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72 results for “Columbia River”
Columbia River spatial water chemistry
We mapped surface water chemistry along a ~600 km segment of the Columbia River. We used a sensor-based and boat-mounted sensing platform to continuously measure underway water chemistry. Measurements were linked with global positioning systems (GPS) to create maps of surface water chemistry. Data were collected over 6 days in July 2018 and include a single longitudinal survey of the Columbia River. Data have been provided in three formats (raw, hydraulic-corrected, and tau-corrected). Additionally, we archive laboratory chemistry data from water samples collected during the project. Sites include a range of main channel, backwaters, and tributaries. Water chemistry samples were analyzed at the North Temperate Lakes - Long Term Ecological Research facility and linked with underway sensor measurements.
Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams
<p>DNA were derived from fin tissue samples taken from individual trout captured from Little Jacks Creek, Big Jacks Creek , and Duncan Creek of the Owyhee mountains and Keithly Creek and Upper Mann Creek in the Hitt mountains of Western Idaho, United States. Fin tissues were collected from individual trout from each stream during monthly sampling events in June through October 2020. </p> <p><em>DNA Extraction:</em> Extraction of DNA from caudal fin tissues were performed using Quick-DNA Miniprep Plus purification kits (Zymo Research Inc.©). Small sections of fin tissue (≤ 25 mg) were collected from each sample. This was mixed with a digesting solution comprised of ultra-pure water, solid tissue buffer (Zymo Research Inc.©) and proteinase K. All tissues were digested in sealed microcentrifuge tubes for at minimum 3 h at 55°C in a water bath. We then aliquoted 100 µL of digestion supernatant and combined with 200 µL of genomic binding buffer (Zymo Research Inc.©). DNA was eluted in 50, 75, and 100 µL of elution buffer to determine which volume provided sufficient DNA concentration for genotyping. After it was determined all quantities produced suitable concentrations, going forward, 50 µL of elution buffer used.</p> <p><em>Genotyping:</em> Following extraction, genotyping-in-thousands sequencing took place at the Hagerman National Fish Hatchery’s genetics research facility with the assistance of the Columbia River Intertribal Fish Commission (CRTFC). Genotyping protocols were as described in Campbell et al. (2015) and summarized below. First, samples were prepared for amplification via PCR by combining DNA extracts with a Qiagen Plus multiplex master mix and a species-specific pooled primer mix. This step added the Illumina sequencing primer sites to amplicons. Following the creation of the PCR cocktail, thermocycling was conducted for amplification. Amplified samples were then diluted 20-fold. Diluted samples were transferred to new 96-well PCR plates where two genetic indexes and barcodes provides a unique set of tagging primers to each well and plate. Tagged plates then underwent a second PCR step. After the second PCR, all DNA were transferred to Charm Biotech normalization plates where DNA was bound to wells, washed, and finally eluted. After normalization, all DNA was pooled together and a purification step using magnetized beads in two steps to selectively remove fragments of DNA that are both too large and too small for sequencing. Following purification, each plate was quantified via qPCR using Life Technologies QuantStudio 6 Flex Instrument (Life Technologies). Finally, sequencing was performed using an Illumina HiSeq 1500 instrument.</p> <p><strong>Ancillary peer-reviewed manuscripts:</strong><br> <em>Genotyping protocols</em><br> Campbell NR, Harmon SA, Narum SR. 2015. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing. Mol Ecol Resour, 15: 855-867. https://doi.org/10.1111/1755-0998.12357<br> <em>SNP loci reference</em><br> Collins EE, Hargrove JS, Delomas TA, Narum SR. 2020. Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin. Ecology and Evolution, 10(17): 9486-9502. https://doi.org/10.1002/ece3.6641 </p> <p><strong>Data Use</strong>:<br> <em>License</em>: <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> <br> <em>Recommended Citation</em>: Wooding AP, Narum SR, Pradhan DS. 2022. Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams (0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7055582</p> <p>Funding for this project is provided by US National Science Foundation and Idaho EPSCoR through award: OIA-1757324 </p>
Dataset from University of Idaho 2004, master's thesis [Littoral ecology of epilithic algae in the Rocky Reach Pool, Mid-Columbia River (Washington State) - The effects of reservoir fluctuations.]
(Abstract from thesis) Epilithic algae, water column physical/chemical properties, and sediments were examined in the impounded Mid-Columbia River including the Rocky Reach Reservoir. Primary objectives included determination of the effects reservoir drawdown has on epilithic algae and potential nutrient enrichment via sediment. Epilithic algae were analyzed by pigment concentration, gravimetrically, and species composition. Reservoir elevation fluctuated at higher rates at tailrace sites (0.41-0.25 m/hr) compared to the forebay site (0.06-0.08 m/hr). Littoral exposure times were also greater at tailrace sites (mean of 8 hrs compared to 0 hr at the forebay site). Mean epilithic algae monochromatic chlorophyll a over all sampling periods at mainstem sites was 76.7 ± 4.8 mg/m2 (95 % C.I.). Epilithic algae monochromatic chlorophyll a in the zone of water fluctuation (0-1 m) was less at Wells tailrace (38.8 mg/m2) compared to Rocky Reach forebay (141.3 mg/m2) during summer, 2000 and 2001. Mean epilithic biofilm ash-free oven-dry weight over all sampling periods at mainstem sites was 25.6 ± 1.5 g/m2 (95 % C.I.). Mean autotrophic index across all mainstem locations was 439 indicating a large heterotrophic component within the epilithic biofilms. Epilithic algae communities were dominated by diatoms (50.2 %) and cyanobacteria (35.9 %), with some green algae (13.8 %). Canonical correlation analysis indicated that temperature, depth, site, and the water elevation change rate were important controllers of epilithic algae chlorophyll pigments. Mean textural characteristics of dredged sediment were 51.1 % sand, 43.2 % silt, and 5.7 % clay. Mean organic matter content in this sediment was 4.1 %. The mean seston sedimentation rate across mainstem locations was 11.3 g m-2 d-1 and organic matter comprised 14.7 % of the material collected from the water column.
Columbia River headwaters - hydroclimate and glacier change, 1977-2017
<p>These data files were used in the production of a manuscript titled "Detecting the effects of sustained glacier wastage on streamflow in variably glacierized catchments" by R.D. Moore, B. Pelto, B. Menounos and D. Hutchinson.</p> <p>cb_shapes - polygons of catchment boundaries for the catchments included in the analysis</p> <p>cq.csv - streamflow and climatic data used in regression and trend analyses within the script "cbt_aug_flow_analysis.r"</p> <p>good_stn.csv - contains station IDs for Water Survey of Canada stations that met selection criteria</p> <p>stn_info.csv - catchment characteristics for Water Survey of Canada stations included in the analysis</p> <p>cbt_metadata.xlsx - full metadata for catchments used in the analysis</p> <p>*.r - R scripts used to conduct analyses and generate figures</p> <p> </p>
Bacteria and archaea of the Columbia and Willamette Rivers, 16S rRNA gene amplicon library metadata
<p>Bacterial and archaeal communities in the Columbia and Willamette Rivers in the Portland, OR, USA, region were characterized by 16S rRNA gene amplicon sequencing as part of the Lewis & Clark College spring 2022 Microbial Ecology course. Whole-water (>0.2 µm) samples were collected from: the Willamette River; the Columbia River above the confluence with the Willamette; and the Columbia River just downstream of the confluence with the Willamette.</p> <p>This dataset provides additional metadata to supplement the DNA sequences archived with the NCBI SRA at <a href="https://www.ncbi.nlm.nih.gov/sra/PRJNA865380">https://www.ncbi.nlm.nih.gov/sra/PRJNA865380</a></p>
Figure 7 in Mechanism of northern pike invasion in the Columbia River Basin
Figure 7. Heat map showing probability of assignment for 77 individuals sampled from Lake Roosevelt to each population sampled in this study. Potential source populations within the Clark Fork River basin, Coeur d'Alene River basin and recently invaded areas are listed in an upstream to downstream order. While many individuals show an elevated assignment probability to Medicine-Cave Lakes (Coeur d'Alene River basin), 71 of the 77 fish had the highest probability of assignment to populations in the recently invaded waterbodies.
Figure 5 in Mechanism of northern pike invasion in the Columbia River Basin
Figure 5. Heat map showing probability of assignment for 145 individuals sampled from recently invaded areas to potential source populations in the Clark Fork and Coeur d'Alene River basins. Recently invaded areas (y-axis) are listed in upstream (top) to downstream (bottom) order. Source populations within each basin (x-axis) are listed in an upstream (left) to downstream (right) order.
Figure 2 in Mechanism of northern pike invasion in the Columbia River Basin
Figure 2. Sampling locations for northern pike in this study. Grey triangles represent hydroelectric dams that prevent upstream movement of fish. Yellow dots represent northern pike sampling locations.
Figure 4 in Mechanism of northern pike invasion in the Columbia River Basin
Figure 4. Plot of principle coordinates analysis on northern pike genotype data from populations in the Clark Fork River basin (pink dots), Coeur d'Alene-Spokane River basin (yellow dots) and recently invaded areas in eastern Washington (green dots). The percent of variation explained by coordinates 1 and 2 are shown in axes labels.
Figure 6 in Mechanism of northern pike invasion in the Columbia River Basin
Figure 6. STRUCUTRE plot showing population groupings of northern pike captured in recently invaded waterbodies of eastern Washington based on K = 2 populations. Waterbodies are listed in an upstream to downstream order. Nearly all fish captured upstream of Lake Roosevelt belong to one group (red bars). Most individuals captured in Lake Roosevelt belong to a second group (pale green bars), but individuals belonging to the red group are also present in Lake Roosevelt.
Figure 1 in Mechanism of northern pike invasion in the Columbia River Basin
Figure 1. Study area map showing (a) the Columbia River basin and major rivers drainages in this study and (b) waterbodies with populations of northern pike sampled in this study. In (b), black triangles represent hydroelectric dams that prevent upstream movement of fish. Waterbodies in red are primarily located in eastern Washington, USA, and represent the most recently invaded areas.
Figure 3 in Mechanism of northern pike invasion in the Columbia River Basin
Figure 3. Invasion scenarios of northern pike in the Columbia River basin compared using microsatellite data in DIYABC. In all scenarios, the Pend Oreille River was the source of fish in Lake Roosevelt. In Scenario 1 (a), Medicine-Cave Lakes share a common ancestor with Lake Pend Oreille, and Medicine-Cave Lakes were the source of fish to the Pend Oreille River. In Scenario 2 (b), Medicine-Cave Lakes share a common ancestor with Lake Pend Oreille, but Lake Pend Oreille was the source of fish to the Pend Oreille River. In Scenario 3 (c); Medicine-Cave Lakes share a common ancestor and admixture of the two was the source of fish in the Pend Oreille River. In Scenario 4 (d), Lake Pend Oreille shares a common ancestor with an unsampled population. The unsampled population was the source of fish to both Medicine-Cave and the Pend Oreille River. Timelines on the left side of each scenario mark the point of coalescent events; all samples were collected at t0.
Quantifying the diets of a non-native and native predator during juvenile salmon out-migrations in the Columbia River
<p>This is the clean and raw data files needed to replicate the analysis for our paper. The data contains carbon and nitrogen stable isotope data from several species of fish collected in the upper John Day Reservoir in Washington State in 2012. The data contains stable isotope signatures from predatory Walleye and Northern Pikeminnow, as well as potential prey species. A spreadsheet with descriptions of the column names is included. </p> <p>All of the code and analysis can be found at Karl Veggerby's Github: https://github.com/veggerk/Columbia-River-predatory-fish-study</p>
Subyearling Chinook salmon diets in Lower Columbia River estuarine habitats
Open the record for dataset details and reuse information.
Species-informative GT-seq markers for Columbia River salmonid fishes: Genotypic data and computing resources
Open the record for dataset details and reuse information.
Data from: Overlap of spatial and temporal spawning distributions of spring and summer Chinook Salmon results in hybridization in the upper Columbia River
<p>The upper Columbia River in Washington State (main-stem and tributary habitat between McNary and Chief Joseph dams) is inhabited by two major lineages of Chinook Salmon (<i>Oncorhynchus tshawytscha</i>); endangered spring Chinook Salmon and summer Chinook Salmon which are not ESA listed. The lineages are highly genetically divergent from one another and historically spatial and temporal isolating mechanisms maintained these genetic differences. Both lineages occur in the Entiat River, a system where anthropogenic activity has changed habitat, flows, species composition, and the distribution of the two lineages over the past century. We examined the spatial and temporal overlap in spawning distributions between Entiat River spring and summer Chinook Salmon and we used genetic markers to assess the level of introgression between lineages. Redd surveys were conducted from 2003 to 2017 to describe spatial and temporal spawning patterns of both lineages. We genotyped sub-yearling juvenile Chinook Salmon captured in the Entiat River from 2009–2014 at 90 SNP loci to determine lineage and hybridization status. There was temporal overlap in spawning between lineages in several years and considerable spatial overlap in redd locations annually. Genetic analysis revealed hybridization between lineages does occur, albeit at relatively low rates (2.6% of sub-yearling juveniles genotyped). We detected hybrids each year samples were collected and they were distributed throughout the Entiat River basin. Hybridization between lineages of Chinook Salmon could result in introgression and a loss of genetic diversity between the lineages, and/or, a loss of production by ESA-listed spring Chinook Salmon. The presence of hybrids warrants concern for ESA-listed spring Chinook Salmon in both the Entiat River system and throughout the upper Columbia River basin.</p>
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>
CMOP 2012 AUV-WP Columbia River estuary benchmark data set
<p>Observational data set from the Columbia River estuary North Channel. The data were collected during two campaigns during May and October-November 2012.</p> <p>Included are Automated Underwater (AUV) mission, and ship-mounted whiched profiler (WP) data sets. Outputs from numerical circulation model are also included.</p> <p>See the README.txt in each zip file for further information.</p>
Microseismic source parameters from induced seismicity in the Horn river basin (British Columbia) [Dataset]
<p>This is a database of results linked to the associated manuscript (Klinger and Werner, 2021) which has been submitted to Geophysical Journal International and is currently in review. </p> <p>We report magnitudes, corner frequencies and stress drops of microseismic events linked to fault reactivation during hydro-fracturing operations in the Horn river basin (British Columbia), as well as the corresponding uncertainties for these parameters. Stress drops are calculated using a Brune model (Brune, 1970) and uncertainties are calculated using a bootstrapping technique. </p> <p>Prior to publication please cite this database using the following two references:</p> <p>Klinger, A.G., Werner, M.J. (2021). Stress drops of hydraulic fracturing induced microseismicity in the Horn River basin: Challenges at high frequencies recorded by borehole geophones. <em>Manuscript submitted to Geophysical Journal International . </em></p> <p>Klinger, A.G., Werner, M.J. (2021). Microseismic source parameters from induced seismicity in the Horn river basin (British Columbia) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5603835.</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Dereplicated Metagenome assembled genomes (MAGs) from Columbia River hyporheic sediments
<p>Fasta file containing 55 metagenome assembled genomes (MAGs) from publication to be submitted titled "<strong>Microbial genome-resolved metaproteomic analyses frame intertwined carbon and nitrogen cycles in river hyporheic sediments". </strong></p>
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