Species occurrence data from the Range-Wide Bull Trout eDNA Project

Metadata:
Identification_Information:
Citation:
Citation_Information:
Originator: Young, Michael K.
Originator: Isaak, Daniel J.
Originator: McKelvey, Kevin S.
Originator: Schwartz, Michael K.
Originator: Carim, Kellie J.
Originator: Fredenberg, Wade
Originator: Wilcox, Taylor M.
Originator: Franklin, Thomas W.
Originator: Chandler, Gwynne L.
Originator: Nagel, David E.
Originator: Parkes-Payne, Sharon L.
Originator: Horan, Dona L.
Originator: Wollrab, Sherry P.
Publication_Date: 2017
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
Description:
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.
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.
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.
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 2014
Ending_Date: 2020
Currentness_Reference:
Observed
Status:
Progress: In work
Maintenance_and_Update_Frequency: Biannually
Spatial_Domain:
Description_of_Geographic_Extent:
Bull trout distribution watersheds in the western United States: Idaho, Montana, Washington, Oregon, and Nevada.
Bounding_Coordinates:
West_Bounding_Coordinate: -124.21406
East_Bounding_Coordinate: -112.31333
North_Bounding_Coordinate: 48.99968
South_Bounding_Coordinate: 41.78174
Keywords:
Theme:
Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: biota
Theme_Keyword: climatologyMeteorologyAtmosphere
Theme_Keyword: environment
Theme_Keyword: inlandWaters
Theme:
Theme_Keyword_Thesaurus: National Research & Development Taxonomy
Theme_Keyword: Climate change
Theme_Keyword: Ecology, Ecosystems, & Environment
Theme_Keyword: Hydrology, watersheds, sedimentation
Theme_Keyword: Forest & Plant Health
Theme_Keyword: Climate effects
Theme_Keyword: Invasive species
Theme_Keyword: Inventory, Monitoring, & Analysis
Theme_Keyword: Monitoring
Theme_Keyword: Natural Resource Management & Use
Theme_Keyword: Landscape management
Theme_Keyword: Wildlife (or Fauna)
Theme_Keyword: Fish
Theme_Keyword: Habitat management
Theme:
Theme_Keyword_Thesaurus: None
Theme_Keyword: eDNA
Theme_Keyword: environmental DNA
Theme_Keyword: bull trout
Theme_Keyword: presence
Theme_Keyword: population
Theme_Keyword: location
Theme_Keyword: status
Theme_Keyword: survey
Theme_Keyword: bull trout habitat
Theme_Keyword: occurrence
Theme_Keyword: sample
Theme_Keyword: study
Theme_Keyword: fish
Place:
Place_Keyword_Thesaurus: None
Place_Keyword: western United States
Place_Keyword: Idaho
Place_Keyword: Montana
Place_Keyword: Washington
Place_Keyword: Oregon
Place_Keyword: Nevada
Access_Constraints: None
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.
Point_of_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
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).
Native_Data_Set_Environment:
Microsoft Windows 7 Version 6.1 (Build 7601) Service Pack 1; Esri ArcGIS 10.2.1.3497
Cross_Reference:
Citation_Information:
Originator: McKelvey, Kevin S.
Originator: Young, Michael K.
Originator: Knotek, W. Ladd
Originator: Carim, Kellie J.
Originator: Wilcox, Taylor M.
Originator: Padgett-Stewart, Ticha M.
Originator: Schwartz, Michael K.
Publication_Date: 2016
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
Cross_Reference:
Citation_Information:
Originator: Carim, Kellie J.
Originator: McKelvey, Kevin S.
Originator: Young, Michael K.
Originator: Wilcox, Taylor M.
Originator: Schwartz, Michael K.
Publication_Date: 2016
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
Cross_Reference:
Citation_Information:
Originator: Isaak, Daniel J.
Originator: Young, Michael K.
Originator: Nagel, David E.
Originator: Horan, Dona L.
Originator: Groce, Matthew C.
Publication_Date: 2015
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
Analytical_Tool:
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.
Tool_Access_Information:
Online_Linkage: https://www.fs.usda.gov/rm/boise/AWAE/projects/ClimateShield.html
Tool_Access_Instructions:
See website
Tool_Citation:
Citation_Information:
Originator: Isaak, Daniel J.
Originator: Young, Michael K.
Originator: Nagel, David E.
Originator: Horan, Dona L.
Originator: Groce, Matthew C.
Publication_Date: 2015
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
Data_Quality_Information:
Attribute_Accuracy:
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.
Logical_Consistency_Report:
See the Process Steps below.
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
Lineage:
Source_Information:
Source_Citation:
Citation_Information:
Originator: Isaak, Daniel J.
Originator: Wenger, Seth J.
Originator: Peterson, Erin E.
Originator: Ver Hoef, Jay M.
Originator: Hostetler, Steven W.
Originator: Luce, Charlie H.
Originator: Dunham, Jason B.
Originator: Kershner, Jeffrey L.
Originator: Roper, Brett B.
Originator: Nagel, David E.
Originator: Chandler, Gwynne L.
Originator: Wollrab, Sherry P.
Originator: Parkes, Sharon L.
Originator: Horan, Dona L.
Publication_Date: 2016
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
Type_of_Source_Media: Online
Source_Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 1993
Ending_Date: 2011
Source_Currentness_Reference:
Ground Condition
Source_Citation_Abbreviation:
NorWeST
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.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Isaak, Daniel J.
Originator: Young, Michael K.
Originator: Nagel, David E.
Originator: Horan, Dona L.
Originator: Groce, Matthew C.
Publication_Date: 2015
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
Type_of_Source_Media: Online
Source_Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 2017
Ending_Date: 2015
Source_Currentness_Reference:
Ground Condition
Source_Citation_Abbreviation:
Climate Shield
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
Source_Information:
Source_Citation:
Citation_Information:
Originator: U.S. Fish and Wildlife Service
Publication_Date: Unpublished material
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
Type_of_Source_Media: Map
Source_Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 2017
Ending_Date: 2010
Source_Currentness_Reference:
Ground Condition
Source_Citation_Abbreviation:
FWS Bull Trout
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.
Source_Information:
Source_Citation:
Citation_Information:
Originator: U.S. Environmental Protection Agency (USEPA) and the U.S. Geological Survey (USGS)
Publication_Date: 2012
Title:
National Hydrography Dataset Plus - NHDPlus, Version 2
Geospatial_Data_Presentation_Form: Database
Online_Linkage: http://www.horizon-systems.com/NHDPlus/NHDPlusV2_home.php
Type_of_Source_Media: Online
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2012
Source_Currentness_Reference:
Ground Condition
Source_Citation_Abbreviation:
NHDPlusV2
Source_Contribution:
NHD flowlines
Process_Step:
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.
Source_Used_Citation_Abbreviation:
NHDPlusV2
Process_Date: Unknown
Process_Step:
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
Process_Date: Unknown
Process_Step:
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***
Process_Date: Unknown
Process_Step:
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
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
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.
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”.
Process_Date: 2020
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.
Process_Date: 2021
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Spatial_Data_Organization_Information:
Direct_Spatial_Reference_Method: Vector
Point_and_Vector_Object_Information:
SDTS_Terms_Description:
SDTS_Point_and_Vector_Object_Type: Entity point
Point_and_Vector_Object_Count: 41653
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Spatial_Reference_Information:
Horizontal_Coordinate_System_Definition:
Planar:
Map_Projection:
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
Planar_Distance_Units: meter
Geodetic_Model:
Horizontal_Datum_Name: D WGS 1984
Ellipsoid_Name: WGS 1984
Semi-major_Axis: 6378137.0000
Denominator_of_Flattening_Ratio: 298.257223563
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Entity_and_Attribute_Information:
Detailed_Description:
Entity_Type:
Entity_Type_Label: BullTrout_eDNA_FieldSampleResults
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.
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.
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
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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