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At least 559 records · Page 31Linked to original sources
USGS2021

Reduced recruitment of Chinook salmon in a leveed bar-built estuary

Estuaries are commonly touted as nurseries for salmonids, providing numerous advantages for smolts prior to ocean entry. In bar-built estuaries, sandbars form at the mouth of rivers during periods of low stream flow, closing access to the ocean and preventing outmigration. We evaluated how summer residency in a leveed bar-built estuary affects the growth, survival, and recruitment of a Chinook salmon ( Oncorhynchus tshawytscha ) population. We performed a mark–recapture study on outmigrants to determine juvenile estuary abundance, growth, and survival. We used returning adult scales and otoliths to determine the relative proportion of summer estuary residents in spawning adults. Juveniles in the estuary grew less after mouth closure, and ultimately summer estuary residents had lower smolt-to-adult survival and contributed disproportionately less to the spawning population than juveniles that reared in the ocean their first summer. Mouth closure may lower food availability and deteriorate estuary conditions by reducing marine prey influx and estuary circulation. This research demonstrates the complexity of estuary dynamics and function as salmonid nurseries, particularly when considering the extensive modification of estuaries.

California↗
USGS2023

Territories within groups: The dynamic competition of drift-feeding juvenile Chinook salmon in 3-dimensional space

Salmonid populations are often regulated by territorial competition among juveniles for food and space. In the canonical view, salmonid territories are spaced horizontally across the river bottom in a 2-D mosaic. However, some juveniles instead feed in tight, three-dimensional (3-D) social groups. To investigate whether territoriality is possible within such groups, we applied a new concept—the momentary home range—to quantify the size, exclusivity, and temporal dynamics of 3-D space use by juvenile Chinook Salmon ( Oncorhynchus tshawytscha ) in the Chena River, Alaska. Individual strategies spanned a broad continuum of exclusivity and stationarity. However, some of the largest, most dominant fish in each group aggressively defended stationary, exclusive feeding spaces and thus were unambiguously territorial. Transient floaters entered and left the group quickly. A majority of fish were not aggressive but nevertheless occupied exclusive, stationary spaces that probably function as territories with regard to resource distribution and population regulation. The presence of territoriality within social groups, in a 3-D configuration, expands the known domain of this important behavior.

Alaska↗
USGS2025

Native Yellowstone cutthroat trout Oncorhynchus virginalis bouvieri growth and survival in a headwater stream primarily driven by warming stream temperatures, with non-native brown trout Salmo trutta posing an additional threat to survival

Warming rivers and interactions with non-native species impact salmonid species globally. Understanding how hydroclimatic conditions synergistically and independently interact with non-native species is critical for effectively managing salmonids into the future. We used a 10-year mark–recapture dataset to assess how native Yellowstone cutthroat trout (YCT) Oncorhynchus virginalis bouvieri and non-native brown trout Salmo trutta growth rates and apparent survival were affected by hydroclimatic conditions and (for YCT) the presence of brown trout in a tributary. Growth (YCT) and survival (both species across size classes) were negatively related to warming stream temperatures. Brown trout growth was positively related to increasing daily streamflow variability (a proxy for streamflow), but this variable was not included in the top YCT growth model. Density-dependent effects appeared to be non-existent (growth) or weakly positive (survival). When sympatric with brown trout, YCT displayed worse survival than allopatric YCT across environmental conditions. Broadly, we found native and non-native trout respond to different hydroclimatic conditions that shift with changing climatic conditions, and brown trout represent an additional threat to YCT survival.

Montana↗
USGS2026

Patterns of recent brook trout invasion in bull trout streams in relation to habitat, source connectivity, biotic resistance, and disturbance

Knowledge of which habitats are at risk of invasion by nonnative species is essential to conservation, but a changing climate often complicates assessments of where future invasions may occur. Nonnative brook trout Salvelinus fontinalis threaten cold-adapted native salmonids throughout western North America, and the extent of future invasions in coldwater streams is recognized as an area of uncertainty with important consequences. We addressed this uncertainty using spatial-stream-network (SSN) modeling to develop a species distribution model (SDM) for brook trout in Idaho, creating high-resolution prediction maps of suitable (i.e., invadable) habitat under baseline (1990–2015) and future (2080s) climate scenarios, and querying predictions within natal bull trout S. confluentus habitat patches (stream–subwatershed scale) for each scenario. Results indicated that brook trout will experience a net loss of suitable habitat in Idaho, but a large increase of suitable habitat in cold streams. The total proportion of bull trout habitat invadable by brook trout increased from 0.33 during the baseline scenario to 0.44 during the future scenario—a result of upstream expansions of brook trout habitat that were partially offset by contractions in bull trout habitat. Changes in the proportion of invadable habitat varied widely among bull trout patches. Between scenarios, the largest increases in suitable habitat occurred in small, low-gradient, unconfined streams with mean August water temperatures of 7–9 °C during the baseline period. A relatively small proportion of patches contained the majority of invadable habitat in both scenarios, particularly patches in “U-shaped” glacial valleys. A changing climate will broadly increase the threat that brook trout pose to bull trout, but the degree of change experienced by individual populations will vary with local context. The high-resolution prediction maps created by our SSN model will help conservation planners identify and prioritize control efforts on the small proportion of brook trout populations that most threaten bull trout.

Idaho↗
USGS2008

Analysis of trade-offs between threats of invasion by nonnative brook trout (Salvelinus fontinalis) and intentional isolation for native westslope cutthroat trout (Oncorhynchus clarkii lewisi)

Native salmonid fishes often face simultaneous threats from habitat fragmentation and invasion by nonnative trout species. Unfortunately, management actions to address one may create or exacerbate the other. A consistent decision process would include a systematic analysis of when and where intentional use or removal of barriers is the most appropriate action. We developed a Bayesian belief network as a tool for such analyses. We focused on native westslope cutthroat trout (Oncorhynchus clarkii lewisi) and nonnative brook trout (Salvelinus fontinalis) and considered the environmental factors influencing both species, their potential interactions, and the effects of isolation on the persistence of local cutthroat trout populations. The trade-offs between isolation and invasion were strongly influenced by size and habitat quality of the stream network to be isolated and existing demographic linkages within and among populations. An application of the model in several sites in western Montana (USA) showed the process could help clarify management objectives and options and prioritize conservation actions among streams. The approach can also facilitate communication among parties concerned with native salmonids, nonnative fish invasions, barriers and intentional isolation, and management of the associated habitats and populations. ?? 2008 NRC.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2005

Combined use of the ASK and SHK-1 cell lines to enhance the detection of infectious salmon anemia virus

Infectious salmon anemia (ISA) is a severe disease primarily affecting commercially farmed Atlantic salmon (Salmo salar) in seawater. The disease has been reported in portions of Canada, the United Kingdom, the Faroe Islands, and the United States. Infectious salmon anemia virus (ISAV), the causative agent of ISA, has also been isolated from several asymptomatic marine and salmonid fish species. Diagnostic assays for the detection of ISAV include virus isolation in cell culture, a reverse transcriptase-PCR, an enzyme-linked immunosorbent assay, and an indirect fluorescent antibody test. Virus isolation is considered the gold standard, and 5 salmonid cell lines are known to support growth of ISAV. In this study, the relative performance of the salmon head kidney 1 (SHK-1), Atlantic salmon kidney (ASK), and CHSE-214 cell lines in detecting ISAV was evaluated using samples from both experimentally and naturally infected Atlantic salmon. Interlaboratory comparisons were conducted using a quality control-quality assurance ring test. Both the ASK and SHK-1 cell lines performed well in detecting ISAV, although the SHK-1 line was more variable in its sensitivity to infection and somewhat slower in the appearance of cytopathic effect. Relative to the SHK-1 and ASK lines, the CHSE-214 cell line performed poorly. Although the ASK line appeared to represent a good alternative to the more commonly used SHK-1 line, use of a single cell line for diagnostic assays may increase the potential for false-negative results. Thus, the SHK-1 and ASK cell lines can be used in combination to provide enhanced ability to detect ISAV.

Journal of Veterinary Diagnostic Investigation↗
USGS2013

Identifying when tagged fishes have been consumed by piscivorous predators: application of multivariate mixture models to movement parameters of telemetered fishes

Background Consumption of telemetered fishes by piscivores is problematic for telemetry studies because tag detections from the piscivore could introduce bias into the analysis of telemetry data. We illustrate the use of multivariate mixture models to estimate group membership (smolt or predator) of telemetered juvenile Chinook salmon ( Oncorhynchus tshawytscha ), juvenile steelhead trout ( O. mykiss ), striped bass ( Morone saxatilis ), smallmouth bass ( Micropterus dolomieu ) and spotted bass ( M. punctulatus ) in the Sacramento River, CA, USA. First, we estimated two types of track statistics from spatially explicit two-dimensional movement tracks of telemetered fishes: the Lévy exponent ( b ) and tortuosity ( τ ). Second, we hypothesized that the distribution of each track statistic would differ between predators and smolts. To estimate the distribution of track statistics for putative predators and smolts, we fitted a bivariate normal mixture model to the mixed distribution of track statistics. Lastly, we classified each track as a smolt or predator using parameter estimates from the mixture model to estimate the probability that each track was that of a predator or smolt. Results Tracks classified as predators exhibited movement that was tortuous and consistent with prey searching tactics, whereas tracks classified as smolts were characterized by directed, linear downstream movement. The estimated mean tortuosity was 0.565 (SD = 0.07) for predators and 0.944 (SD = 0.001) for smolts. The estimated mean Lévy exponent was 1.84 (SD = 1.23) for predators and -0.304 (SD = 1.46) for smolts. We correctly classified 90% of the Micropterus species and 72% of the striped bass as predators. For tagged smolts, 80% of Chinook salmon and 74% of steelhead trout were not classified as predators. Conclusions Mixture models proved valuable as a means to differentiate between salmonid smolts and predators that consumed salmonid smolts. However, successful application of this method requires that telemetered fishes and their predators exhibit measurable differences in movement behavior. Our approach is flexible, allows inclusion of multiple track statistics and improves upon rule-based manual classification methods.

California↗
USGS2015

Recovery of a mining-damaged stream ecosystem

This paper presents a 30+ year record of changes in benthic macroinvertebrate communities and fish populations associated with improving water quality in mining-influenced streams. Panther Creek, a tributary to the Salmon River in central Idaho, USA suffered intensive damage from mining and milling operations at the Blackbird Mine that released copper (Cu), arsenic (As), and cobalt (Co) into tributaries. From the 1960s through the 1980s, no fish and few aquatic invertebrates could be found in 40 km of mine-affected reaches of Panther Creek downstream of the metals contaminated tributaries, Blackbird and Big Deer Creeks. Efforts to restore water quality began in 1995, and by 2002 Cu levels had been reduced by about 90%, with incremental declines since. Rainbow Trout ( Oncorhynchus mykiss ) were early colonizers, quickly expanding their range as areas became habitable when Cu concentrations dropped below about 3X the U.S. Environmental Protection Agency's biotic ligand model (BLM) based chronic aquatic life criterion. Anadromous Chinook Salmon ( O. tshawytscha ) and steelhead ( O. mykiss ) have also reoccupied Panther Creek. Full recovery of salmonid populations occurred within about 12-years after the onset of restoration efforts and about 4-years after the Cu chronic criteria had mostly been met, with recovery interpreted as similarity in densities, biomass, year class strength, and condition factors between reference sites and mining-influenced sites. Shorthead Sculpin ( Cottus confusus ) were slower than salmonids to disperse and colonize. While benthic macroinvertebrate biomass has increased, species richness has plateaued at about 70 to 90% of reference despite the Cu criterion having been met for several years. Different invertebrate taxa had distinctly different recovery trajectories. Among the slowest taxa to recover were Ephemerella , Cinygmula and Rhithrogena mayflies, Enchytraeidae oligochaetes , and Heterlimnius aquatic beetles. Potential reasons for the failure of some invertebrate taxa to recover include competition, and high sensitivity to Co and Cu.

Idaho↗
USGS2025

Leveraging detection uncertainty to estimate Renibacterium salmoninarum infection status among multiple tissues and assays

Effective disease surveillance relies on accurate pathogen testing and robust prevalence estimates. Diagnostic specificity (DSp), the probability that an uninfected animal tests negative, is high when false positives are low. Diagnostic sensitivity (DSe) is the probability an infected animal tests positive; higher DSe means fewer false negatives. However, sensitivity and false negatives are harder to estimate without a "gold standard", an assay that can detect between 90 - 100% of true positive infections. Occupancy estimation of infection prevalence offers one solution by allowing for imperfect detection of the pathogen. Testing potentially infected tissues multiple times allows for the use of a Bayesian multistate occupancy model to estimate the probability of pathogen infection in tissues [Formula: see text] and detection probabilities [Formula: see text] for different assays. Using [Formula: see text] and [Formula: see text] from the posterior distribution, the conditional probability of detecting the pathogen can be modeled, allowing for the calculation of DSe. Renibacterium salmoninarum is a bacterial pathogen causing bacterial kidney disease among salmonid species and was the model pathogen we used to train our model. The current testing standard for salmonids combines initial screening for antibodies using direct fluorescent antibody test (DFAT) with polymerase chain reaction (PCR) confirmation to detect R. salmoninarum. However, detection of R. salmoninarum still varies between species, tissues, and assays. Here, a multi-state occupancy model was used to estimate detection probability among individual and dual kidney/liver infections with DFAT and qPCR in fish with an unknown infection status. Both assays produced false negatives, but qPCR had fewer than DFAT and a higher DSe. Infection state was often misclassified, but multiple surveys per individual or combining tissues for testing improved DSe for both assays.

conterminous United States↗
USGS2020

Disease in Central Valley salmon: Status and lessons from other systems

Chinook Salmon ( Oncorhynchus tshawytscha ) are increasingly vulnerable to anthropogenic activities and climate change, especially at their most southern species range in California’s Central Valley. There is considerable interest in understanding stressors that contribute to population decline and in identifying management actions that reduce the impacts of those stressors. Along the west coast of North America, disease has been linked to declining numbers of salmonids and identified as a key stressor resulting in mortality. In the Central Valley, targeted studies have revealed extremely high prevalence of infectious agents and disease. However, there has been insufficient monitoring to understand the effect that disease may have on salmon populations. In order to inform future research, monitoring, and management efforts, a two-day workshop on salmon disease was held at UC Davis on March 14-15, 2018. This paper summarizes the science presented at this workshop, including the current state of knowledge of salmonid disease in the Central Valley and current and emerging tools to better understand its impacts on salmon. We highlight case studies from other systems where successful monitoring programs have been implemented. First, in the Klamath River where the integration of several data collection and modeling approaches led to the development of successful management actions, and second in British Columbia where investment in researching novel technologies led to breakthroughs in the understanding of salmon disease dynamics. Finally, we identify key information and knowledge gaps necessary to guide research and management of disease in Central Valley salmon populations.

California↗
USGS1991

Benzocaine as an anesthetic for striped bass

Benzocaine was tested as an anesthetic on juvenile and mature adult striped bass ( Morone saxatilis ). Concentrations of 55 mg/L at 22°C to 80 mg/L at 11°C effectively anesthetized fish in about 3 min. Recovery was more rapid as temperature increased. Fish survived concentrations of twice the effective concentration and exposure times up to 60 min at the effective concentration. Striped bass required higher concentrations for anesthetization than had been previously demonstrated for salmonid fishes, but safety margins for both concentration and exposure time were wider than for the salmonids.

Progressive Fish-Culturist↗
USGS1991

Choline requirement of swim-up rainbow trout fry

Triplicate 150‐fish lots of first‐feeding fry of rainbow trout ( Oncorhynchus mykiss ; initial mean weight, 0. 12 g) were fed casein–gelatin‐based diets containing 0, 200, 400, 800, 1,000, 2,000, 4,000, or 8,000 mg choline/kg of feed for 12 weeks to determine their need for dietary choline. Although the growth rates of fry were suboptimal, results showed that fry needed no more than 4,000 mg choline/kg casein–gelatin diet for maximum growth and 2,000 mg/kg for maximum body fat and minimum protein. Survival was significantly lower for fish fed 800 mg choline/kg of diet than for those fed greater amounts of the nutrient. These results suggest that the dietary choline requirement of early feeding salmonids is greater than that previously reported for older salmonids. The amount of choline needed by fishes apparently decreases with age or size.

Progressive Fish-Culturist↗
USGS1993

Prolonged swimming performance of northern squawfish

We determined the prolonged swimming performance of two size-classes of northern squawfish Ptychocheilus oregonensis at 12 and 18°C. The percentage of fish fatigued was positively related to water velocity and best described by an exponential model. At 12°C, the velocity at which 50% of the fish fatigued (FV50) was estimated to be 2.91 fork lengths per second (FL/s; 100 cm/s) for medium-sized fish (30–39 cm) and 2.45 FL/s (104 cm/s) for large fish (40–49 cm). At 18°C, estimated FV50 was 3.12 FL/s (107 cm/s) for medium fish and 2.65 FL/s (112 cm/s) for large fish. Rate of change in percent fatigue was affected by fish size and water temperature. Large fish fatigued at a higher rate than medium-sized fish; all fish fatigued faster at 12 than at 18°C. The mean times to fatigue at velocities of 102–115 cm/s ranged from 14 to 28 min and were not affected by fish size or water temperature. Our results indicate that water velocities from 100 to 130 cm/s may exclude or reduce predation by northern squawfish around juvenile salmonid bypass outfalls at Columbia River dams, at least during certain times of the year. We recommend that construction or modification of juvenile salmonid bypass facilities place the outfall in an area of high water velocity and distant from eddies, submerged cover, and littoral areas.

Oregon, Washington↗
USGS1960

Ovarian fluid: Its role in fertilization

FISH-CULTURISTs, in general, do not agree as to the time of actual fertilization of artificially spawned salmonid eggs. Some fish-culturists believe that the eggs are fertilized in the milt before water is added, while others are equally certain that fertilization is not achieved until after water is added. This difference of opinion has probably existed since the advent of the dry spawning method, in which milt is added to the eggs without the presence of water in the spawning pan. According to the "Manual of Fish-Culture" published by the U. S. Commission of Fish and Fisheries in 1900, it was known that eggs and milt from salmon maintain their viability for many hours if held in open containers, that both eggs and milt soon lose their viability when water is added, and that the milt and fluid around the eggs can be "utilized in impregnating masses of eggs when there is a scarcity of males, as sometimes occurs toward the close of the spawning season." The object of the studies reported here was to confirm some of the foregoing observations and to determine whether salmonid eggs could be fertilized without the supportive action of water.

Progressive Fish-Culturist↗
USGS1963

The Hexamita (= Octomitus ) problem: A preliminary report

THE INTESTINAL FLAGELLATE, Hexamita salmonis (Moore), was described in 1922 from trout in hatcheries throughout New York State. At first associated with the so-called whirling disease of brook trout ( Salvelinus fontinalis ), now believed to be a virus disease, Hexamita was subsequently held responsible for practically any otherwise unexplainable mortality in underyearling salmonids. Over the years, Hexamita , ostensibly H. salmonis , has been the most readily recognized parasite of juvenile salmonids.

Progressive Fish-Culturist↗
USGS1981

Estimation of alewife biomass in Lake Michigan, 1967-1978

The buildup of salmonid populations in Lake Michigan through annual stockings of hatchery-reared fish may become limited by the quantity of forage fish, mainly alewives Alosa pseudoharengus, available for food. As a part of a continuing examination of salmonid predator-prey relations in Lake Michigan, we traced changes in alewife biomass estimated from bottom-trawl surveys conducted in late October and early November 1967–1978. Weight of adult alewives trawled per 0.5 hectare of bottom (10-minute drag) at 16 depths along eight transects between 1973 and 1977 formed a skewed distribution: 72 of 464 drags caught no alewives; 89 drags caught less than 1 kg; and 2 drags caught more than 100 kg (maximum 159 kg). Analysis of variance in normalized catch per tow indicated highly significant differences between the main effects of years and depths, and highly significant differences in the interactions of years and transects, years and depths, and transects and depths. Five geographic and depth strata, formed by combining parts of transects wherein mean catch rate did not differ significantly, were the basis for calculating annual estimates of adult alewife biomass (with 90% confidence intervals). Estimated biomass of alewives (±90% confidence limits) in Lake Michigan proper (Green Bay and Grand Traverse Bay excluded) rose gradually from 46,000 (±9,000) t in 1967 to 114,000 (±17,000) t in 1973, declined to 45,000 (±8,000) t in 1977, and rose to 77,000 (±19,000) t in 1978.

Transactions of the American Fisheries Society↗
USGS1992

Predation by northern squawfish on live and dead juvenile Chinook salmon

Northern squafish Ptychocheilus oregonensis is a major predator of juvenile salmonids Oncorhynchus spp. migrating downstream through the Columbia River. High predation rates occur just below dams. If northern squafish selectively consume salmonids killed or injured during dam passage, previous estimates of predation mortality may be too high. We conducted laboratory experiments that indicate northern squafish prefer dead juvenile chinook salmon O. tshawytscha over live individuals. When equal numbers of dead and live chinook salmon were offered to northern squafish maintained on a natural photoperiod (15 h light: 9 h darkness), significantly more ( P < 0.05) dead than live fish were consumed, both in 1,400-L circular tanks and in an 11,300-L raceway (62% and 79% of prey consumed were dead, respectively). When dead and live juvenile chinook salmon were provided in proportions more similar to those below dams (20% dead, 80% live), northern squafish still selected for dead prey (36% of fish consumed were dead). In additional experiments, northern squafish were offered a proportion of 20% dead juvenile chinook salmon during 4-h periods of either light or darkness. The predators were much more selective for dead chinook salmon during bright light (88% of fish consumed were dead) than during darkness (31% were dead).

Transactions of the American Fisheries Society↗
USGS1997

Fish assemblages and environmental correlates in least-disturbed streams of the upper Snake River basin

Fish assemblages and environmental variables were evaluated from 37 least‐disturbed, 1st‐ through 6th‐order streams and springs in the upper Snake River basin, western USA. Data were collected as part of the efforts by the U.S. Geological Survey National Water Quality Assessment Program and the Idaho State University Stream Ecology Center to characterize aquatic biota and associated habitats in least‐disturbed coldwater streams. Geographically, the basin comprises four ecoregions. Environmental variables constituting various spatial scales, from watershed characteristics to instream habitat measures, were used to examine distribution patterns in fish assemblages. Nineteen fish species in the families Salmonidae, Cottidae, Cyprinidae, and Catostomidae were collected. Multivariate analyses showed high overlap in stream fish assemblages among the ecoregions. Major environmental factors determining species distributions in the basin were stream gradient, watershed size, conductivity, and percentage of the watershed covered by forest. Lowland streams (below 1,600 m in elevation), located mostly in the Snake River Basin/High Desert ecoregion, displayed different fish assemblages than upland streams (above 2,000 m elevation) in the Northern Rockies, Middle Rockies, and Northern Basin and Range ecoregions. For example, cottids were not found in streams above 2,000 m in elevation. In addition, distinct fish assemblages were found in tributaries upstream and downstream from the large waterfall, Shoshone Falls, on the Snake River. Fish metrics explaining most of the variation among sites included the total number of species, number of native species, number of salmonid species, percent introduced species, percent cottids, and percent salmonids. Springs also exhibited different habitat conditions and fish assemblages than streams. The data suggest that the evolutionary consequences of geographic features and fish species introductions transcend the importance of ecoregion boundaries on fish distributions in the upper Snake River basin.

Idaho, Oregon, Washington, Wyoming↗