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Restoration of movement corridors is a key management action used to address threats to migratory and other mobile species. Yet, we lack restoration effectiveness studies that allow for species to reestablish naturally (i.e. without supplementation) following habitat reconnection that capture all phases (dispersal, growth, and regulation) of recovery, and that takes an ecosystems approach. We investigated the natural recovery of migratory anadromous Coho salmon following habitat reconnection across a 5‐km section of Rock Creek, a forested tributary of the Cedar River, Washington, United States, 3 km upstream of Landsburg Dam. The dam blocked upstream fish movement for 102 years until the completion of a fish ladder in 2003. We also evaluated the response of non‐migratory trout, which are closely related to Coho salmon. Juvenile Coho salmon natal to the Cedar River dispersed into Rock Creek for rearing until spawning there in 2007. After restoration, juvenile Coho salmon density (fish/m2) increased 18‐fold, approaching an asymptote (i.e. regulation phase) a decade later. Coho salmon recovery in Rock Creek was spatially variable, however, slowing with distance from the site of restoration. Trout density was also higher after restoration relative to before, likely due to several mechanisms, including increased capacity resulting from the reestablishment of marine organic matter subsidies delivered by spawning anadromous fish. Our study demonstrates that migratory species can recover naturally after the restoration of habitat connectivity and associated movement corridors. Furthermore, our results suggest that such actions can also benefit nontarget species by reestablishing key ecosystem links driven by the target species. [ABSTRACT FROM AUTHOR]

Snorkel surveys are frequently used to monitor stream-dwelling fish. Inferring local abundance from snorkel surveys is complicated by two primary factors: variable fish detection probabilities and the relative abundance of fish in habitat types below the recommended minimum depth for snorkeling. We examine these factors across three salmonid species (Oncorhynchus spp.), 4 years, and 113 location-years in Oregon coastal streams. We calibrate snorkel counts to mark-recapture estimates and develop mathematically explicit expressions that convert a new snorkel count into a probability density of abundance for streams containing mixed habitat types that were and were not snorkeled. Snorkelers detected 63%, 47%, and 39% of juvenile coho salmon (Oncorhynchus kitsutch), steelhead trout (Oncorhynchus mykiss), and cutthroat trout (Oncorhynchus clarkii clarkia) estimated by mark-recapture, respectively, but uncertainty within and among sampling units was high. Further, analytics developed here can be used to infer abundance and uncertainty for habitat types that were not snorkeled. Our quantification of uncertainty arising from using snorkel counts as a proxy for abundance will help managers balance biological risks with available resources. [ABSTRACT FROM AUTHOR]

Concern over rising water temperatures for freshwater ectotherms has led to application of experimentally derived thermal thresholds to stream temperature models for estimation of streams at high risk of exceeding thermal thresholds under current and future climate conditions. We optimised an approach that links field‐relevant thermal maxima experiments to corresponding stream temperature models and identifies opportunities to reduce stream temperatures through riparian tree growth.We conducted a thermal maxima experiment on cold‐water adapted juvenile Chinook (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch) that reflected natural temperatures by using incremental temperature ramping with diel fluctuations (IT‐Dmax) and refit a regionally specific stream temperature model for British Columbia, Canada to directly relate to lab‐derived thresholds. Salmon‐bearing streams across British Columbia were categorised by threshold exceedance risk (i.e., low, moderate, high, severe) based on risk tolerance scenarios for management decision making (i.e., considering a range of prediction intervals [PIs] and stream thermal sensitivities to air temperature). We linked these results directly to riparian management and restoration actions by estimating the potential for riparian tree growth to reduce threshold exceedance risk.Lab‐derived IT‐Dmax endpoints were consistently 24°C (based on the median value between the 7‐day average of the daily maximum and the mean weekly average temperature) across acclimation treatments for both species. Under current conditions, most stream reaches (99.6% using an intermediate risk tolerance scenario) were below the thermal threshold; streams with moderate to high risk of threshold exceedance were projected to increase from 0.4% to 1.5% (total linear stream length of 6,929 km) by end of century. The risk‐averse (high sensitivity, 75% PI) and risk‐tolerant (low sensitivity, 95% PI) scenarios differed by 1,107 km of streams predicted to have a moderate to severe risk of exceeding thresholds by end of century. Maximal riparian tree growth was predicted to shift 670 km of streams from moderate to low exceedance risk under end‐of‐century conditions and intermediate risk tolerance, showing the potential for mitigation from thermal impacts.Our integrative approach tackled several key considerations in identifying streams at high temperature risk for freshwater ectotherms that to date have not been addressed. Furthermore, we showcased the delineation of spatially comprehensive estimates that identify where management mitigation and a specific restoration activity may be most needed to reduce impacts of rising temperatures on rearing salmonids across an extensive region. [ABSTRACT FROM AUTHOR]

Background: Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. Results: We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. Conclusions: Our results highlight the key role of keratinocytes in coho salmon's sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance. [ABSTRACT FROM AUTHOR]

Simple Summary: Phyto-based foods are becoming more and more popular worldwide, and people are consuming phyto-active components for purposes other than traditional health and nutrition. The study aimed to ascertain the impact of tea polyphenols (TPs) on fish. The outcomes showed that cold-water coho salmon exhibit improved growth, feed intake, and immunity. These results are helpful in promoting the development of novel feed additives for the aquaculture industry. To evaluate the impact of nutritional tea polyphenols (TPs) on body composition, growth, biochemical markers, antioxidant capacity, and hemato-immunological levels, a ten-week feeding experiment was carried out on coho salmon (Oncorhynchus kisutch, 180.51 ± 0.15 g). The control group was fed a basal diet; the T1, T2, T3, and T4 groups were fed 0.005%, 0.01%, 0.02%, and 0.04% TPs, respectively. These results demonstrate that adding TPs significantly (p < 0.05) increased the coho salmon fish's weight gain (WG), relative growth rate (RGR), condition factor (CF), feed efficacy (FE), daily growth rate (DGR), and specific growth rate (SGR). There was no discernible difference in the body compositions of the treated TPs and the control group (p > 0.05). In addition, the T3 group showed a significant (p < 0.05) decrease in GPT, LDL, HDL, TC, and CAT. Fish given a 0.02% diet containing TPs had significantly lower levels of malondialdehyde (MDA) in their liver; yet, the TP-treated groups had higher levels of SOD and CAT than the control (p < 0.05). The data analysis shows a significant rise in lysozyme, respiratory burst activity, bactericidal activity, and blood hematological parameters in the 0.01–0.04% TP groups. According to these findings, TPs could be a useful dietary supplement for raising the antioxidant status, growth parameters, haemato-immunological response, and whole-body composition of coho salmon fish. [ABSTRACT FROM AUTHOR]

Flavobacterium psychrophilum, the causative agent of bacterial cold-water disease, is a devastating, worldwide distributed, fish pathogen causing significant economic loss in inland fish farms. Previous epidemiological studies showed that prevalent clonal complexes (CC) differ in fish species affected with disease such as rainbow trout, coho salmon and ayu, indicating significant associations between particular F. psychrophilum genotypes and host species. Yet, whether the population structure is driven by the trade of fish and eggs or by host-specific pathogenicity is uncertain. Notably, all F. psychrophilum isolates retrieved from ayu belong to Type-3 O antigen (O-Ag) whereas only very few strains retrieved from other fish species possess this O-Ag, suggesting a role in outbreaks affecting ayu. Thus, we investigated the links between genotype and pathogenicity by conducting comparative bath infection challenges in two fish hosts, ayu and rainbow trout, for a collection of isolates representing different MLST genotypes and O-Ag. Highly virulent strains in one host species exhibited low to no virulence in the other. F. psychrophilum strains associated with ayu and possessing Type-3 O-Ag demonstrated significant variability in pathogenicity in ayu, ranging from avirulent to highly virulent. Strikingly, F. psychrophilum strains retrieved from rainbow trout and possessing the Type-3 O-Ag were virulent for rainbow trout but not for ayu, indicating that Type-3 O-Ag alone is not sufficient for pathogenicity in ayu, nor does it prevent pathogenicity in rainbow trout. This study revealed that the association between a particular CC and host species partly depends on the pathogen's adaptation to specific host species. [ABSTRACT FROM AUTHOR]

N-(1,3-Dimethyl butyl)-N′-phenyl-phenylenediamine-quinone (6PPD-Q) is a derivative of the widely used rubber tire antioxidant 6PPD, which was first found to be acutely toxic to coho salmon. Subsequent studies showed that 6PPD-Q had species-specific acute toxicity in fishes and potential hepatotoxicity in mice. In addition, 6PPD-Q has been reported in human urine, demonstrating the potential widespread exposure of humans to this chemical. However, whether 6PPD-Q poses a higher risk to humans than its parent compound, 6PPD, and could cause adverse effects in humans is still unclear. In this study, we utilized two human liver cell models (the human proto-hepatocyte model L02 and the human hepatocellular carcinoma cell line HepG2) to investigate the potentially differential effects of these two chemicals. Cell viability curve analysis showed that 6PPD-Q had lower IC50 values than 6PPD for both liver cell lines, suggesting higher toxicity of 6PPD-Q to human liver cells than 6PPD. In addition, L02 cells are more sensitive to 6PPD-Q exposure, which might be derived from its weaker metabolic transformation of 6PPD-Q, since significantly lower levels of phase I and phase II metabolites were detected in 6PPD-Q-exposed L02 cell culture medium. Furthermore, pathway analysis showed that 6PPD-Q exposure induced changes in phenylalanine, tyrosine, and tryptophan biosynthesis and tyrosine metabolism pathways in L02 cells, which might be the mechanism underlying its liver cell toxicity. Gene expression analysis revealed that exposure to 6PPD-Q induced excessive ROS production in L02 cells. Our results further supported the higher risk of 6PPD-Q than 6PPD and provided insights for understanding the effects of 6PPD-Q on human health. [ABSTRACT FROM AUTHOR]

The relationship of histopathological changes and the infection of Piscine orthoreovirus 2 (PRV‐2) was investigated in coho salmon that were suffering from the erythrocytic inclusion body syndrome (EIBS). Immunohistochemical observations revealed abundant σ1 protein of PRV‐2 in the spongy layer of the ventricle of the heart, where severe myocarditis was observed. In the spleen, the virus protein was detected in many erythrocytes, some of which were spherical‐shaped and apparently dead. The number of erythrocytes was decreased in the spleen compared to the apparently healthy fish. The virus protein was also detected in some erythrocytes in blood vessels. The viral protein was often detected in many macrophages ingesting erythrocytes or dead cell debris in the spleen or in the kidney sinusoids. Large amounts of the viral genomic segment L2 were also detected in these organs by RT‐qPCR. Many necrotic foci were found in the liver, although the virus protein was not detected in the hepatocytes. These results suggest that the primary targets of PRV‐2 are myocardial cells and erythrocytes and that clinical symptoms such as anaemia or jaundice and histopathological changes such as myocarditis in EIBS‐affected coho salmon are caused by PRV‐2 infection. [ABSTRACT FROM AUTHOR]

N‐(1,3‐dimethylbutyl)‐N′‐phenyl‐p‐phenylenediamine‐quinone (6PPD‐quinone) is a widespread contaminant of emerging concern resulting from oxidation of 6PPD, which is an antidegradant substance added to tires. The recent identification of 6PPD‐quinone as the cause of acute mortality in coho salmon has quickly motivated studies on 6PPD‐quinone toxicity to other species. Subsequent findings have shown that 6PPD‐quinone toxicity is highly species specific. Closely related species can differ widely in response to 6PPD‐quinone from extremely sensitive to tolerant. Hence toxicity testing is currently the only way to establish whether a species exhibits 6PPD‐quinone toxicity. We investigated the acute toxicity of 6PPD‐quinone in pink salmon alevins (sac fry). This species has is the only Pacific salmon that so far has not been tested for 6PPD‐quinone sensitivity. Fish were exposed in static water in eight treatments with initial concentrations ranging from 0.1 to 12.8 μg/L. Fish were observed for 48 h, and changes in concentrations of 6PPD‐quinone were monitored throughout the experiment. No mortalities or substantial changes in behavior were recorded. Environ Toxicol Chem 2024;43:1332–1338. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. [ABSTRACT FROM AUTHOR]

Cool‐water habitats provide increasingly vital refuges for cold‐water fish living on the margins of their historical ranges; consequently, efforts to enhance or create cool‐water habitat are becoming a major focus of river restoration practices. However, the effectiveness of restoration projects for providing thermal refuge and creating diverse temperature regimes at the watershed scale remains unclear. In the Klamath River in northern California, the Karuk Tribe Fisheries Program, the Mid‐Klamath Watershed Council, and the U.S. Forest Service constructed a series of off‐channel ponds that recreate floodplain habitat and support juvenile coho salmon (Oncorhynchus kisutch) and steelhead (O. mykiss) along the Klamath River and its tributaries. We instrumented these ponds and applied multivariate autoregressive time series models of fine‐scale temperature data from ponds, tributaries, and the mainstem Klamath River to assess how off‐channel ponds contributed to thermal regime diversity and thermal refuge habitat in the Klamath riverscape. Our analysis demonstrated that ponds provide diverse thermal habitats that are significantly cooler than creek or mainstem river habitats, even during severe drought. Wavelet analysis of long‐term (10 years) temperature data indicated that thermal buffering (i.e. dampening of diel variation) increased over time but was disrupted by drought conditions in 2021. Our analysis demonstrates that in certain situations, human‐made off‐channel ponds can increase thermal diversity in modified riverscapes even during drought conditions, potentially benefiting floodplain‐dependent cold‐water species. Restoration actions that create and maintain thermal regime diversity and thermal refuges will become an essential tool to conserve biodiversity in climate‐sensitive watersheds. [ABSTRACT FROM AUTHOR]

We performed a diagnostic disease investigation on a cohort of coho salmon (Oncorhynchus kisutch) fingerlings in Alaska exhibiting anorexia, gaping mouths, anemia, and increased mortality. Histologic examination revealed mild-to-severe myocardial degeneration and lymphohistiocytic and neutrophilic myocarditis, moderate splenic histiocytosis, and mild renal histiocytosis. Piscine orthoreoviruses 1 and 3 were not detected by molecular methods, and no other viruses could be cultured on 3 common diagnostic fish cell lines. De novo assembly produced a viral genome of 10 linear segments with >80% homology to piscine orthoreovirus 2 (PRV2) encoding all 11 PRV2 proteins. An in situ hybridization probe using RNAscope was developed against 697 viral nucleotides identified by sequencing, which revealed viral genome in heart, spleen, gill, kidney, liver, blood, and the lamina propria of the intestines. Our findings are supportive of a novel piscine orthoreovirus most closely related to PRV2 associated with morbidity and mortality of coho salmon in the northeastern Pacific. [ABSTRACT FROM AUTHOR]

The purpose of this experiment was to investigate the effects of Bacillus pumilus (GXUN613L) on the growth performance, serum biochemical indexes, antioxidant capacity, and intestinal health of coho salmon. A total of 240 coho salmon with initial body mass of (130.2±10.1) g were randomly divided into four groups with three replicates in each group and 20 coho salmon in each replicate. Bacillus pumilus (GXUN613L) was supplemented with 0, 2x107, 4x109, and 8x1011 CFU/g in basal diet in CK group, LL group, LM group, and LH group, respectively. The trial period was six weeks. The results showed that the weight gain rate and specific growth rate of coho salmon in LL group and LM group were significantly higher than those in CK group (P<0.05), the protein efficiency ratio of coho salmon in LM group was significantly higher than that in CK group (P<0.05), and the feed conversion ratio was significantly lower than that in CK group (P<0.05). Serum total protein, albumin and total cholesterol in LL group, LM group, and LH group were significantly higher than those in CK group (P<0.05). Serum glucose content and alkaline phosphatase activity in LM group were significantly higher than those in CK group (P<0.05). The total antioxidant capacity, catalase activity, superoxide dismutase, and glutathione peroxidase activity of liver in LM group were significantly higher than those in CK group (P<0.05). The muscular layer thickness and villus height of foregut and hindgut in LM group were significantly higher than those in CK group (P<0.05), and the intestinal microbial diversity was better. The result shows that the addition of Bacillus pumilus (GXUN613 L) in feed can promote the growth, improve the serum indexes and intestinal health, and enhance the antioxidant capacity of coho salmon. The suitable addition amount of GXUN613L is 4x109 CFU/g. [ABSTRACT FROM AUTHOR]

How has parasitism changed for Alaskan salmon over the past several decades? Parasitological assessments of salmon are inconsistent across time, and though parasite data are sometimes noted when processing fillets for the market, those data are not retained for more than a few years. The landscape of parasite risk is changing for salmon, and long‐term data are needed to quantify this change. Parasitic nematodes of the family Anisakidae (anisakids) use salmonid fishes as intermediate or paratenic hosts in life cycles that terminate in marine mammal definitive hosts. Alaskan marine mammals have been protected since the 1970s, and as populations recover, the density of definitive hosts in this region has increased. To assess whether the anisakid burden has changed in salmonids over time, we used a novel data source: salmon that were caught, canned, and thermally processed for human consumption in Alaska, USA. We examined canned fillets of chum (Oncorhynchus keta, n = 42), coho (Oncorhynchus kisutch, n = 22), pink (Oncorhynchus gorbuscha, n = 62), and sockeye salmon (Oncorhynchus nerka, n = 52) processed between 1979 and 2019. We dissected each fillet and quantified the number of worms per gram of salmon tissue. Anisakid burden increased over time in chum and pink salmon, but there was no change in sockeye or coho salmon. This difference may be due to differences in the prey preferences of each species, or to differences in the parasite species detected across hosts. Canned fish serve as a window into the past, providing information that would otherwise be lost, including information on changes over time in the parasite burden of commercially, culturally, and ecologically important fish species. [ABSTRACT FROM AUTHOR]

Piscine orthoreovirus (PRV) is a pathogen that causes heart and skeletal muscle inflammation in Salmo salar and has also been linked to circulatory disorders in other farmed salmonids, such as Oncorhynchus kisutch and Oncorhynchus mykiss. The virus has a segmented, double-stranded RNA genome, which makes it possible to undergo genetic reassortment and increase its genomic diversity through point mutations. In this study, genetic reassortment in PRV was assessed using the full genome sequences available in public databases. This study used full genome sequences that were concatenated and genome-wide reassortment events, and phylogenetic analyses were performed using the recombination/reassortment detection program version 5 (RDP5 V 5.5) software. Additionally, each segment was aligned codon by codon, and overall mean distance and selection was tested using the Molecular Evolutionary Genetics Analysis X software, version 10.2 (MEGA X version 10.2). The results showed that there were 17 significant reassortment events in 12 reassortant sequences, involving genome exchange between low and highly virulent genotypes. PRV sequences from different salmonid host species did not appear to limit the reassortment. This study found that PRV frequently undergoes reassortment events to increase the diversity of its segmented genome, leading to antigenic variation and increased virulence. This study also noted that to date, no reassortment events have been described between PRV-1 and PRV-3 genotypes. However, the number of complete genomic sequences within each genotype is uneven. This is important because PRV-3 induces cross-protection against PRV-1, making it a potential vaccine candidate. [ABSTRACT FROM AUTHOR]

How has parasitism changed for Alaskan salmon over the past several decades? Parasitological assessments of salmon are inconsistent across time, and though parasite data are sometimes noted when processing fillets for the market, those data are not retained for more than a few years. The landscape of parasite risk is changing for salmon, and long‐term data are needed to quantify this change. Parasitic nematodes of the family Anisakidae (anisakids) use salmonid fishes as intermediate or paratenic hosts in life cycles that terminate in marine mammal definitive hosts. Alaskan marine mammals have been protected since the 1970s, and as populations recover, the density of definitive hosts in this region has increased. To assess whether the anisakid burden has changed in salmonids over time, we used a novel data source: salmon that were caught, canned, and thermally processed for human consumption in Alaska, USA. We examined canned fillets of chum (Oncorhynchus keta, n = 42), coho (Oncorhynchus kisutch, n = 22), pink (Oncorhynchus gorbuscha, n = 62), and sockeye salmon (Oncorhynchus nerka, n = 52) processed between 1979 and 2019. We dissected each fillet and quantified the number of worms per gram of salmon tissue. Anisakid burden increased over time in chum and pink salmon, but there was no change in sockeye or coho salmon. This difference may be due to differences in the prey preferences of each species, or to differences in the parasite species detected across hosts. Canned fish serve as a window into the past, providing information that would otherwise be lost, including information on changes over time in the parasite burden of commercially, culturally, and ecologically important fish species. [ABSTRACT FROM AUTHOR]

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

The value of estuaries as nursery habitat for juvenile anadromous salmon is likely variable across estuaries and species. Here, we compiled published empirical data on juvenile salmon estuarine growth and residency. We aimed to quantify the range and variability of these aspects for five species of Pacific salmon across estuaries, methodologies, and life histories. The majority of studies focused on Chinook and coho salmon, largely from their southern range. While there is some evidence of higher growth in wild-origin fish relative to hatchery-origin fish, the wide range of metrics employed made identification of trends among life histories challenging, and unification of reporting could strengthen future research. Different salmon life histories exhibited different residencies, with natural-origin subyearling coho exhibiting the longest mean residency (∼3 months) and 1+ sockeye salmon exhibiting the shortest (3.7 days). Across life histories, hatchery fish exhibited much shorter estuary residencies than wild fish. Collectively, our review highlights key patterns in salmon estuary ecology, identifies knowledge gaps, and lays the foundation for future studies to quantify the importance of estuaries for specific salmon. [ABSTRACT FROM AUTHOR]

Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage‐based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species‐specific Genotyping‐in‐Thousands by sequencing (GT‐seq) panels. For laboratories involved in large‐scale genotyping efforts, diagnosing non‐target species and reassigning them to the appropriate monitoring program can be costly and time‐consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross‐species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species‐specific GT‐seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species‐informative amplicons (16) were newly identified from the four existing GT‐seq panels, thus demonstrating a low‐cost approach to species identification when using targeted sequencing methods. A species‐calling script was developed that is tailored for routine GT‐seq genotyping pipelines and automates the identification of non‐target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low‐frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost‐effective approach to species identification for genetic monitoring programs. [ABSTRACT FROM AUTHOR]

Human stressors block, eliminate, and simplify habitat mosaics, eroding landscapes' life history diversity and thus biological resilience. One goal of restoration is to alleviate human stressors that suppress life history diversity, but life history responses to these efforts are still coming into focus. Here, we report life history diversity emerging in threatened salmonids (Oncorhynchus spp.) repopulating the recently undammed Elwha River (WA, United States) in adjacent but environmentally distinct tributaries. The ~20km tributaries entered the Elwha River <1km apart, but one had a colder stream temperature regime and swifter waters due to its high, snow-dominated elevation and steep valley gradient (~3%), while the other had a warmer stream temperature regime and slower waters because it drained a lake, was at lower elevation, and had a lower stream gradient (~1.5%). Following the 2012 removal of Elwha Dam, the tributaries' salmonids generally became more abundant and expressed diverse life histories within and among species. The warmer, low-gradient tributary produced more age-1+coho salmon and steelhead. Additionally, salmonids exiting the warmer tributary were older and possibly larger for their age class, emigrated ~23 days earlier, and included age-0 Chinook salmon that were larger. Also, assemblage composition varied among years, with the most abundant species shifting between Chinook salmon and coho salmon, while steelhead abundances generally increased but were patchy. These patterns are consistent with a newly accessible, heterogeneous landscape generating life history diversity against the backdrop of patchy recruitment as salmonids -- some with considerable hatchery-origin ancestry -- repopulate an extirpated landscape. Overall, dam removal appears to have promoted life history diversity, which may bolster resilience during an era of rapid environmental change and portend positive outcomes for upcoming dam removals with similar goals. [ABSTRACT FROM AUTHOR]

Objective: Coho Salmon Oncorhynchus kisutch provide an important resource for recreational, commercial, and Indigenous fisheries in the Pacific Northwest. The goal of this study was to improve our understanding of how marine mammal predation may be impacting the survival and productivity of Coho Salmon in the Strait of Georgia, British Columbia. Specifically, we quantified the impact of harbor seal Phoca vitulina predation on juvenile Coho Salmon during their first several months at sea. Early marine survival is believed to be the limiting factor for the recovery of Coho Salmon populations in this region. Methods: To estimate the number of juvenile Coho Salmon consumed by harbor seals, we developed a mathematical model that integrates predator diet data and salmon population and mortality dynamics. Result: Our analysis estimated that harbor seals consumed an annual average of 46−59% of juvenile Coho Salmon between 2004–2016, providing the first quantitative estimate of seal predation in the Strait of Georgia. Conclusion: Marine mammal predation on juvenile Coho Salmon is potentially a very important factor limiting survival and recovery of Coho Salmon in the Strait of Georgia. Impact statementCoho Salmon populations in the Strait of Georgia have experienced precipitous declines in marine survival over the last four decades. In this study, we used predator diet data to quantify the potential impact of harbor seals on juvenile Coho Salmon. Our results suggest seal predation may strongly influence survival of young salmon during their first several months at sea, and should be considered in future recovery efforts. [ABSTRACT FROM AUTHOR]

This study investigated the effect of replacing a portion of fish meal with unfermented and/or fermented soybean meal in juvenile coho salmon (Oncorhynchus kisutch). Four groups of juveniles (initial weight 110.31 ± 3.12 g) in triplicate were fed for 90 days on four different iso‐nitrogen and iso‐lipid diets. The G0 diet comprised 28% fish meal protein (control group). In the other three diets (G1, G2, and G3), 10% of the fish meal protein was replaced with unfermented and/or fermented soybean meal protein. The main results were: Compared with G0, the WGR, SGR, CF; the contents of GLU, TP, ALB, T‐CHO, and T‐AOC, the activities of AKP, CAT, SOD, GST, GSH‐PX, O2·‐CR, OH·‐CR, and GSH and the expressions of SOD, GSH‐PX, GST, CAT, and Nrf2 genes of juvenile coho salmon in G3 were significantly (p < 0.05) increased, However, the FCR, HSI, the content of MDA, and the expressions of TNF‐α and IL‐6 genes of juvenile coho salmon in G3 were significantly (p < 0.05) decreased. There was no significant effect (p > 0.05) of diet on their survival rate (SR). In conclusion, the fermented soybean meal in the juvenile coho salmon diet can replace 10% of the fish meal protein. [ABSTRACT FROM AUTHOR]

By the 1980s, after decades of declining numbers in the mid‐1900s, Coho salmon (Oncorhynchus kisutch) were considered extirpated from the interior Columbia River. In the mid‐1990s, the Confederated Tribes of the Umatilla Indian Reservation, the Confederated Tribes and Bands of the Yakama Nation, and the Nez Perce Tribe began successful reintroduction programs of Coho salmon upstream of Bonneville Dam, but which were initially sourced from lower Columbia River hatcheries. Here we present the first Coho salmon parentage‐based tagging (PBT) baseline from seven hatchery programs located in the interior Columbia River basin, and two sites at or downstream of Bonneville Dam, composed of over 32,000 broodstock samples. Analyses of baseline collections revealed that genetic structure followed a temporal pattern based on 3‐year broodlines rather than geographic location or stocking history. Across hatchery programs, similar levels of genetic diversity was present. The PBT baseline provided multiple direct applications such as identification of origin for Coho salmon collected in a mixed stock at Priest Rapids Dam and the detection of the proportion and distribution of hatchery‐origin fish on the spawning grounds in the Methow River basin. The PBT baseline for Coho salmon is freely available for use and can be downloaded from FishGen.net. [ABSTRACT FROM AUTHOR]

A total of 122 coho salmon specimens were examined. The fish were caught in the coastal zone and in the rivers of Iturup Island (southern Kuril Islands) during their spawning migration in August–October 2021. Almost all females and males close to maturity in that year had spent 1 year at sea and were at ages of 1.1+ (66.7%) and 2.1+ (30.0%). Fish that had spent 2 years at sea were found singly: one specimen at an age of 1.2+ and three specimens at an age of 2.2+ (2.5%). Taking into account the age at maturity and the body weight (an average of 2.63 kg for females and 2.44 kg for males), an assumption can be made that the examined fish bred in short streams. The high value of the gonadosomatic index (up to 20–22% for some females) did not indicate that all the fish caught in the coastal waters would have run to other spawning grounds. At least a portion of them should have spawned in the water courses of Iturup Island, as was evidenced by the captures of a few coho salmon immediately in the rivers. Along with the fish running to the spawning grounds, two actively feeding coho females at an age of 0.0+ (0.55 kg) and 1.0+ (1.11 kg) were also caught with stake nets. [ABSTRACT FROM AUTHOR]

Simple Summary: With the increasing demand for aquaculture, the resource of high-quality traditional protein (such as fishmeal) becomes limited, and plant ingredients are often used as substitutes for fishmeal because of their low price and wide availability. However, plant proteins are usually deficient in certain essential amino acids (EAAs), which adversely affects the growth performance of aquatic animals. Lysine is generally the first limiting amino acid in plant protein ingredients used to formulate the aquafeed, and it plays an important role in physiological processes including antioxidant, differentiation, growth, immunity, and reduction of nitrogen emission. In this study, the effects of dietary graded L-lysine concentrations on the growth, proximate composition, and AA (amino acid) profile of coho salmon alevins were evaluated by a feeding trial. The results showed that an adequate dietary lysine level significantly improved the specific growth rate (SGR), protein efficiency ratio (PER), body protein deposition (BPD), and feed conversion ratio (FCR). The dietary optimum L-lysine requirements for coho salmon alevins were 3.74%, 3.73%, 3.91%, and 3.77% of the diet or 6.80%, 6.78%, 7.11%, and 6.85% of dietary proteins against the SGR, PER, BPD, and FCR, respectively. The suitable dietary L-lysine concentration for coho salmon (Oncorhynchus kisutch) alevins was assessed by a dose response feeding trial. Six experimental diets were made with graded L-lysine concentrations of 2.29%, 2.81%, 3.32%, 3.80%, 4.27%, and 4.78% of the dry matter, respectively, each of which was fed to triplicate groups of 100 alevins (initial body weight: 0.30 ± 0.01 g) in 18 plastic baskets (water volume 240 L). The alevins were cultured in a flowing freshwater system and fed manually to apparent satiation four times a day for 12 weeks. The survival rate of alevins did not differ significantly among the dietary groups. The specific growth rate (SGR), protein efficiency ratio (PER), and body protein deposition (BPD) increased significantly (p < 0.05) with the increase in dietary lysine concentration up to 3.80% and then reduced as lysine level further increased. The feed conversion ratio (FCR) had an inverse trend to SGR. The whole-body crude protein content of the alevins increased significantly with increasing dietary lysine level, while crude lipid content showed the opposite trend. In comparison, the contents of morphological indices, whole-body moisture, and ash were not affected significantly (p > 0.05) by the different dietary lysine concentrations. The highest contents of lysine, arginine, and total essential amino acids (EAAs) were observed in the group with 4.27% dietary lysine concentration, which did not differ significantly from those in the 3.32%, 3.80%, and 4.78% groups but was significantly higher than those in the 2.29% and 2.81% groups. Similarly, valine had the highest content in the group with 4.78%. The variations in dietary lysine had no significant impacts on other EAA and non-EAA contents except glycine, which increased with increasing dietary lysine level. Second-order polynomial model analyses based on SGR, PER, BPD, and FCR evaluated the optimum L-lysine requirements of coho salmon alevins as 3.74%, 3.73%, 3.91%, and 3.77% of the diet or 6.80%, 6.78%, 7.11%, and 6.85% of dietary proteins, respectively. [ABSTRACT FROM AUTHOR]

An analysis of the biological value of chum salmon showed that, in terms of the balance of the amino-acid composition of the protein, chum salmon with spawning changes is not inferior to chum salmon without spawning changes (silver chum salmon). A higher content of polyunsaturated fatty acids in total lipids, including omega-3, was noted in chum salmon with spawning changes compared to silver chum salmon. The metabolic profile of chum salmon samples obtained by NMR spectroscopy showed that the levels of Asp, Glu, and glucose markedly increase during spawning migration, which is explained by the limited feeding of fish. The calculated total taste index of silver chum salmon was 4.06 ± 0.11, and that of chum salmon with spawning changes was 3.46 ± 0.09. Therefore, according to taste sensations, the silver chum salmon has a richer taste compared to the chum salmon with spawning changes. The results of the analysis of the nutritional value and metabolic profile of chum salmon with spawning changes can be used in the manufacture of minced fish for the subsequent production of specialized food products by introducing functional additives that balance the consistency and color, as well as in production of functional food additives. [ABSTRACT FROM AUTHOR]

Environmental laws around the world require some version of an environmental‐impact assessment surrounding construction projects and other discrete instances of human development. Information requirements for these assessments vary by jurisdiction, but nearly all require an analysis of the biological elements of ecosystems. Amplicon‐sequencing—also called metabarcoding—of environmental DNA (eDNA) has made it possible to sample and amplify the genetic material of many species present in those environments, providing a tractable, powerful, and increasingly common way of doing environmental‐impact analysis for development projects. Here, we analyze an 18‐month time series of water samples taken before, during, and after two culvert removals in a salmonid‐bearing freshwater stream. We also sampled multiple control streams to develop a robust background expectation against which to evaluate the impact of this discrete environmental intervention in the treatment stream. We generate calibrated, quantitative metabarcoding data from amplifying the 12s MiFish mtDNA locus and complementary species‐specific quantitative PCR data to yield multispecies estimates of absolute eDNA concentrations across time, creeks, and sampling stations. We then use a linear mixed effects model to reveal patterns of eDNA concentrations over time, and to estimate the effects of the culvert removal on salmonids in the treatment creek. We focus our analysis on four common salmonid species: cutthroat trout (Oncorhynchus clarkii), coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka). We find that one culvert in the treatment creek seemed to have no impact while the second culvert had a large impact on fish passage. The construction itself seemed to have only transient effects on salmonid species during the two construction events. In the context of billions of dollars of court‐mandated road culvert replacements taking place in Washington State, USA, our results suggest that culvert replacement can be conducted with only minimal impact of construction to key species of management concern. Furthermore, eDNA methods can be an effective and efficient approach for monitoring hundreds of culverts to prioritize culverts that are required to be replaced. More broadly, we demonstrate a rigorous, quantitative method for environmental‐impact reporting using eDNA that is widely applicable in environments worldwide. [ABSTRACT FROM AUTHOR]

Climatic warming elevates mortality for many salmonid populations during their physically challenging up-river spawning migrations, yet, the mechanisms underlying the increased mortality remain elusive. One hypothesis posits that a cardiac oxygen insufficiency impairs the heart's capacity to pump sufficient oxygen to body tissues to sustain up-river swimming, especially in warm water when oxygen availability declines and cardiac and whole-animal oxygen demand increases. We tested this hypothesis by measuring cardiac and metabolic (cardiorespiratory) performance, and assessing the upper thermal tolerance of coho salmon (Oncorhynchus kisutch) during sustained swimming and acute warming. By surgically ligating the coronary artery, which naturally accumulates arteriosclerotic lesions in migrating salmon, we partially impaired oxygen supply to the heart. Coronary ligation caused drastic cardiac impairment during swimming, even at benign temperatures, and substantially constrained cardiorespiratory performance during swimming and progressive warming compared to sham-operated control fish. Furthermore, upper thermal tolerance during swimming was markedly reduced (by 4.4 °C) following ligation. While the cardiorespiratory capacity of female salmon was generally lower at higher temperatures compared to males, upper thermal tolerance during swimming was similar between sexes within treatment groups. Cardiac oxygen supply is a crucial determinant for the migratory capacity of salmon facing climatic environmental warming. [ABSTRACT FROM AUTHOR]

Stopover habitats allow migratory animals to bolster energy stores prior to the resumption of migration, which can increase an individual's likelihood of survival. Carryover effects from prior habitats may mediate stopover behavior: evidence suggests that low‐condition migrants exhibit longer stopovers and attain more growth during stopover than high‐condition individuals. For Pacific salmon (Oncorhynchus spp.), estuaries may be important stopover habitats during juvenile emigration from natal freshwaters to the ocean. Favorable foraging conditions in high‐productivity estuaries could boost growth, and body size at marine entry is generally positively correlated with survival to adulthood. However, the contribution of the estuarine life stage to individual fitness across the salmon life cycle remains poorly understood. Here, we show that body size at freshwater exit mediates estuary stopover behavior by juvenile coho salmon (O. kisutch) and that estuary growth can increase the probability of marine survival. We performed a multiyear mark–recapture study of juvenile coho salmon in the Koeye River and its estuary, located on the Central Coast of British Columbia. We found that stopover duration decreased with increasing body size: small juveniles spent more than three times longer in the estuary than their larger conspecifics. Mean annual estuary growth rates ranged from 0.58 to 0.95 mm/day, and the smallest juveniles grew by nearly 30% in fork length during estuary stopover. Consequently, each out‐migrating juvenile cohort entered the ocean larger and less variable in body size than it was at freshwater exit. Analysis of returning spawners from two juvenile cohorts (2017, 2018) indicated that larger individuals had higher ocean survival rates. Using a simplistic analytical extrapolation, we demonstrate that estuary stopover could increase marine survival: For median‐sized juveniles, growth achieved in the estuary was associated with 39.8% (34.0%–46.2%) higher survival for the 2017 cohort and 39.1% (31.6%–47.0%) higher survival for the 2018 cohort. These results, from a watershed unaltered by intensive logging or development, suggest that growth achieved during estuary stopover can mitigate freshwater carryover effects and buffer size‐selective survival in a changing ocean. More broadly, these findings highlight the importance of state‐dependent use of stopover habitats in the study of migration ecology and conservation of migratory species. [ABSTRACT FROM AUTHOR]

Undesired maturation and reproduction are major challenges in fish aquaculture regarding genetic introgression, precocious maturation, and reproduction-related mortality, which can have profound ecological or economic impacts. Farming reproductively sterile fish can effectively mitigate these challenges. In this paper, we transferred and applied a novel immersion-based, non-transgenic gene silencing technology to sterilize coho salmon for the first time. Unfertilized eggs were bath immersion-treated with csdnd-MO-Vivo in different immersion media. Eyed rates of treated groups ranged from 0.9 to 63.5%. Sterile fish lacking germ cells, and those with arrested germ cells/atretic oocytes, were obtained at 14 and 20 months of age, albeit at a low percentage (2.3 to 10.0% based on females). Gonadal histology and vasa/nanos3 gene expression profile were provided for comparing fertile and sterile gonads, as well as retarded ovaries. Future directions and strategies for optimizing the technology and improving sterility induction were also proposed. The successful production of sterile coho salmon achieved in this study demonstrates the proof of principle for this new sterilization technology. As we continue to expand upon these findings and refine the technology, achieving coho salmon sterile population farming would facilitate the future transfer and application to other commercially important aquaculture fish. [ABSTRACT FROM AUTHOR]

Pulsed subsidy events create ephemeral fluxes of hyper‐abundant resources that can shape annual patterns of consumption and growth for recipient consumers. However, environmental conditions strongly affect local resource availability for much of the year, and can heavily impact consumer foraging and growth patterns prior to pulsed subsidy events. Thus, a consumer's capacity to exploit pulse subsidy resources may be influenced by antecedent environmental conditions, but this has rarely been shown in nature and is unknown in aquatic ecosystems.Here, we sought to understand the importance of hydrologic variation and a salmon pulse subsidy on the foraging and growth patterns of two stream salmonids in a coastal southeast Alaska drainage.To do this, we sampled fish stomach contents at a high temporal frequency (daily–weekly measurements) and analyzed fish consumption rates in relation to streamflow and pulse subsidy resource availability. We then explored the influence of interannual hydrologic variation on access to pulse subsidy resources (i.e. whether fish exceeded an egg consumption gape limit) in a bioenergetic simulation.Prior to Pink Salmon spawning, Dolly Varden and Coho Salmon displayed distinct and nonlinear flow‐foraging relationships, where forage for both species consisted primarily of macroinvertebrates. During this time period, consumption maxima coincided with baseflow and the highest observed flow conditions, and consumption minima were observed at severe low‐water and intermediate flow values. After salmon spawning began, forage was not significantly related to flow and consisted primarily of salmon eggs. Further, consumption rates increased overall, and foraging patterns did not appear to be affected by flow in either species. Bioenergetic simulations revealed that patterns of interannual hydrologic variation may shift Coho Salmon growth trajectories among years.Together, our results suggest that access to marine pulse subsidy resources may depend on whether antecedent hydrologic conditions are suitable for juvenile salmonids to grow large enough to consume salmon eggs by the onset of spawning. [ABSTRACT FROM AUTHOR]

A total of 122 coho salmon specimens were examined. The fish were caught in the coastal zone and in the rivers of Iturup Island (southern Kuril Islands) during their spawning migration in August–October 2021. Almost all females and males close to maturity in that year had spent 1 year at sea and were at ages of 1.1+ (66.7%) and 2.1+ (30.0%). Fish that had spent 2 years at sea were found singly: one specimen at an age of 1.2+ and three specimens at an age of 2.2+ (2.5%). Taking into account the age at maturity and the body weight (an average of 2.63 kg for females and 2.44 kg for males), an assumption can be made that the examined fish bred in short streams. The high value of the gonadosomatic index (up to 20–22% for some females) did not indicate that all the fish caught in the coastal waters would have run to other spawning grounds. At least a portion of them should have spawned in the water courses of Iturup Island, as was evidenced by the captures of a few coho salmon immediately in the rivers. Along with the fish running to the spawning grounds, two actively feeding coho females at an age of 0.0+ (0.55 kg) and 1.0+ (1.11 kg) were also caught with stake nets. [ABSTRACT FROM AUTHOR]

Simple Summary: Our results indicate activation of the kynurenine pathway and serotonin activity when stimulated with tryptophan and cortisol supplementation. An amount of 95% of tryptophan is degraded by the kynurenine pathway, indicating the relevance of knowing how this pathway is activated and if stress levels associated with fish culture trigger its activation. Additionally, it is essential to know the consequence of increasing KYNA levels in different species in the short and long term, and even during the fish ontogeny. Aquaculture fish are kept for long periods in sea cages or tanks. Consequently, accumulated stress causes the fish to present serious problems with critical economic losses. Fish food has been supplemented to reduce this stress, using many components as amino acids such as tryptophan. This study aims to determine the transcriptional effect of tryptophan and cortisol on primary cell cultures of salmon head and posterior kidney. Our results indicate activation of the kynurenine pathway and serotonin activity when stimulated with tryptophan and cortisol. An amount of 95% of tryptophan is degraded by the kynurenine pathway, indicating the relevance of knowing how this pathway is activated and if stress levels associated with fish culture trigger its activation. Additionally, it is essential to know the consequence of increasing kynurenic acid "KYNA" levels in the short and long term, and even during the fish ontogeny. [ABSTRACT FROM AUTHOR]

Background: Recently, we have developed a method to identify IgE cross-reactive allergens. However, the mechanism by which IgE cross-reactive allergens cause food allergy is not yet fully understood how. In this study, we aimed to understand the underlying pathogenesis by identifying food allergens that cross-react with house dust mite allergens in a murine model. Material and methods: Allergenic protein microarray analysis was conducted using serum from mice intraperitoneally injected with Dermatophagoides pteronyssinus (Der p) extract plus alum or alum alone as controls. Der p, Dermatophagoides farinae (Der f), coho salmon extract-sensitized and control mice were analyzed. Serum levels of IgE against Der p, Der f, coho salmon extract, protein fractions of coho salmon extract separated by ammonium sulfate precipitation and anion exchange chromatography, and recombinant coho salmon tropomyosin or actin were measured by an enzyme-linked immunosorbent assay. A murine model of cutaneous anaphylaxis or oral allergy syndrome (OAS) was established in Der p extract-sensitized mice stimulated with coho salmon extract, tropomyosin, or actin. Results: Protein microarray analysis showed that coho salmon-derived proteins were highly bound to serum IgE in Der p extract-sensitized mice. Serum IgE from Der p or Der f extract-sensitized mice was bound to coho salmon extract, whereas serum IgE from coho salmon extract-sensitized mice was bound to Der p or Der f extract. Analysis of the murine model showed that cutaneous anaphylaxis and oral allergic reaction were evident in Der p extract-sensitized mice stimulated by coho salmon extract. Serum IgE from Der p or Der f extractsensitized mice was bound strongly to protein fractions separated by anion exchange chromatography of coho salmon proteins precipitated with 50% ammonium sulfate, which massively contained the approximately 38 kDa protein. We found that serum IgE from Der p extract-sensitized mice was bound to recombinant coho salmon tropomyosin. Der p extract-sensitized mice exhibited cutaneous anaphylaxis in response to coho salmon tropomyosin. Conclusion: Our results showed IgE cross-reactivity of tropomyosin between Dermatophagoides and coho salmon which illustrates salmon allergy following sensitization with the house dust mite Dermatophagoides. Our method for identifying IgE cross-reactive allergens will help understand the underlying mechanisms of food allergies. [ABSTRACT FROM AUTHOR]

How various factors, including demography, recombination or genome duplication, may impact the efficacy of natural selection and the burden of deleterious mutations,is a central question in evolutionary biology and genetics. In this study, we show that key evolutionary processes, including variations in i) effective population size (Ne) ii) recombination rates and iii) chromosome inheritance, have influenced the genetic load and efficacy of selection in Coho salmon (Oncorhynchus kisutch), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different migratory distances from their southern glacial refugium, we found evidence supporting gene surfing, wherein reduced Ne at the postglacial recolonization front, leads to a decrease in the efficacy of selection and a surf of deleterious alleles in the northernmost populations. Furthermore, our results indicate that recombination rates play a prime role in shaping the load along the genome. Additionally, we identified variation in polyploidy as a contributing factor to within-genome variation of the load. Overall, our results align remarkably well with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics. Author summary: Understanding how historical processes, such as past glaciations, may have impacted variations in population size and genetic diversity along the genome is a fundamental question in evolution. In this study, we investigated how recent postglacial demographic expansion has affected the distribution of deleterious genetic variants and the resulting deleterious mutation load in Coho salmon (Oncorhynchus kisutch), throughout its native range in North America. By sequencing the entire genome of 71 Coho salmon, we reveal that postglacial expansion has led to allele surfing, a process where alleles increase in frequency in populations that are expanding or colonizing new environments. Here, allele surfing resulted in an increased deleterious mutation load at the colonization front. Furthermore, we demonstrated that the efficacy of natural selection scales with variation in effective population size among populations. We showed that the specific genomic features of Coho salmon, namely variation in local recombination rate and variation in chromosomal inheritance, strongly impacted the segregation of deleterious mutations. [ABSTRACT FROM AUTHOR]

Simple Summary: As an excellent but most expensive source of protein, fish meal (FM) is commonly used in 30–60% of the aquafeed for salmon fish species including coho salmon. However, the high cost and unstable supply of FM led it no longer to be considered as a sustainable protein source for aquafeeds. Accordingly, alternative protein sources with low cost and high availability have become a research hotspot in aquafeed for carnivorous species. Poultry by-product meal (PBPM), one of the rendered animal protein sources, can be used as protein substitute of FM in aquafeed due to its economical availability and high protein content and growth promotion effects in comparison to plant proteins. Until now, little information has been available on evaluating the effects of replacing FM by animal proteins including PBPM for coho salmon. In this study, the effects of PBPM instead of FM on growth, muscle composition, and tissue biochemical indexes of coho salmon were investigated. The results showed that the growth performance, feed utilization, muscle composition, serum biochemical indices, and liver antioxidant enzyme activities of coho salmon were negatively affected by high dietary inclusion level of PBPMs, and the optimum substitution level was evaluated based on the specific growth rate (SGR). The present study evaluated the effects of partially substituting fish meal (FM) with poultry by-product meal (PBPM) on the growth, muscle composition, and tissue biochemical parameters of coho salmon (Oncorhynchus kisutch) post-smolts. Five isonitrogenous (7.45% nitrogen) and isoenergetic (18.61 MJ/kg gross energy) experimental diets were made by substituting 0%, 10%, 20%, 40%, and 60% FM protein with PBPM protein, which were designated accordingly as PBPM0 (the control), PBPM10, PBPM20, PBPM40, and PBPM60, respectively. Each diet was fed to triplicates of ten post-smolts (initial individual body weight, 180.13 ± 1.32 g) in three floating cages three times daily (6:50, 11:50, and 16:50) to apparent satiation for 84 days. Both specific growth rate (SGR) and protein efficiency ratio did not differ significantly (p > 0.05) among the control, PBPM10, and PBPM20 groups, which were remarkably (p < 0.05) higher than those of the PBPM40 and PBPM60 groups. Feed conversion ratio varied inversely with SGR. The PBPM replacement had no remarkable effects on the morphological indices and proximal muscle components. The control and PBPM10 groups led to significantly higher muscle contents of leucine, lysine, and methionine than groups of higher PBPM inclusion. The groups of PBPM40 and PBPM60 obtained significantly (p < 0.05) higher serum alanine aminotransferase and aspartate aminotransferase activities than the control and low PBPM inclusion groups. The control group had significantly higher albumin and total cholesterol contents than the groups with PBPM inclusion. The control group had significantly higher triglycerides content than the PBPM60 group. The PBPM60 group had significantly lower contents of high-density lipoprotein, low-density lipoprotein, and total protein than the control and PBPM10 groups. The high PBPM replacement level up to 40% and 60% had adverse effects on hepatic malondialdehyde levels. The catalase and superoxide dismutase activities were not affected by low PBPM inclusion, but significantly decreased in high-PBPM-inclusion groups. Based on broken-line regression analysis of SGR and PER, the optimum dietary PBPM replacing level was evaluated to be 16.63–17.50% of FM protein for coho salmon post-smolts. [ABSTRACT FROM AUTHOR]

Sea lice infestations have the largest economic and biological impact on salmon farming in Chile, similar to that seen in salmon‐producing countries in the northern hemisphere. Caligus teres infesting coho salmon (Oncorhynchus kisutch) was first recorded in 1981, but Caligus rogercresseyi has been the predominant species infesting Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) from 1997. In contrast, coho salmon has been shown to be resistant to this sea louse species. Regulations to establish integrated pest management of sea lice were implemented by the Chilean authority in 2007. However, to date, pharmacological medicines have been the main tool used by the salmon farming industry in Chile to manage sea lice, although non‐pharmacological treatments have been available since 2016. Production of farmed salmon reached 978.274 tons in 2021 and 7.72 g of medicines was prescribed per ton of harvested salmon. The highest volumes used in that year were Azamethiphos (47%) and hexaflumuron (45.5%), in addition to 5532 tons of hydrogen peroxide. This review updates the current management of sea lice in Chile and also summarizes the biological knowledge of this important parasite. [ABSTRACT FROM AUTHOR]

This experiment aims to investigate the effects of partial replacement of fish meal (FM) by soybean meal (SBM) and/or fermented soybean meal (FSBM) on the growth, serum biochemistry, digestion, antioxidation, immunity, and mTOR signaling pathway of juvenile coho salmon (Oncorhynchus kisutch). Four iso-nitrogen and iso-lipid diets were designed and fed to four groups of juvenile coho salmon (152.25 ± 2.96 g) in triplicate for 10 weeks. The four diets were the G0 diet (control group, containing 28% FM protein), the G1 diet (containing 10% SBM protein and 18% FM protein), the G2 diet (containing 5% SBM protein, 5% FSBM protein, and 18% FM protein), and the G3 diet (containing 10% FSBM protein and 18% FM protein). It was found that compared with the G0 diet (control group), the activities of catalase (CAT), superoxide dismutase (SOD), pepsin, trypsin, α-amylase, and lipase, and the expression levels of mammalian target of rapamycin (mtor), protein kinase B (akt), phosphatidylinositol 3-kinase (pi3k), plant ribosome S6K protein kinase (s6ks), and lysozyme (lyz) genes, of juvenile coho salmon fed the G3 diet increased significantly (p < 0.05), and the expression levels of tumor necrosis factor (tnf-α), interleukin-1β (il-1β), and interleukin-6 (il-6) genes of juvenile coho salmon fed the G3 diet decreased significantly (p < 0.05). However, there were no significant differences in growth, muscle composition, and serum biochemistry of juvenile coho salmon fed the G3 diet compared with the G0 diet (p > 0.05). In conclusion, replacing 10% FM protein with FSBM protein could improve the digestion, antioxidation, immunity, and mTOR signaling pathway of juvenile coho salmon. [ABSTRACT FROM AUTHOR]

Antioxidants which are indispensable functional additives used in rubber tires, are released into aquatic habitats from tire wear particles (TWP), collected in water bodies, and threaten the aquatic ecosystem. This study aimed to design eco-friendly derivatives of 2,2,4-trimethyl-1,2-dihydroquinoline (TMQ) with increased antioxidant activity to use as tire antioxidants. Initially, seventy highly efficient derivatives of TMQ were designed by hydroxylation modifications at multiple sites. The antioxidant activity of hydroxyl derivatives was characterized based on DFT method and compared with TMQ. Twenty derivatives showing a significant (greater than 9%) increase in antioxidant activity compared to TMQ were selected for the next stage. The toxicity risk of these twenty TMQ derivatives was assessed using various toxicokinetic methods. Finally, six TMQ derivatives with significantly lower toxicity risk compared to that of TMQ were evaluated for potential developmental toxicity. They were characterized using molecular docking and molecular dynamics techniques to assess the developmental toxicity risk in silver salmon by absorption of their ROO·, HO·, O2·– and O3 derivatives. TMQ-6 and TMQ-48 showed the lowest toxicity among all TMQ derivatives by a rather large margin. The study throws light on the path of future endeavors to develop highly efficient and greener tire antioxidants. [ABSTRACT FROM AUTHOR]

Aim: Freshwater invasions are a global conservation issue. Emerging tools for biogeographical analyses can provide critical information for their effective management and monitoring. Here, we propose a method to assess the distribution of environmental resistance of stream ecosystems to biological invasions by coupling multi‐stage habitat potential models for non‐native species. Location: Andean Patagonia (Chile and Argentina). Taxa: North American beaver (Castor canadensis), Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch). Methods: Environmental resistance to invasive species was mapped throughout a large region of Patagonia by stacking multi‐stage habitat relationships for each target species and assessing the complementation between critical habitats at multiple scales. We generated an environmental model of stream networks derived from high‐resolution topographic and climatic data representing 15,406 drainage basins (>1 km2) covering an area of 369,791 km2. We quantified the intrinsic potential of stream‐reaches (100‐m and 1000‐m) to sustain high‐quality habitats and assessed habitat complementation (i.e., abundance and proximity) at the sub‐basin scale as a proxy for environmental resistance. Results: Our model revealed high heterogeneity in the distribution of environmental resistance to invasions throughout the study region, providing case‐specific insights for the research and management of invaders. Main Conclusions: Environmental resistance modelling is a novel method to study the biogeography of riverine invasions. Our approach is compatible with additional sources of information about species and the environment and shows versatility to diverse invasion scenarios and data sources. This method can be useful in prioritising research and management of incipient and spreading invasions, especially for large and data‐poor regions. [ABSTRACT FROM AUTHOR]

North‐east Pacific juvenile salmon and forage fishes, including the endangered salmon species Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), chum (Oncorhynchus keta), and pink (Oncorhynchus gorbuscha), and the forage fishes species of Pacific herring (Clupea pallasi), surf smelt (Hypomesus pretiosus), and sand lance (Ammodytes hexapterus), utilize kelp environments. Many details of the kelp forest ecosystem function for these fishes are lacking.Kelp forests, salmon, and forage fishes are declining precipitously as the global climate shifts and developments along coastal shorelines expand. It is therefore essential to understand kelp forest function for these species.Analysis of 7 years of snorkelling survey videos indicates that both forage fishes and salmon use kelp forests throughout the outmigration season, and that their interactions occur in small and large groups, primarily along the outer edge of kelp beds. Over the course of outmigration, juvenile Chinook and coho salmon encounter sand lance first, followed by smelt and herring. The majority of interactions are intermingling, in which a subset proceed to predation, primarily on herring.It is important to develop and implement specific fishery and habitat conservation measures to preserve and restore these functions. Long‐term research has shown that intact, conserved nearshore habitats function better ecologically than restored habitats, and individual kelp forests can function differently for forage fishes and salmon. Therefore, conservation plans should be developed to conserve wild kelp forests which are documented to provide ecosystem function for salmon and forage fishes, by protecting them from various development impacts, including dredging, filling, and water‐quality decline.Coastal restoration is often only successful when ecosystem‐limiting factors that result in a loss of habitat are resolved. Kelp forest restoration, therefore, should be prioritized for regions of known high historical kelp forest importance, with restoration actions focused on correcting the limiting factors that caused loss and/or degradation. [ABSTRACT FROM AUTHOR]

Alternative life‐history tactics are predicted to affect within‐population genetic processes but have received little attention. For example, the impact of precocious males on effective population size (Ne) has not been quantified directly in Pacific salmon Oncorhynchus spp., even though they can make up a large percentage of the total male spawners. We investigated the contribution of precocial males ("jacks") to Ne in a naturally spawning population of Coho Salmon O. kisutch from the Auke Creek watershed in Juneau, Alaska. Mature adults that returned from 2009 to 2019 (~8000 individuals) were genotyped at 259 single‐nucleotide polymorphism (SNP) loci for parentage analysis. We used demographic and genetic methods to estimate the effective number of breeders per year (Nb). Jack contribution to Nb was assessed by comparing values of Nb calculated with and without jacks and their offspring. Over a range of Nb values (108–406), the average jack contribution to Nb from 2009 to 2015 was 12.9% (SE = 3.8%). Jacks consistently made up over 20% of the total male spawners. The presence of jacks did not seem to influence Nb/N. The linkage disequilibrium Ne estimate was lower than the demographic estimate, possibly due to immigration effects on population genetic processes: based on external marks and parentage data, we estimated that immigrant spawners produced 4.5% of all returning offspring. Our results demonstrate that jacks can influence Nb and Ne and can make a substantial contribution to population dynamics and conservation of threatened stocks. [ABSTRACT FROM AUTHOR]

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In this study, we evaluated the effects of fermented soybean meal (FSBM) or/and unfermented SBM replacing a portion of fish meal (FM) on the growth performance, antioxidant capacity, immunity, and mechanistic target of rapamycin (mTOR) signaling pathway of juvenile coho salmon (Oncorhynchus kisutch). Four groups of juvenile coho salmon (initial weight 152.23 ± 3.21 g) in triplicate were fed for 12 weeks on four different iso-nitrogen and iso-lipid experimental diets: G0 diet (28% FM protein, control group), G1 diet (18% FM protein and 10% SBM protein), G2 diet (18% FM protein, 5% SBM protein, and 5% FSBM protein), and G3 diet (18% FM protein and 10% FSBM protein). The main results were compared with the G0 diet; the weight gain rate, specific growth rate, and condition factor of juveniles in G3 were increased significantly (p < 0.05). The content of muscle crude protein, the total protein, glucose, albumin, total cholesterol in serum, and the total antioxidant capacity in the liver of juveniles in G3 was increased significantly (p < 0.05). The activities of pepsin, trypsin, α-amylase, and lipase in the intestine, the superoxide dismutase, catalase, and alkaline phosphatase in the liver of juveniles in G3 were increased significantly (p < 0.05). The expression levels of phosphatidylinositide 3-kinases, serine/threonine kinase, mTOR, and ribosomal protein S6 kinase 1 genes in the liver of juveniles in G3 were upregulated significantly (p < 0.05). The feed coefficient ratio, viscerosomatic index, the contents of muscle moisture, and malondialdehyde in the liver of juveniles in G3 were decreased significantly (p < 0.05). The expression levels of tumor necrosis factor α, interleukin 1β, and interleukin 6 genes in the liver of juveniles in G3 were downregulated significantly (p < 0.05). However, there was no significant effect (p > 0.05) on the survival rate, food intake, and muscle crude lipid and ash of juveniles among the experimental groups. In conclusion, FSBM to replace a portion FM had a positive effect on the growth performance, protein deposition, antioxidant enzyme activity, digestive enzyme activity, protein synthesis, and immune-related genes of juvenile coho salmon. [ABSTRACT FROM AUTHOR]

Simple Summary: Protecting the welfare of animals and the 3Rs rule are very relevance, and for this reason cell culture is an important tool. In fish it has importance in several fields such as virology, toxicology, pathology and immunology. The objective was to carry out a primary culture of the head kidneys of Atlantic salmon (Salmo salar), Pacific salmon (Oncorhynchus kisutch) and rainbow trout (Oncorhynchus mykiss), and to characterize how they respond to bacterial and viral stimuli by analyzing molecules that participate in the innate and adaptive immune response. The primary cell cultures of the head kidney (HK) from the three salmonids studied were cultured and exposed to two substances that mimic molecular patterns of different pathogens, i.e., Lipopolysaccharide (LPS) and Polyinosinic: polycytidylic acid (POLY I:C). The HK primary cell cultures from the three species grown in vitro responded differently to POLY I:C and LPS. This is the first study to demonstrate and characterize the expression of immune genes in head kidney primary cell cultures isolated from three salmonid species. It also indicates their potential role in developing immune responses as defense response agents and targets of immunoregulatory factors. Fish cell culture is a common in vitro tool for studies in different fields such as virology, toxicology, pathology and immunology of fish. Fish cell cultures are a promising help to study how to diagnose and control relevant viral and intracellular bacterial infections in aquaculture. They can also be used for developing vaccines and immunostimulants, especially with the ethical demand aiming to reduce and replace the number of fish used in research. This study aimed to isolate head kidney primary cell cultures from three Chilean salmonids: Salmo salar, Oncorhynchus kisutch, and Oncorhynchus mykiss, and characterize the response to bacterial and viral stimuli by evaluating various markers of the innate and adaptive immune response. Specifically, the primary cell cultures of the head kidney from the three salmonids studied were cultured and exposed to two substances that mimic molecular patterns of different pathogens, i.e., Lipopolysaccharide (LPS) (bacterial) and Polyinosinic: polycytidylic acid (POLY I:C). Subsequently, we determined the mRNA expression profiles of the TLR-1, TLR-8, IgM, TLR-5, and MHC II genes. Head kidney primary cell cultures from the three species grown in vitro responded differently to POLY I:C and LPS. This is the first study to demonstrate and characterize the expression of immune genes in head kidney primary cell culture isolated from three salmonid species. It also indicates their potential role in developing immune responses as defense response agents and targets of immunoregulatory factors. [ABSTRACT FROM AUTHOR]

A correction is presented to the article "When overextended surface allocation turns to groundwater: a Q-methodology of well users in Oregon's high desert" published in the previous issue of a periodical.

There is tremendous variation in life-history strategies among anadromous salmonids. Species that enter the ocean environment at small sizes (< 20 g) are likely under more physiological pressure from pathogens; however, little data is available on responses at these early stages. With this in mind, we performed salmon louse challenges with Coho salmon either immediately after seawater entry (SW; ca. 10 g) or after 30 days in SW (ca. 20 g). Irrespective of size or time in SW, parasites were rapidly rejected by the host, with > 90% of all parasites lost by 16 days post-infection (dpi). Rejection was concomitant with host epithelial granulomatous infiltrations that initially targeted the embedded frontal filament (4 dpi) and the entire parasite by 10 dpi. Illumina sequencing, followed by functional enrichment analysis, revealed a concerted defense response in the fin within 1 dpi that included multiple innate and adaptive immunity components. Strikingly, early indications of an allergic-type inflammatory response were associated with chitin sensing pathways orchestrated by early overexpression of the IgE-receptor, fcer1g. Additionally, there was profound overexpression of several classes of c-type lectin receptors, including dectin-2, mincle, and dc-sign at 1 dpi onward. These profiles and upregulation of cellular effector markers were corroborated by histopathological evaluation, revealing the simultaneous presence of mast cell/eosinophilic granular cells, sacciform cells, macrophages/histiocytes, and granulocytes in fin. At 10 dpi and concurrent with parasite expulsion, there was evidence of immunoregulation in addition to tissue remodelling pathways. At 16 dpi, the response was effectively abrogated. Simultaneous profiling of the parasite transcriptome revealed early induction of chitin metabolism and immunomodulation, toxin production and ECM degradation; however, after 7 dpi, these were replaced with overexpression of stress and immune defense genes. These data present the first evidence for Coho salmon demonstrating chitin- and sugar moiety-sensing as key drivers of salmon louse rejection. [ABSTRACT FROM AUTHOR]

Estimating juvenile salmon habitat carrying capacities is a critical need for restoration planning. We assimilated more than 4500 unique estimates of published juvenile densities (e.g., fish/m2) in estuarine and floodplain habitats. These density data were categorized by species and life stage, habitat type, seasonal period, and geographic region to develop frequency statistics (e.g., 25th and 75th percentiles, or quartiles). These frequency statistics were then used in a habitat expansion approach to estimate carrying capacities based on habitat extent. We demonstrate the habitat expansion approach by applying the quantiles of observed juvenile Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) densities (fish/ha) to spatial data describing current, historical or potential, and predicted (based on seal level rise) habitat extents for 16 coastal Oregon estuaries to estimate carrying capacities. Current carrying capacities based on 75th percentile springtime (Apr–Jun) densities ranged from 2902 to 33,817 fish/delta for Chinook salmon and 2507 to 20,206 fish/delta for coho salmon. Historic carrying capacities during the peak rearing period (spring) ranged from 3869 to 71,844 fish/delta for Chinook salmon and 3201 to 38,337 fish/delta for coho salmon, representing a 3 to 72% loss in Chinook salmon capacity and 2 to 67% loss in coho salmon capacity. Estimated carrying capacities were predicted to decline by 2 to 54% with 1.4 m of sea level rise in systems that are projected to lose vegetated tidal wetland habitat, while a 1 to 320% increase in capacity was predicted for systems that are predicted to increase in area with sea level rise. Finally, we demonstrate how the carrying capacity estimates can be used to estimate changes in juvenile Chinook and coho salmon capacity following restoration, which can be used to both design and evaluate restoration projects. [ABSTRACT FROM AUTHOR]

Piscine orthoreovirus from western North America is transmissible to Atlantic salmon and Sockeye salmon but fails to cause Heart and Skeletal Muscle Inflammation. De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection. Keywords: Piscine orthoreovirus; Salmon; Respiratory performance EN Piscine orthoreovirus Salmon Respiratory performance 1 4 4 05/23/23 20230519 NES 230519 This is a reply to a correspondence from Mordecai G et al. (https://doi.org/10.1186/s12915-023-01548-8) on our research article "Innate antiviral defense demonstrates high energetic efficiency in a bony fish. [Extracted from the article]

Background: Infection with the myxozoan parasite Parvicapsula pseudobranchicola causes disease in wild and farmed salmonids in Norway. In the northeast Pacific Ocean, the parasite has been reported in Pacific salmon Oncorhynchus spp. without evidence of disease. The objectives of the present study were to confirm the identity of P. pseudobranchicola in the Pacific, document its host and geographic ranges, and describe associated pathological changes. Methods: Ocean-entry year wild pink salmon Oncorhynchus gorbuscha, chum salmon O. keta, Chinook salmon O. tshawytscha, coho salmon O. kisutch and sockeye salmon O. nerka were collected in summer and autumn surveys near Vancouver Island (VI) and from a winter survey in the Gulf of Alaska. Samples were also obtained from farmed Atlantic salmon Salmo salar and Chinook salmon near VI. Samples were analysed by qPCR and histology using conventional staining or in situ hybridisation. Parasite sequence was obtained from small subunit ribosomal RNA gene (SSU rDNA). Results: Identical 1525 base-pair SSU rDNA sequences from infected pink salmon, chum salmon and Chinook salmon shared 99.93% identity with a P. pseudobranchicola sequence from Norwegian Atlantic salmon. In autumn surveys, the prevalence was greatest in chum salmon (91.8%) and pink salmon (85.9%) and less so in Chinook salmon (68.8%) and sockeye salmon (8.3%). In farmed salmon, the prevalence was zero in Atlantic salmon (n = 967) and 41% in Chinook salmon (n = 118). Infections were preferentially sited in pseudobranch and visualised by in situ hybridisation. Heavy parasite burdens in all species of Pacific salmon were inconsistently associated with focal granulomatous pseudobranchitis. Conclusions: In the northeast Pacific, widespread occurrence of P. pseudobranchicola in Pacific salmon together with its absence or sporadic occurrence in farmed Atlantic salmon differs from its epidemiology in Norway, despite similar pathological development in the pseudobranch. Consequences of the infections to the health of wild Pacific salmon, identity of the invertebrate host and the distribution and abundance of infective actinospores are unknown and remain high priorities for research. [ABSTRACT FROM AUTHOR]