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eDNA

Water sampling

Imagine looking out across an enormous landscape filled with brooks, creeks, rivers, ponds or lakes. Now imagine your task is to determine if a new ecological threat, such as an invasive species, has begun to invade this landscape. A nearly impossible task! Scientists in the USDA Forest Service are working on ways to determine where a species has invaded by simply sampling a cup of water from locations across the landscape. This is the exciting new field of environmental DNA, or eDNA.

eDNA is DNA that has been separated from organisms into the surrounding environment. For example, DNA in skin cells sloughed from a fish can be found in water, or DNA in plant pollen can be found in the air. Ecologists are able to collect and analyze this DNA to detect organisms of interest. eDNA has great potential as a monitoring tool for wildlife and fish management, particularly in the detection of threatened and endangered species, or individuals at the leading edge of an invasion. For example, scientists used filtered water samples to detect the spread of invasive feral pigs in the Southwestern United States and Burmese python in Florida. Scientists are using similar techniques in the Rocky Mountains to determine the distribution of endangered Bull Trout and invasive Brook Trout.

The use of eDNA is an innovative way to inventory and monitoring fish and wildlife. eDNA is a highly sensitive method for detecting organisms in low abundance and is generally faster and more cost effective than traditional sampling methods. eDNA allows researchers to inexpensively screen for the presence of these aquatic species using specialized technology, such as quantitative polymerase chain reaction (qPCR), which is able to detect DNA from just a couple cells in an environmental sample. Using eDNA is one method of non-invasive genetic sampling, a field in which Forest Service scientists at the Rocky Mountain Research Station have been leaders for years.

Ongoing Projects

Forest Service scientists at the Rocky Mountain Research Station are leaders in developing eDNA tools and applications for detecting aquatic species of high ecological and social interest. These include invasive Brook Trout in the Intermountain West, as well as Bull Trout, which are listed as threatened under the U.S. Endangered Species Act. Forest Service scientists have also optimized sampling protocols, providing easy instructions for any biologist to collect their own eDNA samples in the field. Using these tools and protocols, Forest Service scientists are collaborating with biologists across the nation, including those employed by states and tribes, to inform management decisions. In addition to the more common approach of detecting a single species at a time, the agency is piloting eDNA use for broad-scale biodiversity monitoring.

To effectively apply this relatively new technology in the field, it is critical that researchers and managers understand both the strengths and limitations of this monitoring tool. Forest Service scientists are working to determine the probability of detection for aquatic species under a range of environmental conditions.

Services

Water sampling
  • Protocols and equipment for collecting aquatic eDNA samples
  • Analysis of eDNA samples for:
    • Any salmonid
    • Any sculpin
    • Arctic grayling
    • Boreal toad
    • Brook Trout
    • Brown Trout
    • Bull Trout
    • Canada lynx
    • Chinook Salmon
    • Chum Salmon
    • Coho Salmon
    • Fisher
    • Grizzly bear
    • Harlequin duck
    • Lake Trout
    • Loach Minnow
    • Mysis (Opossum) Shrimp
    • North American River Otter
    • Northern Leatherside
    • Northern Pike
    • Pacific Lamprey
    • Rainbow Trout
    • Rio Grande chub
    • Rio Grande sucker
    • Rocky Mountain sculpin
    • Sacramento pikeminnow
    • Sauger
    • Slimy sculpin (Rocky Mountain variant)
    • Smallmouth bass
    • Snake River Physa snail
    • Spikedace
    • Sturgeon chub
    • Walleye
    • Western pearlshell mussel
    • Western spadefoot toad
    • Westslope Cutthroat Trout
    • Wolverine
    • Yellowstone Cutthroat Trout
    • Coming soon: Bluehead Sucker, Burbot, California Floater, Channel catfish, Coastal Cutthroat Trout, Dolly Varden Trout, Green Sunfish Lahontan Cutthroat Trout, Lampetra spp., Mountain Sucker, Oregon Floater, Plains Killifish, Plains Topminnow, Umpqua Chub, Umpqua Pikeminnow, Yaqui Catfish
  • Marker development for species detection
  • Analysis for detection of other species with developed eDNA markers upon request

A protocol for collecting environmental DNA samples

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.

Selected Publications

Carim, K. J., K. R. Christianson, K. S. McKelvey, W. M. Pate, D. B. Silver, B. M. Johnson, B. T. Galloway, M. K. Young, and M. K Schwartz.  2016. Environmental DNA marker development with sparse biological information: a case study on opossum shrimp (Mysis diluviana). PLoS ONE 11:e0161664. doi:10.1371/journal.pone.0161664

Dysthe, J. C., T. Rodgers, T. W. Franklin, K. J. Carim, M. K. Young, K. S. McKelvey, K. E. Mock, and M. K. Schwartz. 2018. Repurposing environmental DNA samples: detecting the western pearlshell (Margaritifera falcata) as a proof of concept.  Ecology and Evolution. DOI: 10.1002/ece3.3898

McKelvey, K. S., M. K. Young, T. M. Wilcox, D. Bingham, K. L. Pilgrim, and M. K. Schwartz. 2016. Patterns of hybridization among cutthroat trout and rainbow trout in northern Rocky Mountain streams.  Ecology and Evolution 6:688-06. doi: 10.1002/ece3.1887

Jane, S. F., T. M. Wilcox, K. S. McKelvey, M. K. Young, M. K. Schwartz, W. H. Lowe, B. H. Letcher, and A. R. Whiteley. 2015. Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams. Molecular Ecology Resources 15:216-227.

Wilcox T. M., K. S. McKelvey, M. K. Young, S. F. Jane, W. H. Lowe, A. R. Whitely, and M.K. Schwartz. 2013. Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS ONE 8: e59520.

Wilcox, T. M, K. S. McKelvey, M. K. Young, A. J. Sepulveda, B. B. Shepard, S. F. Jane, A. R. Whiteley, W. H. Lowe, and M. K. Schwartz. 2016. Understanding environmental DNA detection probabilities: a case study using a stream-dwelling char Salvelinus fontinalis.  Biological Conservation 194:209-216.

For more publications on eDNA research at the Forest Service, visit Treesearch.