USGS Science⌕ Search

SEARCH · USGS Science

Results for “Salmonid”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,027 records · Page 57Linked to original sources
USGS2014

A legacy of divergent fishery management regimes and the resilience of rainbow and cutthroat trout populations in Lake Crescent, Olympic National Park, Washington

As a means to increase visitation, early fisheries management in the National Park Service (NPS) promoted sport harvest and hatchery supplementation. Today, NPS management objectives focus on the preservation of native fish. We summarized management regimes of Olympic National Park's Lake Crescent, which included decades of liberal sport harvest and hatchery releases of 14.3 million salmonids. Notably, nonnative species failed to persist in the lake. Complementary analyses of annual redd counts (1989–2012) and genetics data delineated three sympatric trout (one rainbow; two cutthroat) populations that exhibited distinct spatial and temporal spawning patterns, variable emergence timings, and genetic distinctiveness. Allacustrine rainbow trout spawned in the lake outlet from January to May. Cutthroat trout spawned in the major inlet tributary (Barnes Creek) from February to June and in the outlet river (Lyre) from September to March, an unusual timing for coastal cutthroat trout. Redd counts for each species were initially low (rainbow = mean 89; range 37–159; cutthroat = mean 93; range 18–180), and significantly increased for rainbow trout (mean 306; range 254–352) after implementation of catch-and-release regulations. Rainbow and cutthroat trout reached maximum sizes of 10.4 kg and 5.4 kg, respectively, and are among the largest throughout their native ranges. Morphometric analyses revealed interspecific differences but no intraspecific differences between the two cutthroat populations. Genetic analyses identified three distinct populations and low levels (9–17%) of interspecific hybridization. Lake Crescent rainbow trout were genetically divergent from 24 nearby Oncorhynchus mykiss populations, and represented a unique evolutionary legacy worthy of protection. The indigenous and geographically isolated Lake Crescent trout populations were resilient to overharvest and potential interactions with introduced fish species.

Washington↗
USGS2020

Anadromous coastal cutthroat trout Oncorhynchus clarkii clarkii as a host for Argulus pugettensis (Crustacea, Branchiura): Parasite prevalence, intensity and distribution

Coastal cutthroat trout [ Oncorhynchus clarkii clarkii (Richardson, 1836)] from the marine waters of Puget Sound, WA, was documented as a new host for the ectoparasite Argulus pugettensis ( Dana, 1852 ). The prevalence of A. pugettensis was 66% (49 of 74) on cutthroat trout and 0% (0 of 55) on coho salmon [ O. kisutch (Walbaum, 1792)] collected during the winter of 2017/2018. Infestations occurred most frequently on the dorsal surface, with intensities ranging from 1 to 26 argulids per fish (mean intensity 3.94 ± 4.93 S.D.). In contrast, the prevalence of the common salmon louse [ Lepeophtheirus salmonis (Krøyer, 1837)] was 72% for cutthroat trout and 31% for coho salmon. Relative to other native salmonids, little is known regarding the status, ecology and threats for coastal cutthroat trout. New information reported here is a first step in understanding the relationship between this wild, native trout and infestations by parasitic sea lice and should be followed by future studies aimed to identify population level consequences.

Northwest Science↗
USGS2024

Spatial and temporal surveys of salmon environmental DNA (eDNA) in a Seattle urban creek

Seattle Public Utilities (SPU) has a history of conducting traditional fish surveys in urban streams of Seattle, Washington. Limited staff resources have reduced SPU's capacity to monitor fish, and environmental DNA (eDNA) was recognized as an alternative survey method that could potentially improve the efficiency and capacity of SPU-sponsored fish surveys. We performed spatiotemporal surveys of eDNA to assess occupancy and distribution of Chinook Salmon ( Oncorhynchus tshawytscha ), Coho Salmon ( O . kisutch ), and Coastal Cutthroat Trout ( O . clarkii clarkii ) in Thornton Creek, Seattle, between October 2018 and December 2020. Peak Chinook and Coho eDNA detections occurred in October and October–November, respectively, coinciding with expected adult return time. Chinook and Coho eDNA was detected in May at the time when juveniles outmigrate through the Lake Washington basin. Coastal Cutthroat Trout eDNA was widespread and detected at high rates across seasons, reflecting their ubiquitous distribution. Results from multiscale occupancy modeling suggested that distance upstream affected site-level occupancy probabilities for adult Chinook, but not Coho. Model results also suggested that the probability of Coho and Chinook eDNA occurring in water samples was affected by survey year. Finally, model results suggested that the probability of detecting Chinook eDNA in PCR technical replicates was affected by survey year and collection day but detection of Coho eDNA was only affected by collection day. This study indicates eDNA surveys are effective for assessing distribution and occupancy of salmonids in Seattle's urban streams. Integrating eDNA surveys into urban stream monitoring programs can help alleviate the burden of limited assets facing many resource managers.

Washington↗
USGS2025

Gas bubble trauma progression and mortality in sculpin, threespine stickleback, and Northern pikeminnow

We examined the progression of gas bubble trauma (GBT) and associated mortality in sculpin ( Cottus spp.), threespine stickleback ( Gasterosteus aculeatus ), and Northern pikeminnow ( Ptychocheilus oregonensis ) exposed to three levels of total dissolved gas (TDG; 120, 125, and 130% saturation) in laboratory experiments. Sculpin were most sensitive to elevated TDG followed by stickleback and then pikeminnow, which were least sensitive. This was evidenced by GBT and associated mortality progressing fastest in sculpin and slowest in pikeminnow. GBT incidence and severity increased through time at all TDG levels tested, but relationships between severity and exposure time were statistically weak or nonexistent. GBT mortality progressed more rapidly as TDG increased in all species. Regional criteria developed to rank GBT in salmonids did not fully capture the incidence and severity of GBT in the three nonsalmonids we examined. Rather, using criteria that considered all areas of the fish provided more accurate data. The lateral line, body, dorsal fin, and pectoral fins were common locations of GBT in sculpin whereas in stickleback and pikeminnow, GBT was most common on the head and body. The proximate cause of GBT-related death was bubbles in the gills and heart, but unlike in other species, bubbles in these organs appeared rapidly just before the point of death. Our findings provide some of the first information on TDG effects on these little-studied species.

Oregon, Washington↗
USGS2011

Adaptive management of bull trout populations in the Lemhi Basin

The bull trout Salvelinus confluentus , a stream-living salmonid distributed in drainages of the northwestern United States, is listed as threatened under the Endangered Species Act because of rangewide declines. One proposed recovery action is the reconnection of tributaries in the Lemhi Basin. Past water use policies in this core area disconnected headwater spawning sites from downstream habitat and have led to the loss of migratory life history forms. We developed an adaptive management framework to analyze which types of streams should be prioritized for reconnection under a proposed Habitat Conservation Plan. We developed a Stochastic Dynamic Program that identified optimal policies over time under four different assumptions about the nature of the migratory behavior and the effects of brook trout Salvelinus fontinalis on subpopulations of bull trout. In general, given the current state of the system and the uncertainties about the dynamics, the optimal policy would be to connect streams that are currently occupied by bull trout. We also estimated the value of information as the difference between absolute certainty about which of our four assumptions were correct, and a model averaged optimization assuming no knowledge. Overall there is little to be gained by learning about the dynamics of the system in its current state, although in other parts of the state space reducing uncertainties about the system would be very valuable. We also conducted a sensitivity analysis; the optimal decision at the current state does not change even when parameter values are changed up to 75% of the baseline values. Overall, the exercise demonstrates that it is possible to apply adaptive management principles to threatened and endangered species, but logistical and data availability constraints make detailed analyses difficult.

Lemhi River Basin↗
USGS2016

Growth, food consumption, and energy status of juvenile pallid sturgeon fed natural or artificial diets

Stocking of hatchery-raised fish is an important part of the pallid sturgeon Scaphirhynchus albus recovery program. In the wild, juvenile pallid sturgeon consume primarily aquatic insects, although little is known about specific dietary needs. In hatchery settings, pallid sturgeon are fed commercial diets that are formulated for salmonids. To compare food consumption, growth, and energy status of pallid sturgeon fed artificial or natural diets, we conducted a laboratory study using 24 juvenile pallid sturgeon (initial fork length 153–236 mm). Pallid sturgeon were fed a daily ration of either commercial pellets (1 mm, slow sinking; 45% protein, 19% fat) or chironomid larvae for 5 wk. Natural-fed pallid sturgeon exhibited a greater specific growth rate (2.12% d −1 ) than pellet-fed fish (0.06% d −1 ). Similarly, relative condition was greater for natural-fed sturgeon ( K n = 1.11) than that observed for pellet-fed fish ( K n = 0.87). In contrast, the hepatosomatic index was significantly higher in pellet-fed fish (2.5%), indicating a high lipid diet compared with natural-fed sturgeon (1.4%). Given the importance of natural diets to fish digestion and growth, it is suggested that a more holistic approach be applied in the development of a practical diet for pallid sturgeon that incorporates attributes of natural prey.

Journal of Fish and Wildlife Management↗
USGS2009

Warmwater and coldwater fish in two-story stranding waters

Two-story fisheries occur in lakes or reservoirs characterized by two distinct spatial strata, warmwater and coldwater. These strata develop as the system begins to warm in the spring or summer in response to solar radiation and then separate into an upper warmwater stratum (epilimnion, hereafter referred to as the upper stratum) and a lower coldwater stratum (hypolimnion, hereafter referred to as the lower stratum) separated by the thermocline, a zone of rapidly declining temperatures with depth (i.e., stratification; Figure 10.1). Each stratum or story is dominated by fish species with different physiological constraints, dietary preferences, and behavior. The original use of the term “two-story” described lentic systems in which the lower stratum was less than 21°C during summer and dominated by stocked salmonids, the upper stratum was dominated by sunfishes or perches, and attempts were made to simultaneously manage both strata as sport fisheries (e.g., Jones 1982). However, the terminology is now used more generally to describe any two-stratum system where a coldwater species dominates the lower stratum, often piscivores; a warmwater species dominates the upper stratum, often a planktivore or omnivore; and both contribute to the sport fishery. In general, the upper stratum is characterized by a large, relatively shallow, littoral zone where a diverse assemblage of fishes interact with the bottom, whereas the lower stratum is characterized as deep and pelagic with fewer fish species.

Book chapter↗
USGS2012

Design and performance of radio telemetry systems for assessing juvenile fish passage at three hydroelectric dams

Studies of the effects of hydroelectric dams on fish populations are common (Williams 2008). Dams block passage of migratory and resident fish, alter habitats from free-flowing to lacustrine, and can alter water temperatures both upstream and downstream. At some dams, structures or operations are modified to reduce their effects on fish populations. In these cases, it is recommended that a series of studies be conducted before and after the alterations to help assess the effectiveness of the actions. We will describe three studies at hydroelectric dams on the Columbia and Snake rivers in the Pacific Northwest of the United States prompted by a need to reduce their effects on fishes, primarily salmonids, listed under the Endangered Species Act (ESA 1973). Hydroelectric development on the Columbia and Snake rivers occurred chiefly between the early 1930s and the late 1970s. Fish originating in the upper portions of the Columbia and Snake rivers must pass as many as eight dams on these rivers during their seaward migration and again on their trip back to their natal waters. Small changes in passage survival at each dam can be important, due to the multiplicative effects of the series of dams. For example, if downstream passage survival at each of eight dams and reservoirs was 90% and it was increased by only 3% per dam, the numbers of fish surviving through the entire hydro system would increase from 43% to 56%. Thus, precisely measuring small changes in passage survival are important to the overall program. This has been achieved by designing efficient telemetry systems and releasing large numbers of tagged fish.

Book chapter↗
USGS2012

Developing a quality assurance plan for telemetry studies: A necessary management tool for an effective study

Telemetry has been used to answer various questions associated with research, management, and monitoring programs and to monitor animal behavior and population dynamics throughout the world. Many telemetry projects have been developed to study the passage, behavior, and survival of migrating adult and juvenile salmonids at hydroelectric projects on the mainstem Columbia and Snake rivers (Skalski et al. 2001a, 2001b; Skalski et al. 2002; Keefer et al. 2004; Goniea et al. 2006; Plumb et al. 2006). Telemetry based field evaluations of the survival of salmon through hydroelectric projects are costly because of the technology (tags, telemetry systems, infrastructure, etc.) and personnel required to conduct the evaluations. Given the cost of implementing these projects, and the financial and conservation implications of the decisions made from the research results (e.g., forgone electricity production and conservation of threatened and endangered animals), ensuring quality data are collected by documenting all procedures, training, data checks, and that sound protocols and quality assurance and control procedures are in place is paramount. Telemetry studies can pose unique data collection, processing, and analysis challenges. For instance, inferences about entire populations of animals are made from study animals that are captured, held, and tagged at disparate locations. Consequently great care must be taken to ensure that any potential biases that could arise from field procedures must be minimized (Peven et al. 2005). Interrogations of released study animals are remotely conducted by telemetry systems throughout the study area. The continuous recording of telemetry systems can result in large numbers of detections over a short time frame and the potential for false positive detections from records that are weak or erroneous. Thus, there is the potential to generate large data sets (many thousands of lines) that require significant postprocessing. Data reduction can be done using software or programming code within a software package or manually to discern noise from valid data and pull out the pertinent information for analysis. In either case, consistent well-documented procedures need to be in place to ensure quality results and allow for repeatability of study methods.

Book chapter↗
USGS2026

A genomic tool to tackle cryptic diversity demonstrates the potential for off-target use of GT-seq panels

A comprehensive understanding of life history is vital to successful species conservation and management. When different life history stages are accompanied by considerable morphological or cryptic variation, such as the egg and larval phases exhibited by most fishes, genomic tools are essential for identifying species so that early-life ecology questions can be studied. Genotyping-in-thousands by sequencing (GT-seq) has recently emerged as a targeted and efficient approach for species identification. We leveraged existing genomic and transcriptomic data to develop a GT-seq panel capable of differentiating the members of the Coregonus artedi complex, a radiation of salmonids in the Laurentian Great Lakes whose members are indistinguishable with mitochondrial DNA barcoding loci and are the focus of bi-national conservation initiatives. Our panel of 494 loci was able to assign fishes in the C. artedi complex to species and lake. We examined cross-amplification in other coregonines with overlapping distributions and found that congeneric Lake Whitefish ( C. clupeaformis ) cross-amplified at 94% of loci and confamilial Round and Pygmy Whitefish ( Prosopium spp.) cross-amplified at 42% and 38% of loci, respectively. We adapted bioinformatic probes to account for Prosopium -specific variants including 22 new SNPs and developed a whitelist of 428 SNPs capable of distinguishing these whitefishes. Finally, we demonstrated performance by identifying 3,066 coregonine larvae and juveniles collected in spring 2019-2021 from Lake Superior. These results hold promise for future insights into the species-specific ecology of early life coregonines and demonstrate the flexibility of GT-seq panels, which may cross-amplify hundreds of informative genome-wide loci in related taxa.

BioRxiv↗
USGS2026

A Lake Charr pangenome reveals highly conserved Ohnologs as drivers of phenotypic diversity

Whole-genome duplication (WGD) is hypothesized to spur evolutionary diversification by producing genome-wide duplicate gene sets (Ohnologs) that are initially functionally redundant but can diverge markedly as the effects of relaxed selection accumulate over time. However, the underlying mechanisms remain unclear, in part because genomic studies often reconstruct Ohnolog evolution over millions of years, during which subsequent mutations can obscure deep-time signals. Investigating the relationship between Ohnolog evolution and diversification on a contemporary timescale offers clearer insights. We explore this relationship in Lake Charr ( Salvelinus namaycush ), where ∼10% of genes are retained highly conserved polyploid duplicates following the Salmonid-Specific Fourth Round WGD. Using 31 chromosome-level assemblies of Lake Charr from morphologically and ecologically diverse populations, joined into a pangenome graph, we characterized 189,555 structural variants (SVs) that were significantly less likely to affect genes retained as sequence-conserved Ohnolog pairs, nuancing the hypothesis that gene redundancy, relaxed selection, and functional diversification are intertwined. However, we found that SVs affecting such conserved Ohnologs may be potent drivers of adaptive evolution. Notably, we identified a putative 938-Kb interchromosomal translocation containing 25 genes with highly conserved Ohnologs in a paralogous (but untranslocated) genomic block. This putative translocation appears to have facilitated Ohnolog divergence in ankrd11 and hp , genes putatively linked to craniofacial and lipid metabolic diversity in sympatric Lake Superior morphs. This research reveals that conserved Ohnologs previously presumed to be redundant remain a reservoir for adaptive change.

BioRxiv↗
USGS1994

In vitro growth of the bacterial kidney disease organism Renibacterium salmoninarum on a nonserum, noncharcoal-based "homospecies-metabolite" medium

Laboratory and field trials were conducted to evaluate in vitro growth of Renibacterium salmoninarum in media without serum or charcoal. Growth of this bacterium, the cause of bacterial kidney disease (BKD) in salmonids, is accelerated by addition of a growth enhancing “metabolite” of unknown composition to KDM2 medium, the medium commonly used for isolation of R. salmoninarum . KDM2 medium supplemented with greater than 1% (v/v) metabolite enhanced growth even without addition of either serum or charcoal. Medium containing 5% metabolite (denoted Five-M) allowed optimal growth in laboratory studies and was further evaluated as a primary plating medium for recovery of the bacterium isolated from chinook salmon ( Oncorhynchus tshawytscha ) exhibiting clinical BKD. Recovery rates of R. salmoninarum using Five-M medium were 4% and 36% higher, respectively, than comparable rates using a serum-based medium for the two salmon populations evaluated. Five-M medium is an effective, inexpensive alternative to serum-based or charcoal-based media.

Journal of Wildlife Diseases↗
USGS2004

Organochlorine pesticides and thiamine in eggs of largemouth bass and American alligators and their relationship with early life-stage mortality

Thiamine deficiency has been linked to early mortality syndrome in salmonids in the Great Lakes. This study was conducted to compare thiamine concentrations in American alligators ( Alligator mississippiensis ) and Florida largemouth bass ( Micropterus salmoides floridanus ) eggs from sites with high embryo mortality and high exposure to organochlorine pesticides (OCPs) (Lakes Apopka and Griffin, and Emeralda Marsh, Florida, USA) to those from sites that have historically exhibited low embryo mortality and low OCPs (Lakes Woodruff and Orange, Florida). During June-July 2000, 20 alligator clutches were collected from these sites, artificially incubated, and monitored for embryo mortality. Thiamine and OCPs were measured in one egg/clutch. During February 2002, 10 adult female bass were collected from Emeralda Marsh and Lake Woodruff and mature ovaries analyzed for thiamine and OCP concentrations. Although ovaries from the Emeralda Marsh bass contained almost 1,000-fold more OCPs compared with the reference site, Lake Woodruff, there were no differences in thiamine concentrations between sites (11,710 vs. 11,857 pmol/g). In contrast, alligator eggs from the reference site had five times the amount of thiamine compared with the contaminated sites (3,123 vs. 617 pmol/g). Similarly, clutches with > 55% hatch rates had significantly higher concentrations of thiamine compared with clutches with <54% hatch rates (1,119 vs. 201 pmol/g). These results suggest that thiamine deficiency might be playing an important role in alligator embryo survival but not in reproductive failure and recruitment of largemouth bass. The cause(s) of this thiamine deficiency are unknown but might be related to differences in the nutritional value of prey items across the sites studied and/or to the presence of high concentration of contaminants in eggs.

Florida↗
USGS1970

Immunization of fishes: A review

Immune response in fishes, which are ectothermic animals, depends on temperature. The optimum response is at the optimum temperature for the species. It is, however, slower in coldwater fishes, such as salmonids, and faster in warmwater fishes. Serum of fishes contains proteins very similar, but not identical, with those of mammals. Immune bodies are contained in gamma, beta, and alpha globulins. Gamma globulin is absent in some fishes. Fishes can be effectively immunized by injection of antigens, however, this is not a practical method. For this reason oral immunization has been attempted repeatedly but the effectiveness is variable.

Journal of Wildlife Diseases↗
USGS1929

Coregonid fishes of the Great Lakes

Wherever they occur, the coregonids, like the salmonids, are important food fishes; but probably nowhere do they attain so much importance in the fisheries as in the region of the Great Lakes. This investigation has as its object the determination of the forms of coregonid fishes that occur in these lakes and the collection of data on their natural history. In addition to its economic significance, the problem is one of scientific interest. It concerns not merely the ecology of the Great Lakes species but it involves also the ultimate consideration of their origin and evolution and of their relationships with one another and with the coregonids of Asia and Europe, as well as with those of other parts of America.

Bulletin of the United States Bureau of Fisheries↗
USGS1994

Life-history organization of Yellowstone cutthroat trout (Oncorhynchus clarki bouvieri) in Yellowstone Lake

Life-history organization of the cutthroat trout (Oncorhynchus clarki) may be viewed at various levels, including species, subspecies, metapopulation, population, or individual. Each level varies in spatial scale and temporal persistence, and components at each level continually change with changes in environment. Cutthroat trout are widely distributed throughout the western United States, occurring in such diverse environments as coastal rivers of the Pacific Northwest and interior streams of the Great Basin. During its evolution the species has organized into 14 subspecies with many different life-history characteristics and habitat requirements. Within subspecies, organization is equally complex. For example, life-history traits, such as average size and age, migration strategy, and migration timing, vary among individual spawning populations of Yellowstone cutthroat trout (Oncorhynchus clarki bouvieri) in tributary streams of Yellowstone Lake. Understanding the effects of human perturbations on life-history organization is critical for management of the cutthroat trout and other polytypic salmonid species. Loss of diversity at any hierarchical level jeopardizes the long-term ability of the species to adapt to changing environments, and it may also lead to increased fluctuations in abundance and yield and increase the risk of extinction.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS1994

Diet affects body composition of chinook salmon

Hatchery-reared salmonids often contain proportionally greater amounts of body lipid (storage fat) and proportionally lesser amounts of body protein (muscle) and ash (bone) than do their wild counterparts of equal size. The effect of body composition on postrelease survival and subsequent return of mature adults is presently unknown. High lipid deposits may benefit the fish by providing reserve energy during adaptation to the wild, or may hinder the fish by delaying transformation and downstream migration. Compositional differences between hatchery and wild fish may be attributed to various factors, including altered environment, feeding rate, level of exercise, or diet. Diets presently fed to chinook salmon (Oncorhynchus tshawytscha) fingerlings are formulated to produce maximum growth, and they contain higher levels of lipid in proportion to protein than would be found in natural prey. Our objective was to determine what relation exists between dietary protein level and body composition in cultured chinook salmon.

Research Information Bulletin↗
USGS2002

Invasive plant species: Inventory, mapping, and monitoring - A national strategy

America is under siege by invasive species of plants and animals, and by diseases. The current environmental, economic, and health-related costs of invasive species could exceed $138 billion per year-more than all other natural disasters combined. Notorious examples include West Nile virus, Dutch elm disease, chestnut blight, and purple loose- strife in the Northeast; kudzu, Brazilian peppertree, water hyacinth, nutria, and fire ants in the Southeast; zebra mussels, leafy spurge, and Asian long-horn beetles in the Midwest; salt cedar, Russian olive, and Africanized bees in the Southwest; yellow star thistle, European wild oats, oak wilt disease, Asian clams, and white pine blister rust in California; cheatgrass, various knapweeds, and thistles in the Great Basin; whirling disease of salmonids in the Northwest; hundreds of invasive species from microbes to mammals in Hawaii; and the brown tree snake in Guam. Thousands of species from other countries are introduced intentionally or accidentally into the United States each year. Based on past experience, 10-15 percent can be expected to establish free-living populations and about 1 percent can be expected to cause significant impacts to ecosystems, native species, economic productivity, and (or) human health.

Information and Technology Report↗