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58 results for “Steelhead”
Lower American River steelhead and Chinook stranding surveys, California, 2016 - 2025
Steelhead stranding surveys have been conducted on the Lower American River (LAR) for the years 2016-2025. Reclamation’s mission is to manage, develop and protect water and related resources in an environmentally and economically sound manner in the interest of the American people. In the National Marine Fisheries Service (NMFS) most recent biological opinion (2009), the presence of dams was identified as the most influential stressor to steelhead on the American River because it blocks passage to historic spawning and rearing habitat. Thus, Reclamation is required to monitor the effects of flow regulation by dams on the steelhead life stages present in the river system. Congruently, Reclamation has committed to significant restoration actions including salmonid spawning and rearing habitat rehabilitation on the Lower American River, which also require accurate and robust monitoring. These surveys support the mission and monitoring requirements of Reclamation by collecting the stranding data required to effectively conduct analyses of the effects of regulating Folsom and Nimbus dams on this federally listed species’ critical life stage development and support operational decision making.
Distribution and habitat use of juvenile steelhead and other fishes of the lower Feather River
Understanding how fish presence is related to habitat features is useful in restoration planning and monitoring as better information about how fish use habitat may lead to more impactful restoration projects. The California Department of Water Resources (DWR), conducted a two-year study of microhabitat and mesohabitat in Feather River. The goal of this study was to identify relationships between habitat conditions (depth, substrate, velocity, and cover) and where juvenile Chinook salmon and steelhead occur. Snorkel surveys were conducted monthly March through August in 2001 and 2002 across 29 different sites, which were selected at random (13 in Low Flow Channel, and 16 in High Flow Channel). Each sampling section covered an area 25 meters long by 4 meters wide, running parallel to riverbank. These data were published to support the Healthy Rivers and Landscapes Science Program.
Lower American River steelhead spawning surveys (Chinook and lamprey data included), California, 2002 to 2025
Steelhead spawning surveys have been conducted on the Lower American River (LAR) for the years 2002-2005, 2007, and 2009-2025. These surveys in conjunction with annual escapement estimates to Nimbus Fish Hatchery, are used to provide a yearly index of in-river and over all spawning abundance. Reclamation’s mission is to manage, develop and protect water and related resources in an environmentally and economically sound manner in the interest of the American people. In the National Marine Fisheries Service (NMFS) most recent biological opinion (2009), the presence of dams was identified as the most influential stressor to steelhead on the American River because it blocks passage to historic spawning and rearing habitat. Thus, Reclamation is required to monitor the effects of flow regulation by dams on the steelhead life stages present in the river system. Congruently, Reclamation has committed to significant restoration actions including salmonid spawning and rearing habitat rehabilitation on the Lower American River, which also require accurate and robust monitoring. These surveys support the mission and monitoring requirements of Reclamation by collecting the spawning data required to effectively conduct analyses of the effects of regulating Folsom and Nimbus dams on this federally listed species’ critical life stage development and support operational decision making.
Stanislaus River Steelhead Life Cycle Monitoring Program
The Stanislaus River Steelhead Life Cycle Monitoring Program is an ongoing survey starting in 2021 that aims to estimate the amount of steelhead (Onocorhynchus mykiss) present in the Stanislaus River by recording steelhead and redds observed. In addition to estimating the amount of steelhead, the survey aims to collect data relevant to steelhead spawning, documenting environmental conditions such as temperature and flow, and recording other fish activity present.
Hydrodynamic modeling data for Synthesis of Juvenile Steelhead Responses to Hydrodynamic Conditions in the Sacramento-San Joaquin Delta
This data release includes the output variables extracted from the UnTRIM Bay-Delta hydrodynamic model (hydrodynamic model) for use in evaluating the effects of hydrodynamics on the behavior of acoustically-tagged juvenile steelhead in the Sacramento-San Joaquin Delta. Work was funded by Proposition 1 and completed by Anchor QEA, LLC, and U.S. Geological Survey for the State Water Contractors under a Proposition 1 Grant (Evaluating Juvenile Salmonid Behavioral Responses to Hydrodynamic Conditions in the Sacramento-San Joaquin Delta), contracted by Delta Stewardship Council. Not all the hydrodynamic model output variables in the output provided with this memorandum were used in the final fish models used to analyze steelhead responses. Model output for additional variables and locations were included for completeness and to make these output files more broadly useful to researchers interested in other locations or variables in the Sacramento-San Joaquin Delta. Hydrodynamic model simulations were conducted for 2011, 2012, 2013, 2014, 2015, and 2016, with hydrodynamic model output variables provided at the same locations for each period simulated. The model simulation for each year spanned the full period of steelhead detections in the telemetry data collected during that year.
South Bay Salt Pond Restoration Project – Phase-1 (2014-2017) Steelhead Outmigration and Entrainment in the A8 Complex.
The South Bay Salt Pond Restoration Project, the largest wetland restoration project in the western United States, is conducting an adaptive management experiment to restore tidal flows to the tidally muted pond A8 complex. The A8 pond complex is a series of interconnected ponds (A8, A7, and A5) located at the interface of the Guadalupe River with Alviso Marsh in Lower South San Francisco Bay that has had a legacy of mercury contamination from cinnabar open-pit mining in the Guadalupe River watershed. As a result, restoration of salt pond habitats in the Alviso Marsh has taken an adaptive management approach whereby the A8 complex was constructed with operable tide gates to facilitate a stepped approach to opening the pond to tidal action. Fish populations, water and sediment were monitored for mercury contamination before and after opening the tide gates and data was used to inform further restoration actions in the A8 complex. However, Central Coast Steelhead Trout, a threatened species inhabit the streams that enter into the Alviso Marsh and the A8 complex, causing management concern for entrainment of outmigration smolts into the A8 complex. In this study, UC Davis conducted back-pack electrofishing in the streams that enter the Alviso Marsh during the late-fall winter of 2013 and 2014. The primary objective of the electrofishing was to collect Steelhead Trout juveniles prior to outmigration to tag with Passive Integrated Transponder (PIT) tags for detection of outmigration and potential entrainment into the A8 complex. In addition to the capture and tagging of Steelhead Trout, we collected data on water quality and catch of non-target fishes. To detect outmigration Steelhead Trout we installed a RFID stream antennae in the lower reaches of the Guadalupe River and to detect entrainment into the A8 complex we installed RFID antennas on the A8 water control structure. A total of 106 Steelhead Trout were captured during the two years of stream electrofishing, and 1
Data on aquifer regeneration and steelhead response in the Carmel River, California
<p>Original datasets and model code used in the paper "Focused aquifer regeneration produced outsized gains for a threatened fish in a populated, dryland watershed," by David A. Boughton and Haley A. Ohms</p> <p> </p>
Data from: Distinct patterns of inheritance shape life-history traits in steelhead trout
<p>Life-history variation is the raw material of adaptation, and understanding its genetic and environmental underpinning is key to designing effective conservation strategies. We used large-scale genetic pedigree reconstruction of anadromous steelhead trout (<em>Oncorhynchus</em> <em>mykiss</em>) from the Russian River, California, USA to elucidate sex-specific patterns of life-history traits and their heritability. SNP data from adults returning from sea over a 14-year period were used to identify 13,474 parent-offspring trios. These pedigrees were used to determine age structure, size distributions, and family sizes for these fish, as well as to estimate the heritability of two key life-history traits, spawn date and age at maturity (first reproduction). Spawn date was highly heritable (h<sup>2</sup> = 0.73) and had a cross-sex genetic correlation near unity. We provide the first estimate of heritability for age at maturity in ocean-going fish from this species and found it to be high heritable (h<sup>2</sup> from 0.29–0.62, depending upon sex and calculation), with a much lower genetic correlation across sexes. We also evaluated genotypes at a migration-associated inversion polymorphism and found sex-specific correlations with age at maturity. The significant heritability of these two key reproductive traits in these imperiled fish, and their patterns of inheritance in the two sexes, is consistent with predictions of both natural and sexually antagonistic selection (sexes experience opposing selection pressures). This emphasizes the importance of anthropogenic factors, including hatchery practices and ecosystem modifications, in shaping the fitness of this species, thus providing important guidance for management and conservation efforts.</p>
Data from: Distinct patterns of inheritance shape life-history traits in steelhead trout
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Genetic parentage reveals the (un)natural history of Central Valley Hatchery steelhead
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Quantifying component mortality estimates of out-migrating juvenile steelhead (<em>Oncorhynchus mykiss</em>)
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Steelhead passage at a mid-sized dam in California assessed using PIT-tags
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Genotype and phenotype data for Columbia River steelhead.
<p>As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age-at-maturity in steelhead (<i>Oncorhynchus mykiss</i>) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead (R<sup>2</sup> 0.51 vs 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R<sup>2</sup> = 0.139-0.170; females R<sup>2</sup> = 0.096-0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management.</p> <p> </p>
Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes
<p>Multiple evolutionary processes influence genome‐wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (<em>Oncorhynchus mykiss</em>) populations that have declined in abundance due to anthropogenic impacts. Whole‐genome resequencing of 74 populations of steelhead revealed genome‐wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.</p>
Data from: Changes to climate patterns significantly alter the growth of juvenile Chinook and steelhead in the Salmon River, Idaho
<p>dataset used for: Changes to climate patterns significantly alter the growth of juvenile Chinook and steelhead in the Salmon River, Idaho</p>
Data from: Limited, asymmetric hybridization between coastal cutthroat trout and steelhead in a Northern California river
<p>Hybridization between coastal cutthroat trout (<em>Oncorhynchus clarkii clarkii</em>) and steelhead (<em>O. mykiss</em>) was assessed in the Smith River, California. Individuals were categorized as pure or as one of 10 hybrid classes using 30 'diagnostic' single-nucleotide polymorphisms positioned on 26 separate chromosomes. Most of the individuals examined (n = 876), were pure coastal cutthroat trout (n = 634) or pure steelhead (n = 213), and 29 individuals were identified as having hybrid ancestry. Among hybrids, first generation hybrids (n = 15) and coastal cutthroat trout backcrosses (n = 12) were the most common. No individuals were identified as backcrosses to SH, suggesting the presence of genetic or behavioral mechanisms constraining such backcrosses, or the growth and survival of their progeny. Mitochondrial DNA of 14 of 15 F1 hybrids was of steelhead origin, suggesting that hybridization was driven primarily by sneak-mating of male coastal cutthroat trout with female steelhead. Evaluation of classical phenotypic characters for coastal cutthroat trout and steelhead (i.e., jaw slash, maxillary length, and hyoid teeth) were not reliable by themselves for identification of either pure parental fish or hybrids. In contrast, analysis with geometric morphometrics revealed distinctive body shapes for pure coastal cutthroat trout and steelhead, and the combination of classical traits and geometric morphology was mostly accurate in distinguishing them. However, first generation hybrids and backcrosses overlapped completely with parental types, highlighting challenges in hybrid identification using phenotypic traits.</p>
Genetic monitoring of steelhead in the Klickitat River to estimate productivity, straying, and migration timing
<div> <p>Salmonids with complex life history variation present challenges for conservation management, but genetic approaches alongside fisheries monitoring can address questions regarding viability of natural populations. We genotyped adult (n=3,108) and juvenile (n=2,624) samples of anadromous <em>Oncorhynchus</em> <em>mykiss</em> that were collected in the Klickitat River, WA, USA at traps in the lower drainage to examine tributary level productivity, straying from outside sources and variation in adult migration timing. Genetic assignment of steelhead from this system indicated that the majority were produced within or near tributaries of the middle Klickitat River (juvenile mean = 72.8%; adult mean = 87.3%). Analyses with parentage-based tagging identified that most hatchery-origin adults were assigned to the Skamania Hatchery (80.8%) as expected since this has been the release stock for decades within the Klickitat River drainage. Hatchery-origin adults were also identified from programs operating outside the Klickitat River, which were primarily strays from Snake River hatcheries. Most natural-origin steelhead were assigned to the Klickitat River, but there were also natural-origin fish identified as strays from other regions of the Columbia River (22.3% of natural returns). We also examined genes known to be associated with migration timing in adult steelhead observed at the trap and observed a strong relationship between migration date and alleles for early and late migration, but individual outliers were detected across seasons. Our results indicate that genetic variation of steelhead in the Klickitat River has been influenced by hatchery programs as well as natural-origin straying from other sub-basins, but genetic diversity remains high throughout the sub-basin, and both early and late migration alleles are maintained. The genetic diversity present in Klickitat River steelhead may enable this Endangered Species Act listed (threatened) species to better adapt to stochastic environmental conditions compared to less diverse populations. </p> </div>
Genotype data for: Demographic and genetic consequences of a steelhead supplementation program
<p>Supplementation of naturally-spawning populations by the addition of hatchery-spawned individuals is commonly conducted for recovery of threatened and endangered populations and to support harvest opportunities. We present an analysis of steelhead, the anadromous form of Rainbow Trout (<em>Oncorhynchus</em> <em>mykiss</em>), returning to an integrated supplemented population in Southwest Washington over the course of 15 years. The goal of the supplementation program was to evaluate whether use of a juvenile captive broodstock and an integrated paradigm could be used to increase adult returns while avoiding negative genetic impacts to the population. Estimates of relative reproductive success (RRS) for fish spawned in the hatchery ranged from 2.4 for hatchery-origin females to 6.4 for natural-origin males, indicating that fish spawned in the hatchery produced more returning adult progeny than did fish allowed to spawn in the natural environment. We observed a slight reduction in reproductive success (RS) for hatchery-origin (relative to natural-origin) fish when spawning in the natural environment, but the difference was non-significant for males and marginally significant for females. In contrast to the relatively weak relationship between RS and origin (male P = 0.347, η<sup>2</sup> = 0.008; female P = 0.066, η<sup>2</sup> = 0.037), we observed a strong relationship between RS and return year (male P < 0.001, η<sup>2</sup> = 0.896; female P < 0.001, η<sup>2</sup> = 0.867) (i.e., hatchery- and natural-origin fish did well or poorly together each year). Hatchery-origin fish exhibited reduced genetic diversity, as well as evidence of increased temporal population structure among hatchery fish. We suspect the latter is an artifact of cultural practices that reduce diversity in age at smoltification. We conclude that the program was successful in achieving an increase in adult return, but not in avoiding negative genetic effects on the population, and that any lasting impacts of supplementation remain to be determined.</p>
Data from: Limited, asymmetric hybridization between coastal cutthroat trout and steelhead in a Northern California river
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Genotype and phenotype data for Columbia River steelhead.
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