United States Department of Agriculture
National Genomics Center for Fish and Wildlife Conservation
Case Study: Bull Trout
The National Genomics Center for Fish and Wildlife Conservation offers cost effective and
reliable genetic and genomic data to enhance fish and wildlife monitoring. Since 2008, Forest
Service scientists at the Rocky Mountain Research Station have contributed to monitoring
and assessment efforts of the threatened bull trout, with an emphasis on genetic approaches.
Background
Bull trout (Salvelinus confluentus) are native to portions of
western North America. This species is a cold-water specialist
that relies on large river basins with clean water and wellconnected habitat to persist. Reductions in habitat connectivity
and quality, along with interactions with introduced trout
(e.g., brook trout: Salvelinus fontinalis), have led to rangewide declines in bull trout. This species is currently listed
as Threatened under the U.S. Endangered Species Act and
several lineages are designated as Threatened or of Special
Concern by the Committee on the Status of Endangered
Wildlife in Canada. Even in high-quality habitat, bull trout
tend to be found in low numbers, and they are among the
most difficult species to monitor using traditional sampling
Bull trout spawning.
Credit: Joel Sartore (National Geographic) & Wade
methods. Yet doing so is critical, because land management
Fredenberg (U.S. Fish and Wildlife Service).
and recreational angling are significantly influenced by
whether or not bull trout are present in a given watershed. Moreover, bull trout are likely to be the species most sensitive
to warming stream temperatures associated with climate change, and localized extirpations have already occurred.
The Rocky Mountain Research Station (RMRS) has long been involved in monitoring and assessment of bull trout, with
an emphasis on genetic approaches since 2008. In collaboration with Region 1 of the Forest Service, Station scientists
conducted one of the first systematic, comprehensive inventories of bull trout presence in small streams in this area,
sampling nearly 900 sites on over 400 streams. The Center now harbors what may be the largest tissue archive of bull
trout from the Northern Rocky Mountains. RMRS scientists and University of Montana researchers recently completed
the first work in North America to describe losses in bull trout populations (or of any freshwater fish) related to climate
change. Ongoing work combines spatially specific occupancy models and climate data to make highly accurate
predictions about locations of currently occupied bull trout habitat, as well as projections about those habitats likely to be
occupied under moderate and extreme climate change. Validating those predictions and projections is crucial, but doing so
using conventional sampling is not feasible due to low detection probabilities when sampling bull trout and the scope and
inaccessibility of the intended monitoring area. Thus, Station scientists have pioneered environmental-DNA, or eDNA,
based methods to detect the presence of bull trout. Station scientists have refined the sampling methods needed to make
eDNA surveys a reliable and accessible option for managers, and have collaborated with managers throughout the Western
United States to conduct eDNA studies of bull trout and of their primary nonnative competitor, brook trout.
Forest Service Research & Development
Continued on back
National Genomics Center for Fish and Wildlife Conservation
Case Study: Bull Trout
Next Steps
The next steps are to optimize those methods to permit their application at spatial scales ranging from local to regional.
That is, we would go from determining the upstream extent of populations in individual streams, to identifying species
presence within entire watersheds, to assessing species distribution and trends at the scale of the Columbia River basin,
the Western United States, and the entire range of a species.
Partial List of Partners
• U.S. Forest Service: Washington Office, Region 1, Bitterroot National Forest, Idaho Panhandle National Forest, Lolo
National Forest, Kootenai National Forest, Nez Perce-Clearwater National Forest, Payette National Forest, SalmonChallis National Forest, Sawtooth National Forest Idaho Department of Fish and Game
• Montana Fish, Wildlife and Parks
• Oregon Department of Fish and Wildlife
• Nez Pierce Tribe
• University of Montana
• University of Massachusetts
• U.S. Fish and Wildlife Service
Select Publications
TM Wilcox, MK Schwartz, KS McKelvey, MK Young, WH Lowe (2014) A blocking primer increases specificity in
environmental DNA detection of bull trout (Salvelinus confluentus). Conservation Genetics Resources, 6, 283–284.
LA Eby, O Helmy, LM Holsinger, MK Young (2014) Evidence of climate-induced range contractions in bull trout
Salvelinus confluentus in a Rocky Mountain watershed, USA. PloS ONE, 9, e98812.
SF Jane, TM Wilcox, KS McKelvey, MK Young, MK Schwartz, WH Lowe, BH Letcher, AR Whiteley (2014) Distance,
flow and PCR inhibition: eDNA dynamics in two headwater streams. Molecular Ecology Resources. doi: 10.1111/17550998.12285.
TM Wilcox, KS McKelvey, MK Young, SF Jane, WH Lowe, AR Whiteley, MK Schwartz (2013) Robust detection of rare
species using environmental DNA: the importance of primer specificity. PloS ONE, 8, e59520.
SJ Wenger, NA Som, DC Dauwalter, DJ Isaak, HM Neville, CH Luce, JB Dunham, MK Young, KD Fausch, BE Rieman
(2013) Probabilistic accounting of uncertainty in
forecasts of species distributions under climate change.
Global Change Biology, 19, 3343–3354
Photo to Right: Bull trout spawning.
Credit: Joel Sartore (National Geographic) & Wade
Fredenberg (U.S. Fish and Wildlife Service).
Forest Service
Research & Development For more information, contact: Michael Schwartz, PhD
Center Director
michaelkschwartz@fs.fed.us