Supporting Science

Aquatic environmental DNA (eDNA) sampling is the collection of DNA released by a target species into streams, rivers, ponds, lakes, and wetlands. Detection of stream fish with eDNA can be 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 single-pass electrofishing (Wilcox et al. 2016). The simplicity and expedience of sample collection coupled with the potential for accurate estimates of species presence has led to widespread interest in this technique. At the National Genomics Center for Wildlife and Fish Conservation (NGC), scientists have been at the forefront of investigating and applying eDNA sampling for aquatic species, including developing 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). The papers and other contributions by the NGC are detailed below. For a broader perspective on the burgeoning literature on eDNA sampling, please see the eDNA reference page maintained at Washington State University.

Key References

Carim KJ, Bean NJ, Connor JM, Baker WP, Jaeger M, Ruggles MP, McKelvey KS, Franklin TW, Young MK, Schwartz MK. 2020. Environmental DNA Sampling Informs Fish Eradication Efforts: Case Studies and Lessons Learned. North American Journal of Fisheries Management 40:488–508. 

Carim KJ, McKelvey KS, Young MK, Wilcox TM, Schwartz MK. 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.J., M.K. Young, C. McConnell, B.B. Roper, E.K. Archer, B. Staab, C. Hirsch, D.E. Nagel, M.K. Schwartz, and G.L. Chandler. 2018. Crowd-sourced databases as essential elements for Forest Service partnerships and aquatic resource conservation. Fisheries 43, DOI: 10.1002/fsh.10083.

Kronenberger, J.A., Wilcox, T.M., Mason, D.H., Franklin, T.W., McKelvey, K.S., Young, M.K. and Schwartz, M.K., 2022. eDNAssay: a machine learning tool that accurately predicts qPCR cross‐amplification. Molecular Ecology Resources DOI: 10.1111/1755-0998.13681

Kronenberger, John K.; Wilcox, Taylor M.; Young, Michael K.; Mason, Daniel H.; Franklin, Thomas W.; Schwartz, Michael K. 2024. Large-scale validation of 46 invasive species assays using an enhanced in silico framework.

https://www.int-res.com/abstracts/esr/v53/p569-586/

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, 216-227.

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, 88, 1215-1222.

Morisette, Jeffrey; Burgiel, Stanley; Brantley, Kelsey; Daniel, Wesley; Darling, John; Davis, Jeanette; Franklin, Thomas; Gaddis, Keith; Hunter, Margaret; Lance, Richard; Leskey, Tracy; Passamaneck, Yale; Piaggio, Antoinette; Rector, Brian; Sepulveda, Adam; Smith, Melissa; Stepien, Carol; Wilcox, Taylor. 2021. Strategic considerations for invasive species managers in the utilization of environmental DNA (eDNA): Steps for incorporating this powerful surveillance tool. Management of Biological Invasions. 12(3): 747-775. https://doi.org/10.3391/mbi.2021.12.3.15.

Robinson, A.T., Y.M. Paroz, M.J. Clement, T.W. Franklin, J.C. Dysthe, M.K. Young, K.S. McKelvey, and K.J. Carim. 2019. Environmental DNA sampling of small-bodied minnows: performance relative to location, species, and traditional sampling. North American Journal of Fisheries Management. DOI: 10.1002/nafm.10344.

Rubenson, E.S., and J.D. Olden. 2020. An invader in salmonid rearing habitat: current and future distributions of smallmouth bass (Micropterus dolomieu) in the Columbia River Basin. Canadian Journal of Fisheries and Aquatic Sciences 77: 314–325

Steward, David R.; Hafen, Thomas; Hendrickson, Dean A.; Taylor, Andrew T.; Varela-Romero, Alejandro; Mason, Daniel H.; Dysthe, Joseph C.; Franklin, Thomas W.; Young, Michael K.; McKelvey, Kevin S; Schwartz, Michael K; Long, James M. 2024. Environmental DNA mitochondrial markers to assess potential occupancy of Endangered Yaqui catfish in the Yaqui River basin, Mexico.

https://doi.org/10.1002/edn3.548              

Wilcox, T.M., K. J. Carim, M. K. Young, K. S. McKelvey, T. W. Franklin, M. K. Schwartz. 2018. Comment: The Importance of Sound Methodology in Environmental DNA Sampling. North American Journal of Fisheries Management DOI: 10.1002/nafm.10055.

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, Taylor M.; Kronenberger, John A.; Young, Michael K.; Mason, Daniel H.; Franklin, Thomas W.; Schwartz, Michael K. 2024. The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa. Molecular Ecology Resources. 00: e13932.

Wilcox, T. M, McKelvey, K. S, Young, M. K, Engkjer, C., Lance, R. F., Lahr, A., Eby, L. A., Schwartz, M. K. 2020. Parallel, targeted analysis of environmental samples via high throughput quantitative PCR (HT-qPCR). Environmental DNA. DOI: 10.1002/edn3.80

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, 7, 639-641.

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.

Wilcox, T.M., Young, M.K., McKelvey, K.S., Isaak, D.J., Horan, D.L. and Schwartz, M.K., 2018. Fine-scale environmental DNA sampling reveals climate-mediated interactions between native and invasive trout species. Ecosphere. 9: e02500. 

Wilcox, T.M., Zarn, K.E., Piggott, M.P., Young, M.K., McKelvey, K.S. and Schwartz, M.K. 2018. Capture enrichment of aquatic environmental DNA: A first proof of concept. Molecular Ecology Resources 18:1392-1401.

Yates, M.C., Wilcox, T.M., McKelvey, K.S., Young, M.K., Schwartz, M.K. and Derry, A.M. 2021. Allometric scaling of eDNA production in stream‐dwelling brook trout (Salvelinus fontinalis) inferred from population size structure. Environmental DNA 3:553-560. 

Young, Michael K.; Isaak, Daniel J.; Nagel, David; Horan, Dona L.; Carim, Kellie J.; Franklin, Thomas W.; Zeller, Victoria A.; Roper, Brett; Schwartz, Michael K. 2022. Broad-scale eDNA sampling for describing aquatic species distributions in running waters: Pacific lamprey Entosphenus tridentatus in the upper Snake River, USA. Journal of Fish Biology. 101: 1312-1325.

Species Assays

(list of assays completed or in development at NGC)

(eDNA assay development protocol)

Carim KJ, Christianson KR, McKelvey KS, Pate WM, Silver DB, Johnson BM, Galloway BT, Young MK, Schwartz MK. 2016. Environmental DNA marker development with sparse biological information: A case study on opossum shrimp (Mysis diluviana). PLoS ONE. 11: e0161664.

Carim, K.J., Dysthe, J.C., McLellan, H., Young, M.K., McKelvey, K.S. and Schwartz, M.K., 2019. Using environmental DNA sampling to monitor the invasion of nonnative Esox lucius (northern pike) in the Columbia River basin, USA. Environmental DNA 1:215-226.

Carim KJ, Dysthe JC, Young MK, McKelvey KS, Schwartz MK. 2017. A noninvasive tool to assess the distribution of Pacific lamprey (Entosphenus tridentatus) in the Columbia River basin. PLoS ONE. 12(1): e0169334.

Carim KJ, Dysthe JC, Young MK, McKelvey KS, Schwartz MK. 2016. An environmental DNA assay for detecting Arctic grayling in the upper Missouri River basin, North America. Conservation Genetics Resources. 8, 197-199.

Carim, K. J.; Wilcox, T. M.; Anderson, M.; Lawrence, D.; Young, M. K.; McKelvey, K. S.; Schwartz, M. K. 2016. An environmental DNA marker for detecting nonnative brown trout (Salmo trutta). Conservation Genetics Resources, 8, 259-261.

Dysthe JC, Carim KJ, Franklin TW, Kikkert D, Young MK, McKelvey KS, Schwartz MK. 2018. Molecular detection of northern leatherside chub (Lepidomeda copei) DNA in environmental samples. Northwest Science, 78, 92–99.

Dysthe, Joseph C.; Carim, Kellie J.; Paroz, Yvette M.; McKelvey, Kevin S.; Young, Michael K.; Schwartz, Michael K. 2016. Quantitative PCR assays for detecting loach minnow (Rhinichthys cobitis) and spikedace (Meda fulgida) in the southwestern United States. PLoS One. 11: e0162200.

Dysthe, Joseph C.; Carim, Kellie J.; Ruggles, Michael; McKelvey, Kevin S.; Young, Michael K.; Schwartz, Michael K. 2017. Environmental DNA assays for the sister taxa sauger (Sander canadensis) and walleye (Sander vitreus). PLoS ONE 12: e0176459.

Dysthe JC, Rodgers T, Franklin TW, Carim KJ, Young MK, McKelvey KS, Mock KE, Schwartz MK. 2018. Repurposing environmental DNA samples—detecting the western pearlshell (Margaritifera falcata) as a proof of concept. Ecology and Evolution, 8, 2659–2670.

Dysthe, J.C., Franklin, T.W., McKelvey, K.S., Young, M.K. and Schwartz, M.K., 2018. An improved environmental DNA assay for bull trout (Salvelinus confluentus) based on the ribosomal internal transcribed spacer I. PLoS One. 13: e0206851., 13, p.e0206851.

Franklin TW et al. 2019. Using environmental DNA methods to improve winter surveys for rare carnivores: DNA from snow and improved noninvasive techniques. Biological Conservation 229:50–58. 

Franklin, Thomas W.; Dysthe, Joseph C.; Golden, Michael; McKelvey, Kevin S.; Hossack, Blake R.; Carim, Kellie J.; Tait, Cynthia; Young, Michael K.; Schwartz, Michael K. 2018. Inferring presence of the western toad (Anaxyrus boreas) species complex using environmental DNA. Global Ecology and Conservation. 15: e00438.

Franklin, Thomas W.; Wilcox, Taylor M.; McKelvey, Kevin S.; Greaves, Samuel E.; Dysthe, Joseph C.; Young, Michael K.; Schwartz, Michael K. 2019. Repurposing environmental DNA samples to verify the distribution of Rocky Mountain tailed frogs in the Warm Springs Creek Basin, Montana. Northwest Science. 93(1): 85-92.

Franklin, Thomas W.; Dysthe, Joseph C.; Neville, Helen; Young, Michael K.; McKelvey, Kevin M.; Schwartz, Michael K. 2022. Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) and Paiute cutthroat trout (Oncorhynchus clarkii seleniris) detection from environmental DNA samples: A dual-purpose assay. Western North American Naturalist. 82(2): 388-397.

Franklin, Thomas W.; Dysthe, Joseph C.; Rubenson, Erika S.; Carim, Kellie J.; Olden, Julian D.; McKelvey, Kevin S.; Young, Michael K.; Schwartz, Michael K. 2018. A non-invasive sampling method for detecting non-native smallmouth bass (Micropterus dolomieu). Northwest Science. 92(2): 149-157.

Homel, K.M., Franklin, T.W., Carim, K.J., McKelvey, K.S., Dysthe, J.C. and Young, M.K. 2020. Detecting spawning of threatened chum salmon Oncorhynchus keta over a large spatial extent using eDNA sampling: Opportunities and considerations for monitoring recovery. Environmental DNA. doi: 10.1002/edn3.159. 

Mason, D.H., Dysthe, J.C., Franklin, T.W., Skorupski, J.A., Young, M.K. and McKelvey, K.S., 2018. qPCR detection of Sturgeon chub (Macrhybopsis gelida) DNA in environmental samples. PLoS ONE, 13(12), p.e0209601.

Mason, D.H., Dysthe, J.C., Franklin, T.W., Williams, C.L., Young, M.K., McKelvey, K.S. and Schwartz, M.K. 2021. Certain detection of uncertain taxa: eDNA detection of a cryptic mountain sucker (Pantosteus jordani) in the Upper Missouri River, USA. Environmental DNA 3:449-457. 

Padgett-Stewart, Ticha M.; Wilcox, Taylor M.; Carim, Kellie J.; McKelvey, Kevin S.; Young, Michael K.; Schwartz, Michael K. 2016. An eDNA assay for river otter detection: A tool for surveying a semi-aquatic mammal. Conservation Genetics Resources. 8: 5-7.

Rodgers, T.W., Dysthe, J.C., Tait, C., Franklin, T.W., Schwartz, M.K. and Mock, K.E. 2020. Detection of 4 imperiled western North American freshwater mussel species from environmental DNA with multiplex qPCR assays. Freshwater Science 39:762-772. 

Wilcox TM, Caragiulo A, Dysthe JC, Franklin TW, Mason DH, McKelvey KS, Zarn KE, Schwartz MK. 2021. Detection of Jaguar (Panthera onca) From Genetic Material in Drinking Water. Frontiers in Ecology and Evolution 9:613200.