United States Department of Agriculture
National Genomics Center for Fish and Wildlife Conservation
Case Study: Cutthroat 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 been investigating the
ecology and status of cutthroat trout, with an emphasis on genetic approaches.
Background
Cutthroat trout (Oncorhynchus clarkii) are native
throughout western North America. There are 12 extant
subspecies, and all occupy cold water with the majority
of populations found on public lands. Cutthroat trout
are considered habitat generalists, but are particularly
sensitive to the presence of other introduced trout, such
as rainbow trout (Oncorhynchus mykiss), brook trout
(Salvelinus fontinalis), and brown trout (Salmo trutta).
Most subspecies have undergone substantial habitat
losses (>50%) relative to their historical ranges, primarily
because of habitat degradation and negative interactions
with introduced trout species. Nearly all populations have
been petitioned for listing under the U.S. Endangered
Cutthroat trout specimen. Credit: Morgan Sparks, University of
Species Act, and two subspecies have already gone
Alaska-Fairbanks, SFOS/IAB.
extinct. Nonnative fishes influence cutthroat trout either
via hybridization (with rainbow trout) or a combination of competition and predation (brook trout, to an extent brown
trout). Understanding the genetic integrity and population distribution of cutthroat trout and the presence of nonnative
fishes are critical for conservation management of the species.
The Rocky Mountain Research Station is a leader in investigating the ecology, status, and genetic patterns of cutthroat
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 cutthroat trout presence in small streams in
this area, sampling nearly 900 sites on over 400 streams that are part of ongoing habitat monitoring (PIBO: PACFISH/
INFISH Biological Opinion). The National Genomics Center for Fish and Wildlife Conservation now harbors the largest
tissue archive of cutthroat trout from the Northern Rocky Mountains. In part based on that archive, Station scientists
developed one of the largest panels of genetic markers for evaluating hybridization in cutthroat trout, as well as the first
range-wide assessment of units of conservation within westslope cutthroat trout (Onchorhynchus clarkii lewisi).
Ongoing work combines spatially specific occupancy models and climate data to make highly accurate predictions about
locations of currently occupied cutthroat 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 the high cost and effort required to sample the large geographic area under
study. Thus, Forest Service scientists have pioneered environmental-DNA (eDNA) based methods to detect the presence
of cutthroat trout, as well as invasive species that pose a threat.
Forest Service Research & Development
Continued on back
National Genomics Center for Fish and Wildlife Conservation
Case Study: Cutthroat Trout
Background Continued
Recently completed work includes the development of taxon-specific eDNA markers for westslope cutthroat trout,
Yellowstone cutthroat trout (O.c. bouvieri), and rainbow trout, with a similar marker for brown trout in production and
complementing markers already developed for brook trout and bull trout (S. confluentus). Station scientists have refined
the sampling methods needed to make eDNA surveys a reliable and accessible option for managers, particularly with
respect to detecting early invasions of brook trout and evaluating the effectiveness of migration barriers and mechanical
or chemical treatments for their removal. For all trout species, the next steps are to optimize and apply eDNA methods
broadly across local and regional scales. Specifically, eDNA applications could range 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 a species’s entire range.
Partial List of Partners
• U.S. Forest Service: Washington Office, Pacific
Northwest Research Station, Region 1, Region 3,
Bitterroot National Forest, Grand Mesa-UncompahgreGunnison National Forests, Idaho Panhandle National
Forest, Lolo National Forest, Kootenai National
Forest, Nez Perce-Clearwater National Forests, Payette
National Forest, Salmon-Challis National Forest,
Sawtooth National Forest Arizona Game and Fish
Department
• California Department of Fish and Wildlife
• Idaho Department of Fish and Game
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Montana Fish, Wildlife and Parks
Oregon Department of Fish and Wildlife
Utah Division of Wildlife
Washington Department of Ecology
Columbia River Inter-Tribal Fish Commission
Nez Perce Tribe
Idaho State University
University of Montana
University of Massachusetts
U.S. Fish and Wildlife Service
Wildlife Conservation Society
Select Publications
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. Distance, flow and PCR inhibition: eDNA dynamics in two headwater
streams. Molecular Ecology Resources. doi: 10.1111/1755-0998.12285.
Wilcox, Taylor M.; Schwartz, Michael K.; McKelvey, Kevin S.; Young, Michael K.; Lowe, Winsor H. 2014. A blocking
primer increases specificity in environmental DNA detection of bull trout (Salvelinus confluentus). Conservation Genetics
Resources. 6: 283-284.
Wilcox, Taylor M.; McKelvey, Kevin S.; Young, Michael K.; Jane, Stephen F.; Lowe, Winsor H.; Whiteley, Andrew
R.; Schwartz, Michael K. 2013. Robust detection of rare species using environmental DNA: The importance of primer
specificity. PLoS ONE 8(3): e59520. doi: 10.1371/journal.pone.0059520
Young, Michael K.; McKelvey, Kevin S.; Pilgrim, Kristine L.; Schwartz, Michael K. 2013. DNA barcoding at riverscape
scales: Assessing biodiversity among fishes of the genus Cottus (Teleostei) in northern Rocky Mountain streams.
Molecular Ecology. doi: 10.1111/1755-0998.12091
Hansen, Michael M.; Olivieri, Isabelle; Waller, Donald M.; Nielsen, Einar E.; Allendorf, F. W.; Schwartz, M. K.; Baker,
C. S.; Gregovich, D. P.; Jackson, J. A.; Kendall, K. C.; Laikre, L.; McKelvey, K.; Neel, M. C.; Ryman, N.; Short Bull, R.;
Stetz, J. B.; Tallmon, D. A.; Vojta, C. D.; Waples, R. S. 2012. Monitoring adaptive genetic responses to environmental
change. Molecular Ecology. doi: 10.1111/j.1365-294X.2011.05463.x
Forest Service
Research & Development For more information, contact: Michael Schwartz, PhD
Center Director
michaelkschwartz@fs.fed.us