Species occurrence data from the Range-Wide Bull Trout eDNA Project
Metadata:
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Identification_Information:
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Citation:
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Citation_Information:
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Originator: Young, Michael K.
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Originator: Isaak, Daniel J.
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Originator: McKelvey, Kevin S.
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Originator: Schwartz, Michael K.
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Originator: Carim, Kellie J.
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Originator: Fredenberg, Wade
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Originator: Wilcox, Taylor M.
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Originator: Franklin, Thomas W.
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Originator: Chandler, Gwynne L.
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Originator: Nagel, David E.
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Originator: Parkes-Payne, Sharon L.
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Originator: Horan, Dona L.
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Originator: Wollrab, Sherry P.
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Publication_Date: 2017
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Title:
Species occurrence data from the Range-Wide Bull Trout eDNA Project- Geospatial_Data_Presentation_Form: vector digital data
- Publication_Information:
- Publication_Place: Fort Collins, CO
- Publisher: Forest Service Research Data Archive
- Other_Citation_Details:
- Updated 05 June 2021
- Online_Linkage: https://doi.org/10.2737/RDS-2017-0038
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Description:
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Abstract:
- These data include 2014 - 2020 eDNA field sample points indicating lab results for presence or absence of bull trout. Sample sites are spaced at a 1 kilometer interval throughout the historical range of bull trout. eDNA stream samples are collected and species presence/absence is determined by analyses at the National Genomics Center. Results are recorded in the feature attribute table of the eDNA sample site shapefile. One point feature in the shapefile was generated for each 1 kilometer sample point in the bull trout eDNA feature class. Where multiple samples were collected at a single eDNA sample site, replicate point features will occur at a single location in the shapefile.
The bull trout is an ESA-listed species with a historical range that encompasses many waters across the Northwest. Though once abundant, bull trout have declined in many locations and are at risk from a changing climate, nonnative species, and habitat degradation. Informed conservation planning relies on sound and precise information about the distribution of bull trout in thousands of streams, but gathering this information is a daunting and expensive task. To overcome this problem, we coupled 1) predictions from the range-wide, spatially precise Climate Shield model on the location of natal habitats of bull trout with 2) a sampling template for every 8-digit hydrologic unit in the historical range of bull trout, based on the probability of detecting bull trout presence using environmental DNA (eDNA) sampling (McKelvey et al. 2016). The template consists of a master set of geospatially referenced sampling locations at 1-kilometer intervals within each cold-water habitat. We also identified sampling locations at this same interval based on the U.S. Fish and Wildlife Service's (USFWS) designation of critical spawning and rearing habitat. Based on field tests of eDNA detection probabilities conducted by the National Genomics Center for Wildlife and Fish Conservation, this sampling approach will reliably determine the presence of populations of bull trout, as well as provide insights on non-spawning habitats used by adult and subadult fish. The completed bull trout eDNA survey results are available through an interactive ArcGIS Online Map. The map provides the ability to zoom in and look at an area of interest, as well as to create queries or select an area to download points as a shapefile.
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Purpose:
- Results from collected eDNA field sample locations indicating presence or absence of bull trout. The points represent lab results starting in 2015 and updated at least once a year based on participation. Points taken prior to 2015 were sampled using effectively identical protocols and are added to the eDNAtlas Database from previous databases as time allows.
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Supplemental_Information:
- For more information on The Range-Wide Bull Trout eDNA Project see: https://www.fs.usda.gov/rm/boise/AWAE/projects/BullTrout_eDNA.html
Original metadata date was 08/15/2017. Minor metadata updates were made on 09/01/2017. On 07/03/2018 the metadata was updated to denote that 2018 data are now included. On 04/09/2019 the metadata was updated to reflect changes made to the data on 03/14/2019: added more sample results as well as added the Sample_Visit field to indicate if a sample was collected at more than one time at a single location on the sample day. On 09/18/2019 more sample results were added, as well as changing the Sample_Visit field name to SampleVisi. Some location field names were added or edited to clarify sample grid locations from field collection locations. On 11/08/2019 the metadata was updated to reflect changes made to the data. On 12/09/2019 metadata were updated to include information regarding data prior to 2015 that are available. On 07/24/2020 an “ID_Tag” field to specify for the lab which Unique ID was assigned to the sample for the PCR run. Additional minor metadata updates were included. More sample results were added, as well as changing the Sample_Visit field name to Samp_Visit. On 10/23/2020 a few data corrections were made, see Process Steps for details. On 06/05/2021 the metadata was updated to reflect the changes in the attribute table. There are two new fields: Field_Lon and Field_Lat. Those and other coordinate attribute definitions were edited to clarify which were grid point coordinates and which were GPS coordinates the contributor gave as the location of the field sample. The Samp_Visit field was deleted since the ID_Tag can be used to differentiate between samples at the same location and date. On 07/27/22 the metadata was updated to correct old URLs.
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Time_Period_of_Content:
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Time_Period_Information:
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Range_of_Dates/Times:
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Beginning_Date: 2014
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Ending_Date: 2020
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Currentness_Reference:
- Observed
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Status:
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Progress: In work
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Maintenance_and_Update_Frequency: Biannually
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Spatial_Domain:
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Description_of_Geographic_Extent:
- Bull trout distribution watersheds in the western United States: Idaho, Montana, Washington, Oregon, and Nevada.
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Bounding_Coordinates:
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West_Bounding_Coordinate: -124.21406
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East_Bounding_Coordinate: -112.31333
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North_Bounding_Coordinate: 48.99968
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South_Bounding_Coordinate: 41.78174
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Keywords:
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Theme:
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Theme_Keyword_Thesaurus: ISO 19115 Topic Category
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Theme_Keyword: biota
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Theme_Keyword: climatologyMeteorologyAtmosphere
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Theme_Keyword: environment
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Theme_Keyword: inlandWaters
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Theme:
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Theme_Keyword_Thesaurus: National Research & Development Taxonomy
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Theme_Keyword: Climate change
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Theme_Keyword: Ecology, Ecosystems, & Environment
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Theme_Keyword: Hydrology, watersheds, sedimentation
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Theme_Keyword: Forest & Plant Health
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Theme_Keyword: Climate effects
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Theme_Keyword: Invasive species
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Theme_Keyword: Inventory, Monitoring, & Analysis
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Theme_Keyword: Monitoring
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Theme_Keyword: Natural Resource Management & Use
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Theme_Keyword: Landscape management
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Theme_Keyword: Wildlife (or Fauna)
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Theme_Keyword: Fish
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Theme_Keyword: Habitat management
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Theme:
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Theme_Keyword_Thesaurus: None
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Theme_Keyword: eDNA
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Theme_Keyword: environmental DNA
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Theme_Keyword: bull trout
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Theme_Keyword: presence
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Theme_Keyword: population
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Theme_Keyword: location
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Theme_Keyword: status
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Theme_Keyword: survey
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Theme_Keyword: bull trout habitat
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Theme_Keyword: occurrence
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Theme_Keyword: sample
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Theme_Keyword: study
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Theme_Keyword: fish
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Place:
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Place_Keyword_Thesaurus: None
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Place_Keyword: western United States
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Place_Keyword: Idaho
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Place_Keyword: Montana
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Place_Keyword: Washington
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Place_Keyword: Oregon
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Place_Keyword: Nevada
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Access_Constraints: None
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Use_Constraints:
- These species occurrence data and accompanying geospatial datasets were created using funding from the U.S. Government and can be used without additional permissions or fees. If you use these data in a publication, presentation, or other research product please use the following citation:
Young, Michael K.; Isaak, Daniel J.; McKelvey, Kevin S.; Schwartz, Michael K.; Carim, Kellie J.; Fredenberg, W.; Wilcox, Taylor M.; Franklin, T.; Chandler, Gwynne L.; Nagel, David E.; Parkes-Payne, Sharon L.; Horan, Dona L.; Wollrab, Sherry P. 2017. Species occurrence data from the Range-Wide Bull Trout eDNA Project. Fort Collins, CO: Forest Service Research Data Archive. Updated 05 June 2021. https://doi.org/10.2737/RDS-2017-0038
The USDA Forest Service makes no warranty, expressed or implied, including the warranties of merchantability and fitness for a particular purpose, nor assumes any legal liability or responsibility for the accuracy, reliability, completeness or utility of these geospatial data, or for the improper or incorrect use of these geospatial data. These geospatial data and related maps or graphics are not legal documents and are not intended to be used as such. The data and maps may not be used to determine title, ownership, legal descriptions or boundaries, legal jurisdiction, or restrictions that may be in place on either public or private land. Natural hazards may or may not be depicted on the data and maps, and land users should exercise due caution. The data are dynamic and may change over time. The user is responsible to verify the limitations of the geospatial data and to use the data accordingly.
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Point_of_Contact:
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Contact_Information:
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Contact_Person_Primary:
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Contact_Person: Sharon Parkes-Payne
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Contact_Organization: USDA Forest Service, Rocky Mountain Research Station, Boise Aquatic Sciences Lab
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Contact_Position: GIS Specialist
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Contact_Address:
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Address_Type: mailing and physical
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Address: 322 East Front Street
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City: Boise
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State_or_Province: ID
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Postal_Code: 83702
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Country: USA
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Contact_Voice_Telephone: 208-373-4356
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Contact_Electronic_Mail_Address:
Sharon.L.Payne@usda.gov
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Data_Set_Credit:
- Funding for this project was provided by USDA Forest Service, Rocky Mountain Research Station, AWAE Program (Air, Water, and Aquatic Environments Program). Funding was also provided by the USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation (https://www.fs.usda.gov/rmrs/ngc).
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Native_Data_Set_Environment:
- Microsoft Windows 7 Version 6.1 (Build 7601) Service Pack 1; Esri ArcGIS 10.2.1.3497
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Cross_Reference:
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Citation_Information:
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Originator: McKelvey, Kevin S.
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Originator: Young, Michael K.
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Originator: Knotek, W. Ladd
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Originator: Carim, Kellie J.
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Originator: Wilcox, Taylor M.
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Originator: Padgett-Stewart, Ticha M.
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Originator: Schwartz, Michael K.
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Publication_Date: 2016
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Title:
Sampling large geographic areas for rare species using environmental DNA: A study of bull trout Salvelinus confluentus occupancy in western Montana- Geospatial_Data_Presentation_Form: Journal Article
- Series_Information:
- Series_Name: Journal of Fish Biology
- Issue_Identification: 88: 1215-1222
- Online_Linkage: https://doi.org/10.1111/jfb.12863
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Cross_Reference:
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Citation_Information:
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Originator: Carim, Kellie J.
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Originator: McKelvey, Kevin S.
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Originator: Young, Michael K.
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Originator: Wilcox, Taylor M.
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Originator: Schwartz, Michael K.
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Publication_Date: 2016
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Title:
A protocol for collecting environmental DNA samples from streams- Geospatial_Data_Presentation_Form: document
- Series_Information:
- Series_Name: Gen. Tech. Rep.
- Issue_Identification: RMRS-GTR-355
- Publication_Information:
- Publication_Place: Fort Collins, CO
- Publisher: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station
- Other_Citation_Details:
- 18 p.
- Online_Linkage: https://www.fs.usda.gov/treesearch/pubs/52466
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Cross_Reference:
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Citation_Information:
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Originator: Isaak, Daniel J.
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Originator: Young, Michael K.
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Originator: Nagel, David E.
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Originator: Horan, Dona L.
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Originator: Groce, Matthew C.
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Publication_Date: 2015
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Title:
The cold-water climate shield: Delineating refugia for preserving salmonid fishes through the 21st century- Geospatial_Data_Presentation_Form: Journal Article
- Series_Information:
- Series_Name: Global Change Biology
- Issue_Identification: 21: 2540-2553
- Online_Linkage: https://doi.org/10.1111/gcb.12879
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Analytical_Tool:
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Analytical_Tool_Description:
- Climate Shield: Populations of many cold-water species are likely to decline this century with global warming, but declines will vary spatially and some populations will persist even under extreme climate change scenarios. Especially cold habitats could provide important refugia from both future environmental change and invasions by non-native species that prefer warmer waters. The Climate Shield website hosts geospatial data and related information that describes specific locations of cold-water refuge streams for native Cutthroat Trout and Bull Trout across the American West. Forecasts about the locations of refugia could enable the protection of key watersheds, be used to rally support among multiple stakeholders, and provide a foundation for planning climate-smart conservation networks that improve the odds of preserving native trout populations through the 21st century.
Climate Shield was inspired by the landscapes of the Rocky Mountains and people everywhere that are working to preserve native trout. The Northern Rockies Adaptation Partnership (http://adaptationpartners.org/nrap/) provided a valuable forum that accelerated this work. The Great Northern and North Pacific Landscape Conservation Cooperatives generously funded the NorWeST project (https://www.fs.usda.gov/rm/boise/AWAE/projects/NorWeST.html), which serves as the foundation for Climate Shield.
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Tool_Access_Information:
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Online_Linkage:
https://www.fs.usda.gov/rm/boise/AWAE/projects/ClimateShield.html
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Tool_Access_Instructions:
- See website
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Tool_Citation:
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Citation_Information:
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Originator: Isaak, Daniel J.
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Originator: Young, Michael K.
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Originator: Nagel, David E.
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Originator: Horan, Dona L.
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Originator: Groce, Matthew C.
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Publication_Date: 2015
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Title:
The cold-water climate shield: Delineating refugia for preserving salmonid fishes through the 21st Century- Geospatial_Data_Presentation_Form: Journal Article
- Series_Information:
- Series_Name: Global Change Biology
- Issue_Identification: 21: 2540-2553
- Online_Linkage: https://doi.org/10.1111/gcb.12879
Back to Top
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Data_Quality_Information:
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Attribute_Accuracy:
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Attribute_Accuracy_Report:
- The laboratory controls are checked for proper amplification (negative = no wells of amplification, positive = 3 wells of amplification). Samples are again checked for inhibition (> 1 CT delay in the internal positive control compared to the IPC of the negative control). Further, the number of positive wells and the corresponding CT well values are checked for accuracy. If a sample showed positive amplification, the shape of the amplification curve is checked to assure a true detection was present.
Bull trout are indicated as present in the shapefile if Positive Wells is > 0. The BT_Present field is populated as follows:
Positive Wells = 0; absent = 2
Positive Wells > 0; present = 3
Other BT_Present fields were populated with:
Value = 1 (not sampled)
Value = 4 (sampled, being processed)
Additional details about quality assurance and quality control checks can be found in the Process Steps below.
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Logical_Consistency_Report:
- See the Process Steps below.
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Completeness_Report:
- The only data missing are the site locations that have samples, but haven’t been run yet OR samples that are being re-run due to ambiguous results.
A database of the distribution of bull trout across their U.S. range based on eDNA sampling of habitats with a > 25% probability of occupancy by juvenile bull trout. Probability of occupancy is from the Climate Shield model for juvenile bull trout under the baseline climate scenario. Data collection period is 2014–2018.
Protocols: The NGCWFC protocol: https://www.fs.usda.gov/rmrs/publications/protocol-collecting-edna-samples-streams-version-23
Quality Checks: Field data collection follows the protocol. Standard laboratory protocols are followed. Data are reviewed for consistency by inspection.
Data Processing & Scientific Workflows: Field data are accompanied by a spreadsheet. Spreadsheet data are examined for consistency and completeness. Laboratory data are directly uploaded to spreadsheets and matched with field data. Data are again reviewed for consistency of results. Suspect results are re-analyzed.
Backup & Storage: eDNA samples are stored in -20 degrees Celsius (ºC) freezers. Data are stored on multiple computers in Missoula. USDA Forest Service NAS server, Boise.
Link: https://www.fs.usda.gov/rm/boise/AWAE/projects/BullTrout_eDNA.html
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Lineage:
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Source_Information:
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Source_Citation:
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Citation_Information:
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Originator: Isaak, Daniel J.
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Originator: Wenger, Seth J.
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Originator: Peterson, Erin E.
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Originator: Ver Hoef, Jay M.
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Originator: Hostetler, Steven W.
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Originator: Luce, Charlie H.
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Originator: Dunham, Jason B.
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Originator: Kershner, Jeffrey L.
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Originator: Roper, Brett B.
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Originator: Nagel, David E.
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Originator: Chandler, Gwynne L.
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Originator: Wollrab, Sherry P.
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Originator: Parkes, Sharon L.
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Originator: Horan, Dona L.
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Publication_Date: 2016
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Title:
NorWeST modeled summer stream temperature scenarios for the western U.S.- Geospatial_Data_Presentation_Form: tabular and vector digital data
- Publication_Information:
- Publication_Place: Fort Collins, CO
- Publisher: Forest Service Research Data Archive
- Online_Linkage: https://doi.org/10.2737/RDS-2016-0033
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Type_of_Source_Media: Online
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Source_Time_Period_of_Content:
-
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Time_Period_Information:
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Range_of_Dates/Times:
-
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Beginning_Date: 1993
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Ending_Date: 2011
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Source_Currentness_Reference:
- Ground Condition
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Source_Citation_Abbreviation:
- NorWeST
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Source_Contribution:
- Mean August predicted stream temperatures at 1-kilometer intervals along a reconditioned NHDPlus stream network. NorWeST Attribute S1_93_11 - Scenario 1, modeled stream temperature from 1993-2011 at the sample point.
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Source_Information:
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Source_Citation:
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Citation_Information:
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Originator: Isaak, Daniel J.
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Originator: Young, Michael K.
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Originator: Nagel, David E.
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Originator: Horan, Dona L.
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Originator: Groce, Matthew C.
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Publication_Date: 2015
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Title:
Climate Shield 1.0 - Cold water habitat patches for bull trout- Geospatial_Data_Presentation_Form: Database
- Online_Linkage: https://www.fs.usda.gov/rm/boise/AWAE/projects/ClimateShield.html
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Type_of_Source_Media: Online
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Source_Time_Period_of_Content:
-
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Time_Period_Information:
-
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Range_of_Dates/Times:
-
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Beginning_Date: 2017
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Ending_Date: 2015
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Source_Currentness_Reference:
- Ground Condition
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Source_Citation_Abbreviation:
- Climate Shield
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Source_Contribution:
- Predictions from the range-wide Climate Shield model on the location of natal habitats of bull trout
The Climate Shield fish distribution models provide stream-specific probabilistic predictions about the occurrence of juvenile bull trout and cutthroat trout in association with different scenarios for climate change and brook trout invasions. Descriptions of all potential cold-water habitats < 11ºC are provided in tables associated with ArcGIS shapefiles downloadable from the project website. https://www.fs.usda.gov/rm/boise/AWAE/projects/ClimateShield.html.
For more details about how the values in the tables were derived, please see the Climate Shield manuscript (Isaak et al. 2015).
Isaak, Daniel J.; Young, Michael K.; Nagel, David E.; Horan, Dona L.; Groce, Matthew C. 2015. The cold-water climate shield: Delineating refugia for preserving salmonid fishes through the 21st Century. Global Change Biology. 21:2540-2553. https://doi.org/10.1111/gcb.12879
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Source_Information:
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Source_Citation:
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Citation_Information:
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Originator: U.S. Fish and Wildlife Service
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Publication_Date: Unpublished material
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Title:
U.S. Fish and Wildlife Service critical bull trout habitat- Geospatial_Data_Presentation_Form: Database
- Online_Linkage: https://www.fws.gov/pacific/bulltrout/Habitat.cfm
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Type_of_Source_Media: Map
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Source_Time_Period_of_Content:
-
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Time_Period_Information:
-
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Range_of_Dates/Times:
-
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Beginning_Date: 2017
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Ending_Date: 2010
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Source_Currentness_Reference:
- Ground Condition
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Source_Citation_Abbreviation:
- FWS Bull Trout
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Source_Contribution:
- The Fish and Wildlife spawning and rearing critical habitat is not part of the data available for download. It is on the map as a way to help users visualize the habitats the present/absent data as it relates to the critical habitat. Those streamlines on the map are only available when zoomed in and aren’t part of the Field Collection Sites table.
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Source_Information:
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Source_Citation:
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Citation_Information:
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Originator: U.S. Environmental Protection Agency (USEPA) and the U.S. Geological Survey (USGS)
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Publication_Date: 2012
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Title:
National Hydrography Dataset Plus - NHDPlus, Version 2- Geospatial_Data_Presentation_Form: Database
- Online_Linkage: http://www.horizon-systems.com/NHDPlus/NHDPlusV2_home.php
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Type_of_Source_Media: Online
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Source_Time_Period_of_Content:
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Time_Period_Information:
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Single_Date/Time:
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Calendar_Date: 2012
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Source_Currentness_Reference:
- Ground Condition
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Source_Citation_Abbreviation:
- NHDPlusV2
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Source_Contribution:
- NHD flowlines
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Process_Step:
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Process_Description:
- STEP 1: BT eDNA Metadata for Generating Sample Points
Sample points were generated using NHDPlus Version 2 (NHDPlusV2) flowlines (McKay et al. 2012) as the spatial foundation. The points were only located on a portion of the NHDPlusV2 flowlines that corresponded with Climate Shield (Isaak et al. 2015) cold water habitat patches or U.S. Fish and Wildlife Service designated critical bull trout habitat (U.S. Fish and Wildlife Service 2014). Sample points were generally spaced at a 1 kilometer (km) intervals along the stream network. Specifically, an initial sample point was placed 100 meters (m) upstream from each confluence or outlet. Subsequent sample points along the reach were spaced at 1 km intervals up to the next confluence or headwater initiation point. Reaches between confluences that were shorter than 200 meters had a sample point placed only at the midpoint of the reach. Slope was computed for stream reaches. USGS 30 m DEM data were used to compute channel gradient from the focal point, upstream to the next sample point, confluence, or headwater initiation point.
Isaak, Daniel J.; Young, Michael K.; Nagel, David E.; Horan, Dona L.;Groce, Matthew C. 2015. The cold-water climate shield: Delineating refugia for preserving salmonid fishes through the 21st Century. Global Change Biology. 21:2540-2553. https://doi.org/10.1111/gcb.12879
McKay L.; Bondelid T.; Dewald T. 2012. NHDPlus Version 2: User Guide. U.S. EPA and USGS.
U.S. Fish and Wildlife Service. 2014. Bull Trout Recovery Plan. Website: https://www.fws.gov/pacific/bulltrout/. Visited July 14, 2017.
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Source_Used_Citation_Abbreviation:
- NHDPlusV2
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Process_Date: Unknown
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Process_Step:
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Process_Description:
- STEP 2: Various contributors collect samples in the field at the sample point locations. Protocols are described in Carim et al. 2016.
Carim, Kellie J.; McKelvey, Kevin S.; Young, Michael K.; Wilcox, Taylor M.; Schwartz, Michael K. 2016. A protocol for collecting environmental DNA samples from streams. Gen. Tech. Rep. RMRS-GTR-355. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. 18 p. https://doi.org/10.2737/RMRS-GTR-355
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Process_Date: Unknown
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Process_Step:
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Process_Description:
- STEP 3: Samples are tested at the National Genomics Center for Wildlife and Fish Conservation (https://www.fs.usda.gov/rmrs/ngc).
Quality Assurance/Quality Control Procedures (QAQC) - Thomas Franklin (thomas.franklin@usda.gov):
The final QAQC process involves checking all of the data from each sample’s qPCR analyses. The raw data (in the form of an amplification plot viewed in StepOnePlus or QuantStudio Design & Analysis Software) are compared to the data in the Mastersheet. The laboratory controls are check for proper amplification (negative = no wells of amplification, positive = 3 wells of amplification). Samples are again checked for inhibition (> 1 CT delay in the internal positive control compared to the IPC of the negative control). Further, the number of positive wells and the corresponding CT well values are checked for accuracy. If a sample showed positive amplification, the shape of the amplification curve is checked to assure a true detection was present. Any notes about the sample are added to the “PCR Notes” or “Comments” column. After a sample has been QAQC’d, the QAQC completion date and initials of the researcher are placed in the “Comments” column. Lastly, a “1” or “0” is placed in the final data column. A “1” represents a sample in which the data in that row are ready to be published. A “0” represents a sample in which the data in that row are not ready to be published (sample is inhibited, needs to be reanalyzed, etc.).
Sharon Payne (this information was used to create the BT_Present column in the shapefile):
PCR Date = Date PCR was run
Inhibited (0,1,2,3) =
0 = PCR Ran, not inhibited;
1 = PCR Ran, sample inhibited. Blank in Positive wells - CT Well 3 if no results can be gathered due to inhibition. If results can still be gathered even though sample is inhibited, the Positive wells - CT Well 3 columns will have CT numbers in them.;
2 = Treated for inhibition, PCR Ran, still inhibited. Nothing entered in Positive wells through CT Well 3 if no results can be gathered due to sustained inhibition. If results can still be gathered even though sample is inhibited, the Positive wells through CT Well 3 columns will have CT numbers in them;
3 = Treated for inhibition, PCR ran, sample no longer inhibited.
Positive Wells = Number of positive wells (1-9)
CT Well 1 = CT result. Real number <= 45. 45 indicates negative result for species
CT Well 2 = CT result. Real number <= 45. 45 indicates negative result for species
CT Well 3 = CT result. Real number <= 45. 45 indicates negative result for species
CT Well 4 = CT result. Real number <= 45. 45 indicates negative result for species
CT Well 5 = CT result. Real number <= 45. 45 indicates negative result for species
CT Well 6 = CT result. Real number <= 45. 45 indicates negative result for species
CT Well 7 = CT result. Real number <= 45. 45 indicates negative result for species
CT Well 8 = CT result. Real number <= 45. 45 indicates negative result for species
CT Well 9 = CT result. Real number <= 45. 45 indicates negative result for species
eDNA Quant = Mean eDNA quantity if a standard curve was used.
PCR Notes = Notes for run. If PCR ran and sample was inhibited but positive results could be verified, enter # of positive wells and CT results but note that sample was inhibited and CT values could be delayed/skewed. Note if diluted to treat for inhibition.
Comments = Any comments about the sample or run
Final Data =
0 = Data in this row are not to be published. This sample has been (or will be) reanalyzed and the final data can be found in a new row. For example, if an ID Tag was analyzed multiple times for the same species (example - reran sample to confirm DNA present not from contamination) and therefore has multiple rows of data (new row for each PCR data) but we only want to report one outcome for the ID Tag/Species Code combination.
1 = Data have been QAQC'd and are ready to be published for this ID Tag/Species Code combination. This represents the final data for that ID Tag/Species Code combination.
2 = Sample has been collected for this site. Results are being processed.
***Please note the 0/1 has nothing to do with the presence/absence of a species at that given site***
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Process_Date: Unknown
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Process_Step:
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Process_Description:
- STEP 4: Shapefile of sample points is updated to include lab sample results and field collection information
a. The laboratory controls are checked for proper amplification (negative = no wells of amplification, positive = 3 wells of amplification). Samples are again checked for inhibition (> 1 CT delay in the internal positive control compared to the IPC of the negative control). Further, the number of positive wells and the corresponding CT well values are checked for accuracy. If a sample showed positive amplification, the shape of the amplification curve is checked to assure a true detection was present.
Bull trout are indicated as present in the shapefile if Positive Wells is > 0. The BT_Present field is populated as follows:
Positive Wells = 0; absent = 2
Positive Wells > 0; present = 3
Other BT_Present fields were populated with:
Value = 1 (not sampled)
Value = 4 (sampled, being processed)
b. Fields also populated at the lab include: DD_X and DD_Y (coordinates) as collected in the field; Date_Coll (date collected); and Datasource (agency of the individual who collected the field sample).
-
Process_Date: Unknown
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Process_Step:
-
-
Process_Description:
- STEP 5: Shapefile is populated with other attributes deemed useful to the user
a. S1_93_11 – NorWeST - Scenario 1, modeled stream temperature from 1993-2011 at the sample point. Derived through a spatial join of the point with the NorWeST stream line.
b. Ownership - Land ownership at the field sample point from the Protected Areas Database of the United States (PADUS). Derived through a spatial join. Note that these attributes may have been slightly modified from the underlying data to have consistent naming.
c. SummerQ - Mean summer flow in cubic feet per second (cfs) at the sample point from the VIC flow model (https://www.fs.usda.gov/rm/boise/AWAE/projects/modeled_stream_flow_metrics.shtml) Derived through a spatial join.
d. eDNA_Slope - Stream channel slope averaged to the next upstream field sample point or tributary
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Process_Date: 2017
-
Process_Step:
-
-
Process_Description:
- STEP 6: Shapefile is made available as a geoprocessing service on ArcGIS Online and can be filtered and downloaded.
-
Process_Date: Unknown
-
Process_Step:
-
-
Process_Description:
- 2019 UPDATES:
On 03/14/2019 we added more sample results as well as added the Sample_Visit field to indicate if a sample was collected at more than one time at a single location on the sample day. On 09/18/2019 more sample results were added, as well as changing the Sample_Visit field name to SampleVisi. Some location field names were added or edited to clarify sample grid locations from field collection locations.
Points taken prior to 2015 were sampled using effectively identical protocols and are added to the eDNAtlas Database from previous databases as time allows.
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Process_Date: 2019
-
Process_Step:
-
-
Process_Description:
- 2020 UPDATES:
On 07/24/2020 an “ID_Tag” field was added to specify for the lab which Unique ID was assigned to the sample for the PCR run. Additional minor metadata updates were included, and the Sample Visit field name was changed back to Samp_Visit. This update included many more sample results.
On 10/23/2020 additional data edits were made. The original results of 7 samples were erroneously overwritten with the results of other samples after they had already been QAQC’d. The ID_Tag for those previously incorrect bull trout results are as follows: MT_082118_ANT_16, MT_082118_RAM_1, MT_082218_RAM_3, MT_082218_RAMT_7, MT_082218_REN_11, MT_082218_REN_12, MT_082218_REN_14. This update changed the BT_Present attributes for those points from a “3” back to the original results from the qPCR plate of “2”, showing that lab had not detected bull trout in that sample. The BTPresentT text field was also changed to indicate “sampled, bull trout absent”.
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Process_Date: 2020
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Process_Step:
-
-
Process_Description:
- 2021 UPDATES:
On 06/05/2021 the metadata was updated to reflect the changes in the attribute table. There are two new fields: Field_Lon and Field_Lat. Those and other coordinate attribute definitions were edited to clarify which were grid point coordinates and which were GPS coordinates the contributor gave as the location of the field sample. The Samp_Visit field was deleted since the ID_Tag can be used to differentiate between samples at the same location and date. This update also included many more sample results.
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Process_Date: 2021
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Spatial_Data_Organization_Information:
-
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Direct_Spatial_Reference_Method: Vector
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Point_and_Vector_Object_Information:
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SDTS_Terms_Description:
-
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SDTS_Point_and_Vector_Object_Type: Entity point
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Point_and_Vector_Object_Count: 41653
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Spatial_Reference_Information:
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Horizontal_Coordinate_System_Definition:
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Planar:
-
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Map_Projection:
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-
Map_Projection_Name: WGS 1984 Web Mercator Auxiliary Sphere
-
Planar_Coordinate_Information:
-
-
Planar_Coordinate_Encoding_Method: coordinate pair
-
Coordinate_Representation:
-
-
Abscissa_Resolution: 0.00000000671487310199836
-
Ordinate_Resolution: 0.00000000671487310199836
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Planar_Distance_Units: meter
-
Geodetic_Model:
-
-
Horizontal_Datum_Name: D WGS 1984
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Ellipsoid_Name: WGS 1984
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Semi-major_Axis: 6378137.0000
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Denominator_of_Flattening_Ratio: 298.257223563
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Entity_and_Attribute_Information:
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Detailed_Description:
-
-
Entity_Type:
-
-
Entity_Type_Label: BullTrout_eDNA_FieldSampleResults
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Entity_Type_Definition:
- Attribute Table
-
Entity_Type_Definition_Source:
- ESRI
-
Attribute:
-
-
Attribute_Label: FID
-
Attribute_Definition:
- Internal feature number.
-
Attribute_Definition_Source:
- ESRI
-
Attribute_Domain_Values:
-
-
Unrepresentable_Domain:
- Sequential unique whole numbers that are automatically generated.
-
Attribute:
-
-
Attribute_Label: Shape
-
Attribute_Definition:
- Feature geometry.
-
Attribute_Definition_Source:
- ESRI
-
Attribute_Domain_Values:
-
-
Unrepresentable_Domain:
- Coordinates defining the features.
-
Attribute:
-
-
Attribute_Label: eDNA_ID
-
Attribute_Definition:
- Full eDNA Project ID number for the sample point derived from concatenating the HUC8 number and the unique eDNA sample Site_ID
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: HUC8
-
Attribute_Definition:
- Watershed Boundary Dataset 8-digit subbasin number
-
Attribute_Definition_Source:
- USDA Forest Service (via USGS - https://water.usgs.gov/GIS/wbd_huc8.pdf)
-
Attribute:
-
-
Attribute_Label: HUC8_Name
-
Attribute_Definition:
- Watershed Boundary Dataset 8-digit subbasin name
-
Attribute_Definition_Source:
- USDA Forest Service (via USGS - https://water.usgs.gov/GIS/wbd_huc8.pdf)
-
Attribute:
-
-
Attribute_Label: Site_ID
-
Attribute_Definition:
- eDNA Field sample point unique ID
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: COMID
-
Attribute_Definition:
- Common identifier (COMID) of the underlying NHDFlowline (version 2).
-
Attribute_Definition_Source:
- USDA Forest Service (via NHD, EPA, USGS)
-
Attribute:
-
-
Attribute_Label: GNIS_NAME
-
Attribute_Definition:
- Feature Name from the Geographic Names Information System (GNIS_NAME) NHD Plus version 2
-
Attribute_Definition_Source:
- USDA Forest Service (via NHD, EPA, USGS)
-
Attribute:
-
-
Attribute_Label: REACHCODE
-
Attribute_Definition:
- REACHCODE of the underlying NHD Plus version 2 NHDFlowline
-
Attribute_Definition_Source:
- USDA Forest Service (via NHD, EPA, USGS)
-
Attribute:
-
-
Attribute_Label: TotDASqKM
-
Attribute_Definition:
- Total Upstream Cumulative Drainage Area, in square kilometers, at the downstream end of the NHDFlowline feature.
-
Attribute_Definition_Source:
- USDA Forest Service (via NHD, EPA, USGS)
-
Attribute:
-
-
Attribute_Label: DD_X
-
Attribute_Definition:
- grid point x-coordinate in Decimal Degrees - contributor field coordinates
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: DD_Y
-
Attribute_Definition:
- grid point y-coordinate in Decimal Degrees - contributor field coordinates
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: UTM_Zone
-
Attribute_Definition:
- UTM Zone
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: UTM_X
-
Attribute_Definition:
- UTM x-coordinate; Universal Transverse Mercator (UTM) conformal projection uses a 2-dimensional Cartesian coordinate system to give locations on the surface of the Earth
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: UTM_Y
-
Attribute_Definition:
- UTM y-coordinate; Universal Transverse Mercator (UTM) conformal projection uses a 2-dimensional Cartesian coordinate system to give locations on the surface of the Earth
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: SummerQ
-
Attribute_Definition:
- Mean summer flow in cubic feet per second (cfs) at the sample point from the VIC flow model - https://www.fs.usda.gov/rm/boise/AWAE/projects/modeled_stream_flow_metrics.shtml (NOTE: “-9999” was added to some points that had issues with the spatial join and getting the correct underlying data)
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: eDNA_Slope
-
Attribute_Definition:
- Stream channel slope averaged to the next upstream field sample point or tributary
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: Ownership
-
Attribute_Definition:
- Land ownership at the field sample point from the Protected Areas Database of the United States (PADUS).
-
Attribute_Definition_Source:
- USDA Forest Service (via USGS - See PAD-US Standards Manual Document, https://gapanalysis.usgs.gov/padus/data/standards/ )
-
Attribute:
-
-
Attribute_Label: Field_Zone
-
Attribute_Definition:
- UTM zone for the coordinates where the sample was collected in the field.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: Field_East
-
Attribute_Definition:
- UTM easting (X) coordinate where the sample was collected in the field.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: Field_Nrth
-
Attribute_Definition:
- UTM northing (Y) coordinate where the sample was collected in the field.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: Field_Lon
-
Attribute_Definition:
- Sample point x-coordinate in Decimal Degrees where the sample was collected in the field. Contributor field coordinates.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: Field_Lat
-
Attribute_Definition:
- Sample point y-coordinate in Decimal Degrees where the sample was collected in the field. Contributor field coordinates.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: Field_DD_X
-
Attribute_Definition:
- Grid point x-coordinate in Decimal Degrees - contributor field coordinates.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: Field_DD_Y
-
Attribute_Definition:
- Grid point y-coordinate in Decimal Degrees - contributor field coordinates.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: Date_Coll
-
Attribute_Definition:
- Date the sample was collected in the field. A NULL value indicates the collection date is not known or the site location has not yet been sampled.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: Datasource
-
Attribute_Definition:
- Agency of the individual who collected the field sample.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: BT_Present
-
Attribute_Definition:
- Indicates if a site has been sampled and if bull trout is present.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute_Domain_Values:
-
-
Enumerated_Domain:
-
-
Enumerated_Domain_Value: 1
-
Enumerated_Domain_Value_Definition:
- not sampled
-
Enumerated_Domain_Value_Definition_Source:
- USDA Forest Service
-
Enumerated_Domain:
-
-
Enumerated_Domain_Value: 2
-
Enumerated_Domain_Value_Definition:
- sampled, bull trout absent
-
Enumerated_Domain_Value_Definition_Source:
- USDA Forest Service
-
Enumerated_Domain:
-
-
Enumerated_Domain_Value: 3
-
Enumerated_Domain_Value_Definition:
- sampled, bull trout present
-
Enumerated_Domain_Value_Definition_Source:
- USDA Forest Service
-
Enumerated_Domain:
-
-
Enumerated_Domain_Value: 4
-
Enumerated_Domain_Value_Definition:
- sampled, being processed. Note that the July 2020 update does not have any samples that have been submitted and not processed.
-
Enumerated_Domain_Value_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: S1_93_11
-
Attribute_Definition:
- NorWeST - Scenario 1, modeled stream temperature from 1993-2011 at the sample point.
https://www.fs.usda.gov/rm/boise/AWAE/projects/NorWeST.html
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: ID_Tag
-
Attribute_Definition:
- Unique ID assigned to each eDNA sample stored/processed at the National Genomics Center for Wildlife and Fish Conservation.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute:
-
-
Attribute_Label: BTPresentT
-
Attribute_Definition:
- Bull Trout Present - text corresponding to the BT_Present attribute.
-
Attribute_Definition_Source:
- USDA Forest Service
-
Attribute_Domain_Values:
-
-
Enumerated_Domain:
-
-
Enumerated_Domain_Value: not sampled
-
Enumerated_Domain_Value_Definition:
- The National Genomics Center for Wildlife and Fish Conservation indicates they have not received a sample from this location. If you would like to contribute a sample at this location, see https://www.fs.usda.gov/rm/boise/AWAE/projects/BullTrout_eDNA/Participating.html.
-
Enumerated_Domain_Value_Definition_Source:
- USDA Forest Service
-
Enumerated_Domain:
-
-
Enumerated_Domain_Value: sampled, bull trout absent
-
Enumerated_Domain_Value_Definition:
- The National Genomics Center for Wildlife and Fish Conservation indicates they have received a sample from this site and have tested it to find no bull trout eDNA present.
-
Enumerated_Domain_Value_Definition_Source:
- USDA Forest Service
-
Enumerated_Domain:
-
-
Enumerated_Domain_Value: sampled, bull trout present
-
Enumerated_Domain_Value_Definition:
- The National Genomics Center for Wildlife and Fish Conservation indicates they have received a sample from this site and have tested it to find bull trout eDNA present at the location.
-
Enumerated_Domain_Value_Definition_Source:
- USDA Forest Service
-
Enumerated_Domain:
-
-
Enumerated_Domain_Value: sampled, being processed
-
Enumerated_Domain_Value_Definition:
- The National Genomics Center for Wildlife and Fish Conservation indicates they have received a sample from this site and the sample is still being processed. Note that the July 2020 update does not have any samples that have been submitted and not processed.
-
Enumerated_Domain_Value_Definition_Source:
- USDA Forest Service
-
Overview_Description:
-
-
Entity_and_Attribute_Overview:
- The data available for download from the ArcGIS Online map contain bull trout eDNA lab results from field samples contributed to National Genomics Center for Wildlife and Fish Conservation, as well as information about the date and agency that collected the genetic material. This attribute table also contains other useful information including slope, stream temperature, and other additional about the sample site location.
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Entity_and_Attribute_Detail_Citation:
- See the User Guide for more specifics: https://www.fs.usda.gov/rm/boise/AWAE/projects/BullTrout_eDNA/SurveyStatus.html.
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Distribution_Information:
-
-
Distributor:
-
-
Contact_Information:
-
-
Contact_Person_Primary:
-
-
Contact_Person: Sharon (Parkes) Payne
-
Contact_Organization: USDA Forest Service, Rocky Mountain Research Station, Boise Aquatic Sciences Lab
-
Contact_Address:
-
-
Address_Type: mailing and physical
-
Address: 322 East Front Street, Suite 401
-
City: Boise
-
State_or_Province: ID
-
Postal_Code: 83702
-
Country: USA
-
Contact_Voice_Telephone: 208-373-4356
-
Contact_Electronic_Mail_Address:
Sharon.L.Payne@usda.gov
-
Resource_Description: RDS-2017-0038
-
Distribution_Liability:
- Metadata documents have been reviewed for accuracy and completeness. Unless otherwise stated, all data and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. However, neither the author, the Archive, nor any part of the federal government can assure the reliability or suitability of these data for a particular purpose. The act of distribution shall not constitute any such warranty, and no responsibility is assumed for a user's application of these data or related materials.
The metadata, data, or related materials may be updated without notification. If a user believes errors are present in the metadata, data or related materials, please use the information in (1) Identification Information: Point of Contact, (2) Metadata Reference: Metadata Contact, or (3) Distribution Information: Distributor to notify the author or the Archive of the issues.
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Standard_Order_Process:
-
-
Digital_Form:
-
-
Digital_Transfer_Information:
-
-
Format_Name: SHP
-
Format_Version_Number: See Format Specification
-
Format_Specification:
- ArcGIS Shapefile
-
File_Decompression_Technique: No compression applied
-
Digital_Transfer_Option:
-
-
Online_Option:
-
-
Computer_Contact_Information:
-
-
Network_Address:
-
-
Network_Resource_Name:
https://www.fs.usda.gov/rm/boise/AWAE/projects/BullTrout_eDNA.html
-
Digital_Form:
-
-
Digital_Transfer_Information:
-
-
Format_Name: PDF
-
Format_Version_Number: See Format Specification
-
Format_Specification:
- Adobe Acrobat PDF file
-
File_Decompression_Technique: No compression applied
-
Digital_Form:
-
-
Digital_Transfer_Information:
-
-
Format_Name: XLS
-
Format_Version_Number: See Format Specification
-
Format_Specification:
- Microsoft Excel worksheet
-
File_Decompression_Technique: No compression applied
-
Digital_Transfer_Option:
-
-
Online_Option:
-
-
Computer_Contact_Information:
-
-
Network_Address:
-
-
Network_Resource_Name:
https://www.fs.usda.gov/rm/boise/AWAE/projects/BullTrout_eDNA.html
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Fees: None
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Metadata_Reference_Information:
-
-
Metadata_Date: 20220727
-
Metadata_Contact:
-
-
Contact_Information:
-
-
Contact_Person_Primary:
-
-
Contact_Person: Sharon Parkes-Payne
-
Contact_Organization: USDA Forest Service, Rocky Mountain Research Station, Boise Aquatic Sciences Lab
-
Contact_Position: GIS Specialist
-
Contact_Address:
-
-
Address_Type: mailing and physical
-
Address: 322 East Front Street
-
City: Boise
-
State_or_Province: ID
-
Postal_Code: 83702
-
Country: USA
-
Contact_Voice_Telephone: 208-373-4356
-
Contact_Electronic_Mail_Address:
Sharon.L.Payne@usda.gov
-
Metadata_Standard_Name: FGDC Content Standard for Digital Geospatial Metadata
-
Metadata_Standard_Version: FGDC-STD-001-1998
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