Bull Trout eDNA
The bull trout has a historical range that encompasses many waters across the Northwest. Though once abundant, bull trout have declined in many locations and is now federally listed and protected under the Endangered Species Act. Bull trout populations are at risk to further declines 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, Rocky Mountain Research Station scientists initiated the range-wide bull trout eDNA project in partnership with biologists from more than 20 organizations.
Environmental DNA (eDNA) sampling in streams is the collection of DNA released by a target species into the water. Scientists at the U.S. Forest Service’s National Genomics Center for Wildlife and Fish Conservation have pioneered developments in this field—including the first reliable eDNA assay for salmonid fish species, the first that distinguishes bull trout from other species of char (Wilcox et al. 2013, 2014), and the first that distinguishes among subspecies of cutthroat trout (Wilcox et al. 2015a). Detection of stream fish with eDNA is remarkably sensitive—100% detection efficiency of target species has been achieved despite order-of-magnitude changes in stream discharge (Jane et al. 2015). Field experiments indicate that detection probability of a single trout in 100 m of stream exceeds 85%, an efficiency several-fold better than one-pass electrofishing (Wilcox et al. 2016). We have also developed an easy-to-learn, field-proven eDNA sampling protocol that requires only 15 minutes of effort by a single person to collect a sample (Carim et al. 2016). Collected samples are portable, readily stored while in the field, and can be processed in the lab in as little as 3 days. The ease of use has led this protocol to be adopted by biologists from partner agencies in every western state.
Bull trout have been a focus of these eDNA surveys. The initial studies have been directed at precisely delineating the distribution of bull trout within select watersheds, as well as confirming their absence from potential habitats and discovering previously unknown populations (McKelvey et al. 2016). In 2015, we paired predictions of bull trout habitat occupancy from the Climate Shield model with an optimized eDNA protocol to survey all juvenile bull trout habitats throughout two 8-digit HUC river basins in Montana and Idaho, and to begin these surveys in 10 additional 8-digit HUC basins. In 2016–2018, we extend this sampling to the entire range of bull trout in the U.S.
This was initially a 3-year project. Original samples were collected and submitted from 2016-2018. More recent bull trout data were added from samples from the eDNAtlas project, which also includes samples taken prior to 2016.
The range-wide bull trout eDNA project 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.
The template consisted of a master set of geospatially referenced sampling locations at 1-km intervals within each cold-water habitat. Researchers also identified sampling locations at this same 1-km intervals based on the U.S. Fish and Wildlife Service's 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 reliably determined the presence of populations of bull trout, as well as provided insights on non-spawning habitats used by adult and subadult fish. The result was a rapid, robust, and repeatable range-wide assessment of natal habitats of this species.
Bull Trout eDNA Survey Participation
The goal of this project was to collect eDNA samples at regular intervals in most cold-water habitats throughout the U.S. bull trout range that have a greater than 25% probability of occupancy by juvenile bull trout, that are regarded as critical habitat for spawning and rearing, or that historically supported bull trout. To achieve that goal participants were provided:
- A protocol that explains how to collect eDNA samples.
- There is a short video available on the protocol for collecting environmental DNA samples from streams.
- Additional guidelines specific to the bull trout eDNA survey project.
- A map and spreadsheet of eDNA points to guide sampling.
- The loan of a pump set with a battery & charger from our “tool library”.
- Field kits for the collection and storage of eDNA samples. To ensure consistency in sampling and guarantee sterility of the supplies.
A few weeks after samples were collected, we provided results on whether and where bull trout were present. At the end of each year, we posted an interactive map of the results of sampling across the range of bull trout.
Deliverables
The completed bull trout eDNA survey results Online Map allows users to view the survey results in an interactive 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. Please note that there are some issues with IE and it's recommended to use a different browser.
Online Map
PDF Maps by HUC 8
AGOL User Guide
Metadata
Bull Trout eDNA shapefile
Citation
If you use these data, please cite as: 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 digital maps and sample coordinates in the table below were used to guide your eDNA surveys for determining the occurrence of bull trout in spawning and rearing habitats anywhere throughout their historical range in the Northwest. Most of the potential bull trout streams (>5,000) were identified using the Climate Shield habitat occupancy model developed from >4,000 fish surveys in 512 streams, but USFWS-designated critical habitats for bull trout spawning and rearing are also shown on the maps.
- PDF index map of HUCs
- Shapefile of WBD HUCs
- Map Documentation
- Import Excel spreadsheet coordinates to Garmin GPS procedures
HUC 8 | BTeDNA Sample Sites Map Name | Sample Coordinates Excel Spreadsheet |
09040001 | ||
17010101 | ||
17010102 | ||
17010103 | ||
17010104 | ||
17010105 | ||
17010106 | ||
17010201 | Upper Clark Fork | |
17010202 | ||
17010203 | Blackfoot | |
17010204 | ||
17010205 | ||
17010206 | ||
17010207 | ||
17010208 | ||
17010209 | ||
17010210 | ||
17010211 | ||
17010212 | ||
17010213 | ||
17010214 | ||
17010215 | ||
17010216 | ||
17010301 | ||
17010302 | ||
17010304 | St. Joe | |
17020001 | ||
17020002 | ||
17020003 | ||
17020004 | ||
17020005 | ||
17020006 | ||
17020007 | ||
17020008 | ||
17020009 | ||
17020010 | ||
17020011 | ||
17030001 | ||
17030002 | ||
17030003 | ||
17040217 | ||
17050102 | ||
17050111 | ||
17050112 | ||
17050113 | ||
17050116 | ||
17050120 | ||
17050121 | ||
17050122 | ||
17050123 | ||
17050124 | ||
17050201 | ||
17050202 | ||
17050203 | ||
17060101 | ||
17060102 | ||
17060103 | ||
17060104 | ||
17060105 | ||
17060106 | ||
17060107 | ||
17060201 | ||
17060202 | ||
17060203 | ||
17060204 | ||
17060205 | ||
17060206 | ||
17060207 | ||
17060208 | ||
17060209 | ||
17060210 | ||
17060301 | ||
17060302 | ||
17060303 | ||
17060305 | ||
17060307 | ||
17060308 | ||
17070102 | ||
17070103 | ||
17070105 | ||
17070106 | ||
17070201 | ||
17070202 | ||
17070203 | ||
17070301 | ||
17070302 | ||
17070306 | ||
17080001 | ||
17080002 | ||
17080003 | ||
17080004 | ||
17080005 | ||
17090001 | ||
17090004 | ||
17090005 | ||
17090011 | ||
17100101 | ||
17100102 | ||
17100104 | ||
17100105 | ||
17110001 | ||
17110004 | ||
17110005 | ||
17110006 | ||
17110007 | ||
17110008 | ||
17110009 | ||
17110010 | ||
17110012 | ||
17110013 | ||
17110014 | ||
17110015 | ||
17110017 | ||
17110018 | ||
17110020 | ||
18010202 | ||
18010203 |
Staff
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Person
Michael K. Young, PhD
Emeritus Scientisthttps://research.fs.usda.gov/about/people/michael.k.young -
Person
Daniel J. Isaak, PhD
Research Fish Biologisthttps://research.fs.usda.gov/about/people/daniel.isaak -
Person
Sharon L. Payne
RMRS GIS Specialist and W&W Web Managerhttps://research.fs.usda.gov/about/people/sharon.l.payne -
Person
Thomas W. Franklin
Ecologist / eDNA Program Leaderhttps://research.fs.usda.gov/about/people/thomas.franklin -
Person
Kevin S. McKelvey, PhD
Emeritus Scientisthttps://research.fs.usda.gov/about/people/kevin.mckelvey -
Person
Michael K. Schwartz, PhD
Director, National Genomics Center for Wildlife and Fish Conservationhttps://research.fs.usda.gov/about/people/michael.k.schwartz -
Person
Kellie Carim, PhD
Research Ecologisthttps://research.fs.usda.gov/about/people/kellie.carim -
Person
Taylor Wilcox, PhD
Research Geneticisthttps://research.fs.usda.gov/about/people/taylor.wilcox -
Person
Gwynne L. Chandler
Fish Biologisthttps://research.fs.usda.gov/about/people/gwynne.chandler -
Person
David E. Nagel
Physical Scientist/Spatial Analysthttps://research.fs.usda.gov/about/people/david.nagel -
Person
Dona Horan
Fish Biologisthttps://research.fs.usda.gov/about/people/dona.horan -
Person
Sherry P. Wollrab
Ecologisthttps://research.fs.usda.gov/about/people/sherry.p.wollrab
Data and Tools
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Dataset
https://research.fs.usda.gov/rmrs/products/dataandtools/bull-trout-edna-sample-site-locations
Documents
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https://research.fs.usda.gov/sites/default/files/2023-03/rmrs-range-wide-bull-trout-edna-project-arcgis-online-map-guide.pdfFile Type: pdf
File Size: 1.10MB -
https://research.fs.usda.gov/sites/default/files/2023-03/rmrs-btedna_indexmap_fullsize.pdfFile Type: pdf
File Size: 1.05MB -
https://research.fs.usda.gov/sites/default/files/2023-03/rmrs-bull-trout-edna-extracted-points-metadata.pdfFile Type: pdf
File Size: 303KB -
https://research.fs.usda.gov/sites/default/files/2023-03/rmrs-additional_guidelines_for_the_bull_trout_edna_surveys.pdfFile Type: pdf
File Size: 216KB -
https://research.fs.usda.gov/sites/default/files/2023-03/rmrs-edna_bull_trout_-_partners.pdfFile Type: pdf
File Size: 287KB -
https://research.fs.usda.gov/sites/default/files/2023-03/rmrs-edna_fieldsite_posterdocumentation.pdfFile Type: pdf
File Size: 72KB -
https://research.fs.usda.gov/sites/default/files/2023-03/rmrs-converting_edna_pointsexcelarcgis_basemap.pdfFile Type: pdf
File Size: 1.94MB
Publications
- Lisa A. Eby, Olga Helmy, Lisa M. Holsinger, Michael K. Young. 2014. Evidence of climate-induced range contractions in bull trout Salvelinus confluentus in a Rocky Mountain watershed, U.S.A.
- Kellie Carim, K. R. Christianson, Kevin S. McKelvey, W. M. Pate, D. B. Silver, B. M. Johnson, B. T. Galloway, Michael K. Young, Michael K. Schwartz. 2016. Environmental DNA marker development with sparse biological information: A case study on opossum shrimp (Mysis diluviana)
- Kellie Carim, Joseph Dysthe, Michael K. Young, Kevin S. McKelvey, Michael K. Schwartz. 2017. A noninvasive tool to assess the distribution of Pacific lamprey (Entosphenus tridentatus) in the Columbia River basin
- Kellie Carim, Joseph Dysthe, Michael K. Young, Kevin S. McKelvey, Michael K. Schwartz. 2016. An environmental DNA assay for detecting Arctic grayling in the upper Missouri River basin, North America
- Kellie Carim, Kevin S. McKelvey, Michael K. Young, Taylor Wilcox, Michael K. Schwartz. 2016. A protocol for collecting environmental DNA samples from streams
- Daniel J. Isaak, Michael K. Young, David E. Nagel, Dona Horan, Matthew C. Groce. 2015. The cold-water climate shield: Delineating refugia for preserving salmonid fishes through the 21st century
- Stephen F. Jane, Taylor M. Wilcox, Kevin S. McKelvey, Michael K. Young, Michael K. Schwartz, Winsor H. Lowe, Benjamin H. Letcher, Andrew R. Whiteley. 2014. Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams
- Kevin S. McKelvey, Michael K. Young, W. L. Knotek, Kellie Carim, T. M. Wilcox, T. M. Padgett-Stewart, Michael K. Schwartz. 2016. Sampling large geographic areas for rare species using environmental DNA: A study of bull trout Salvelinus confluentus occupancy in western Montana
- Taylor M. Wilcox, Kellie Carim, Kevin S. McKelvey, Michael K. Young, Michael K. Schwartz. 2015. The dual challenges of generality and specificity when developing environmental DNA markers for species and subspecies of Oncorhynchus
- Taylor M. Wilcox, Kevin S. McKelvey, Michael K. Young, Stephen F. Jane, Winsor H. Lowe, Andrew R. Whiteley, Michael K. Schwartz. 2013. Robust detection of rare species using environmental DNA: The importance of primer specificity
- Taylor M. Wilcox, Michael K. Schwartz, Kevin S. McKelvey, Michael K. Young, Winsor H. Lowe. 2014. A blocking primer increases specificity in environmental DNA detection of bull trout (Salvelinus confluentus)
- Taylor M. Wilcox, Kevin S. McKelvey, Michael K. Young, Winsor H. Lowe, Michael K. Schwartz. 2015. Environmental DNA particle size distribution from Brook Trout (Salvelinus fontinalis)
- Taylor M. Wilcox, Kevin S. McKelvey, Michael K. Young, Adam J. Sepulveda, Bradley B. Shepard, Stephen F. Jane, Andrew R. Whiteley, Winsor H. Lowe, Michael K. Schwartz. 2016. Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis
- Michael K. Young, Daniel J. Isaak, Kevin S. McKelvey, Taylor M. Wilcox, Daniel M. Bingham, Kristine L. Pilgrim, Kellie Carim, Matthew R. Campbell, Matthew P. Corsi, Dona Horan, David E. Nagel, Michael K. Schwartz. 2016. Climate, demography, and zoogeography predict introgression thresholds in salmonid hybrid zones in Rocky Mountain streams
External Publications
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U.S. Fish and Wildlife Service (2014) Revised draft recovery plan for the coterminous United States population of bull trout (Salvelinus confluentus). Portland, Oregon. xiii + 151 pp.
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U.S. Fish and Wildlife Service (2008) Bull trout recovery monitoring and evaluation guidance. Report prepared for the U.S. Fish and Wildlife Service by the Bull Trout Recovery and Monitoring Technical Group (RMEG). Portland, OR.