Freshwater Life Stages Research Articles

Assessing climate change impacts on North American freshwater habitat of wild Atlantic salmon - urgent needs for collaborative research

Climate change and human activities have dramatically affected all ecosystems inhabited by Atlantic salmon, causing drastic population declines. Change in river temperature dynamics (e.g. daily variability, frequency, and duration of summer maximum, warmer thermal regimes) is of special concern as it impacts growth rates, reproductive success, prey abundance and phenology, timing of migration, and ultimately survival. The Atlantic Salmon Research Joint Venture held a workshop to address the effects of climate change on freshwater habitats of Atlantic salmon and identify research gaps and priorities. Here we summarize the state of the science for three key themes identified by workshop participants: (1) Effects of climate change on in-river habitat conditions, (2) Physiological and behavioral responses of salmon to temperature, and (3) Population-level responses of salmon to climate change. The group highlighted the crucial importance of understanding and monitoring the links between river temperature dynamics and physiological requirements of Atlantic salmon across different life stages and habitat conditions, with a focus on freshwater life stages. Climate change will undoubtedly continue to affect instream habitats across all seasons and render challenging conditions for all freshwater Atlantic salmon life stages. Hence, we call for urgent interdisciplinary collaborations and partnerships among scientists and managers to address the pressing research gaps that require large-scale data integration across life cycle stages and ecosystems. More collaboration between scientists, managers, and interest groups is needed to ensure that fundamental science directly addresses the knowledge-action gap to enhance evidence-based decision-making and conservation.

Population variability in thermal performance of pre-spawning adult Chinook salmon.

Climate change is causing large declines in many Pacific salmon populations. In particular, warm rivers are associated with high levels of premature mortality in migrating adults. The Fraser River watershed in British Columbia, Canada, supports some of the largest Chinook salmon (Oncorhynchus tshawytscha) runs in the world. However, the Fraser River is warming at a rate that threatens these populations at critical freshwater life stages. A growing body of literature suggests salmonids are locally adapted to their thermal migratory experience, and thus, population-specific thermal performance information can aid in management decisions. We compared the thermal performance of pre-spawning adult Chinook salmon from two populations, a coastal fall-run from the Chilliwack River (125km cooler migration) and an interior summer-run from the Shuswap River (565km warmer migration). We acutely exposed fish to temperatures reflecting current (12°C, 18°C) and future projected temperatures (21°C, 24°C) in the Fraser River and assessed survival, aerobic capacity (resting and maximum metabolic rates, absolute aerobic scope (AAS), muscle and ventricle citrate synthase), anaerobic capacity (muscle and ventricle lactate dehydrogenase) and recovery capacity (post-exercise metabolism, blood physiology, tissue lactate). Chilliwack Chinook salmon performed worse at high temperatures, indicated by elevated mortality, reduced breadth in AAS, enhanced plasma lactate and potassium levels and elevated tissue lactate concentrations compared with Shuswap Chinook salmon. At water temperatures exceeding the upper pejus temperatures (Tpejus, defined here as 80% of maximum AAS) of Chilliwack (18.7°C) and Shuswap (20.2°C) Chinook salmon populations, physiological performance will decline and affect migration and survival to spawn. Our results reveal population differences in pre-spawning Chinook salmon performance across scales of biological organization at ecologically relevant temperatures. Given the rapid warming of rivers, we show that it is critical to consider the intra-specific variation in thermal physiology to assist in the conservation and management of Pacific salmon.

Basin-scale spatiotemporal distribution of ayu Plecoglossus altivelis and its relationship with water temperature from summer growth to autumn spawning periods

As climate warming progresses, it becomes necessary to study the effects of water temperature on the basin-scale dynamic distribution of riverine fish. This study examined the spatiotemporal distribution of Plecoglossus altivelis using the environmental DNA approach and its relationship with water temperature from summer growth to autumn spawning periods in the Nagara River basin, central Japan. The overall results of the spatiotemporal distribution of P. altivelis were consistent with the known life history: a wide-range distribution in the basin during summer and aggregation in the middle mainstem during autumn. Additionally, this study found three intriguing distribution patterns depending on water temperature. During summer (August), the warmest period, P. altivelis was distributed in the upper mainstem, one tributary, and the mainstem downstream of the tributary confluences in relation to the relatively colder water (< 25 °C). During early autumn (September–early October), it spread widely in the middle and upper mainstem without the constraint of the upper limit of water temperature. During late autumn (late October–November), it steadily aggregated to the middle mainstem because of downstream migration for spawning at water temperatures below 20 °C. This study suggests the importance of river connectivity for P. altivelis migration to suitable habitats during its freshwater life stages, upper mainstem and tributaries as summer growth habitats, and cooling effects of tributaries on the mainstem during mid-summer.

Dietary plant oil supplemented with arachidonic acid and eicosapentaenoic acid affects the fatty acid composition and eicosanoid metabolism of Atlantic salmon (Salmo salar L.) during smoltification

This study sought to investigate whether a “natural diet” (mimicking the fatty acid composition of freshwater aquatic insects eaten by salmon parr) during the freshwater (FW) life stage of pre-smolt Atlantic salmon (Salmo salar L.) affected red blood cells and gill fatty acid composition as well as eicosanoid metabolism in gill during smolting at different temperatures. Before being transferred to seawater (SW), salmon parr were fed with a modified (MO) diet containing vegetable oils (rapeseed, palm, and linseed oils) supplemented with eicosapentaenoic acid (EPA) and arachidonic acid (ARA) to completely replace the fish oil (FO). Fatty acid composition in red blood cells and gill tissues was determined before SW transfer and six weeks after. Additionally, the expression of genes associated with eicosanoid metabolism and Na+/K+-ATPase (NKA) activity in salmon gill was examined at different temperatures before SW transfer and 24 h after. The results showed the changes in fatty acid composition, including sum monounsaturated fatty acids (MUFAs), docosahexaenoic acid (DHA), ARA, EPA, and sum n-6 polyunsaturated fatty acids (n-6 PUFA) in both red blood cells and gill tissues at the FW stage were consistent with the fatty acid profiles of the supplied MO and FO fish diets; however sum EPA and DHA composition exhibited opposite trends to those of the FO diet. The proportion of ARA, EPA, and n-6 PUFA increased, whereas sum MUFAs and DHA decreased in the red blood cells and gill tissues of MO-fed fish compared to those fed with the FO diet at FW stage. Additionally, 5-lipoxygenase-activating protein (Flap) expression was downregulated in MO-fed fish prior to SW transfer. During the process of SW transfer at different temperatures, the MO diet remarkably suppressed NKAα1a expression in MO-fed fish both at 12 and 16 °C. The MO diet also upregulated phospholipase A2 group IV (PLA2g4) expression in gills at 8, 12, and 16 °C, but suppressed phospholipase A2 group VI (PLA2g6) expression in gills at 12 °C compared to FO-fed fish at 12 °C and MO-fed fish at 8 °C. The MO diet also upregulated Cyclooxygenase 2 (Cox-2) expression at 8 °C compared to FO-fed fish and increased Arachidonate 5-lipoxygenase (5-Lox) expression in MO-fed fish at 16 °C compared to both FO-fed fish at 16 °C and MO-fed fish at 8 °C. Our study also determined that both SW transfer water temperatures and diets during the FW period jointly influenced the mRNA expression of PLA2g4, PLA2g6, and Lpl, whereas 5-Lox was more sensitive to dietary changes. In conclusion, the MO diet affected the fatty acid composition in gill and in red blood cells. When transferred to SW, dietary ARA supplementation could promote the bioavailability for eicosanoid synthesis in gill mainly via PLA2g4 activation, and potentially inhibit the stress and inflammatory response caused by different water temperatures through dietary EPA supplementation.

Quantification of thermal impacts across freshwater life stages to improve temperature management for anadromous salmonids.

Water temperature is the major controlling factor that shapes the physiology, behaviour and, ultimately, survival of aquatic ectotherms. Here we examine temperature effects on the survival of Chinook salmon (Oncorhynchus tshawytscha), a species of high economic and conservation importance. We implement a framework to assess how incremental changes in temperature impact survival across populations that is based on thermal performance models for three freshwater life stages of Chinook salmon. These temperature-dependent models were combined with local spatial distribution and phenology data to translate spatial–temporal stream temperature data into maps of life stage-specific physiological performance in space and time. Specifically, we converted temperature-dependent performance (i.e. energy used by pre-spawned adults, mortality of incubating embryos and juvenile growth rate) into a common currency that measures survival in order to compare thermal effects across life stages. Based on temperature data from two abnormally warm and dry years for three managed rivers in the Central Valley, California, temperature-dependent mortality during pre-spawning holding was higher than embryonic mortality or juvenile mortality prior to smolting. However, we found that local phenology and spatial distribution helped to mitigate negative thermal impacts. In a theoretical application, we showed that high temperatures may inhibit successful reintroduction of threatened Central Valley spring-run Chinook salmon to two rivers where they have been extirpated. To increase Chinook salmon population sizes, especially for the threatened and declining spring-run, our results indicate that adults may need more cold-water holding habitat than currently available in order to reduce pre-spawning mortality stemming from high temperatures. To conclude, our framework is an effective way to calculate thermal impacts on multiple salmonid populations and life stages within a river over time, providing local managers the information to minimize negative thermal impacts on salmonid populations, particularly important during years when cold-water resources are scarce.

Physical and biological constraints on the capacity for life-history expression of anadromous salmonids: an Eel River, California, case study

Recovery of anadromous salmonid populations is complicated by their complex life histories. We examined the spatiotemporal interplay of stream temperature, geomorphic features, and a species’ thermal sensitivity mediated by biological interactions in a case study of steelhead trout (Oncorhynchus mykiss) and Chinook salmon (Oncorhynchus tshawytscha) in California’s Eel River watershed. We estimated habitat suitability and fish capacity for each salmonid run and freshwater life stage during average, cool, and warm years in each of the watershed’s subbasins, including a historically occupied high-elevation subbasin upstream of an impassable dam. Our estimates varied depending on whether we accounted for exposure to the Sacramento pikeminnow (Ptychocheilus grandis), an introduced predator and competitor. Our results indicate that the dammed subbasin has substantial salmonid capacity relative to the rest of the watershed and could provide an important cool-water refuge during warm years and from pikeminnow, potentially improving the productivity and resilience of multiple anadromous salmonid populations. Our approach can be applied in any setting where spatially explicit habitat metrics can be estimated and population-specific and life-stage-specific habitat criteria can be specified.

Trace element content in tissues of sockeye salmon from several waterbodies of the Kamchatka Peninsula

The results of the study of macro- (Ca, Mg) and micro- (Mn, Zn, Cu, Fe) elements content in the pectoral fin tissue of adult sockeye salmon Oncorhynchus nerka from the rivers Bolshaya and Kamchatka as well as from Azabachye Lake (Kamchatka Peninsula) are presented. The significant differences in the contents in samples from the three waterbodies were found. It was ascertained that the largest ash proportion (and the mass fraction of trace elements) in dry matter contained in the tissues of sockeye salmon from Kamchatka River, the smallest in the sample of Azabachye Lake. The Ca content was 98 % of the ash mass in all samples; Mg accounted for slightly less than 2 %. The proportion of the remaining elements varied within 0.1 %, and exactly in this range the differences in the microelement composition between the samples were revealed. In sockeye salmon tissues from the Kamchatka River, the content of heavy metals as well as Ca and Mg was higher than in other samples, and their percentage ratio considerably differed from the others. Obviously, the water bodies studied sufficiently distinguish in hydrochemical indices, and that is the cause of differences in bioaccumulation intensities of trace elements in fish tissues at the freshwater life stage.

Vertebral deformities in interspecific diploid and triploid salmonid hybrids.

Vertebral deformities in salmonid interspecific hybrids, some of which were triploidised, were assessed across three separate year classes during the freshwater life stage. Initially, eggs from a farmed Atlantic salmon Salmo salar were crossed with the sperm from a S. salar, arctic char Salvelinus alpinus or brown trout Salmo trutta. For S. salar × S. trutta, half the eggs were triploidised. In a second- and third-year class, the eggs from a farmed S. salar were crossed with the sperm from either a S. salar or a S. trutta, and half of each group was triploidised. In the two initial-year classes, all hybrids were larger than the S. salar controls, and triploid S. salar × S. trutta were larger than diploid counterparts. In the third-year class, the S. salar × S. trutta were smaller than the S. salar, in contrast to the initial 2 year classes, although the triploid hybrids were still larger than the diploids. In the third-year class, a high degree of spontaneous triploidy was also observed in the putative diploid groups (between 16 and 39%). Vertebral deformities were consistently higher in pressure-shocked triploids than diploids, irrespective of hybridisation, but there was no consistent effect of hybridisation among experiments. Although this study was not able to explain the contrasting results for vertebral deformities between year classes, triploid S. salar × S. trutta can demonstrate impressive freshwater growth that could be of interest for future farming programmes.

Oversummer growth and survival of juvenile coho salmon (Oncorhynchus kisutch) across a natural gradient of stream water temperature and prey availability: an in situ enclosure experiment

Conservation efforts for Pacific salmon (Oncorhynchus spp.) increasingly prioritize maintenance of cool water temperatures that protect all freshwater life stages. However, development of appropriate temperature standards requires a robust understanding of the interactions among water temperature, ecosystem productivity, and fish performance. We used a series of in situ enclosures to examine how natural spatiotemporal gradients in thermal conditions and prey availability affected the summer growth and survival of age-0+ coho salmon (Oncorhynchus kisutch). Coho salmon absolute growth rates peaked at a mean daily average water temperature (mean T) of 16.6 °C and an associated maximum weekly maximum temperature (MWMT) of 21.1 °C. Juvenile growth under these thermal conditions was sixfold greater than the growth rates observed for conspecifics rearing in the coolest study reach (mean T = 13.0 °C; MWMT = 16.0 °C). Even at the highest rearing temperature (mean T = 18.1 °C; MWMT = 24.0 °C), growth rates remained positive and above the study-wide average, although overall survival was reduced. Among the predictor variables examined, invertebrate prey abundance was the predominant factor influencing age-0+ coho salmon growth. These results suggest that abundant prey resources may mitigate the negative effects of elevated water temperature on fish growth in riverine environments. Given the likelihood of increasing stream temperatures with climate change, productive ecosystems may provide critical refuges for juvenile salmonids.

Insights from an individual based model of a fish population on a large regulated river

On regulated rivers, managers must understand how drivers they can influence interact with the system to affect the health of resident fish populations. One potential way to gain insight into how these drivers interact or act in insolation is with individual based models (IBM), which can take numerous environmental drivers as inputs and mechanistically simulate their effects on the individuals in the system. This paper uses inSALMO, a spatially explicit IBM for salmon freshwater life stages, to examine how eight different drivers affect nine response variables for winter run Chinook salmon on the Sacramento River, CA. This paper examines the effects spawner numbers, spawner timing, water temperature, flow rate, turbidity, habitat cover, gravel area, and food concentration on superimposition, temperature induced egg mortality, predation, stranding, poor condition mortality, age at out-migration, length at out-migration, number of out-migrants, and juvenile size distribution. Notable results included: flow’s lack of effect on juvenile stranding and small effect on final out-migrant count, the degree to which flow affects superimposition risk, temperature having the largest effect on final juvenile out-migrant count, the interaction between predation and temperature induced egg mortality which produces a constantly decreasing out-migration count with temperature, and the level at which gravel additions would not have added benefits for superimposition mortality. While this method uses simulations, and thus will not have perfectly fidelity to the system, it is a cost-effective and quick method for gaining a mechanistically derived understanding of the complex relationships between numerous drivers and response variables.

Atlantic salmon return rate increases with smolt length

AbstractRecent declines in Atlantic salmon Salmo salar populations are generally attributed to factors in their marine life-phase. However, it is postulated that factors affecting their freshwater life-phase might impact their marine survival, such as the influence of body size. While larger smolts are widely hypothesized to have higher marine survival rates, empirical support remains scant, in part due to inadequate data and ambiguous statistical analyses. Here, we test the influence of smolt body size on marine return rates, a proxy for marine survival, using a 12-year dataset of 3688 smolts tagged with passive integrated transponders in the River Frome, Southern England. State-space models describe the probability of smolts surviving their marine phase to return as 1 sea-winter (1SW) or multi-sea-winter adults as a function of their length, while accounting for imperfect detection and missing data. Models predicted that larger smolts had higher return rates; the most parsimonious model included the effect of length on 1SW return rate. This prediction is concerning, as freshwater juvenile salmon are decreasing in size on the River Frome, and elsewhere. Thus, to maximize adult returns, restoration efforts should focus on freshwater life-stages, and maximize both the number and the size of emigrating smolts.

Climbing the ladder: an evaluation of three different anguillid eel climbing substrata and placement of upstream passage solutions at migration barriers

AbstractConservation programmes for endangered, long‐lived and migratory species often have to target multiple life stages. The bottlenecks associated with the survival of juvenile anguillid eels migrating into inland waters, the survival and growth of the freshwater life stage, as well as the recruitment and survival of silver eels, migrating back to the ocean to spawn, must be resolved. In this study, we focus on the efficiency of passage solutions for upstream‐migrating juveniles. Such solutions can consist of inclined ramps lined with wetted climbing substrata. We evaluated different commonly used substrata in a controlled experiment, recorded eel behaviour at the entrance of the ramp with infrared videography and validated the experimental results at a hydropower dam, where we also investigated the effects of ramp placement on performance. In the experiment on eel substratum selection, 40% of the eels passed in lanes with studded substratum, whereas only 21 and 5% passed using open weave and bristle substrata respectively. Video analysis revealed that the studded substratum attracted more approaches and initiated climbs than the other substrata, but once a climb had been initiated, passage success rates did not differ between substrata. Eels using the studded substratum climbed 26% faster than those using the bristle substratum and almost four times as fast as those climbing in the open weave. The superior performance of the studded substratum was supported by data from the field validation. Moreover, ramps positioned by the bank with low water velocities caught the most eels, but proximity to the dam had no effect on performance. To strengthen the European eel population, more juveniles need to reach their freshwater feeding grounds. A critical step to achieve this increase is to equip upstream passage solutions with suitable substrata and to optimize ramp placement at migration obstacles.

Condition-dependent skipped spawning in anadromous brown trout (Salmo trutta)

Repeat spawners of anadromous salmonids may contribute significantly to population resilience by providing multiple cohorts to both seawater and freshwater life stages. In this study, winter survival of sea trout (Salmo trutta Linnaeus, 1758) post spawners (kelts) was 89%. Sea survival increased linearly with female length with a return probability between 30% and 50%, whereas males attained a maximum return probability of 60% at 520 mm. Of the returning sea trout, 40% skipped spawning and they had significantly lower condition factor as kelts compared with those who returned after one summer. These results suggest that sex-specific differences in individual post-spawning growth–survival trade-off exist and that energetic status of descending kelts may influence the probability to skip spawning. We discuss to what extent hydropower may reduce post-spawning survival due to blocking of river descent opportunities, potentially altering the fitness landscape and favouring new life-history adaptations. From a management perspective, it is concluded that it is crucial to maintain connectivity in regulated rivers, allowing fish to complete repetitive spawning and feeding migrations, thus contributing to population productivity.

Hydropower and high productivity in the Hanford Reach: A synthesis of how flow management may benefit fall Chinook Salmon in the Columbia River, USA

The fall Chinook Salmon (Oncorhynchus tshawytscha) population that spawns in the Hanford Reach of the Columbia River, USA is paradoxical because it is located above 4 and below 10 main stem Columbia River dams and yet is one of the largest and most productive C. salmon populations in the Pacific Northwest. A synthesis of information collected in the Hanford Reach reveals that the hydrosystem above the Hanford Reach and the management of river flows may have contributed to the recent size and productivity of this salmon population. Mechanisms for high survival and capacity at each freshwater life stage have been identified. Plausible mechanisms for contributing to high spawning capacity include: (a) more spawning habitat available during the spawning period. Plausible mechanisms for high egg‐to‐presmolt survival include: (a) reduced desiccation of redds, (b) reduced scour of redds, (c) reduced sedimentation in redds, (d) improved flow exchange within redds, and (e) increased food availability. Smolt survival may also be enhanced through the large size they attain in the Hanford Reach. This synthesis of information provides an uncommon assessment of some the positive effects of flow management from hydropower dams on a valued native fish that has occurred over the last three decades. WIREs Water 2018, 5:e1275. doi: 10.1002/wat2.1275This article is categorized under: Water and Life &gt; Stresses and Pressures on Ecosystems Water and Life &gt; Conservation, Management, and Awareness

Conservation Challenges and Research Needs for Pacific Lamprey in the Columbia River Basin

The Pacific Lamprey Entosphenus tridentatus, an anadromous fish native to the northern Pacific Ocean and bordering freshwater habitats, has recently experienced steep declines in abundance and range contractions along the West Coast of North America. During the early 1990s, Native American tribes recognized the declining numbers of lamprey and championed their importance. In 2012, 26 entities signed a conservation agreement to coordinate and implement restoration and research for Pacific Lamprey. Regional plans have identified numerous threats, monitoring needs, and strategies to conserve and restore Pacific Lamprey during their freshwater life stages. Prime among these are needs to improve lamprey passage, restore freshwater habitats, educate stakeholders, and implement lamprey‐specific research and management protocols. Key unknowns include range‐wide trends in status, population dynamics, population delineation, limiting factors, and marine influences. We synthesize these key unknowns, with a focus on the freshwater life stages of lamprey in the Columbia River basin.

Upscaling site‐scale ecohydraulic models to inform salmonid population‐level life cycle modeling and restoration actions – Lessons from the Columbia River Basin

AbstractWith high‐resolution topography and imagery in fluvial environments, the potential to quantify physical fish habitat at the reach scale has never been better. Increased availability of hydraulic, temperature and food availability data and models have given rise to a host of species and life stage specific ecohydraulic fish habitat models ranging from simple, empirical habitat suitability curve driven models, to fuzzy inference systems to fully mechanistic bioenergetic models. However, few examples exist where such information has been upscaled appropriately to evaluate entire fish populations. We present a framework for applying such ecohydraulic models from over 905 sites in 12 sub‐watersheds of the Columbia River Basin (USA), to assess status and trends in anadromous salmon populations. We automated the simulation of computational engines to drive the hydraulics, and subsequent ecohydraulic models using cloud computing for over 2075 visits from 2011 to 2015 at 905 sites. We also characterize each site's geomorphic reach type, habitat condition, geomorphic unit assemblage, primary production potential and thermal regime. We then independently produce drainage network‐scale models to estimate these same parameters from coarser, remotely sensed data available across entire populations within the Columbia River Basin. These variables give us a basis for imputation of reach‐scale capacity estimates across drainage networks. Combining capacity estimates with survival estimates from mark–recapture monitoring allows a more robust quantification of capacity for freshwater life stages (i.e. adult spawning, juvenile rearing) of the anadromous life cycle. We use these data to drive life cycle models of populations, which not only include the freshwater life stages but also the marine and migration life stages through the hydropower system. More fundamentally, we can begin to look at more realistic, spatially explicit, tributary habitat restoration scenarios to examine whether the enormous financial investment on such restoration actions can help recover these populations or prevent their extinction. Copyright © 2017 John Wiley &amp; Sons, Ltd.

Incorporating thermal requirements into flow regime development for multiple Pacific salmonid species in regulated rivers

It has long been recognized that altered flow regimes and warm water temperature are among major stressors that have contributed to the precipitous decline of salmonid populations in California’s Central Valley, resulting in many of them being listed as endangered or threatened pursuant to the U.S. Endangered Species Act. While it is widely acknowledged that water temperature affects all freshwater life stages of salmonids, it has not been a focus when developing instream flow requirements. In this study, we developed a framework that incorporates water temperature requirements into flow regime development for multiple Pacific salmonid species. We applied this framework to Clear Creek, an upper Central Valley stream that supports three salmonid species and has been regulated by reservoir releases for instream flow since 1963 when Whiskeytown dam was built. The analysis of flow data indicated that from the pre-project (i.e., pre-dam) period to post- project period, flow magnitude was reduced by 45–76% for flood flows, 43% for spring pulse flows, and 27–53% for monthly average flows from January through May. Water temperature from 1996 to 2013 exceeded the U.S. Environmental Protection Agency recommended criteria for salmonids from May to October, with most exceedances occurring in September, followed by May and October. Statistical analyses suggested that the abundances of both adult and juvenile salmonids in Clear Creek were strongly correlated to flow magnitude, water temperature, or both. Higher flows that coincided with adult immigration were correlated to higher numbers of adults spawning in Clear Creek, which in turn produced a higher number of juveniles; however, higher flows that occurred during the early life stages (e.g., fry) appeared to reduce the number of outmigrating juveniles. Higher water temperatures in the immigration, spawning, and juvenile rearing periods were correlated with reduced numbers of both adult and juvenile spring-run Chinook salmon in Clear Creek. High water temperatures in June and July were correlated with reduced number of outmigrating juvenile steelhead. Adult or juvenile fall-run Chinook salmon showed either a curvilinear or linear relationship with water temperature during their immigration, spawning, and rearing periods. Based on the pre-project flow and strong correlation between fish abundance and flow or water temperature, we developed a flow regime that incorporates water temperature requirements and other needs of different life stages of salmonids. The flow regime includes the following elements: winter and spring base flow, summer and fall water temperature sustaining flow, winter floodplain inundation flow, and spring pulse flow. This approach can be applied to other regulated streams for developing flow regimes to conserve and recover listed salmonid species.

Transcriptional Response to Acute Thermal Exposure in Juvenile Chinook Salmon Determined by RNAseq.

Thermal exposure is a serious and growing challenge facing fish species worldwide. Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range are particularly likely to encounter warmer water due to a confluence of factors. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and pose a threat to dwindling salmon populations. To better understand how acute thermal exposure affects the biology of salmon, we performed a transcriptional analysis of gill tissue from Chinook salmon juveniles reared at 12° and exposed acutely to water temperatures ranging from ideal to potentially lethal (12° to 25°). Reverse-transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. In addition to a high degree of downregulation of a wide range of genes, we found upregulation of genes involved in protein folding/rescue, protein degradation, cell death, oxidative stress, metabolism, inflammation/immunity, transcription/translation, ion transport, cell cycle/growth, cell signaling, cellular trafficking, and structure/cytoskeleton. These results demonstrate the complex multi-modal cellular response to thermal stress in juvenile salmon.

Freshwater movement patterns by juvenile Pacific salmon Oncorhynchus spp. before they migrate to the ocean: Oh the places you'll go!

Juvenile movement patterns for coho salmon Oncorhynchus kisutch and Chinook salmon Oncorhynchus tshawytscha from two large interior rivers of British Columbia, Canada, were examined. Otoliths from post-spawned fishes were collected on spawning grounds and elemental signatures were determined through transects from sectioned otoliths using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). Large variations in otolith elemental signatures were found during the freshwater life stage indicative of movement downstream to rivers and tributaries that differed in elemental signature. This study highlights that downstream movements occur before migration to the ocean during the parr-smolt transformation. Extensive downstream movements of parr appear to be a successful life-history strategy based on variations observed in the otolith elemental signatures of spawners. Movements downstream in parr and the remarkable homing ability of adults also suggest that imprinting to natal streams must occur prior to the parr-smolt transformation.

Linking climate change projections for an Alaskan watershed to future coho salmon production

Climate change is predicted to dramatically change hydrologic processes across Alaska, but estimates of how these impacts will influence specific watersheds and aquatic species are lacking. Here, we linked climate, hydrology, and habitat models within a coho salmon (Oncorhynchus kisutch) population model to assess how projected climate change could affect survival at each freshwater life stage and, in turn, production of coho salmon smolts in three subwatersheds of the Chuitna (Chuit) River watershed, Alaska. Based on future climate scenarios and projections from a three-dimensional hydrology model, we simulated coho smolt production over a 20-year span at the end of the century (2080-2100). The direction (i.e., positive vs. negative) and magnitude of changes in smolt production varied substantially by climate scenario and subwatershed. Projected smolt production decreased in all three subwatersheds under the minimum air temperature and maximum precipitation scenario due to elevated peak flows and a resulting 98% reduction in egg-to-fry survival. In contrast, the maximum air temperature and minimum precipitation scenario led to an increase in smolt production in all three subwatersheds through an increase in fry survival. Other climate change scenarios led to mixed responses, with projected smolt production increasing and decreasing in different subwatersheds. Our analysis highlights the complexity inherent in predicting climate-change-related impacts to salmon populations and demonstrates that population effects may depend on interactions between the relative magnitude of hydrologic and thermal changes and their interactions with features of the local habitat.