cues present to measure their reaction to a predator. Hatchery salmon had the least predator experience, followed by wild salmon captured upstream (wild‐upstream) and wild‐salmon captured downstream (wild‐downstream).Both wild salmon groups slowed down in response to predator cues, whereas hatchery salmon did not change travel speed. The magnitude of reaction to predator cues by salmon group followed the gradient of previous predator experience, supporting the sensitization hypothesis.Moving animals are conspicuous and vulnerable to predators. Here we provide a novel conceptual framework for understanding how directionally moving prey perceive risk and make antipredator decisions. Our study extends the scope of economic escape theory and improves general understanding of non‐lethal effects of predators on moving prey.

Effect of release timing on apparent survival of juvenile fall run Chinook Salmon from Coleman National Fish Hatchery

Hatchery production of Pacific salmon for release into the environment is a common tool for conservation and supplementation of depleted stocks. Hatchery conditions are controlled to support high survival rates; however, once released into the environment, managers have little control over conditions experienced by juveniles. Thus, release timing is a critical decision in hatchery operations. This 3-year study used acoustic telemetry to estimate release timing effects on migration survival of fall run Chinook Salmon from the largest hatchery in California: the Coleman National Fish Hatchery. Juvenile Chinook Salmon implanted with JSATS transmitters were released in two or more groups each year, concomitant with the regular hatchery production. Arrays of acoustic monitors were deployed at six locations within the 517 km migration route to estimate reach-specific survival of each release. Mark-recapture models identified both year and release timing effects on reach-specific survival. In years when release effects were well-supported, survival was higher in the earlier release group. Survival in subsequent releases was similar or significantly lower indicating that conditions in the river may decline or stay the same but improvement was not observed. Survival was consistently high in the first 92 km of the migration route and may be related to predator swamping from the release of millions of hatchery fish. Survival declined, and became more variable, within the lower 425 km of the river with the lowest rates observed in the tidal bay-delta. These results indicate that both year and release timing can strongly influence survival and that time between releases likely influences the magnitude of the effect.

Density‐dependent marine survival of hatchery‐origin Chinook salmon may be associated with pink salmon

AbstractUnderstanding how protected species influence the population dynamics of each other is an essential part of ecosystem‐based management. Chinook salmon (Oncorhynchus tshawytscha) are critical prey for endangered southern resident killer whales (SRKWs; Orcinus orca), and increasing releases of hatchery Chinook salmon has been proposed to aid SRKW recovery. We analyzed 30 yr of data and found that density‐dependent survival of hatchery Chinook salmon released into the central and southern parts of the Salish Sea (Washington, USA; and British Columbia, Canada) may be associated with the presence of naturally produced pink salmon (O. gorbuscha), which are highly abundant as juveniles only in even‐numbered years. We first modeled hatchery Chinook salmon marine survival as a function of the numbers of juvenile Chinook released and the presence of emigrating juvenile pink salmon between 1983 and 2012. Then, we related reconstructed numbers of hatchery Chinook salmon returning to Puget Sound to the abundance of juvenile Chinook released in even (pink emigration) and odd (non‐pink emigration) years from 1980 to 2010. We found that in some regions of the Salish Sea, both hatchery Chinook salmon marine survival and adult Chinook returns varied depending on the number of hatchery Chinook released and the presence of juvenile pink salmon. Specifically, in some regions survival of hatchery Chinook salmon decreased when greater numbers of juveniles were released into the Salish Sea in even years, when large numbers of pink salmon were present, but increased or remained stable when pink salmon were not present in large numbers (in odd years). This suggests lower, density‐dependent survival of juvenile Salish Sea Chinook salmon during even outmigration years. Our analyses suggest that scientists and managers should further investigate potential mechanisms for density‐dependent survival of hatchery Chinook salmon from Salish Sea hatcheries when designing strategies to maximize adult returns.

Combining Models of the Critical Streakline and the Cross-Sectional Distribution of Juvenile Salmon to Predict Fish Routing at River Junctions

Because fish that enter the interior Delta have poorer survival than those emigrating via the Sacramento River, understanding the mechanisms that drive entrainment rates at side channel junctions is critically important for the management of imperiled juvenile salmon. Here, we implement a previously proposed process-based conceptual model to study entrainment rates based on three linked elements: the entrainment zone, critical streakline, and cross-sectional distribution of fish. The critical streakline is the location along a channel cross-section immediately upstream of a junction that forms the spatial divide between parcels of water that enter a side channel or remain in the main channel. The critical streakline therefore divides the main channel into entrainment zones within which fish would likely enter each channel. Combined with information about the cross-sectional distribution of fish upstream of a junction, this conceptual model provides a means to predict fish entrainment into each channel. To apply this conceptual model, we combined statistical models of the critical streakline, the cross-sectional distribution of acoustic tagged juvenile Chinook salmon, and their probability of entrainment into Georgiana Slough. We fit joint beta regression and logistic regression models to acoustic telemetry data gathered in 2011 and 2012 to estimate the cross-sectional distribution of fish upstream of the junction, and to estimate the probability of entrainment for fish on either side of the critical streakline. We show that entrainment rates can be predicted by understanding how the combination of critical streakline position and cross-sectional distribution of fish co-vary as a function of environmental covariates. By integrating over individual positions and entrainment fates to arrive at population-level entrain probability in relation to environmental covariates, our model offers managers a simple but powerful tool to evaluate how alternative actions affect migrating fish.