Modeling possible cooling-water intake system impacts on Ohio River fish populations

To assess the possible impacts caused by cooling-water intake system entrainment and impingement losses, populations of six target fish species near power plants on the Ohio River were modeled. A Leslie matrix model was constructed to allow an evaluation of bluegill, freshwater drum, emerald shiner, gizzard shad, sauger, and white bass populations within five river pools. Site-specific information on fish abundance and length-frequency distribution was obtained from long-term Ohio River Ecological Research Program and Ohio River Sanitation Commission (ORSANCO) electrofishing monitoring programs. Entrainment and impingement data were obtained from 316(b) demonstrations previously completed at eight Ohio River power plants. The model was first run under a scenario representative of current conditions, which included fish losses due to entrainment and impingement. The model was then rerun with these losses added back into the populations, representative of what would happen if all entrainment and impingement losses were eliminated. The model was run to represent a 50-year time period, which is a typical life span for an Ohio River coal-fired power plant. Percent changes between populations modeled with and without entrainment and impingement losses in each pool were compared to the mean interannual coefficient of variation (CV), a measure of normal fish population variability. In 6 of the 22 scenarios of fish species and river pools that were evaluated (6 species x 5 river pools, minus 8 species/river pool combinations that could not be evaluated due to insufficient fish data), the projected fish population change was greater than the expected variability of the existing fish population, indicating a possible adverse environmental impact. Given the number of other variables affecting fish populations and the conservative modeling approach, which assumed 100% mortality for all entrained fish and eggs, it was concluded that the likelihood of impact was by no means assured, even in these six cases. It was concluded that in most cases, current entrainment and impingement losses at six Ohio River power plants have little or no effect at the population level.     

Hatchery practices may result in replacement of wild salmonids: adult trends in the Klamath basin,California

Appraisal of hatchery-related effects on Pacific salmonids (Oncorhynchus spp.) is a necessary component of species conservation. For example, hatchery supplementation can influence species viability by changing genetic, phenotypic and life-history diversity. We analyzed time series data for seven salmonid taxa from the Klamath River basin, California, to investigate trajectories of wild and hatchery adult populations. Linear regression coupled with randomized permutations (n?=?99,999), two- tailed t tests, and Bayesian change point analysis were used to detect trends over time. Cross correlation was also used to evaluate relationships between wild and hatchery populations. The taxa of interest were spring, fall, and late-fall Chinook Salmon (O. tshawytscha); Coho Salmon (O. kisutch); Coastal Cutthroat Trout (O. clarki clarki); and summer and hybrid Steelhead Trout (O. mykiss). Significant decreases were detected for summer and hybrid Steelhead Trout. The proportion of wild fall Chinook has also significantly decreased concurrently with increases in hatchery returns. In comparison, returns of most Chinook and coho runs to the hatcheries, and fall Chinook strays to wild spawning areas from Iron Gate Hatchery have significantly increased since the 1970s. Increases were also detected for wild late-fall Chinook and spring Chinook adults. However, both of these were significantly correlated with Chinook Salmon returns to Trinity River Hatchery, suggesting augmentation by hatchery strays. Changes in abundances appeared related to changing ocean habitat conditions and hatchery practices. Our results suggest that anadromous salmonid populations in the Klamath River basin are becoming increasingly dependent on hatchery propagation, a pattern that can threaten population persistence.     

Native fish entrapment in irrigation systems: A step towards understanding the significance of the problem

Summary   The Australian irrigation industry diverts significant volumes of water from our rivers, and as such, may also divert and entrain riverine fish. Although it is widely acknowledged that our native fish fauna have been greatly affected by a variety of anthropogenic changes, little is known about the extent or significance of fish entrainment in irrigation systems. This paper presents results from a preliminary investigation into the diversion of fish into irrigation channels undertaken in the Goulburn-Murray Irrigation Network, Victoria, Australia. The case study and our knowledge of the life-history strategies of the Basin's fish fauna suggest that the loss of native fish into irrigation networks may be a substantial problem, which, up until recently, has been largely ignored. We strongly suggest that the impact of diversions on native fish populations requires urgent further investigation and quantification, through the cooperation of water management authorities and fish biologists.     

Variability in fish size/otolith radius relationships among populations of Chinook salmon

Back-calculation of growth trajectories from otolith microstructure is a valuable tool for understanding mechanisms underlying variability in growth among fish populations. We analyzed fish length/otolith radius relationships for Snake River spring/summer Chinook and Snake River fall Chinook salmon, listed as separate “Evolutionarily Significant Units” (ESUs) under the US Endangered Species Act, to determine whether these ESUs shared relationships. In addition, we analyzed otoliths from seven separate populations within the Snake River spring/summer Chinook ESU to assess the variability in relationships among populations, which are much more closely related than ESUs. We also examined several potential functional forms for the equations. We found that the separate ESUs had significantly different fish length/otolith radius relationships, but that variability in otolith growth rate could not explain the difference. Relationships among populations within the spring/summer Chinook ESU did not vary nearly as much as those between ESUs. The quadratic model and the power model fit the data equally well, and constraining these models to pass through a biological intercept (estimated fish length and otolith radius at hatching) resulted in only a slight decrease in model fit. To test the ability of the models to back-calculate fish lengths, we predicted the length at tagging for 17 PIT-tagged fall Chinook that were measured at release and at recapture. The back-calculation demonstrated little bias (<1 mm FL, on average) and relatively small standard deviation (～3.5 mm) for the best model. When we repeated the back-calculation with data from both ESUs combined, bias increased substantially (to 15 mm FL), demonstrating the importance of determining the proper taxonomic level at which to combine data within a species.     

Variation of mitochondrial DNA in Chinook salmon Oncorhynchus tschawytscha Walbaum populations from Kamchatka

The variation in mitochondrial DNA (mtDNA) structure among Chinook Salmon Oncorhynchus tschawytscha Walbaum populations from Kamchatka was inferred from restriction length polymorphism analysis using eight restriction endonucleases. The nucleotide sequence variation in three amplified mtDNA regions was examined at seven polymorphic restriction sites in 579 fish from 13 localities. Based on the frequencies of 11 combined haplotypes and the number of nucleotide substitutions, the among- and within-population variation was estimated. The heterogeneity test showed highly significant differences among all the populations. The estimated maximum time of independent divergence of the Asian Chinook salmon populations, whose differences was about 0.02% nucleotide substitutions, did not exceed 10000-20000 years. Apparently, the retreat of the late Pleistocene glacier triggered spreading, recolonization, and formation of the present-day pattern of the species subdivision into structural components.     

Survival of captured and relocated adult spring-run Chinook salmon Oncorhynchus tshawytscha in a Sacramento River tributary after cessation of migration

We studied the efficacy of the process for capture and upstream relocation of 26 adult spring-run Chinook salmon in Butte Creek, California in 2009. These fish had ceased volitional upstream migration prior to reaching their summer holding habitat. The purpose of the relocation was to move fish upstream of two water diversion dams and release them in a part of the stream from which they could presumably swim to cool summer holding habitat, then spawn in the fall. Fish were netted, transported by truck, given an esophageal radio tag/temperature tag, and released. Radio tagging proved to be a useful technique for determining the survival and movement of relocated fish and temperature tags provide useful information to determine thermal exposure and time of death. Twenty-three tags (88 %) were recovered, compared with a 10 % tag recovery rate for an earlier study using fin clips. Most tags were recovered within 3.5 km upstream and 1 km downstream of the release site. A single tag was recovered 6 km upstream. No fish were determined to have survived to spawn. Temperature tag data indicate that most of the salmon died within 2–6 days after the relocation operation. After preventative measures have been exhausted, future relocations efforts, in any setting, should consider (1) intervention as soon as fish cease volitional migration but before they are exposed to further deleterious conditions (2) monitoring environmental conditions to choose appropriate release sites (3) evaluation of disease transmission risk, and (4) handling practices that minimize potential stress due to air immersion and thermal shock.     

Understanding the behavior and ecology of Chinook salmon (Oncorhynchus tshawytscha) on an important feeding ground in the Gulf of Alaska

Population declines and demographic changes of Chinook salmon (Oncorhynchus tshawytscha), have been documented throughout this species’ range, though information on natural and anthropogenic mechanisms related to these changes are not fully understood. To provide insights into marine behaviors and survival of Chinook salmon, 40 pop-up satellite archival tags (PSATs), that collected environmental data, were attached to large (69–100 cm FL) Chinook salmon caught in the marine waters of Cook Inlet, Alaska. PSATs provided evidence of predation on tagged Chinook salmon by ectothermic and unconfirmed predators, and provided valuable information about the migratory characteristics and occupied depths and temperatures of this species while occupying Cook Inlet and the Gulf of Alaska. The results from this study suggest that late-marine mortality of Chinook salmon of a variety of stock-origins by apex predators is more common in Cook Inlet than previously thought, and may be used to improve our understanding this species’ population dynamics. Furthermore, results from this study adds to the existing knowledge of marine habitat use by Chinook Salmon and may be useful in assessing the vulnerability and interactions between this species and anthropogenic activities.

     

Diel movements of out-migrating Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) smolts in the Sacramento/San Joaquin watershed

We used ultrasonic telemetry to describe the movement patterns of late-fall run Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (O. mykiss) smolts during their entire emigration down California’s Sacramento River, through the San Francisco Bay Estuary and into the Pacific Ocean. Yearling hatchery smolts were tagged via intracoelomic surgical implantation with coded ultrasonic tags. They were then released at four upriver locations in the Sacramento River during the winters of 2007 through 2010. Late-fall run Chinook salmon smolts exhibited a nocturnal pattern of migration after release in the upper river. This is likely because individuals remain within a confined area during the day, while they become active at night and migrate downstream. The ratio between night and day detections of Chinook salmon smolts decreased with distance traveled downriver. There was a significant preference for nocturnal migration in every reach of the river except the Estuary. In contrast, steelhead smolts, which reside upriver longer following release, exhibited a less pronounced diel pattern during their entire migration. In the middle river, Delta, and Estuary, steelhead exhibited a significant preference for daytime travel. In the ocean Chinook salmon preferred to travel at night, yet steelhead were detected on the monitors equally during the night and day. These data show that closely related Oncorhynchus species, with the same ontogenetic pattern of out-migrating as yearlings, vary in migration tactic.     

Potential Factors Affecting Survival Differ by Run-Timing and Location: Linear Mixed-Effects Models of Pacific Salmonids (Oncorhynchus spp.) in the Klamath River,California

Understanding factors influencing survival of Pacific salmonids (Oncorhynchus spp.) is essential to species conservation, because drivers of mortality can vary over multiple spatial and temporal scales. Although recent studies have evaluated the effects of climate, habitat quality, or resource management (e.g., hatchery operations) on salmonid recruitment and survival, a failure to look at multiple factors simultaneously leaves open questions about the relative importance of different factors. We analyzed the relationship between ten factors and survival (1980–2007) of four populations of salmonids with distinct life histories from two adjacent watersheds (Salmon and Scott rivers) in the Klamath River basin, California. The factors were ocean abundance, ocean harvest, hatchery releases, hatchery returns, Pacific Decadal Oscillation, North Pacific Gyre Oscillation, El Niño Southern Oscillation, snow depth, flow, and watershed disturbance. Permutation tests and linear mixed-effects models tested effects of factors on survival of each taxon. Potential factors affecting survival differed among taxa and between locations. Fall Chinook salmon O. tshawytscha survival trends appeared to be driven partially or entirely by hatchery practices. Trends in three taxa (Salmon River spring Chinook salmon, Scott River fall Chinook salmon; Salmon River summer steelhead trout O. mykiss) were also likely driven by factors subject to climatic forcing (ocean abundance, summer flow). Our findings underscore the importance of multiple factors in simultaneously driving population trends in widespread species such as anadromous salmonids. They also show that the suite of factors may differ among different taxa in the same location as well as among populations of the same taxa in different watersheds. In the Klamath basin, hatchery practices need to be reevaluated to protect wild salmonids.     

Density of the waterborne parasite Ceratomyxa shasta and its biological effects on salmon

The myxozoan parasite Ceratomyxa shasta is a significant pathogen of juvenile salmonids in the Pacific Northwest of North America and is limiting recovery of Chinook (Oncorhynchus tshawytscha) and coho (O. kisutch) salmon populations in the Klamath River. We conducted a 5-year monitoring program that comprised concurrent sentinel fish exposures and water sampling across 212 river kilometers of the Klamath River. We used percent mortality and degree-days to death to measure disease severity in fish. We analyzed water samples using quantitative PCR and Sanger sequencing, to determine total parasite density and relative abundance of C. shasta genotypes, which differ in their pathogenicity to salmonids. We detected the parasite throughout the study zone, but parasite density and genetic composition fluctuated spatially and temporally. Chinook and coho mortality increased with density of their specific parasite genotype, but mortality-density thresholds and time to death differed. A lethality threshold of 40% mortality was reached with 10 spores liter(-1) for Chinook but only 5 spores liter(-1) for coho. Parasite density did not affect degree-days to death for Chinook but was negatively correlated for coho, and there was wider variation among coho individuals. These differences likely reflect the different life histories and genetic heterogeneity of the salmon populations. Direct quantification of the density of host-specific parasite genotypes in water samples offers a management tool for predicting host population-level impacts.     

Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California river

We reared juvenile Chinook salmon for two consecutive flood seasons within various habitats of the Cosumnes River and its floodplain to compare fish growth in river and floodplain habitats. Fish were placed in enclosures during times when wild salmon would naturally be rearing in floodplain habitats. We found significant differences in growth rates between salmon reared in floodplain and river enclosures. Salmon reared in seasonally inundated habitats with annual terrestrial vegetation experienced higher growth rates than those reared in a perennial pond on the floodplain. Growth of fish in the non-tidal river upstream of the floodplain varied with flow in the river. When flows were high, there was little growth and high mortality, but when the flows were low and clear, the fish grew rapidly. Fish displayed very poor growth in tidally influenced river habitat below the floodplain, a habitat type to which juveniles are commonly displaced during high flow events due to a lack of channel complexity in the main-stem river. Overall, ephemeral floodplain habitats supported higher growth rates for juvenile Chinook salmon than more permanent habitats in either the floodplain or river. Variable responses in both growth and mortality, however, indicate the importance of providing habitat complexity for juvenile salmon in floodplain reaches of streams, so fish can find optimal places for rearing under different flow conditions.     

Spatio-temporal dynamics of alternative male phenotypes in coho salmon populations in response to ocean environment

1. The coexistence of alternative reproductive phenotypes will probably be shaped by spatial and temporal variability in the environment. However, the effects of such variability on coexistence and the scale at which it operates are seldom understood. 2. To quantify such effects, we examined spatial and temporal dynamics in the abundance and frequency of alternative phenotypes of male coho salmon, Oncorhynchus kisutch Walbaum, which mature as either large fighters (age-3 'hooknoses') or small sneakers (age-2 'jacks'). Using over 20 years of data on coded-wire tagged fish released from nine Oregon hatcheries, we tested for the effects of ocean environment independent of those due to freshwater rearing. 3. Annual fluctuations of the abundance of jack and hooknose males within populations were correlated strongly by brood year (cohort) but not by return year (breeding group). This occurred independently of significant effects of release practice (i.e. the number of fish released, body size at release and date of release), indicating that a synchronized fluctuation in mortality during the first year at sea was the predominant cause. As a result, the annual frequency of the alternative phenotypes at breeding varied considerably within populations. 4. Spatial patterns in the annual fluctuations of the two phenotypes were similar (i.e. synchronous among populations), except that jacks showed local spatial structure (decreased synchrony with distance) not evident among hooknoses. This suggests that oceanic processes affecting the two phenotypes operate at different spatial scales. Despite effects on salmon abundance, the ocean environment had little influence through its effects on salmon growth on the relative frequencies of the alternative phenotypes within and among populations. 5. The results provide insight into the evolutionary dynamics of alternative phenotypes, including an intragenerational time lag that increases annual variability in phenotype frequencies at breeding (return years) and the significance of local freshwater processes, rather than oceanic processes, on phenotype expression. Freshwater processes, such as juvenile growth, timing of migration and breeding competition, operating at evolutionary and intragenerational time-scales, are probably the predominant forces affecting phenotype frequency.     

Short‐term response of fish communities and water chemistry to breaching of a causeway in the Sarita River Estuary,British Columbia,Canada

On the west coast of Vancouver Island, Canada, in the Treaty Settlement Lands of the Huu‐ay‐aht First Nation, a causeway isolating the southern portion of the Sarita River estuary was breached in 2018 to enhance juvenile salmon and tidal water access into the southern portion of the estuary. Short‐term goals of breaching were to: (1) enhance juvenile salmon access through the causeway; (2) promote colonization of Chinook and Chum Salmon in pools, while retaining Coho Salmon; (3) monitor the entire estuary fish community, including non‐salmonids, to assess breaching success; and (4) homogenize water chemistry in pool and channel ecosystems currently fragmented by the causeway. Immediately following the breach, both fish community and water chemistry measurements indicate that these goals were achieved. Chinook and Chum Salmon utilization increased inside and outside of the causeway following breaching. Similarly, Chinook and Chum salmon were observed in pool ecosystems, and Coho Salmon were also retained in pools following breaching. Water chemistry was homogenized post‐breach, primarily due to increased saltwater penetration. While continued monitoring is required, short‐term indicators suggest that breaching was effective in increasing connectivity of the Sarita Estuary, allowing access to 1.4 km² of habitat that had previously been inaccessible to juvenile salmon.     

Signals of large scale climate drivers,hatchery enhancement,and marine factors in Yukon River Chinook salmon survival revealed with a Bayesian life history model

Understanding how species might respond to climate change involves disentangling the influence of co‐occurring environmental factors on population dynamics, and is especially problematic for migratory species like Pacific salmon that move between ecosystems. To date, debate surrounding the causes of recent declines in Yukon River Chinook salmon (Oncorhynchus tshawytscha) abundance has centered on whether factors in freshwater or marine environments control variation in survival, and how these populations at the northern extremity of the species range will respond to climate change. To estimate the effect of factors in marine and freshwater environments on Chinook salmon survival, we constructed a stage‐structured assessment model that incorporates the best available data, estimates incidental marine bycatch mortality in trawl fisheries, and uses Bayesian model selection methods to quantify support for alternative hypotheses. Models fitted to two index populations of Yukon River Chinook salmon indicate that processes in the nearshore and marine environments are the most important determinants of survival. Specifically, survival declines when ice leaves the Yukon River later in the spring, increases with wintertime temperature in the Bering Sea, and declines with the abundance of globally enhanced salmon species consistent with competition at sea. In addition, we found support for density‐dependent survival limitations in freshwater but not marine portions of the life cycle, increasing average survival with ocean age, and age‐specific selectivity of bycatch mortality in the Bering Sea. This study underscores the utility of flexible estimation models capable of fitting multiple data types and evaluating mortality from both natural and anthropogenic sources in multiple habitats. Overall, these analyses suggest that mortality at sea is the primary driver of population dynamics, yet under warming climate Chinook salmon populations at the northern extent of the species’ range may be expected to fare better than southern populations, but are influenced by foreign salmon production.     

Indicators of AEI applied to the Delaware Estuary

We evaluated the impacts of entrainment and impingement at the Salem Generating Station on fish populations and communities in the Delaware Estuary. In the absence of an agreed-upon regulatory definition of "adverse environmental impact" (AEI), we developed three independent benchmarks of AEI based on observed or predicted changes that could threaten the sustainability of a population or the integrity of a community. Our benchmarks of AEI included: (1) disruption of the balanced indigenous community of fish in the vicinity of Salem (the "BIC" analysis); (2) a continued downward trend in the abundance of one or more susceptible fish species (the "Trends" analysis); and (3) occurrence of entrainment/impingement mortality sufficient, in combination with fishing mortality, to jeopardize the future sustainability of one or more populations (the "Stock Jeopardy" analysis). The BIC analysis utilized nearly 30 years of species presence/absence data collected in the immediate vicinity of Salem. The Trends analysis examined three independent data sets that document trends in the abundance of juvenile fish throughout the estuary over the past 20 years. The Stock Jeopardy analysis used two different assessment models to quantify potential long-term impacts of entrainment and impingement on susceptible fish populations. For one of these models, the compensatory capacities of the modeled species were quantified through meta-analysis of spawner-recruit data available for several hundred fish stocks. All three analyses indicated that the fish populations and communities of the Delaware Estuary are healthy and show no evidence of an adverse impact due to Salem. Although the specific models and analyses used at Salem are not applicable to every facility, we believe that a weight of evidence approach that evaluates multiple benchmarks of AEI using both retrospective and predictive methods is the best approach for assessing entrainment and impingement impacts at existing facilities.     

Temperature effects on juvenile anadromous salmonids in California’s central valley: what don’t we know?

The anadromous Chinook salmon (Oncorhynchus tshawytscha) (4 runs) and steelhead (rainbow trout, O. mykiss), are both native to Californias Sacramento-San Joaquin River (SSJR) system, whose watershed encompasses the central valley of California. The SSJR system holds the southernmost extant Chinook salmon populations in the Eastern Pacific Ocean, whereas coastal anadromous steelhead populations are found at more southerly latitudes. Populations of both species of anadromous salmonid have experienced dramatic declines during the past 100 years, at least partly from water impoundments and diversions on most central valley rivers and their tributaries. These changes restricted the longitudinal distribution of these salmonids, often forcing the superimposition of steelhead populations and Chinook salmon populations in the same reaches. This superimposition is problematic in part because the alterations to the river systems have not only changed the historic flow regimes, but have also changed the thermal regimes, resulting in thermally-coupled changes in fish development, growth, health, distribution, and survival. Given the highly regulated nature of the system, resource managers are constantly trying to strike a balance between maintaining or increasing the population size of anadromous fish runs and with other demands for the water, such as irrigation and water quality. To do so, in this review, we summarize the published information on the temperature tolerance and growth of the stream-associated life stages of these two valuable species, which are so central to the natural heritage of the State and its cultures. We show that many of these limits and growth-related effects are specific regarding life stage and that some may be specific to distinct strains or races of Chinook salmon and steelhead within the system. Because the number of published studies on the physiology of central valley salmonids was surprisingly low, we also use this review to highlight critical areas where further research is needed. Overall, this review should assist biologists and resource decision-makers with improved understanding for the protection and enhancement of these native fishes.     

Genetic variation in mortality of chinook salmon during a bloom of the marine alga Heterosigma akashiwo

Mortality in a netpen-reared population of 3-year-old chinook salmon Oncorhynchus tshawytscha during an extensive 1997 bloom of the alga Heterosigma akashiwo in Puget Sound, Washington, was low (7·2%), and corresponded to a reduction in variance effective population size of 9·4%. Under a liability threshold model, the heritability of mortality (± S.E.), based on paternal half-sibs, was estimated at 0·15 ± 0·04. No significant genetic variation was detected for date of death. Despite the low overall mortality, the consequences for variation in family size underscore the importance of maximizing genetic variation in cultured fish populations later released to the wild as a precaution against mortality and losses of genetic variation over the life cycle. The pattern of family variation in response to this algal bloom provides evidence for potentially selective mortality of anadromous salmonids in the marine environment during natural perturbations.     

Holding behavior of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) smolts, as influenced by habitat features of levee banks, in the highly modified lower Sacramento River, California

Using acoustic telemetry methods on large numbers of tagged fish, we studied how the holding behavior of Chinook salmon and steelhead smolts could be related to habitat features and spatial and temporal variables on a highly altered section of the Sacramento River. We viewed downstream migration as a process in which fish transition between moving and holding states, and used a binomial and negative binomial Generalized Linear Model to analyze two aspects of holding: 1) probability of holding, and 2) holding time. For Chinook salmon, the probability of holding increased as wood size and fine substrates increased; holding time increased as overhead shade increased. For steelhead, holding behavior was only weakly related to habitat variables, in contrast to the strong relationships with spatial and temporal variables. For both species, the probability of holding increased when distance from the release location decreased and instream flows decreased. We found support for three main findings: 1) spatial and temporal factors have considerably greater influence on Chinook salmon and steelhead smolt holding behavior than nearshore habitat features; 2) holding behaviors of Chinook salmon smolts are influenced more strongly by habitat features than steelhead smolts; and 3) incorporation of habitat features such as large woody material and overhead shade should be considered when conducting nearshore bank rehabilitation projects to increase cover from predators and provide velocity refuge, improving holding habitat during downstream migration.     

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) within a Snake River watershed

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.     

Thermal biology and bioenergetics of different upriver migration strategies in a stock of summer-run Chinook salmon

By combining biotelemetry with animal-borne thermal loggers, we re-created the thermal histories of 21 summer-run Chinook salmon (Oncorhynchus tshawytscha) migrating in the Puntledge River, a hydropower impacted river system on Vancouver Island, British Columbia, Canada. Daily maximum water temperatures in the Puntledge River during the summer-run adult Chinook salmon migration and residency period frequently exceeded 21 °C, a value that has been observed to elicit behavioral thermoregulation in other Chinook salmon populations. We therefore compared river temperatures to body temperatures of 16 fish that migrated through the river to understand if cool-water refuge was available and being used by migrants. In addition, we used thermal histories from fish and thermal loggers distributed in the river to model the effect of thermal habitat on energy density using a bioenergetics model. In general, we found no evidence that cool-water refuge existed in the river, suggesting that there is no opportunity for fish to behaviorally thermoregulate during upriver migration through the regulated portion of the river. Of the thermal histories used in the bioenergetics model, fish that reached an upstream lake were able to access cooler, deeper waters, which would have reduced energy consumption compared to fish that only spent time in the warmer river. Consequently, the Puntledge River water temperatures are likely approaching and in some cases exceeding the thermal limits of the summer-run Chinook salmon during the spawning migration. Further warming may cause more declines in the stock.