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Detection and range delineation of bull trout using environmental DNA

Date: May 20, 2015

Scientists discover previously unknown populations of bull trout using new technology


Modeled bull trout habitat in western Montana and northern Idaho. Color coding indicates the estimated likelihood of a stream providing spawning and rearing habitat for bull trout (Isaak et al. 2015)
Modeled bull trout habitat in western Montana and northern Idaho. Color coding indicates the estimated likelihood of a stream providing spawning and rearing habitat for bull trout (Isaak et al. 2015)
Bull trout are a critical component of aquatic community assemblages, and a focal species for the Great Northern Landscape Conservation Cooperative in all four ecotypic areas: the Columbia Basin, Rocky Mountains, Sagebrush Steppe, and Cascadia. This species is Endangered Species Act(ESA)-listed and occurs at low densities within thousands of streams designated as critical habitat across the region. Bull trout is also the most thermally restricted salmonid in the Northwest: over 90% of juvenile bull trout observations are in streams with mean August water temperatures < 11°C (Isaak et al. 2015).

Mounting evidence shows that the distribution of bull trout within individuals streams has been contracting in association with climate change; some historically occupied habitats may no longer support populations. Because of the difficulty and expense of sampling bull trout, current information about the species distribution is imprecise and many streams have been sampled infrequently or not at all. That uncertainty comes at a cost. Stakeholders may not be able to efficiently target their limited conservation resources, may forego or delay land management critical for other objectives, and may even avoid monitoring populations because of the added burden of obtaining sampling permits.

To reduce uncertainties (and regulatory gridlock) associated with bull trout, we recently developed and published the Climate Shield Habitat Occupancy Model, which uses NorWeST temperature information and other environmental covariates to accurately predict the probability of bull trout (and cutthroat trout) presence across the Columbia Basin (Fig. 1; Isaak et al. 2015). The fish and temperature data used to develop the NorWeST and Climate Shield databases and models were “crowd-sourced.” That approach was particularly powerful because it engaged hundreds of biologists working for dozens of agencies and leveraged their raw data to develop databases worth over $10,000,000. Building on those efforts, we propose to conduct a precise, up-to-date, range-wide bull trout status assessment through the use of crowd-sourcing, digital media, and new genomic techniques that are revolutionizing the cost-effectiveness of broad-scale species sampling.

Among the array of genomic techniques now available, environmental DNA (eDNA) has emerged as a powerful method for determining the occurrence of many species reliably and inexpensively.  The method involves collecting DNA shed by organisms (i.e., environmental DNA) by pumping water through a filter. We have also developed a field-proven eDNA sampling protocol that requires only 15 minutes of effort by a single person to collect a sample.

For bull trout, initial studies with eDNA have been directed at precisely delineating the their distribution within select watersheds, as well as confirming their absence from potential habitats and discovering previously unknown populations (Fig. 2). Samples collected to evaluate bull trout distributions can be used to evaluate many other species with no additional field costs and can serve as a multi-species baseline for future biodiversity assessments.

A comparison of eDNA detection of bull trout in the headwaters of Lolo Creek, Montana and previous electofishing. The arrow points to a small putative population that was previously undetected.
A comparison of eDNA detection of bull trout in the headwaters of Lolo Creek, Montana and previous electofishing. The arrow points to a small putative population that was previously undetected.

Featured Publications

Isaak, Daniel J. ; Young, Michael K. ; Nagel, David E. ; Horan, Dona ; Groce, Matthew C. , 2015
Wilcox, Taylor M. ; Schwartz, Michael K. ; McKelvey, Kevin S. ; Young, Michael K. ; Lowe, Winsor H. , 2014
Jane, Stephen F. ; Wilcox, Taylor M. ; McKelvey, Kevin S. ; Young, Michael K. ; Schwartz, Michael K. ; Lowe, Winsor H. ; Letcher, Benjamin H. ; Whiteley, Andrew R. , 2014
Wilcox, Taylor M. ; McKelvey, Kevin S. ; Young, Michael K. ; Jane, Stephen F. ; Lowe, Winsor H. ; Whiteley, Andrew R. ; Schwartz, Michael K. , 2013


Forest Service Partners: 
Jim Brammer, USFS Beaverhead-Deer Lodge NF
Casey Watson, USFS Boise NF
George Liknes, USFS Helena NF
Lisa Howden and Dan Scaife, USFS Idaho Panhandle NF
Aubree Benson, Jon Hanson, Shane Hendrickson, and Traci Sylte, USFS Lolo NF
Thomas Cameron, Brian Riggers, and Scott Spaulding, USFS Northern Region
Dan Duffield, Lee Jacobson, and Cynthia Tait, USFS Intermountain Region
John Chatel, USFS Pacific Northwest Region
Brenda Mitchell, USFS Sawtooth NF
External Partners: 
Dimitri Vigergar, Bureau of Reclamation
Will McDowell, Clark Fork Coalition
Bruce Rieman, Clearwater Resource Council
Angelo Vitale, Coeur d'Alene Tribes
Tim Copeland, Matt Corsi, Joe Dupont, Jim Fredericks, and Kevin Meyer, Idaho Department of Fish and Game
Rick Wilkison, Idaho Power Company
Gary Frank, Montana Department of Natural Resources Conservation
Ladd Knotek, Ryan Kreiner, Brad Liermann, Ron Pierce, and Pat Saffel, Montana Fish, Wildlife & Parks
David Lawrence, National Fish and Wildlife Foundation
Steve Kloetzel, The Nature Conservancy
Amy Haak, Trout Unlimited
Dan Brewer and Erin Britton Kuttel, U.S. Fish and Wildlife Service
Kirk Krueger, Washington Department of Fish and Wildlife
Bob Rose, Yakima Nation