Chinook Salmon Oncorhynchus Tshawytscha Research Articles

Comparisons of isotopic niche between females and male alternative reproductive tactics of Chinook salmon (Oncorhynchus tshawytscha) from Lake Ontario

Chinook salmon (Oncorhynchus tshawytscha) have complex life histories with two distinct male alternative reproductive tactics (ARTs). The larger and older “hooknose” males battle for position to spawn with nesting females whereas the precociously maturing “jack” males use a sneaking tactic to gain access to females. Although dietary niche is known to differ between ARTs of other fish taxa, no research to date has examined these differences in a salmonid. Here, we used δ15N and δ13C stable isotope analyses to compare the dietary niches of female, hooknose male, and jack male Chinook salmon sampled from a Lake Ontario tributary. We found that all three life histories shared similar δ15N values, whereas jack males had greater δ13C values compared to hooknose males, with females having intermediate values. Jack males also had notably little overlap in their isotopic niche space with hooknose males and females, indicating that jack males occupy a distinct isotopic niche in Lake Ontario. We discuss habitat partitioning and differences in dietary niche as explanatory factors. Altogether, these data unveil novel distinctions in isotopic niche within the complex life history strategies of Chinook salmon in Lake Ontario that can inform management decisions and provide avenues for future research.

Salmonid Double-stranded RNA-Dependent Protein Kinase Activates Apoptosis and Inhibits Protein Synthesis.

dsRNA-dependent protein kinase R (PKR) is a key factor of innate immunity. It is involved in translation inhibition, apoptosis, and enhancement of the proinflammatory and IFN responses. However, how these antiviral functions are conserved during evolution remains largely unknown. Overexpression and knockout studies in a Chinook salmon (Oncorhynchus tshawytscha) cell line were conducted to assess the role of salmonid PKR in the antiviral response. Three distinct mRNA isoforms from a unique pkr gene, named pkr-fl (full length), pkr-ml (medium length) and pkr-sl (short length), were cloned and a pkr-/- clonal fish cell line was developed using CRISPR/Cas9 genome editing. PKR-FL includes an N-terminal dsRNA-binding domain and a C-terminal kinase domain, whereas PKR-ML and PKR-SL display a truncated or absent kinase domain, respectively. PKR-FL is induced during IFNA2 stimulation but not during viral hemorrhagic septicemia virus (VHSV) infection. Overexpression experiments showed that only PKR-FL possesses antiviral functions, including activation of apoptosis and inhibition of de novo protein synthesis. Knockout experiments confirmed that PKR is involved in apoptosis activation during the late stage of VHSV infection. Endogenous PKR also plays a critical role in translation inhibition upon poly(I:C) transfection after IFNA2 treatment. It is, however, not involved in translational arrest during VHSV infection. Extra- and intracellular titrations showed that endogenous PKR does not directly inhibit viral replication but apparently favors virion release into the supernatant, likely by triggering late apoptosis. Altogether, our data confirm that salmonid PKR has conserved molecular functions that VHSV appears to bypass with subversion strategies.

A new method for regionalization of the vertebral column in salmonids based on radiographic hallmarks.

Current procedures to establish vertebral column regionalization (e.g., histology) in fish are time consuming and difficult to apply. The aim of this study was to develop a more rapid and accurate radiology-based method for Atlantic salmon (Salmo salar). A detailed analysis of 90 animals (4 kg) led to the establishment of region-specific radiographic hallmarks. To elucidate its transferability to other salmonid species, radiography was carried out in brown trout (Salmo trutta), Arctic char (Salvelinus alpinus), rainbow trout (Oncorhynchus mykiss), pink salmon (Oncorhynchus gorbuscha), and Chinook salmon (Oncorhynchus tshawytscha). This method was also evaluated for whole ungutted fish. The vertebral column of Atlantic salmon can be subdivided into five regions (R1-R5) based on anatomy: postcranial (R1, V1, and V2), abdominal (R2, V3-V26), transitional (R3, V27-V36), caudal (R4, V37-V53), and ural (R5, V54-V59). The following specific radiographic hallmarks allow the identification of regions: (i) lack of ribs in R1, (ii) modified parapophysis of the first vertebra of R3, (iii) prominent hemal spine of the first vertebra of R4, and (iv) the separated hemal spine of the most cranial pre-ural vertebra of R5. These hallmarks were all transferable to the other salmonid species assessed. The results include a further description of various region-specific characteristics in Atlantic salmon. The method was found applicable for sedated/whole ungutted fish, verifying it as quick and easy compared to other regionalization methods. The regions defined by radiology in this study agree with the vertebral column regions recently defined for Chinook salmon (O. tshawytscha). Thus, and considering the results of this study on various salmonid species, the currently developed regionalization protocol can be generally used for salmonids.

Initial responses of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) to removal of two dams on the Elwha River, Washington State, U.S.A.

Large dam removal is being used to restore river systems, but questions remain regarding their outcomes. We examine how the removal of two large dams in the Elwha River, coupled with hatchery production and fishing closures, affected population attributes of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss). Initial responses by returning adult Chinook salmon and steelhead was an increase in the number and spatial extent of natural and hatchery origin fish. Although few naturally produced juvenile Chinook salmon and steelhead outmigrants were observed prior to and during dam removal, abundances increased three years after adult fish passage was restored, suggesting that impacts due to downstream sedimentation after dam removal were reduced. The Chinook salmon population demographics remain dominated by hatchery production, while increases in winter steelhead abundance included both hatchery and natural-origin spawners. The spatial expansion of winter steelhead upstream of former dam sites was predominantly by natural-origin spawners. We also observed a natural “reawakening” of summer steelhead that were in part derived from an up-river resident population that returned to the Upper Elwha. Our results showed that a combination of habitat, hatchery, and harvest actions can result in positive responses for salmonid populations.

Diploid and triploid Chinook salmon (Oncorhynchus tshawytscha) exhibit differential immunological responses toacute thermal stress.

Exposure to temperatures outside of a fish's optimal range results in suppression of the immune system, ultimately leaving aquaculture stocks susceptible to disease outbreaks. This effect is exacerbated in triploid fishes, which demonstrate greater susceptibility to stress than their diploid counterparts. This study investigates the impacts of acute heat stress on the abundance of immune transcripts and proteins in diploid and triploid Chinook salmon (Oncorhynchus tshawytscha), an important finfish crop. This study also demonstrates that acute heat stress induces significant increases in the abundance hsp70, hsp90 and il1b transcripts in the head kidneys, gills and heart ventricles of both diploid and triploid Chinook salmon. Widespread dysregulation of antigen-presentation transcripts was also observed in fish of both ploidies. These results suggest that acute heat stress activates acute-phase responses in Chinook salmon and dysregulates antigen presentation, potentially leaving fish more susceptible to infection. At the protein level, IL-1β was differentially expressed in the head kidney and ventricles of diploid and triploid salmon following heat shock. Differential expression of two tapasin-like proteins in diploid and triploid salmon subjected to heat shock was also observed. Altogether, these data indicate that diploid and triploid Chinook salmon respond differently to acute thermal stressors.

Molecular mechanism of TRIM32 in antiviral immunity in rainbow trout (Oncorhynchus mykiss)

TRIM family proteins are widely found in multicellular organisms and are involved in a wide range of life activities, and also act as crucial regulators in the antiviral natural immune response. This study aimed to reveal the molecular mechanism of rainbow trout TRIM protein in the anti-IHNV process. The results demonstrated that 99.1% homology between the rainbow trout and the chinook salmon (Oncorhynchus tshawytscha) TRIM32. When rainbow trout were infected with IHNV, the TRIM32 was highly expressed in the gill, spleen, kidney and blood. Meanwhile, rainbow trout TRIM32 has E3 ubiquitin ligase activity and undergoes K29-linked polyubiquitination modifications dependent on the RING structural domain was determined by immunoprecipitation. TRIM32 could interact with the NV protein of IHNV and degrade NV protein through the ubiquitin-proteasome pathway, and was also able to activate NF-κB transcription, thereby inhibiting the replication of IHNV. Moreover, the results of the animal studies showed that the survival rate of rainbow trout overexpressing TRIM32 was 70.2% which was significantly higher than that of the control group, and stimulating the body to produce high levels of IgM when the host was infected with the virus. In addition, TRIM32 can activate the NF-κB signalling pathway and participate in the antiviral natural immune response. The results of this study will help us to understand the molecular mechanism of TRIM protein resistance in rainbow trout, and provide new ideas for disease resistance breeding, vaccine development and immune formulation development in rainbow trout.

Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population.

Intraspecific biodiversity is vital for species persistence in an increasingly volatile world. By embracing methods that integrate information at different spatiotemporal scales, we can directly monitor and reconstruct changes in intraspecific biodiversity. Here we combined genetics and otolith biochronologies to describe the genotypic and phenotypic diversity of Chinook salmon (Oncorhynchus tshawytscha) in the Yuba River, California, comparing cohorts that experienced a range of hydroclimatic conditions. Yuba River salmon have been heavily impacted by habitat loss and degradation, and large influxes of unmarked hatchery fish each year have led to concern about introgression and uncertainty around the viability of its wild populations, particularly the rarer spring-run salmon. Otolith strontium isotopes showed that Yuba River origin fish represented, on average, 42% (range 7%-73%) of spawners across six return years (2009-2011, 2018-2020), with large interannual variability. The remainder of adult Chinook salmon in the river were primarily strays from the nearby Feather River hatchery, and since 2018 from the Mokelumne River hatchery. Among the Yuba-origin spawners, on average, 30% (range 14%-50%) exhibited the spring-run genotype. The Yuba-origin fish also displayed a variety of outmigration phenotypes that differed in the timing and size at which they left the Yuba river. Early-migrating fry dominated the returns (mean 59%, range 33%-89%), and their contribution rates were negatively correlated with freshwater flows. It is unlikely that fry survival rates are elevated during droughts, suggesting that this trend reflects disproportionately low survival of larger later migrating parr, smolts, and yearlings along the migratory corridor in drier years. Otolith daily increments indicated generally faster growth rates in non-natal habitats, emphasizing the importance of continuing upstream restoration efforts to improve in-river growing conditions. Together, these findings show that, despite a long history of habitat degradation and hatchery introgression, the Yuba River maintains intraspecific biodiversity that should be taken into account in future management, restoration, and reintroduction plans. The finding that genotypic spring-run are reproducing, surviving, and returning to the Yuba River every year suggests that re-establishment of an independent population is possible, although hatchery-wild interactions would need to be carefully considered. Integrating methods is critical to monitor changes in key genetic, physiological, and behavioral traits to assess population viability and resilience.

A new, standardized international Pacific Rim baseline for genetic stock identification (GSI) of Chinook Salmon

AbstractObjectiveGenetic stock identification (GSI) can be an effective tool for fisheries management, but development of reference baselines for species with broad geographic distributions can be challenging. Mixed‐stock fisheries for Chinook Salmon Oncorhynchus tshawytscha have utilized GSI analyses for decades with various genetic baselines, but these have largely become outdated with advances in technology that enable more efficient genotyping. Thus, our goals were to (1) create nested baselines of genotypic data for Chinook Salmon throughout their entire natural range using existing data from multiple sources and (2) evaluate the utility of those nested baselines to conduct accurate hierarchical GSI of mixture proportions or the stock identification of individual fish.MethodsIn this study, we compiled a large genetic baseline of single‐nucleotide polymorphism (SNP) markers for 389 populations that encompass the entire geographic range of Chinook Salmon. We used cross validation and realistic mixture simulations to test the accuracy of the baseline in generating GSI estimates.ResultWe demonstrated that a multi‐tiered assignment approach can provide high accuracy at both tier 1 (broadscale, with three coastwide reporting groups; 97.8% mean accuracy) and tier 2 (fine‐scale regional reporting groups; up to 97.7% mean accuracy) levels. Realistic mixture simulations showed that this multi‐tiered approach can provide highly effective GSI results for several common mixed‐stock fisheries applications in the Pacific Ocean.ConclusionThis new SNP baseline and the multi‐tiered assignment approach provide the most comprehensive rangewide GSI baseline for Chinook Salmon over any previous application and enable highly accurate estimates for GSI purposes.

Remnant salmon life history diversity rediscovered in a highly compressed habitat.

Chinook salmon (Oncorhynchus tshawytscha) display remarkable life history diversity, underpinning their ability to adapt to environmental change. Maintaining life history diversity is vital to the resilience and stability of Chinook salmon metapopulations, particularly under changing climates. However, the conditions that promote life history diversity are rapidly disappearing, as anthropogenic forces promote homogenization of habitats and genetic lineages. In this study, we use the highly modified Yuba River in California to understand if distinct genetic lineages and life histories still exist, despite reductions in spawning habitat and hatchery practicesthat have promoted introgression. There is currently a concerted effort to protect federally listed Central Valley spring-run Chinook salmon populations, given that few wild populations still exist. Despite this, we lack a comprehensive understanding of the genetic and life history diversity of Chinook salmon present in the Yuba River. To understand this diversity, we collected migration timing data and GREB1L genotypes from hook-and-line, acoustic tagging, and carcass surveys of Chinook salmon in the Yuba River between 2009 and 2011. Variation in the GREB1L region of the genome is tightly linked with run timing in Chinook salmon throughout their range, but the relationship between this variation and entry on spawning grounds is little explored in California's Central Valley. We found that the date Chinook salmon crossed the lowest barrier to Yuba River spawning habitat (Daguerre Point Dam) was tightly correlated with their GREB1L genotype. Importantly, our study confirms that ESA-listed spring-run Chinook salmon are spawning in the Yuba River, promoting a portfolio of life history and genetic diversity, despite the highlycompressed habitat. This work highlights the need to identify and protect this life history diversity, especially in heavily impacted systems,to maintain healthy Chinook salmon metapopulations. Without protection, we run the risk of losing the last vestiges of important genetic variation.

Sex-specific diet differences in harbor seals (Phoca vitulina) via spatial assortment.

The lack of recovery of Chinook salmon (Oncorhynchus tshawytscha) in the Pacific Northwest has been blamed in part on predation by pinnipeds, particularly the harbor seal (Phoca vitulina). Previous work at a limited number of locations has shown that male seal diet contains more salmon than that of female seals and that sex ratios at haul-out sites differ spatiotemporally. This intrapopulation variation in predation may result in greater effects on salmon than suggested by models assuming equal spatial distribution and diet proportion. To address the generality of these patterns, we examined the sex ratios and diet of male and female harbor seals from 13 haul-out sites in the inland waters of Washington State and the province of British Columbia during 2012-2018. DNA metabarcoding was conducted to determine prey species proportions of individual scat samples. The sex of harbor seals was then determined from each scat matrix sample with the use of quantitative polymerase chain reaction (qPCR). We analyzed 2405 harbor seal scat samples using generalized linear mixed models (GLMMs) to examine the factors influencing harbor seal sex ratio at haul-out sites and permutational multivariate analysis of variance (PERMANOVA) to examine the influence of sex and haul-out site on harbor seal diet composition. We found that the overall sex ratio was 1:1.02 (female:male) with notable spatiotemporal variation. Salmoniformes were about 2.6 times more abundant in the diet of males than in the diet of females, and Chinook salmon comprised ca. three times more of the average male harbor seal's diet than the average female's diet. Based on site-specific sex ratios and diet data, we identified three haul-out sites where Chinook salmon appear to be under high predation pressure by male harbor seals: Cowichan Bay, Cutts Area, and Fraser River. Our study indicates that combining sex-specific pinniped diet data with the sex ratio of haul-out sites can help identify priority sites of conservation concern.

Comparing standard‐ and reduced‐size passive integrated transponder (PIT) tags for monitoring juvenile wild spring Chinook Salmon

AbstractObjectivesAnnual migration monitoring can help to discern patterns and environmental factors that impact growth, survival, and movement timing in small fish. Mark–recapture methods form the basis for such monitoring, and the standard 12‐mm passive integrated transponder (PIT) tag has emerged as an essential tool for studies of juvenile salmonids. A smaller, 9‐mm PIT tag now provides the potential to conduct mark–recapture studies on smaller fish. We evaluated relative performance of the 9‐mm tag, which is similar in design to its 12‐mm predecessor.MethodsFor this comparison, we tagged and released approximately 8400 wild spring Chinook Salmon Oncorhynchus tshawytscha parr in Valley Creek, Idaho, from 2011 to 2013. Tag‐size cohorts were of similar average body size and were tagged in equal numbers. We estimated survival and detection probability for each cohort over two river segments.ResultsIn both segments, survival varied among years, but we observed no significant differences between tag‐size groups. At Valley Creek, average detection rates of fish with 9‐mm tags were a little less than one‐half the rates of fish with 12‐mm tags and were significantly lower in all 3 years. At Lower Granite Dam, detection rates were again lower for 9‐mm tags, but the differences were much smaller (3%–12%) and were not statistically significant.ConclusionWe found that 9‐mm tags can be as effective as 12‐mm tags and may allow for better inference to smaller (<55‐mm) non‐tagged fish. However, the lower detection rates of the 9‐mm tags could lead to less precise estimates, and site‐specific detection rates should be considered for studies that rely on these tags.

Inferring precocial Chinook Salmon production through single‐parentage assignments

AbstractObjectiveParentage analysis is a routine methodology in fisheries research, but study systems exist where it is impractical to sample both parents. The ability to reliably assign offspring to a single parent is beneficial in these situations. We applied single‐parentage assignments to a naturally spawning population of Chinook Salmon Oncorhynchus tshawytscha to quantify production of anadromous returns by unsampled precocial males.MethodsWe used an approach that focused on two important aspects of parentage analyses: (1) addressing the presence of family structure within the set of sampled parents and (2) controlling for false‐positive and false‐negative assignments.ResultResults indicated that 30% of reproductively successful males were precocial males, which produced 20% of the returning anadromous offspring.ConclusionThis study provides a framework for applying single‐parent assignments in a salmonid study system while explicitly addressing sources of assignment errors.

Back from the brink: Estimating daily and annual abundance of natural-origin salmon smolts from 30-years of mixed-origin capture-recapture data

Evaluating the status and trends of natural-origin anadromous fish populations over time requires robust estimates of out-migrating juvenile abundance. Information on abundance is typically acquired by capturing actively migrating fish as they pass stationary monitoring platforms. Challenges to estimation include protracted migration timing, temporally varying capture probabilities and the contemporaneous presence of unmarked hatchery-origin fish. The confounding effects of unmarked hatchery fish are especially pernicious in systems hosting multiple hatchery programs with variable mark-rates among releases. Here, we address this problem for a regionally and culturally important population of Chinook salmon (Oncorhynchus tshawytscha) supported by a hatchery-supplementation program implemented in response to the listing of this population under the U.S. Endangered Species Act. We developed a model to estimate daily and annual abundance of naturally produced age-0 fall Chinook salmon passing Lower Granite Dam (Snake River, USA) for each of the last 30 years. We accounted for variable hatchery marking rates by integrating two related data sources: 1) release-recapture data of fish with individually identifiable tags and 2) counts of marked and unmarked sample of fish captured each day. We fit joint parameters for daily fish arrival and capture probabilities to these data to estimate the daily abundance of hatchery- and natural-origin fish. Our results show that from 1992 to 2021, the annual abundance of juvenile natural-origin Snake River fall Chinook salmon increased by two orders of magnitude. These results are the first comprehensive evaluation of multi-decadal trends in abundance and run-timing for this population. Our approach can be adapted to other runs and locations within the Columbia River basin or similar systems where out-migrating fish are monitored at fixed locations.

Recreational fishing in the lower basin of the Santa Cruz river(Patagonia, Argentina) in the face of damming scenarios

The Steelhead ecotype (Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytscha) have promoted a recreational fishery in the Santa Cruz river, the last large free flowing river of Patagonia. However, two dams are being built upstream in the middle course, potentially affecting the life cycle of these anadromous salmonids. The study describes the dynamics of the recreational fishing of the Santa Cruz river around Piedrabuena city and anglers perceptions, discussing its trends according to possible river connectivity scenarios. The fishery was assessed through a monthly year-round field sampling from April 2018 to April 2019, developing instantaneous angler counts, discriminating fishing methods, effort, and catch per unit effort; also, in situ interviews were used to collect information on anglers’ motivations and perceptions. In addition, information on fishing tournaments was used. Three fishing zones (FZ) were identified near Piedrabuena city: FZ-1, located downstream where anglers used baited hook and line to catch the native marine Patagonian blenny (Eleginops maclovinus); FZ-2, located in the town where baited hook and line, spinning, and fly-cast are used to catch Patagonian blenny and salmonids; FZ-3 located upstream the town, where fishing effort was mainly directed to salmonids employing spinning and fly-cast. Fishing effort showed a seasonal pa�ern with high values from March to May and September to October, agreeing with Steelhead and Chinook salmon runs, respectively. The most relevant motivations for anglers were nonoriented catch variables. Anglers preferred the capture of salmonids over native species, considering dams to be a major threat to fishery. Although a postdamming scenario could allow the adult salmonids to migrate upstream, the current reproduction grounds of Steelhead will be flooded, and juveniles and adults of both species will be hindered in their downstream migration to sea. These aspects seem to seriously compromise the future of these unique fisheries.

MAVS disruption impairs downstream signaling and results in higher virus replication levels of salmonid alphavirus subtype 3 but not infectious pancreatic necrosis virus in vitro.

The mitochondrial anti-viral signaling (MAVS) protein is an intermediary adaptor protein of retinoic acid-inducible gene-1 (RIG-I) like receptor (RLR) signaling, which activates the transcription factor interferon (IFN) regulatory factor 3 (IRF3) and NF-kB to produce type I IFNs. MAVS expression has been reported in different fish species, but few studies have shown its functional role in anti-viral responses to fish viruses. In this study, we used the transcription activator-like effector nuclease (TALEN) as a gene editing tool to disrupt the function of MAVS in Chinook salmon (Oncorhynchus tshawytscha) embryonic cells (CHSE) to understand its role in induction of interferon I responses to infections with the (+) RNA virus salmonid alphavirus subtype 3 (SAV-3), and the dsRNA virus infectious pancreatic necrosis virus (IPNV) infection. A MAVS-disrupted CHSE clone with a 7-aa polypeptide (GVFVSRV) deletion mutation at the N-terminal of the CARD domain infected with SAV-3 resulted in significantly lower expression of IRF3, IFNa, and ISGs and increased viral titer (1.5 log10) compared to wild-type. In contrast, the IPNV titer in MAVS-disrupted cells was not different from the wild-type. Furthermore, overexpression of salmon MAVS in MAVS-disrupted CHSE cells rescued the impaired type I IFN-mediated anti-viral effect against SAV-3.

Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha).

Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.

Behavioral transcriptomic effects of triploidy and probiotic therapy (Bifidobacterium, Lactobacillus, and Lactococcus mixture) on juvenile Chinook salmon (Oncorhynchus tshawytscha).

Aquaculturists use polyploid fish to maximize production albeit with some unintended consequences including compromised behaviors and physiological function. Given benefits of probiotic therapies (e.g., improved immune response, growth, and metabolism), we explored probiotic supplementation (mixture of Bifidobacterium, Lactobacillus, and Lactococcus), to overcome drawbacks. We first examined fish gut bacterial community composition using 16S metabarcoding (via principal coordinate analyses and PERMANOVA) and determined probiotics significantly impacted gut bacteria composition (p = 0.001). Secondly, we examined how a genomic disruptor (triploidy) and diet supplements (probiotics) impact gene transcription and behavioral profiles of hatchery-reared Chinook salmon (Oncorhynchus tshawytscha). Juveniles from four treatment groups (diploid-regular feed, diploid-probiotic feed, triploid-regular feed, and triploid-probiotic feed; n = 360) underwent behavioral assays to test activity, exploration, neophobia, predator evasion, aggression/sociality, behavioral sensitivity, and flexibility. In these fish, transcriptional profiles for genes associated with neural functions (neurogenesis/synaptic plasticity) and biomarkers for stress response and development (growth/appetite) were (i) examined across treatments and (ii) used to describe behavioral phenotypes via principal component analyses and general linear mixed models. Triploids exhibited a more active behavioral profile (p = 0.002), and those on a regular diet had greater Neuropeptide Y transcription (p = 0.02). A growth gene (early growth response protein 1, p = 0.02) and long-term neural development genes (neurogenic differentiation factor, p = 0.003 and synaptysomal-associated protein 25-a, p = 0.005) impacted activity and reactionary profiles, respectively. Overall, our probiotic treatment did not compensate for triploidy. Our research highlights novel applications of behavioral transcriptomics for identifying candidate genes and dynamic, mechanistic associations with complex behavioral repertoires.

Unique diet and Philonema sp. infections in reservoir‐rearing juvenile Chinook Salmon

AbstractObjectiveDams and reservoirs can alter juvenile growth and survival of migratory salmonids through several physical and biological mechanisms. Juvenile Chinook Salmon Oncorhynchus tshawytscha that are produced upstream of large hydropower dams may have associated passage mortality, but the reservoirs created by these dams can support rapid growth. Characterizing the biotic drivers of growth and mortality in reservoirs may aid in understanding the cumulative effects of river impoundments on migratory salmonid populations. The purpose of this study was to understand how reservoirs facilitate rapid growth in juvenile Chinook Salmon.MethodsWe analyzed stomach contents to determine diet composition throughout the summer and fall. We also recorded prevalence of the parasitic nematode Philonema sp. in the coeloms of fish.ResultWe found that juvenile Chinook Salmon frequently consumed young‐of‐year centrarchids, which likely contributed to rapid growth. Piscivory was highest from July through October and decreased with surface temperature from November through December. Correspondingly, zooplankton and arthropod consumption increased in November and December. Prevalence of visible Philonema sp. infections in the coelom was high (34.6%), negatively associated with time, and nonlinearly associated with fork length.ConclusionThese findings reveal unique diet patterns and suggest potential parasite‐associated mortality in reservoir‐rearing Chinook Salmon, but more detailed studies across a longer time scale are needed to robustly assess the population‐level effects of this parasite.

Variables influencing stream‐type juvenile Chinook Salmon density within floodplain habitat in the Skagit River basin, Washington

AbstractObjectiveDespite decades of restoration work, Chinook Salmon Oncorhynchus tshawytscha in the Pacific Northwest remain under the protection of the U.S. Endangered Species Act (ESA). Chinook Salmon in the Skagit River basin play a vital role in the abundance and recovery of the Puget Sound Chinook Salmon Evolutionarily Significant Unit, which is currently listed as threatened under the ESA. The stream‐type juvenile (STJ) life history pattern of Chinook Salmon in the Skagit River has higher ocean survival to the adult stage (i.e., productivity) than that of parr or fry out‐migrants, and improvement in STJ Chinook Salmon habitat could increase abundance and diversity in the Skagit River basin. Our objective was to provide recommended ranges of variables shown to influence habitat selection in floodplains by STJ Chinook Salmon.MethodsUsing field observations from 70 sites within the Skagit River basin, we developed generalized linear mixed‐effects models across three seasons in floodplain habitats to correlate variable ranges with densities of STJ Chinook Salmon.ResultModel accuracy varied by season (summer: R2 = 0.24; winter: R2 = 0.56; spring: R2 = 0.54), and significant parameters included velocity, substrate, depth range, and distance to the closest connection with the main stem. Additional significant factors included wood cover, maximum water temperature, velocity range, and interaction of the ranges of velocity and depth. Recommended ranges for habitat variables associated with the highest densities of STJ Chinook Salmon include depths of 40–68 cm, velocities of 0.06–0.33 m/s, substrate sizes of 3–36 mm, and distances of 33–119 m to the main‐stem connection. Water temperatures associated with high juvenile densities varied by season (winter: 4–6°C; summer: 9–14°C).ConclusionOur recommended ranges for habitat variables can be used to refine designs for river restoration projects intended to improve habitat for juvenile Chinook Salmon and other salmonids in the Pacific Northwest.

Predicting juvenile-to-adult survival in Chinook salmon using non-lethal scale-derived growth and regeneration indices

ABSTRACT Survival is often associated with body size, growth rate, and stress, but the latter two are more difficult to observe non-lethally. Non-lethal methods can be particularly important for endangered and culturally valuable species. With fish scales, growth and stress indices could be inferred without needing to sacrifice fish. We examined scales from ~350 wild Chinook salmon (Oncorhynchus tshawytscha) in Valley Creek and at Lower Granite Dam (Pacific Northwest, USA) in 2007–2019. From a von Bertalanffy model and scale circulus spacings, we estimated a brood-year-specific growth coefficient K (hereafter K ˆ ). Using the scale-derived K ˆ and other biological and environmental covariates, we examined how these potential predictors associated with juvenile-to-adult survival of >136,000 passive-integrated-transponder-tagged Chinook salmon from the Snake River Basin (Pacific Northwest, USA). We found that the effects on survival from brood-year-specific K ˆ , fork length of the tagged individuals, and interaction between K ˆ and fork length were positive. We also determined that the proportion of fish samples with regenerated scales (an indicator of stress) had a negative effect on survival. For further refinement of non-lethal, scale-derived indices on survival, we encourage examination of indices across populations, juvenile habitats, and juvenile life stages, and not simply a regional, brood-year-specific growth index.