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Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon in Canada and the United States have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated a chromosome-level genome assembly. We also resequenced the genomes of 83 coho salmon across the North American range to identify nucleotide variants and understand the demographic histories of these salmon by modeling effective population size from genome-wide data. From demographic history modeling, we observed reductions in effective population sizes between 3,750 and 8,000 years ago for several northern sampling sites, which may correspond to bottleneck events during recolonization after glacial retreat. [ABSTRACT FROM AUTHOR]

The breakdown product of the rubber tire antioxidant N‐(1,3‐dimethylbutyl)‐N'‐phenyl‐p‐phenylenediamine‐quinone (6PPD)‐6‐PPD‐quinone has been strongly implicated in toxic injury and death in coho salmon (Oncorhynchus kisutch) in urban waterways. Whereas recent studies have reported a wide range of sensitivity to 6PPD‐quinone in several fish species, little is known about the risks to Chinook salmon (Oncorhynchus tshawytscha), the primary prey of endangered Southern Resident killer whales (Orcinus orca) and the subject of much concern. Chinook face numerous conservation threats in Canada and the United States, with many populations assessed as either endangered or threatened. We evaluated the acute toxicity of 6PPD‐quinone to newly feeding (~3 weeks post swim‐up) juvenile Chinook and coho. Juvenile Chinook and coho were exposed for 24 h under static conditions to five concentrations of 6PPD‐quinone. Juvenile coho were 3 orders of magnitude more sensitive to 6PPD‐quinone compared with juvenile Chinook, with 24‐h median lethal concentration (LC50) estimates of 41.0 and more than 67 307 ng/L, respectively. The coho LC50 was 2.3‐fold lower than what was previously reported for 1+‐year‐old coho (95 ng/L), highlighting the value of evaluating age‐related differences in sensitivity to this toxic tire‐related chemical. Both fish species exhibited typical 6PPD‐quinone symptomology (gasping, increased ventilation, loss of equilibrium, erratic swimming), with fish that were symptomatic generally exhibiting mortality. The LC50 values derived from our study for coho are below concentrations that have been measured in salmon‐bearing waterways, suggesting the potential for population‐level consequences in urban waters. The higher relative LC50 values for Chinook compared with coho merits further investigation, including for the potential for population‐relevant sublethal effects. Environ Toxicol Chem 2023;42:815–822. © 2023 His Majesty the King in Right of Canada and The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. Reproduced with the permission of the Minister of Fisheries and Oceans Canada. [ABSTRACT FROM AUTHOR]

Conservation units (CUs) are important tools for supporting the implementation of standardized management practices for exploited species. Following the adoption of the Wild Salmon Policy in Canada, CUs were defined for Pacific salmon based on characteristics related to ecotype, life history and genetic variation using microsatellite markers as indirect measures of local adaptation. Genomic data sets have the potential to improve the definition of CUs by reducing variance around estimates of population genetic parameters, thereby increasing the power to detect more subtle patterns of population genetic structure and by providing an opportunity to incorporate adaptive information more directly with the identification of variants putatively under selection. We used one of the largest genomic data sets recently published for a nonmodel species, comprising 5662 individual Coho salmon (Oncorhynchus kisutch) from 149 sampling locations and a total of 24,542 high‐quality SNPs obtained using genotyping‐by‐sequencing and mapped to the Coho salmon reference genome to (1) evaluate the current delineation of CUs for Coho in Canada and (2) compare patterns of population structure observed using neutral and outlier loci from genotype–environment association analyses to determine whether separate CUs that capture adaptive diversity are needed. Our results reflected CU boundaries on the whole, with the majority of sampling locations managed in the same CU clustering together within genetic groups. However, additional groups that are not currently represented by CUs were also uncovered. We observed considerable overlap in the genetic clusters identified using neutral or candidate loci, indicating a general congruence in patterns of genetic variation driven by local adaptation and gene flow in this species. Consequently, we suggest that the current CU boundaries for Coho salmon are largely well‐suited for meeting the Canadian Wild Salmon Policy's objective of defining biologically distinct groups, but we highlight specific areas where CU boundaries may be refined. [ABSTRACT FROM AUTHOR]

Prompted by a recent report that 6PPD-quinone (6PPD-q), a by-product of a common tire manufacturing additive that is present in road runoff, is toxic to coho salmon (Oncorhynchus kisutch), extracts of water samples collected from an urban river were re-analyzed to determine if this compound was present in stormwater-influenced flows. In addition, extracts were analyzed for 1,3-diphenylguanidine (DPG), which is also used in tire manufacturing. Samples were originally collected in the fall of 2019 and winter of 2020 in the Greater Toronto Area of Canada from the Don River, a highly urbanized watershed in close proximity to several major multi-lane highways. These target compounds were analyzed using ultra-high pressure liquid chromatography with high resolution mass spectrometric detection with parallel reaction monitoring. Both 6PPD-q and DPG were detected above limits of quantification (i.e., 0.0098 µg/L) in all extracts. Maximum concentrations for 6PPD-quinone of 2.30 ± 0.05 µg/L observed in the river during storm events exceeded the LC50 for this compound for coho salmon (i.e., > 0.8 µg/L). In composite samples collected at intervals throughout one rain event, both compounds reached peak concentrations a few hours after initiation of the event (i.e., 0.52 µg/L for DPG and 2.85 µg/L for 6PPD-q), but the concentrations of 6PPD-q remained elevated above 2 µg/L for over 10-h in the middle of the event. Estimates of cumulative loads of these compounds in composite samples indicated that kg amounts of these compounds entered the Don River during each hydrological event, and the loads were proportional to the amounts of precipitation. This study contributes to the growing literature indicating that potentially toxic tire-wear compounds are present at elevated levels and are transported via road runoff into urban surface waters during rain events. [ABSTRACT FROM AUTHOR]

The Strait of Georgia, Canada, has complex interactions among natural and human pressures that confound understanding of changes in this system. We report on the interannual variability in biomass of 12 zooplankton taxonomic groups in the deep (bottom depths greater than 50 m) central and northern Strait of Georgia from 1996 to 2018, and their relationships with 10 physical variables. Total zooplankton biomass was dominated (76%) by large-sized crustaceans (euphausiids, large and medium size calanoid copepods, amphipods). The annual anomaly of total zooplankton biomass was highest in the late 1990s, lowest in the mid-2000s, and generally above its climatological (1996–2010) average after 2011, although many individual groups had different patterns. Two latent trends (derived from dynamic factor analyses) described the variability of annual biomass anomalies underlying all zooplankton groups: a U-shaped trend with its minimum in the mid-2000s, and a declining trend from 2001 to 2011. Two latent trends also described the physical variables. The variability represented by these four latent trends clustered into two periods: 1996–2006, with generally declining zooplankton biomass and increasing salinities, and 2007–2018, with increasing zooplankton biomass and decreasing salinities. ARIMA modelling showed sea surface salinity at Entrance Island in the middle Strait of Georgia, the Pacific Decadal Oscillation, and the peak date of the spring phytoplankton bloom were significantly related to the two latent zooplankton trends. ARIMA models comparing zooplankton and physical variables with the marine survivals of four salmon populations which enter the Strait as juveniles (Chinook: Cowichan River, Puntledge River, Harrison River; Coho: Big Qualicum River) all included zooplankton groups consistent with known salmon prey; prominent among the physical variables were sea surface salinity and variables representing the flow from the Fraser River. These regressions explained (adjR2) 38 to 85% of the annual variability in marine survival rates of these salmon populations over the study time period. Although sea temperature was important in some relationships between zooplankton biomass and salmon marine survival, salinity was a more frequent and more important variable, consistent with its influence on the hydrodynamics of the Strait of Georgia system. [ABSTRACT FROM AUTHOR]

Over 1 billion USD are devoted annually to rehabilitating freshwater habitats to improve survival for the recovery of endangered salmon populations. Mitigation often requires the creation of new habitat (e.g. habitat offsetting) to compensate population losses from human activities, however offsetting schemes are rarely evaluated. Anadromous Pacific salmon are ecologically, culturally, and economically important in the US and Canada, and face numerous threats from degradation of freshwater habitats. Here we used a matrix population model of coho salmon (Oncorhynchus kisutch) to determine the amount of habitat offsetting needed to compensate mortality (2–20% per year) caused by a range of development activities. We simulated chronic mortality to three different life stages (egg, parr, smolt/adult), individually and simultaneously, to mimic impacts from development, and evaluated if the number of smolts produced from constructed side-channels demographically offset losses. We show that under ideal conditions, the typical size of a constructed side-channel in the Pacific Northwest (PNW) (3405 m2) is sufficient to compensate for only relatively low levels of chronic mortality to either the parr or smolt/adult stages (2–7% per year), but populations do not recover if mortality is >10% per year. When we assumed lower productivity (e.g.; 25th percentile), we found that constructed channels would need to be 2.5–4.5 fold larger as compared to the typical size built in the PNW, respectively, to maintain population sizes. Moreover, when we imposed mortality to parr and smolt/adult stages simultaneously, we found that constructed side-channels would need to be between 1.8- and 2.3- fold larger that if the extra chronic mortality was imposed to one life stage only. We conclude that habitat offsetting has the potential to mitigate chronic mortality to early life stages, but that realistic assumptions about productivity of constructed side-channels and cumulative effects of anthropogenic disturbances on multiple life stages need to be considered. [ABSTRACT FROM AUTHOR]

Direct DNA sequencing is powering a revolution in the application of genetics to resource management, with parentage-based tagging (PBT) increasingly applied to salmon fisheries and hatchery brood stock management and assessment. Genetic stock identification (GSI) and PBT were applied to assessment of 2018 coho salmon (Oncorhynchus kisutch) ocean fisheries and hatchery brood stocks in British Columbia (BC), Canada, with 6391 individuals successfully genotyped in fishery samples and 7805 individuals genotyped in 40 hatchery brood stocks. Population-specific contributions to mixed-stock fisheries and exploitation rates were estimated with coded-wire tags (CWTs) and GSI–PBT technologies for six populations. PBT assignments, verified by CWTs, were 100% accurate for 308 individuals with respect to population of origin and age. There was generally reasonably close agreement of estimated population-specific exploitation rates between CWT and genetic methods. We conclude that a genetic approach can improve upon the results available from the current CWT program for assessment and management of coho salmon fisheries and hatchery brood stocks in BC and provide information critical to aid in implementation of Canada's Policy for Conservation of Wild Pacific Salmon. [ABSTRACT FROM AUTHOR]

• Diluted bitumen exposure impairs growth of coho fry and parr. • Cardiorespiratory performance was similarly impaired in both life-stages. • Baseline phase I biotransformation levels are greater in unexposed fry than parr. • Phase I biotransformation response to exposure was distinct for fry and parr. Millions of liters of diluted bitumen (dilbit), a crude oil product from Canada's oil sands region, is transported through critical Pacific salmon habitat each day. While the toxicity of the water-soluble fraction of dilbit (WSFd) to early life-stages of salmon is known, quantitative data on life-stage differences in sensitivity to WSFd is missing. To fill this knowledge gap, we exposed two juvenile life-stages of coho salmon (O. kisutch) in parallel to very low (parts per billion), environmentally-relevant concentrations of WSFd for acute (48 h) and sub-chronic (4 wk) durations. The relative sensitivities of the two life-stages (fry and parr) were assessed by comparing the timing and magnitude of biological responses using common organismal and molecular endpoints of crude oil exposure. A significant reduction in body condition occurred in both fry and parr after 4 wk exposure to WSFd. Both life-stages also experienced a concentration-dependent decrease in time-to-loss-of-equilibrium during a hypoxia challenge test at both 48 h and 4 wk of exposure. Although organismal responses were similar, molecular responses were distinct between life-stages. In general, unexposed fry had higher baseline values of hepatic phase I biotransformation indicators than unexposed parr, but induction of EROD activity and cyp1a mRNA expression in response to WSFd exposure was greater in parr than in fry. Neither gst nor hsp70 mRNA expression, markers of phase II biotransformation and cell stress, respectively, were reliably altered by WSFd exposure in either life-stage. Taken together, results of this study do not support differential sensitivities of coho fry and parr to WSFd. All the same, the potential for ontogenic differences in the expression and induction of phase I biotransformation need to be considered because age does matter for these endpoints if they are used as bioindicators of exposure in post-spill impact assessments. [ABSTRACT FROM AUTHOR]

Genetic stock identification (GSI) and parentage-based tagging (PBT) are being increasingly applied to salmon fisheries and hatchery broodstock management and assessment in Canada. GSI and PBT were applied to assessment of 2019 coho salmon fisheries and hatchery broodstocks in British Columbia (BC), Canada, with 8208 individuals successfully genotyped in fishery samples and 2237 PBT identifications made (27.3% individual identification rate). The observed number of fishery PBT identifications per population corresponded closely with the expected number based upon genetic tagging rate in the populations. Coded-wire tags (CWTs) did not provide an accurate representation of the catch in the northern British Columbia troll fishery or the northwest Vancouver Island inshore recreational fishery, owing to the fact that major components of this fishery were not marked with CWTs. A single population chosen as an indicator in a Conservation Unit (CU) did not display a distribution of captures among fishery areas that was representative of other populations in the CU. There were 6544 individuals genotyped in 25 hatchery broodstocks from which 4019 PBT identifications were made. Population-specific contributions to mixed-stock fisheries and exploitation rates were estimated with CWTs and GSI-PBT technologies for eight hatchery populations. There was generally reasonably close agreement of estimated population-specific exploitation rates between CWT and genetic methods for hatchery populations. We conclude that a genetic approach can improve upon the results available from the current CWT program for assessment and management of coho salmon fisheries and hatchery broodstocks in BC, and provide information critical to aid in implementation of Canada's Policy for Conservation of Wild Pacific Salmon. [ABSTRACT FROM AUTHOR]

Many coho salmon stocks ( Oncorhynchus kisutch) have been in decline during the past three decades. Canada’s most endangered salmon stock, the Thompson River coho salmon, is being studied extensively as managers attempt to reverse these population declines. Investigators are using acoustic telemetry to track the migratory behaviour and survival of the Thompson River (and other) coho salmon stocks. Coho salmon pre-smolts are relatively small compared with salmonid species that are typically studied using acoustic telemetry; therefore the identification of the appropriate sizes of fish and tags to use is critical. This study tested the effects of surgically implanting the three smallest sizes of acoustic tags currently available on the growth, survival, tag retention, swimming performance and physical condition of coho salmon pre-smolts for 300 days post-surgery. Maximum tag size to body size ratios ranged from 15–17% by fork length and 7–8% by mass for the three tag sizes (11 cm fork length for a 6 × 19 mm tag, 12.5 cm for a 7 × 19 mm tag, and 14 cm for a 9 × 21 mm tag). Based on our results, it is unlikely that coho salmon pre-smolts implanted with acoustic transmitters following these size guidelines would have poor survival in studies of freshwater migratory behaviour as a result of the surgery or the tag. [ABSTRACT FROM AUTHOR]

The present study reports measured levels of Hg and other trace elements in commercial salmon feed; farmed Atlantic, coho, and chinook salmon (n = 110); and wild coho, chinook, chum, sockeye, and pink salmon (n = 91). Metal concentrations in farmed and wild salmon from British Columbia, Canada, were relatively low and below human health consumption guidelines. Methylmercury in all salmon samples (range, 0.03-0.1 μg/g wet wt) were below the 0.5 μg/g guideline set by Health Canada. Negligible differences in metal concentrations were observed between the various species of farmed and wild salmon. Metal concentrations generally were higher in commercial salmon feed compared to farmed salmon. Mercury showed slight bioaccumulation potential in farmed salmon, with biomagnification factors (BMFs) ranging between 0.8 and 1.9. Other metals, such as Cd, Pb, and Ni, exhibited biodilution, with BMFs of much less than one. The relatively low degree of biomagnification of metals observed in farmed salmon likely resulted from the combination of low gastrointestinal absorption efficiency, negligible transfer to muscle tissue relative to other compartments, and a high degree of growth dilution in these fish. Human dietary exposure calculations indicate intakes of Hg, Cd, Pb, Cu, As, and Ni via farmed and wild British Columbia salmon are a relatively small percentage of total intakes (0.05-32%) compared to other Canadian foodstuffs, such as fruits, vegetables, chicken, and beef (68-99%). Although total dietary exposure of Cd, Pb, and Cu approached provisional tolerable daily intake levels, the contribution from British Columbia salmon was less than 2%. Our findings indicate farmed and wild British Columbia salmon remain a safe source of omega-3 highly unsaturated fatty acid intake for cardioprotective and, possibly, other health benefits. [ABSTRACT FROM AUTHOR]

We investigated the growth rate, winter survival, presmolt size, and emigration timing of juvenile coho salmon (Oncorhynchus kisutch) in response to salmon carcasses and in-stream wood. Experimental trials were conducted during two consecutive years and pre-winter fish size and densities differed between years. Sixteen pens with emigration traps were built in a side-channel of the Mamquam River, British Columbia. Pens were randomly assigned salmon carcasses, in-stream wood, both carcasses and in-stream wood, or neither (control). Our first trial was conducted between December 1996 and August 1997 and the second between December 1997 and August 1998. Initial rearing densities and average individual body mass were 3.1 fish·m–2 and 2.4 g, respectively, in the first trial and were 1.6 fish·m–2 and 6.6 g, respectively, in the second trial. Results were influenced by both fish initial size and density. During the first trial (smaller-sized fish at high densities), salmon carcasses increased fish growth rates and presmolt size. Winter survival did not increase in response to any treatment; however, a pre-winter size-related survival pattern was observed during the first trial. During the second trial, (larger-sized fish at low densities), no treatment influenced fish growth rates or presmolt size but all treatments augmented fish survival. [ABSTRACT FROM AUTHOR]

For anadromous salmonids, olfaction is a critical sense, enabling return migration. In recent years, several pesticides have been identified that interfere with salmonid olfaction at concentrations in the μg/L range; thus, they may pose a risk to species longe]ity. In the present study, we investigated the acute effects of five agricultural pesticides on juvenile coho salmon (Oncorhynchus kisutch) olfaction using the electro-olfactogram (EOG), a measure of odorant-evoked field potentials. Electro-olfactogram responses to the odorant L-serine were measured during and following a 30-min exposure of the left olfactory rosette to chlorothalonil, endosulfan, glyphosate acid, iodocarb (IPBC), trifluralin, and 2,4-dichlorophenoxyacetic acid. With the relatively insoluble pesticides endosulfan and trifluralin, decreases in EOG amplitude were only apparent at relatively high concentrations (100 and 300 μg/L, respectively) following 20 min of exposure and were absent for chlorothalonil (1 mg/L). With the water-soluble herbicide glyphosate, significant EOG reductions occurred within 10 min of exposure to 1 mg/L and more rapidly with higher concentrations. Recovery of EOG post-glyphosate exposure was concentration-dependent, and complete recovery was not observed with some concentrations at 60 min postexposure. Dichlorophenoxyacetic acid only affected EOG at high concentration (100 mg/L), where it eliminated EOG within 2 min of exposure. With IPBC, EOG was decreased at 25 min of exposure to 1 μg/L; higher concentrations caused decreases to occur more rapidly. Excluding IPBC and glyphosate, all EOG reductions occurred at concentrations greater than the current Canadian water-quality guidelines and reported 96-h lethality values. Our results show that olfactory neurons can be impaired rapidly by some current-use pesticides, even at exposures in the low-μg/L range. [ABSTRACT FROM AUTHOR]

Describes the avoidance of solar ultraviolet radiation by juvenile coho salmon in the Little Qualicum River, British Columbia. Factors affecting the organisms in fresh water; Decline of the salmonid stocks; Formation of epidermal lesions.

This is a synthesis of published and unpublished research on euphausiid and fish populations using the south-west coast of Vancouver Island. Overall, the studies covered 1985–98, when there were two ENSO events and considerable variation in upwelling. The population biology of the dominant euphausiids (Thysanoessa spinifera , Euphausia pacifica ) was monitored during 1991–98. The species abundance trends differed. Results of simple correlation analyses suggested that variations in temperature, salinity and upwelling do not explain variations in the abundance of larval or adult euphausiids, or in the abundance of portions of euphausiid populations on which fish feed. I found significant interannual variations in daily ration of the dominant planktivorous fish species, but euphausiids remained the most important prey. Pacific hake (Merluccius productus ), the dominant planktivore, fed on larger (>17 mm) T. spinifera , even though the biomass of this part of the euphausiid biomass decreased by 75% between 1991 and 1997, but Pacific herring (Clupea pallasi ) may have begun feeding on smaller E. pacifica . Therefore, any study of the relationship between fish production and krill biology must consider that part of the euphausiid biomass exploited by fish. In addition, some fish species and/or life history stages appeared to adapt to changes in euphausiid availability, while others did not. Such variation in adaptations also has to be described and considered to understand how changes in euphausiid biology affect fish productivity. [ABSTRACT FROM AUTHOR]

• In Canada, implementation of the Wild Salmon Policy requires a new approach to management of Chinook and coho salmon fisheries. • Mass marking (removal of adipose fin) of hatchery production for Chinook salmon fits with genetic-based fisheries assessment. • Genetic stock identification (GSI) and parentage-based tagging (PBT) provide a method of salmon fisheries assessment. • GSI and PBT provide an alternate, cheaper, and more effective method in assessment and management of Canadian-origin salmon. • GSI and PBT provide an opportunity for a genetic-based system to replace the current coded-wire tag (CWT) system for salmon assessment. I present responses to arguments offered by coded-wire tag (CWT) proponents supposedly limiting the effectiveness of a genetic stock identification (GSI) and parentage-based tagging (PBT) fisheries assessment method. I demonstrate that a GSI-PBT-based assessment method is cheaper, more powerful, and more informative than traditional CWTs. Implementation of a GSI-PBT for Canadian fisheries assessment can provide information at least equivalent to that derived from the current CWT assessment program. Adoption of a GSI-PBT assessment program will facilitate mass-marking of Chinook salmon (Oncorhynchus tshawytscha) in British Columbia, has allowed for genetic tagging during the COVID pandemic while few Chinook salmon juveniles were marked with CWTs, has allowed for tagging of approximately six times more juveniles than traditionally tagged with CWTs, and at an estimated cost of 23 % of that associated with tagging with CWTs. GSI and PBT provide an alternate, cheaper, and more effective method in the assessment and management of Canadian-origin salmon relative to CWTs, and an opportunity for a genetic-based system to replace the current CWT system for salmon assessment. The time has arrived for agencies managing Pacific salmon fisheries to prepare for a transition from CWTs to a genetics-based fisheries assessment program. [ABSTRACT FROM AUTHOR]

Three microsatellite loci were used to examine genetic variation among 16 coho salmon (Oncorhynchus kisutch) populations within the Fraser River drainage system, in British Columbia, Canada. Each locus was highly polymorphic with 30 alleles at the Ots101 locus, 15 alleles at the Ots3 locus and 38 alleles at the Ots103 locus. Average observed heterozygosities were 86.1%, 70%, and 56.1%, respectively. With the exception of the Dunn and Lemieux River populations, Chi-square tests and FST values indicated that all populations had significantly different allele frequencies. Two distinct population groups within the Fraser River drainage were observed. Lower Fraser River populations were strongly differentiated from populations spawning in the upper Fraser River, which includes the Thompson River (a tributary flowing into the upper Fraser) and the portion of the Fraser River beyond the precipitous Fraser River canyon. This regional population structure may have resulted from colonization of the upper and lower Fraser River regions by different founder populations following Pleistocene glaciation, and be maintained by adaptive differences between the two groups of coho salmon. Coho salmon populations in the upper Fraser and Thompson River drainages form an evolutionarily significant unit (ESU) of importance for conservation of biodiversity in coho salmon. Microsatellite DNA loci show promise as technically simple and highly informative genetic markers for coho salmon population management. [ABSTRACT FROM AUTHOR]