eDNA Sampling & Supporting Science

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 will extend this sampling to the entire range of bull trout in the U.S.

Key References

Eby LA, Helmy O, Holsinger LM, Young MK (2014) Evidence of climate-induced range contractions in Bull Trout Salvelinus confluentus in a Rocky Mountain watershed, USA. PloS ONE, 9, e98812.

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

Carim, Kellie J.; Dysthe, J. Caleb; Young, Michael K.; McKelvey, Kevin S.; Schwartz, Michael K. 2017. A noninvasive tool to assess the distribution of Pacific lamprey (Entosphenus tridentatus) in the Columbia River basin. PLoS ONE. 12(1): e0169334.

Carim, K. J.; Dysthe, J. C. S.; Young, M. K.; McKelvey, K. S.; Schwartz, M. K. 2016. An environmental DNA assay for detecting Arctic grayling in the upper Missouri River basin, North America. Conservation Genetics Resources. doi: 10.1007/s12686-016-0531-1.

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.

Isaak D, Young MK, Nagel D, Horan D, Groce M (2015) The cold-water climate shield: delineating refugia for preserving salmonids through the 21st century. Global Change Biology, 21. doi:10.1111/gcb.12879.

Jane SF, Wilcox TM, McKelvey KS, Young MK, Schwartz MK, Lowe WH, Letcher BH, Whiteley AR (2015) Distance, flow, and PCR inhibition: eDNA dynamics in two headwater streams. Molecular Ecology Resources, 15. doi: 10.1111/1755-0998.12285.

McKelvey KS, Young MK, Knotek WL, Carim KJ, Wilcox TM, Padgett-Stewart TM, Schwartz MK (2016) Sampling large geographic areas for rare species using environmental DNA: a study of bull trout Salvelinus confluentus occupancy in western Montana. Journal of Fish Biology. doi:10.1111/jfb.12863.

Miller, Sue; Carim, Kellie; Schwartz, Mike; Spaulding, Scott; Wilcox, Taylor. 2020. Black and white and shed all over: How eDNA analysis can help to answer your species questions. Science You Can Use Bulletin, Issue 40. Fort Collins, CO: Rocky Mountain Research Station. 11 p.

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.

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.

Wilcox TM, Carim KJ, McKelvey KS, Young MK, Schwartz MK (2015a) The dual challenges of generality and specificity when developing environmental DNA markers for species and subspecies of Oncorhynchus. PLoS ONE, 10, e142008.

Wilcox TM, McKelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS ONE, 8, e59520.

Wilcox TM, Schwartz MK, McKelvey KS, Young MK, Lowe WH (2014) A blocking primer increases specificity in environmental DNA detection of bull trout (Salvelinus confluentus). Conservation Genetics Resources, 6, 283–284.

Wilcox TM, McKelvey KS, Young MK, Lowe WH, Schwartz MK (2015b) Environmental DNA particle size distribution from Brook Trout (Salvelinus fontinalis). Conservation Genetics Resources. DOI 10.1007/s12686-015-0465-z.

Wilcox TM, McKelvey KS, Young MK, Sepulveda AJ, Shepard BB, Jane SF, Whiteley AR, Lowe WH, Schwartz MK (2016) Understanding environmental DNA detection probabilities: a case study using a stream-dwelling char Salvelinus fontinalis. Biological Conservation, 194, 209–216.

Young MK, Isaak DJ, McKelvey KS, Wilcox TM, Bingham DM, Pilgrim KL, et al. (2016) Climate, demography, and zoogeography predict introgression thresholds in salmonid hybrid zones in Rocky Mountain streams. PLoS ONE 11(11): e0163563. doi:10.1371/journal.pone.0163563.