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For almost 200 years, the taxonomy of cutthroat trout (Oncorhynchus clarkii), a salmonid native to Western North America, has been in flux as ichthyologists and fisheries biologists have tried to describe the diversity within these fishes. Starting in the 1950s, Robert Behnke reexamined the cutthroat trout and identified 14 subspecies based on morphological traits, Pleistocene events, and modern geographic ranges. His designations became instrumental in recognizing and preserving the remaining diversity of cutthroat trout. Over time, molecular techniques (i.e. karyotypes, allozymes, mitochondrial DNA, SNPs, and microsatellite arrays) have largely reinforced Behnke's phylogenies, but have also revealed that some relationships are consistently weakly supported. To further resolve these relationships, we generated de novo transcriptomes for nine cutthroat subspecies, as well as a Bear River Bonneville form and two Colorado River lineages (blue and green). We present phylogenies of these subspecies generated from multiple sets of orthologous genes extracted from our transcriptomes. We confirm many of the relationships identified in previous morphological and molecular studies, as well as discuss the importance of significant differences apparent in our phylogenies from these studies within a geological perspective. Specific findings include three distinct clades: (1) Bear River Bonneville form and Yellowstone cutthroat trout; (2) Bonneville cutthroat trout (n = 2); and (3) Greenback and Rio Grande cutthroat trout. We also identify potential gene transfer between Bonneville cutthroat trout and a population of Colorado River green lineage cutthroat trout. Using these findings, it appears that additional groups warrant species‐level consideration if other recent species elevations are retained. [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]

The decomposition of vertebrates in lake ecosystems has been largely understudied despite being a vital part of ecosystem processes. Invasive lake trout (Salvelinus namaycush) invaded Yellowstone Lake and caused a decline in the native Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) population. To restore Yellowstone cutthroat trout, lake trout were suppressed by gillnetting annually since 1995 and has continued to present, with most carcasses deposited in the profundal zone (>70 m). As a part of suppression management, a fraction of carcasses from gillnetting were ground and placed on littoral spawning sites (causing lake trout embryo mortality via hypoxia). We conducted experiments (2018 and 2019) to determine how carcass state (i.e., whole vs. ground) and location of deposition (i.e., profundal or littoral) affected decomposition rates. Whole carcasses in the depths of Yellowstone Lake decomposed nine times slower (rate of decay, k = −0.0075 day−1; 95% CI = −0.0063–−0.0089) than ground carcasses in the littoral zone (k = −0.0679 day−1; 95% CI = −0.0590–−0.0768). Whole carcasses had a half-life of 91 days while ground carcasses had a half-life of 10 days. We showed that carcass state and location cause a differential decomposition for lake trout carcasses in Yellowstone Lake. Understanding carcass persistence in lakes can inform the management of suppression-produced carcasses in large lakes and provide insight into potential effects of carcass deposition from other sources, such as spawning events or fish kills, on nutrient cycling. [ABSTRACT FROM AUTHOR]

The cutthroat trout (Oncorhynchus clarkii (Richardson, 1836)) is one of the most widely distributed species of freshwater fish in western North America. Occupying a diverse range of habitats, they exhibit significant phenotypic variability that is often recognized by intraspecific taxonomy. Recent molecular phylogenies have described phylogenetic diversification across cutthroat trout populations, but no study has provided a range-wide morphological comparison of taxonomic divisions. In this study, we used linear- and geometric-based morphometrics to determine if phylogenetic and subspecies divisions correspond to morphological variation in cutthroat trout, using replicate populations from throughout the geographic range of the species. Our data indicate significant morphological divergence of intraspecific categories in some, but not all, cutthroat trout subspecies. We also compare morphological distance measures with distance measures of mtDNA sequence divergence. DNA sequence divergence was positively correlated with morphological distance measures, indicating that morphologically more similar subspecies have lower sequence divergence in comparison to morphologically distant subspecies. Given these results, integrating both approaches to describing intraspecific variation may be necessary for developing a comprehensive conservation plan in wide-ranging species. [ABSTRACT FROM AUTHOR]

Glaciers have shaped past and present habitats for Pacific salmon (Oncorhynchus spp.) in North America. During the last glacial maximum, approximately 45% of the current North American range of Pacific salmon was covered in ice. Currently, most salmon habitat occurs in watersheds in which glacier ice is present and retreating. This synthesis examines the multiple ways that glacier retreat can influence aquatic ecosystems through the lens of Pacific salmon life cycles. We predict that the coming decades will result in areas in which salmon populations will be challenged by diminished water flows and elevated water temperatures, areas in which salmon productivity will be enhanced as downstream habitat suitability increases, and areas in which new river and lake habitat will be formed that can be colonized by anadromous salmon. Effective conservation and management of salmon habitat and populations should consider the impacts of glacier retreat and other sources of ecosystem change. [ABSTRACT FROM AUTHOR]

Global climate change is shifting the timing of life-cycle events, sometimes resulting in phenological mismatches between predators and prey. Phenological shifts and subsequent mismatches may be consistent across populations, or they could vary unpredictably across populations within the same species. For anadromous Pacific salmon (Oncorhynchus spp.), juveniles from thousands of locally adapted populations migrate from diverse freshwater habitats to the Pacific Ocean every year. Both the timing of freshwater migration and ocean arrival, relative to nearshore prey (phenological match/mismatch), can control marine survival and population dynamics. Here we examined phenological change of 66 populations across six anadromous Pacific salmon species throughout their range in western North America with the longest time series spanning 1951-2019. We show that different salmon species have different rates of phenological change but that there was substantial within-species variation that was not correlated with changing environmental conditions or geographic patterns. Moreover, outmigration phenologies have not tracked shifts in the timing of marine primary productivity, potentially increasing the frequency of future phenological mismatches. Understanding population responses to mismatches with prey are an important part of characterizing overall population-specific climate vulnerability., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Sockeye salmon (Oncorhynchus nerka) stocks throughout the southern part of their North American range have experienced declines in productivity over the past two decades. In this study, we tested the hypothesis that pink (O. gorbuscha) and chum (O. keta) salmon stocks have also experienced recent declines in productivity by investigating temporal and spatial trends in productivity of 99 wild North American pink and chum salmon stocks. We used a combination of population dynamics and time series models to quantify individual stock trends as well as common temporal trends in pink and chum salmon productivity across local, regional, and continental spatial scales. Our results indicated widespread declines in productivity of wild chum salmon stocks throughout Washington (WA) and British Columbia (BC) with 81% of stocks showing recent declines in productivity, although the exact form of the trends varied among regions. For pink salmon, the majority of stocks in WA and BC (65%) did not have strong temporal trends in productivity; however, all stocks that did have trends in productivity showed declining productivity since at least brood year 1996. We found weaker evidence of widespread declines in productivity for Alaska pink and chum salmon, with some regions and stocks showing declines in productivity (e.g., Kodiak chum salmon stocks) and others showing increases (e.g., Alaska Peninsula pink salmon stocks). We also found strong positive covariation between stock productivity series at the regional spatial scale for both pink and chum salmon, along with evidence that this regional-scale positive covariation has become stronger since the early 1990s in WA and BC. In general, our results suggest that common processes operating at the regional or multi-regional spatial scales drive productivity of pink and chum salmon stocks in western North America and that the effects of these process on productivity may change over time. [ABSTRACT FROM AUTHOR]

Knowledge of the spatial and temporal extent of covariation in survival during the critical ocean entry stage will improve our understanding of how changing ocean conditions influence salmon productivity and management. We used data from the Pacific coastwide coded-wire tagging program to investigate local and regional patterns of ocean survival of Chinook salmon (Oncorhynchus tshawytscha) from the Central Valley of California to southeastern Alaska from 1980–2006. Ocean survival of fish migrating as subyearlings covaried strongly from Vancouver Island to California. Short-term correlations between adjacent regions indicated this covariability increased, beginning in the early 1990s. Chinook salmon survivals exhibited a larger spatial scale of variability (50% correlation scale: 706 km) than those reported for other northeast Pacific Ocean salmon. This scale is similar to that of environmental variables related to ecosystem productivity, such as summer upwelling (50% correlation scale: 746 km) and sea surface temperature (50% correlation scale: 500–600 km). Chinook salmon ocean survival rates from southeastern Alaska and south of Vancouver Island were not inversely correlated, in contrast to earlier observations based on catch data, but note that our data differ in temporal and spatial coverage from those studies. The increased covariability in Chinook salmon ocean survival suggests that the marine phase contributes little to the reduction in risk across populations attributable to the portfolio effect. In addition, survival of fish migrating as yearlings from the Columbia River covaried with Chinook salmon survival from the northernmost regions, consistent with our understanding of their migration patterns. [ABSTRACT FROM PUBLISHER]

Natural productivity, the number of natural-origin adult recruits per parent, is an important parameter for assessing population status of steelheadOncorhynchus mykiss(anadromous Rainbow Trout) and Pacific salmonOncorhynchusspp. listed under the U.S. Endangered Species Act. Hatchery-origin adults comprise a majority of many salmon and steelhead spawning populations. In such cases, the utility of natural productivity estimates is affected by uncertain reproductive fitness of hatchery spawners and by possible ecological or genetic interactions among hatchery and natural fish. This study examined options for analyzing population census data to assess hatchery spawner effects on natural productivity of mixed steelhead populations including spawners of hatchery and natural origin. It compared productivity in three mixed and reference (natural) population pairs, and estimated productivity as natural recruits per total spawners of natural and hatchery origin (Rnat/Stot) or as natural recruits per natural spawner (Rnat/Snat). Natural productivity estimated asRnat/Stotreflected hatchery program scale, not productive capacity of natal streams. This analytical approach masked natural production dynamics in populations with a major hatchery spawner proportion, and was therefore of limited use for determining hatchery spawner influence. Productivity estimated asRnat/Snatindicated similar productivity of reference and mixed populations, and an absence of hatchery spawner effect, in the case of (1) a large hatchery stray component, and (2) a hatchery supplementation program. In the third pairing,Rnat/Snatproductivity of the mixed population significantly exceeded that of the reference population, suggesting natural spawner abundance is below carrying capacity. Hatchery spawners contributed to natural productivity in that case, but in the presence of reduced natural spawner density. These findings suggest that hatchery spawners are unlikely to affect natural production of a mixed steelhead population unless natural spawner abundance is below carrying capacity. Received October 28, 2012; accepted July 2, 2013 [ABSTRACT FROM AUTHOR]

When natural populations exchange migrants at a rate proportional to their geographic distance, population genetics theory leads to the expectation of a pattern of isolation-by-distance (IBD), whereby geographic and genetic distance are correlated. However, the presence or absence of such patterns in modern populations may not fully reflect the historical relationships among those populations. Thus, historical samples, collected prior to modern human impacts, can often provide a critical baseline for comparison with modern populations. Steelhead, the anadromous form of rainbow trout, Oncorhynchus mykiss, are native to western North America and are endangered or threatened throughout most of California, near the southern extent of their native range. Population samples of steelhead collected in 1897 and 1909 in Central California rivers provided the opportunity to evaluate the historical genetic composition and population structure of these threatened fish. Here we show that these steelhead populations had a historically strong correlation between genetic and geographic distance that has been virtually erased in modern populations, suggesting that current relationships among modern steelhead populations are no longer reflective of natural migratory pathways. This demonstrates the critical role of migration in maintaining population relationships of threatened species and highlights the importance of natural history museums in providing historical baseline information. [ABSTRACT FROM AUTHOR]

Population structure of coho salmon Oncorhynchus kisutch from Russia to California was examined with a survey of microsatellite variation to describe the distribution of genetic variation. Variation at 17 microsatellite loci was surveyed for approximately 50,000 coho salmon sampled from 318 localities. The genetic differentiation index (FST) over all populations and loci was 0.058, with individual locus FST values ranging from 0.027 to 0.143. The least genetically diverse coho salmon were observed from Russia, the Porcupine River in the Yukon River drainage, and the middle Fraser and Thompson rivers in southern British Columbia. Coho salmon from Vancouver Island, British Columbia; Puget Sound, Hood Canal, and Juan de Fuca Strait, northern Washington; and Oregon displayed the greatest number of alleles compared with coho salmon in other regions. Differentiation in coho salmon allele frequencies among regions and among populations within regions was approximately seven times greater than that of annual variation within populations. A regional structuring of populations was the general pattern observed; coho salmon spawning in different tributaries within a major river drainage or spawning in smaller rivers in a geographic area were generally more similar to each other than to populations in different major river drainages or geographic areas. The distribution of microsatellite variation in coho salmon likely reflects the origins of salmon radiating from refuges after the last glaciation period. [ABSTRACT FROM AUTHOR]

Abstract: Remains of anadromous Pacific salmon and trout (genus Oncorhynchus) are common in archaeological sites from California to Alaska; however, morphological similarity generally precludes species identification, limiting the range of questions that salmonid remains can address in relation to past human use and ongoing efforts in conservation biology. We developed a relatively simple, rapid, and non-destructive way to classify salmon and trout vertebrae from archaeological contexts to species using length, height and the ratio of length to height. Modern reference material was obtained from all seven anadromous Oncorhynchus species native to the west coast of North America. A minimum of ten adult Chinook (Oncorhynchus tshawytscha), chum (Oncorhynchus keta), coho (Oncorhynchus kisutch), pink (Oncorhynchus gorbuscha), and sockeye salmon (Oncorhynchus nerka) and cutthroat (Oncorhynchus clarki clarki) and steelhead trout (Oncorhynchus mykiss) were skeletonized and vertebra length and height were measured. Morphometric analyses compared species classification success based on Linear Discriminant Analysis (LDA), Classification and Regression Trees (CART), and randomForest, with CART performing the best. Classification analyses used all seven species individually, but because of considerable overlap among several species we also conducted analyses on four species groupings. We assigned Chinook salmon and cutthroat to their own groups based on their dissimilarities from each other and the other species. The remaining species were divided into two group complexes (a) chum, coho, and steelhead; and (b) pink and sockeye. When we grouped species according to similar morphology, CART overall success rates increased, ranging from 92 to 100%. Individual species with the highest successful classification rates using CART were Chinook salmon and cutthroat, from 92 to 100%, respectively. We applied our classification to an assemblage of ancient (1000–3000 year old) salmonid vertebrae from the Swiftwater Rockshelters excavations on the upper Wenatchee River in Washington State, U.S.A. [Copyright &y& Elsevier]

The New Zealand mud snail (NZMS) Potamopyrgus antipodarum, a normative species recently introduced into North America, has been shown to negatively influence ecosystem function. Methods to careful or eliminate NZMS are needed. Twenty four-hour treatments with 2 mg of potassium permanganate (KMnO4) per liter of water were evaluated against NZMS held for 24 h in artificial stream sections that contained refuge areas. The snails did not seek refuge when placed into an area that contained KmnO4 and also had neutral preference when provided the opportunity to select between artificial stream sections with and without KMnO4. In a separate series of experiments, NZMS and rainbow trout Oncorhynchus mykiss were placed into hatchery raceway sections that were treated with a 2 mg/L KMnO4 solution for 2 h/d over a period of 14 consecutive days. Mortality of NZMS and rainbow trout was not elevated in these raceways relative to nontreated control raceways. There was evidence, however, that the presence of the KMnO4 depressed fish growth (i.e., Fulton's condition factor). The KMnO4 treatment did not cause significant gill damage in rainbow trout. Our results show that KMnO4 at 2 mg/L is not effective in controlling or eliminating NZMS populations. [ABSTRACT FROM AUTHOR]

Contemporary evolution of Pacific salmon ( Oncorhynchus spp.) is best viewed in the context of the evolutionary history of the species and the dynamic ecosystems they inhabit. Speciation was complete by the late Miocene, leaving c. six million years for intraspecific diversification. Following the most recent glacial maximum, large areas became available for recolonization. Current intraspecific diversity is thus the product of recent evolution overlaid onto divergent historical lineages forged during recurrent episodes of Pleistocene glaciation. In northwestern North America, dominant habitat features have been relatively stable for the past 5000 years, but salmon ecosystems remain dynamic because of disturbance regimes (volcanic eruptions, landslides, wildfires, floods, variations in marine and freshwater productivity) that occur on a variety of temporal and spatial scales. These disturbances both create selective pressures for adaptive responses by salmon and inhibit long-term divergence by periodically extirpating local populations and creating episodic dispersal events that erode emerging differences. Recent anthropogenic changes are replicated pervasively across the landscape and interrupt processes that allow natural habitat recovery. If anthropogenic changes can be shaped to produce disturbance regimes that more closely mimic (in both space and time) those under which the species evolved, Pacific salmon should be well-equipped to deal with future challenges, just as they have throughout their evolutionary history. [ABSTRACT FROM AUTHOR]

Remaining populations of westslope cutthroat trout (Oncorhynchus clarkii lewisi) in western North America are primarily confined to cold headwaters whereas nonnative rainbow trout (Oncorhynchus mykiss) predominate in warmer, lower elevation stream sections historically occupied by westslope cutthroat trout. We tested whether differing thermal preferences could account for the spatial segregation observed in the field. Thermal preferences of age-1 westslope cutthroat trout and rainbow trout (125 to 150 mm total length) were assessed in the laboratory using a modified annular preference chamber at acclimation temperatures of 10, 12, 14, and 16°C. Final preferred temperature of westslope cutthroat trout (14.9°C) was similar to that of rainbow trout (14.8°C) when tested in a thermal gradient of 11-17°C. The high degree of overlap in thermal preference indicates the two species have similar thermal niches and a high potential for competition. We suggest several modifications to the annular preference chamber to improve performance in future studies. [ABSTRACT FROM AUTHOR]

On the Pacific coast of North America, the most abundant vertebrate visitors to estuaries and rivers during salmon migration are gulls, yet the utilization of salmon nutrients by these scavengers, and subsequent ecological impacts are not well documented. On two forested watersheds on the central Coast of British Columbia, we tracked gull abundance during the spawning period for two consecutive years, and estimated consumption of post-reproductive salmon carcasses and eggs, as well as guano production. At Clatse River, gulls (Larus glaucescens, L. argentatus, L. thayerii, L. californicus, L. canus, L. philadelphia) consumed 13-26% of total salmon carcass biomass and 29-36% of all salmon eggs deposited in the system. At Neekas River, gulls consumed 11 - 19% of salmon carcass biomass and 7-18% of total salmon eggs. Local guano production over the 60-day period ranged from 600 kg to 1190 kg at Clatse and from 1200kg to 2100 kg at Neekas River, and was distributed to marine, estuarine, freshwater and riparian habitats. The large aggregations of gulls and subsequent nutrient cycling observed on our study watersheds may represent a once widespread phenomenon that is now largely reduced due to recent declines in salmon populations. [ABSTRACT FROM AUTHOR]

Salmonid cryptobiosis is caused by Cryptobia (Trypanoplasma) salmositica. The haemoflagellate has been reported from all species of Pacific Oncorhynchus spp. on the west coast of North America. It is normally transmitted by the freshwater leech, Piscicola salmositica, in streams and rivers, and sculpins, Cottus spp., are considered important reservoir hosts. The pathogen can also survive on the body surface of fish because it has a contractile vacuole to osmoregulate when the fish is in fresh water. This allows for direct transmission between fish, especially in aquaculture facilities. The parasite divides rapidly by binary fission in the blood to cause disease, the severity of which is directly related to parasitaemia. Cryptobia salmositica has a mitochondrium and it normally undergoes aerobic respiration; however, if its mitochondrium is damaged it will switch to glycolysis. Its glycolytic enzymes and catalase are contained in glycosomes. Cysteine protease is a metabolic enzyme, and its neutralization inhibits oxygen consumption and multiplication of the parasite. An important virulent Factor in cryptobiosis is a secretory metalloprotease. The protective mechanism involves production of complement fixing antibodies, phagocytosis by macrophages, and cell-mediated cytotoxicity. Recovered fish are protected, probably for life as the immunity is non-sterile. Clinical signs of the disease include anaemia, anorexia, splenomegaly, general oedema and abdominal distension with ascites. The metabolism and swimming performance of infected fish are significantly reduced and the bioenergetic cost of the disease is very considerable. Fish are susceptible to hypoxia and their immune system is depressed during acute cryptobiosis. Severity of the disease and mortality rates vary significantly between species and stocks of salmon. Protective strategies include selective breeding of Cryptobia-resistant fish. This is innate resistance to infection and it is controlled by a dominant Mendelian locus. In these fish the parasite is lysed via the alternative pathway of complement activation. In Cryptobia-tolerant fish (infected with the pathogen but which do not suffer from disease) the metalloprotease secreted by the parasite is neutralized by α2 macroglobulin. Hence, the production of a transgenic Cryptobia-tolerant salmon is an option. This strategy has the advantage in that human intervention (e.g. vaccination, chemotherapy) is not required once the transgenic fish is produced. Acquired immunity is another option; a single dose of the attenuated live vaccine protects fish for at least 2 years. The protective mechanism in vaccinated fish is similar to that in recovered fish. The trypanocidal drug, isometamidium chloride, is an effective therapeutic and prophylactic agent. It accumulates in the mitochondrium of the parasite and significantly disrupts aerobic respiration by causing lesions in the organelle. Efficacy of the drug is significantly increased after its conjugation to antibodies. This immuno-chemotherapeutic strategy has the advantage in that it will lower the drug dosage and hence side-effects of chemotherapy. It will probably reduce the accumulation of the drug in fish, and important consideration in food fish. Keywords: biology; control; Cryptobia salmositica, cryptobiosis, host-parasite relationships; salmonids; systematics. [ABSTRACT FROM AUTHOR]

The production characteristics of juvenile rainbow trout, Oncorhynchus mykiss, and brook trout, Salvelinus fontinalis, were compared under winter pond conditions. Juvenile rainbow trout (55.1 1.5 g) and brook trout (28.9 0.4 g) were stocked at a density of 8,750 fish/ha into six 0.04-ha ponds. After 163 days, survival, growth, and feed conversion were similar (P > 0.05). The results of this study suggest that brook trout may attain growth rates similar to rainbow trout under winter pond conditions in temperate regions of North America. [ABSTRACT FROM PUBLISHER]

In temperate regions of North America, the culture of rainbow trout, Oncorhynchus mykiss (Walbaum), in ponds is constrained to the period mid-November to early April by water temperature. Feeding practice may influence production time. The effects of three feeding practices on growth and body composition of rainbow trout raised in ponds during a 142-day winter growth period were investigated. Feeding practices were (1) hand-feeding to satiation, (2) feeding according to a fish size/water temperature chart, and (3) feeding by demand feeder. Fish fed to satiation consumed 66% more diet than fish fed according to a feeding chart and t63% more than fish fed by demand feeders. Fish fed to satiation had significantly higher (P « 0.05) weight gain, harvest weight, specific growth rate, and protein gain with no significant increase (P » 0.05) in percentage body fat or feed conversion ratio (FCR) compared to the other two treatments. Survival percentage did not differ significantly (P » 0.05) between treatments. These data indicate that by using satiation feeding, marketable size rainbow trout can be produced in temperate region ponds without increases in percentage body fat or FCR. [ABSTRACT FROM AUTHOR]

The annual global production of farmed salmon has increased by a factor of 40 during the past two decades. Salmon from farms in northern Europe, North America, and Chile are now available widely year-round at relatively low prices. Salmon farms have been criticized for their ecological effects, but the potential human health risks of farmed salmon consumption have not been examined rigorously. Having analyzed over 2 metric tons of farmed and wild salmon from around the world for organochlorine contaminants, we show that concentrations of these contaminants are significantly higher in farmed salmon than in wild. European-raised salmon have significantly greater contaminant loads than those raised in North and South America, indicating the need for further investigation into the sources of contamination. Risk analysis indicates that consumption of farmed Atlantic salmon may pose health risks that detract from the beneficial effects of fish consumption.