Fall-run Chinook Salmon Research Articles

An evaluation of tradeoffs in restoring ephemeral vs. perennial habitats to conserve animal populations

IntroductionHabitat loss and degradation pose significant threats to global fish and wildlife populations, prompting substantial investments in habitat creation and restoration efforts. Not all habitats provide equal benefits, leading to challenges in prioritizing restoration actions. For example, juvenile anadromous salmonids require high quality rearing aquatic habitats to achieve the physiological requirements needed to successfully migrate to the ocean. However, there are profound disagreements among anadromous salmon restoration managers whether it is best to focus efforts on restoring in-channel habitats that are available for the entire rearing period or floodplain habitats that, while facilitating greater growth and survival than in-channel habitats, are only available for a few weeks at a time and are typically only activated every two-to-three years.MethodsWe used an existing fall-run Chinook salmon decision-support model to evaluate under what conditions floodplain restoration would provide greater benefits than in-channel habitat restoration. The simulations included a wide range of floodplain inundation frequencies and durations and floodplain benefits in the form of increased survival and growth relative to in-channel habitats.ResultsThe simulations results indicated that in-channel habitat restoration was always the best habitat restoration action when there was no existing in-channel habitat despite simulating a wide range of flood frequency, duration, and growth and survival benefits. Floodplain restoration was generally best when there was sufficient in-channel habitat available to successfully rear most of the juveniles produced by the returning adult salmon.DiscussionWe hypothesize that in-channel and floodplain habitats have different roles in salmon population maintenance with in-channel habitats regulating the overall population size and floodplains acting as recurrent resource pulses. Our study provides a quantitative framework to evaluate the benefit of these two habitat types and provides generalizable rulesets that can be used by managers when implementing habitat restoration strategies for species that inhabit both in-channel and floodplain habitats.

The combined effects of predation, fishing, and ocean productivity on salmon species targeted by marine mammals in the northeast Pacific.

Along the northeast Pacific coast, the salmon-eating southern resident killer whale population (SRKW, Orcinus orca) have been at very low levels since the 1970s. Previous research have suggested that reduction in food availability, especially of Chinook salmon (Oncorhynchus tshawytscha), could be the main limiting factor for the SRKW population. Using the ecosystem modelling platform Ecopath with Ecosim (EwE), this study evaluated if the decline of the Pacific salmon populations between 1979 and 2020 may have been impacted by a combination of factors, including marine mammal predation, fishing activities, and climatic patterns. We found that the total mortality of most Chinook salmon populations has been relatively stable for all mature returning fish despite strong reduction in fishing mortality since the 1990s. This mortality pattern was mainly driven by pinnipeds, with increases in predation between 1979 and 2020 mortality ranging by factors of 1.8 to 8.5 across the different Chinook salmon population groups. The predation mortality on fall-run Chinook salmon smolts originating from the Salish Sea increased 4.6 times from 1979 to 2020, whereas the predation mortality on coho salmon (Oncorhynchus kisutch) smolts increased by a factor of 7.3. The model also revealed that the north Pacific gyre oscillation (NPGO) was the most important large-scale climatic index affecting the stock productivity of Chinook salmon populations from California to northern British Columbia. Overall, the model provided evidence that multiple factors may have affected Chinook salmon populations between 1979 and 2020, and suggested that predation mortality by marine mammals could be an important driver of salmon population declines during that time.

Diets of Native and Non-Native Piscivores in the Stanislaus River, California, Under Contrasting Hydrologic Conditions

The fish communities of the Sacramento–San Joaquin Delta and its tributaries in California’s Central Valley have been irreparably altered through introductions of numerous fish species, including Striped Bass (Morone saxatilis), black bass (Micropterus spp.), and catfishes (Ameiurus spp. and Ictalurus spp.). Research into how predation by non-native piscivores affects native anadromous species has focused on the Sacramento and San Joaquin river mainstems and Delta habitats, through which all anadromous species must pass. Yet, the ranges of non-native fishes extend into upstream tributaries. We collected diets from native and non-native piscivores in the Stanislaus River, a tributary to the San Joaquin River and a remaining stronghold for native fishes. Piscivorous fishes primarily consumed invertebrates and the native species fall-run Chinook Salmon (Oncorhynchus tshawytscha) and Pacific Lamprey (Entosphenus tridentatus). Juvenile Chinook Salmon and Pacific Lamprey were consumed at higher frequencies than any other potential fish prey species, particularly by Striped Bass and black bass. The frequency of native fishes in predator diets was similar across years, despite contrasting hydrologic conditions; 2019 (wet year), 2020 (dry year), and 2021 (critically dry year). Our results show that Pacific Lamprey were frequently consumed by native and non-native piscivores, and that juvenile Chinook Salmon experience substantial predation early in their migration, regardless of hydrologic conditions.

Role of maturation and mortality in portfolio effects and climate resilience

The portfolio effect plays a critical role in population productivity and stability. Age structure of spawning salmon represents an example of portfolio effects such that the risks of experiencing unfavorable conditions are spread across time. However, the distribution of maturation ages for Pacific salmon ( Oncorhynchus spp.) is increasingly concentrated into fewer and younger ages, which may impact population resilience to climate change. We explored the population dynamics of Sacramento River fall-run Chinook salmon ( O. tshawytscha) under different age structure scenarios using a life-cycle model and compared two mechanisms that can underlie these changes—mortality and maturation. In addition, we tested whether age structure promotes resilience to drought. We found that high age structure diversity increased the stability of population size and harvest compared with low diversity. However, mean population size responded differently depending on the underlying mechanism. Reduced mortality of adult fish ages 4–5 increased escapement, whereas delayed maturation decreased escapement. Overall, high age structure diversity was able to buffer against the adverse effects of droughts by reducing the variability of population size and harvest compared with low diversity. Our results suggest that age structure promotes stability of salmon in an increasingly variable climate.

Intraspecific variation among Chinook Salmon populations indicates physiological adaptation to local environmental conditions.

Understanding interpopulation variation is important to predicting species responses to climate change. Recent research has revealed interpopulation variation among several species of Pacific salmonids; however, the environmental drivers of population differences remain elusive. We tested for local adaptation and countergradient variation by assessing interpopulation variation among six populations of fall-run Chinook Salmon from the western United States. Juvenile fish were reared at three temperatures (11, 16 and 20°C), and five physiological metrics were measured (routine and maximum metabolic rate, aerobic scope, growth rate and critical thermal maximum). We then tested associations between these physiological metrics and 15 environmental characteristics (e.g. rearing temperature, latitude, migration distance, etc.). Statistical associations between the five physiological metrics and 15 environmental characteristics supported our hypotheses of local adaptation. Notably, latitude was a poor predictor of population physiology. Instead, our results demonstrate that populations from warmer habitats exhibit higher thermal tolerance (i.e. critical thermal maxima), faster growth when warm acclimated and greater aerobic capacity at high temperatures. Additionally, populations with longer migrations exhibit higher metabolic capacity. However, overall metabolic capacity declined with warm acclimation, indicating that future climate change may reduce metabolic capacity, negatively affecting long-migrating populations. Linking physiological traits to environmental characteristics enables flexible, population-specific management of disparate populations in response to local conditions.

Responses to pathogen exposure in sentinel juvenile fall-run Chinook salmon in the Sacramento River, CA.

This study investigated how the deployment of juvenile Chinook salmon in ambient river conditions and the subsequent exposure to and infection by pathogens was associated with the changes in the expression of genes involved in immune system functioning, general stress and host development. Juvenile fish were deployed in sentinel cages for 21days in the Sacramento River, CA, USA. Gill, kidney and intestinal tissue were sampled at 0, 7, 14 and 21days post-deployment. Pathogen detection and host response were assessed by a combination of molecular and histopathological evaluation. Our findings showed that fish became infected by the parasites Ceratonova shasta, Parvicapsula minibicornis and Ichthyophthirius multifiliis, and to a lesser extent, the bacteria Flavobacterium columnare and Rickettsia-like organisms. Co-infection was common among sentinel fish. Expression of investigated genes was altered following deployment and was often associated with pathogen abundance. This study provides a foundation for future avenues of research investigating pathogens that affect out-migrating Chinook salmon in the Sacramento River, and offers crucial knowledge related to conservation efforts.

Increasing objectivity associated with anadromous fish redd identification using a discriminant function analysis

Many fish species reproduce by creating nests (redds) in alluvial stream gravels, which can be used to track population trends. However, temporal and spatial overlap across multiple redd-building species can hinder redd species classification. This is further complicated when the corresponding adult is not present. Spawning surveys on the Lower American River (LAR) have been conducted since 2003 to document fall-run Chinook Salmon and California Central Valley (CCV) steelhead spawning. Other fish species on the LAR have overlapping reproduction timing, including Pacific Lamprey. Prior to 2016, a redd observed during field surveys that was not associated with a fish observation was assigned species identity based on seasonal timing and professional judgement. However, this method has potential to misidentify the species that built the redd due to overlap in spawning season and similarity in redd dimensions among LAR fish species. To decrease subjectivity associated with unoccupied redd identification, we used occupied redd data to build a discriminant function analysis (DFA), which predicts redd species identity based on field-measured parameters that vary across species including time of year, redd dimensions, and ambient conditions. We compared model accuracy across 6 years in which additional “fish on” observations were added annually to the discriminant function to test whether adding observational data improved model accuracy. We also applied the discriminant function to historical redd data in which species identification was made based on professional judgement to compare the two approaches. DFA accuracy improved with additional years of data, and in the iteration that included the most observational data it was highly accurate in identifying fall-run Chinook Salmon and CCV steelhead (96% and 97%, respectively). Accuracies for Pacific Lamprey were slightly lower (91%) than salmonids due to the relatively low number of “fish-on” redd observations for Pacific Lamprey. Comparisons between the DFA and historical identification based on professional opinion were generally similar, but with up to 19.6% disagreement in some years. Our study demonstrates that physical and temporal metrics can support more accurate species identification, and field data can be used to support more robust population estimates and inform future habitat restoration decisions.

Shedding Kinetics of Infectious Hematopoietic Necrosis Virus (IHNV) in Juvenile Spring- and Fall-Run Chinook Salmon of the Columbia River Basin.

Simple SummaryWhen a virus infects a host it reproduces in that host and then sheds from the host in order to find new hosts for more rounds of reproduction. Thus, virus shedding is a critical step in the host-to-host transmission cycles that allow a virus to spread across a landscape and persist over time. In Pacific salmon and trout the virus infectious hematopoietic necrosis virus (IHNV) causes significant disease, with up to 50% mortality in outbreaks in some conservation hatcheries. Chinook salmon have evolved as two distinct life-history types, referred to as spring- and fall Chinook salmon, and they are the most abundant host of IHNV in the Columbia River basin (CRB) of Washington, Oregon, and Idaho. Here we examined the timing and quantity of virus shedding from both spring-run and fall-run CRB Chinook salmon after controlled exposures to three IHNV strains representing different virus subgroups. We observed rapid shedding kinetics with similar timing for two virus strains in both host types. However, spring Chinook salmon shed much more virus from the UC subgroup than fall fish, suggesting that spring Chinook salmon may play a dominant role in the ecology and maintenance of IHNV in the CRB.This investigation sought to characterize the shedding of infectious hematopoietic necrosis virus (IHNV) in two populations of Columbia River Basin (CRB) Chinook salmon (Oncorhynchus tshawytscha). Juvenile spring- and fall-run Chinook salmon were exposed by immersion to each of three IHN virus strains from the UC, MD, and L subgroups, and then monitored for viral shedding from individual fish for 30 days. Detectable quantities of UC, MD and L IHN virus were shed by a subset of fish from each host population (1–9 out of 10 fish total in each treatment group). Viral shedding kinetics were consistent, with a rapid onset of shedding, peak shedding by 2–3 days, and then a rapid decline to below detectable levels by 7 days’ post-exposure to IHNV. Intraspecies variation was observed as spring Chinook salmon shed more UC virus than fall fish: spring Chinook salmon shed UC virus in greater numbers of fish, with 22-fold higher mean peak shedding magnitude, 33-fold higher mean total virus shed per fish, and 900-fold higher total virus shed per treatment group. The L and MD viruses had comparable shedding at intermediate levels in each host population. All viral shedding occurred well before host mortality began, and shedding magnitude did not correlate with virulence differences. Overall, the greater shedding of UC virus from spring Chinook salmon, combined with low virulence, indicates a uniquely high transmission potential that may explain the predominance of UC viruses in CRB Chinook salmon. This also suggests that spring-run fish may contribute more to the ecology of IHNV in the CRB than fall-run Chinook salmon.

How riparian and floodplain restoration modify the effects of increasing temperature on adult salmon spawner abundance in the Chehalis River, WA.

Stream temperatures in the Pacific Northwest are projected to increase with climate change, placing additional stress on cold-water salmonids. We modeled the potential impact of increased stream temperatures on four anadromous salmonid populations in the Chehalis River Basin (spring-run and fall-run Chinook salmon Oncorhynchus tshawytscha, coho salmon O. kisutch, and steelhead O. mykiss), as well as the potential for floodplain reconnection and stream shade restoration to offset the effects of future temperature increases. In the Chehalis River Basin, peak summer stream temperatures are predicted to increase by as much as 3°C by late-century, but restoration actions can locally decrease temperatures by as much as 6°C. On average, however, basin-wide average stream temperatures are expected to increase because most reaches have low temperature reduction potential for either restoration action relative to climate change. Results from the life cycle models indicated that, without restoration actions, increased summer temperatures are likely to produce significant declines in spawner abundance by late-century for coho (-29%), steelhead (-34%), and spring-run Chinook salmon (-95%), and smaller decreases for fall-run Chinook salmon (-17%). Restoration actions reduced these declines in all cases, although model results suggest that temperature restoration alone may not fully mitigate effects of future temperature increases. Notably, floodplain reconnection provided a greater benefit than riparian restoration for steelhead and both Chinook salmon populations, but riparian restoration provided a greater benefit for coho. This pattern emerged because coho salmon tend to spawn and rear in smaller streams where shade restoration has a larger effect on stream temperature, whereas Chinook and steelhead tend to occupy larger rivers where temperatures are more influenced by floodplain connectivity. Spring-run Chinook salmon are the only population for which peak temperatures affect adult prespawn survival in addition to rearing survival, making them the most sensitive species to increasing stream temperatures.

Variation in Juvenile Salmon Growth Opportunities Across a Shifting Habitat Mosaic

Historically, Chinook Salmon in the California Central Valley reared in the vast wetlands of the Sacramento–San Joaquin Delta. However, more than 95% of floodplain, riparian, and wetland habitats in the Delta have become degraded because of anthropogenic factors such as pollution, introduced species, water diversions, and levees. Despite pronounced habitat loss, previous work using otolith reconstructions has revealed that some juvenile salmon continue to successfully rear for extended periods in the Delta. However, the extent to which the Delta functions to promote salmon growth relative to other habitats remains unknown. In this study, we integrated otolith microstructure (daily increment count and width) and strontium isotope (87Sr/86Sr) records to fill this critical knowledge gap by comparing the growth of natural-origin fall-run Chinook Salmon from the American River that reared in the Delta with those that remained in their natal stream. Using generalized additive models, we compared daily otolith growth rates among rearing habitats (Delta vs. American River) and years (2014 to 2018), encompassing a range of hydrologic conditions. We found that juvenile Chinook Salmon grew faster in the Delta in some years (2016), but slower in the Delta during drought conditions (2014 to 2015). The habitat that featured faster growth rates varied within and among years, suggesting the importance of maintaining a habitat mosaic for juvenile salmonids, particularly in a dynamic environment such as the California Central Valley. Linking otolith chemistry with daily growth increments provides a valuable approach to explore the mechanisms governing interannual variability in growth across habitat types, and a useful tool to quantify the effects of large-scale restoration efforts on native fishes.

Variation in Juvenile Salmon Growth Opportunities Across a Shifting Habitat Mosaic

Historically, Chinook Salmon in the California Central Valley reared in the vast wetlands of the Sacramento–San Joaquin Delta. However, more than 95% of floodplain, riparian, and wetland habitats in the Delta have become degraded because of anthropogenic factors such as pollution, introduced species, water diversions, and levees. Despite pronounced habitat loss, previous work using otolith reconstructions has revealed that some juvenile salmon continue to successfully rear for extended periods in the Delta. However, the extent to which the Delta functions to promote salmon growth relative to other habitats remains unknown. In this study, we integrated otolith microstructure (daily increment count and width) and strontium isotope (87Sr/86Sr) records to fill this critical knowledge gap by comparing the growth of natural-origin fall-run Chinook Salmon from the American River that reared in the Delta with those that remained in their natal stream. Using generalized additive models, we compared daily otolith growth rates among rearing habitats (Delta vs. American River) and years (2014 to 2018), encompassing a range of hydrologic conditions. We found that juvenile Chinook Salmon grew faster in the Delta in some years (2016), but slower in the Delta during drought conditions (2014 to 2015). The habitat that featured faster growth rates varied within and among years, suggesting the importance of maintaining a habitat mosaic for juvenile salmonids, particularly in a dynamic environment such as the California Central Valley. Linking otolith chemistry with daily growth increments provides a valuable approach to explore the mechanisms governing interannual variability in growth across habitat types, and a useful tool to quantify the effects of large-scale restoration efforts on native fishes.

Hypolimnetic oxygenation 6. Improvement in fisheries, hydropower, and drought management with costs of installation and operation in Camanche Reservoir, California, United States

Horne AJ, Faisst WK. 2022. Hypolimnetic oxygenation 6. Improvement in fisheries, hydropower, and drought management with costs of installation and operation in Camanche Reservoir, California, United States. Lake Reserv Manage. XX:XXX–XXX. A hypolimnetic oxygenation system (HOS) was installed in Camanche Reservoir, California, in 1993 to eliminate hatchery fish kills caused by hydrogen sulfide in dam tailwaters. It operates from about June through October each year. Algae, nutrients, heavy metals, and turbidity also declined. Fall run Chinook salmon (Oncorhynchus tshawytscha) increased by 3550/yr or 265%. Threatened steelhead trout (O. mykiss), which spend more time in the river than Chinook, benefited more (625%). A 3 yr delay in elevated adult returns indicated that the HOS’s main effect was improved in-river water quality for juvenile fish, rather than better adult attraction flows. Using the California State economist’s value of $1172 for an adult Chinook to freshwater anglers, the increase due to HOS added $6.5 million/yr to California’s recreation. The in-reservoir coldwater fishery improved because dissolved oxygen in the hypolimnion increased from <1 mg/L to ∼5 mg/L. Oxygenation allowed summer operation of a 10.7 MW hydropower plant, making HOS carbon neutral. During droughts, improved water quality at lower reservoir levels reduced dependence on alternative supplies and supported full hatchery operation and in-river spawning. Oxygen addition ($0.64/kg) was much cheaper than nitrate addition ($104/kg). Averaged over 20 yr, HOS reduced phosphorus ($19.3/kg vs. alum addition at $16/kg) and ammonia/nitrate ($2/kg). Iron ($0.0005/kg) and manganese were reduced at lower cost than for conventional methods ($9/kg). Copper ($4441/kg) and zinc ($2169/kg) fell below chronic toxicity levels. Capital cost for HOS was $1.87 million in 1993 or $30,390/km2 ($1248/acre). Operation and management averaged $191,288/yr (1993–2000).

Phenomenological and mechanistic modeling of recreational angling behavior using creel data

Improved understanding of angling behavior in recreational fisheries can help managers account for partial controllability in systems in which angling effort is not directly regulated. Relevant aspects of angling behavior include fishing participation, site choice, and catch-and-release actions and can be considered at scales of both aggregate fishing effort and individual-decision-making. Using creel survey data collected across eight fishery seasons, we predicted aggregate angling effort (e.g., daily number of boating trips engaged in fishing) and characterized influences of individual trip-based site choice for recreational fisheries acting on fall-run Chinook salmon and coho salmon near the mouth of the Columbia River, United States of America. We applied an overdispersed Poisson likelihood-based generalized linear model with an autoregressive structure to aggregate boating effort and a multinomial logit model to trip-based site choice decisions among separate ocean and estuary fishing zones. Predictive models explained 71% and 79% of out-of-sample and in-sample variability in aggregate effort, respectively, and included the covariates weekend status, Chinook salmon catch rate, tidal range, and pre-season expectations of fish abundance. In addition to reinforcing the importance of Chinook salmon catch rate and tidal range, site choice model selection revealed influences of weather, fishery restrictions, expected fishery season lengths, and the individual-specific characteristics of boat length and guide status on decision-making. Model results provide predictive models for short-term fishery planning, highlight heterogeneity in individual decision-making, and illustrate the value of standardized creel data for evaluating angling behavior.

The effect of temperature on specific dynamic action of juvenile fall-run Chinook salmon, Oncorhynchus tshawytscha.

Juvenile fall-run Chinook salmon (Oncorhynchus tshawytscha) in the Sacramento-San Joaquin River Basin experience temporally and spatially heterogenous temperature regimes, between cool upper tributaries and the warm channelized Delta, during freshwater rearing and outmigration. Limited water resources necessitate human management of dam releases, allowing temperature modifications. The objective of this study was to examine the effect of temperature on specific dynamic action (SDA), or the metabolic cost associated with feeding and digestion, which is thought to represent a substantial portion of fish energy budgets. Measuring SDA with respect to absolute aerobic scope (AAS), estimated by the difference between maximum metabolic rate (MMR) and standard metabolic rate (SMR), provides a snapshot of its respective energy allocation. Fish were acclimated to 16°C, raised or lowered to each acute temperature (13°C, 16°C, 19°C, 22°C or 24°C), then fed a meal of commercial pellets weighing 2% of their wet mass. We detected a significant positive effect of temperature on SMR and MMR, but not on AAS. As expected, there was no significant effect of temperature on the total O2 cost of digestion, but unlike other studies, we did not see a significant difference in duration, peak metabolic rate standardized to SMR, time to peak, percent of meal energy utilized, nor the ratio of peak O2 consumption to SMR. Peak O2 consumption represented 10.4-14.5% of AAS leaving a large amount of aerobic capacity available for other activities, and meal energy utilized for digestion ranged from 5.7% to 7.2%, leaving substantial remaining energy to potentially assimilate for growth. Our juvenile fall-run Chinook salmon exhibited thermal stability in their SDA response, which may play a role in maintaining homeostasis of digestive capability in a highly heterogeneous thermal environment where rapid growth is important for successful competition with conspecifics and for avoiding predation.

Identifying the potential of anadromous salmonid habitat restoration with life cycle models.

An investigation into the causes of species decline should include examination of habitats important for multiple life stages. Integrating habitat impacts across life stages with life-cycle models (LCMs) can reveal habitat impairments inhibiting recovery and help guide restoration efforts. As part of the final elements of the Habitat Restoration Planning model (HARP; Beechie et al. this volume), we developed LCMs for four populations of three species of anadromous salmonids (Oncorhynchus kisutch, O. tshawytscha, and O. mykiss), and ran diagnostic scenarios to examine effects of barrier removal, fine sediment reduction, wood augmentation, riparian shade, restoration of the main channel and bank conditions, beaver pond restoration, and floodplain reconnection. In the wood scenario, spawner abundance for all populations increased moderately (29–48%). In the shade scenario, spring-run Chinook salmon abundance increased the most (48%) and fall-run Chinook salmon and steelhead were much less responsive. Coho responded strongly to the beaver pond and floodplain scenarios (76% and 54%, respectively). The fine sediment scenario most benefitted fall- and spring-run Chinook salmon (32–63%), whereas steelhead and coho were less responsive (11–21% increase). More observations are needed to understand high fine sediment and its impacts. Our LCMs were region-specific, identifying places where habitat actions had the highest potential effects. For example, the increase in spring-run Chinook salmon in the wood scenario was driven by the Cascade Mountains Ecological Region. And, although the overall response of coho salmon was small in the barrier removal scenario (6% increase at the scale of the entire basin), barrier removals had important sub-regional impacts. The HARP analysis revealed basin-wide and regional population-specific potential benefits by action types, and this habitat-based approach could be used to develop restoration strategies and guide population rebuilding. An important next step will be to ground-truth our findings with robust empirically-based estimates of life stage-specific survivals and abundances.

Reconciling fish and farms: Methods for managing California rice fields as salmon habitat.

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in California’s Central Valley have emerged as ecologically functioning floodplain rearing habitat for juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods to enhance habitat benefits for fall-run Chinook Salmon reared on winter-flooded rice fields in the Yolo Bypass, a modified floodplain managed for flood control, agriculture, and wildlife habitat in the Sacramento River Valley of California. Investigations included studying the effect of 1) post-harvest field substrate; 2) depth refugia; 3) duration of field drainage; and 4) duration of rearing occupancy on in-situ diet, growth and survival of juvenile salmon. Post-harvest substrate treatment had only a small effect on the lower trophic food web and an insignificant effect on growth rates or survival of rearing hatchery-origin, fall-run Chinook Salmon. Similarly, depth refugia, created by trenches dug to various depths, also had an insignificant effect on survival. Rapid field drainage yielded significantly higher survival compared to drainage methods drawn out over longer periods. A mortality of approximately one third was observed in the first week after fish were released in the floodplain. This initial mortality event was followed by high, stable survival rates for the remainder of the 6-week duration of floodplain rearing study. Across years, in-field survival ranged 7.4–61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in California’s recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incremental improvements in design to increase survival. Zooplankton (fish food) in the winter-flooded rice fields were 53-150x more abundant than those sampled concurrently in the adjacent Sacramento River channel. Correspondingly, observed somatic growth rates of juvenile hatchery-sourced fall-run Chinook Salmon stocked in rice fields were two to five times greater than concurrently and previously observed growth rates in the adjacent Sacramento River. The abundance of food resources and exceptionally high growth rates observed during these experiments illustrate the potential benefits of using existing agricultural infrastructure to approximate the floodplain wetland physical conditions and hydrologic patterns (shallow, long-duration inundation of cool floodplain habitats in mid-winter) under which Chinook Salmon evolved and to which they are adapted.

Differential sensitivity to warming and hypoxia during development and long-term effects of developmental exposure in early life stage Chinook salmon.

Warming and hypoxia are two stressors commonly found within natural salmon redds that are likely to co-occur. Warming and hypoxia can interact physiologically, but their combined effects during fish development remain poorly studied, particularly stage-specific effects and potential carry-over effects. To test the impacts of warm water temperature and hypoxia as individual and combined developmental stressors, late fall-run Chinook salmon embryos were reared in 10 treatments from fertilization through hatching with two temperatures [10°C (ambient) and 14°C (warm)], two dissolved oxygen saturation levels [normoxia (100% air saturation, 10.4-11.4mg O2/l) and hypoxia (50% saturation, 5.5mg O2/l)] and three exposure times (early [eyed stage], late [silver-eyed stage] and chronic [fertilization through hatching]). After hatching, all treatments were transferred to control conditions (10°C and 100% air saturation) through the fry stage. To study stage-specific effects of stressor exposure we measured routine metabolic rate (RMR) at two embryonic stages, hatching success and growth. To evaluate carry-over effects, where conditions during one life stage influence performance in a later stage, RMR of all treatments was measured in control conditions at two post-hatch stages and acute stress tolerance was measured at the fry stage. We found evidence of stage-specific effects of both stressors during exposure and carry-over effects on physiological performance. Both individual stressors affected RMR, growth and developmental rate while multiple stressors late in development reduced hatching success. RMR post-hatch showed persistent effects of embryonic stressor exposure that may underlie differences observed in developmental timing and acute stress tolerance. The responses to stressors that varied by stage during development suggest that stage-specific management efforts could support salmon embryo survival. The persistent carry-over effects also indicate that considering sub-lethal effects of developmental stressor exposure may be important to understanding how climate change influences the performance of salmon across life stages.

Assessing contributions of cold-water refuges to reproductive migration corridor conditions for adult salmon and steelhead trout in the Columbia River, USA

Diadromous fish populations face multiple challenges along their migratory routes. These challenges include suboptimal water quality, harvest, and barriers to longitudinal and lateral connectivity. Interactions among factors influencing migration success make it challenging to assess management options for improving migratory fish conditions along riverine migration corridors. We describe a spatially explicit simulation model that integrates complex individual behaviors of fall-run Chinook Salmon (Oncorhynchus tshawytscha) and summer-run steelhead trout (O. mykiss) during migration, responds to variable habitat conditions over a large extent of the Columbia River, and links migration corridor conditions to fish condition outcomes. The model is built around a mechanistic behavioral decision tree that drives individual interactions of fish within their simulated environments. By simulating several thermalscapes with alternative scenarios of thermal refuge availability, we examined how behavioral thermoregulation in cold-water refuges influenced migrating fish conditions. Outcomes of the migration corridor simulation model show that cold-water refuges can provide relief from exposure to high water temperatures, but do not substantially contribute to energy conservation by migrating adults. Simulated cooling of the Columbia River decreased reliance on cold-water refuges and there were slight reductions in migratory energy expenditure. This modeling of simulated thermalscapes provides a framework for assessing the contribution of cold-water refuges to the success of migrating fishes, but any final determination will depend on analyzing fish survival and health for their entire migration, water temperature management goals and species recovery targets.

Contrasting the migratory behavior and stranding risk of White Sturgeon and Chinook Salmon in a modified floodplain of California

While navigating through the same migratory corridor, different species may experience differing reproductive success due the interaction of species-specific movement behavior with habitat configuration. We contrasted the migratory behavior of White Sturgeon Acipenser transmontanus and fall-run Chinook Salmon Oncorhynchus tshawytscha, two native fishes in Central Valley of California. These species co-occur in the region’s Yolo Bypass floodplain seasonally, but they represent disparate reproductive strategies: White Sturgeon are iteroparous, spawning multiple times throughout their lifespan, while Chinook Salmon are semelparous, spawning only once in their lifespan. Except for brief windows when the Yolo Bypass connected to the Sacramento River during flood conditions, migrating White Sturgeon and Chinook Salmon that entered the Bypass from 2012 to 2018 had to turn around and exit it in order to complete a successful spawning migration up the Sacramento River. This “exit behavior” was critical to migratory success when the Bypass was not flooded. Between March 2012 and May 2018, the median probability of acoustically-tagged fall-run Chinook Salmon exiting the Yolo Bypass at its southern extent was estimated to be 0.74 (0.58–0.87 95% credible interval), while an individual White Sturgeon had a median exit probability of 0.99 (0.96–1.00 95% credible interval). Our results suggest that White Sturgeon successfully exit the Yolo Bypass more consistently than fall-run Chinook Salmon, indicating that fall-run Chinook Salmon are at higher risk of stranding in the Yolo Bypass. The difference in probability of exit between these two species has implications for how to manage for migratory success in altered habitats. Floodplain · Fish passage · Bayesian · Telemetry · Behavioral ecology · Movement · Stranding.

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.