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Detecting rare species using environmental DNA

Status: 
Action
Dates: 
April, 2013

One person can collect a water sample in about 15 minutes, and use that sample to detect many species.
One person can collect a water sample in about 15 minutes, and use that sample to detect many species.
Animals in aquatic environments—such as fish, amphibians, crayfish, and mussels—release DNA into the water via their feces, urine, and skin. This external DNA is called environmental DNA (eDNA). By filtering water samples and analyzing them for eDNA, one can determine whether a species is present without actually capturing or seeing an individual. Different species can be identified by using genetic markers that are unique to them.

Because of its greater efficiency and reduced cost, eDNA sampling may revolutionize the monitoring and assessment of freshwater species.

Approach

Researchers at the U.S. Forest Service’s National Genomics Center for Wildlife and Fish Conservation (NGC) have pioneered developments in this field—including the first reliable eDNA assay for salmonid fish species. NGC scientists developed a rapid, field-proven eDNA sampling protocol that is remarkably sensitive—100% detection efficiency of target species has been attained across order-of-magnitude changes in stream discharge, and detection rates of rare species can be much higher than with traditional sampling methods. Moreover, collected samples are easily stored in the field, can be processed in the lab in under 48 hours, and cost relatively little to analyze. Assays are available or being developed for an array of native and nonnative species.

Scientists at the NGC have collaborated with biologists from across the West to use eDNA sampling for answering questions about the presence of native and nonnative trout.
Scientists at the NGC have collaborated with biologists from across the West to use eDNA sampling for answering questions about the presence of native and nonnative trout.
NGC scientists introduced biologists from partner agencies across the West to this approach by providing training and lending equipment from our “tool library.” Successful projects have included finding new populations of sensitive species, delineating the boundaries of habitats occupied by fish, and gauging the effectiveness of efforts to remove nonnative species.

Key Findings

  • Even a single DNA molecule on a filter—and thus a species in a stream—can be detected with high reliability.
  • Detection probability of a single trout in 100 m of stream exceeds 85%, an efficiency several-fold better than one-pass electrofishing.
  • Often an entire 6th-code subwatershed (~20–40 km of stream) can be sampled by a single person in one day.
  • Our protocol has been adopted by biologists from partner agencies in most western states, on projects ranging from population inventories to gauging the effectiveness of efforts to remove nonnative species.
  • Samples collected to evaluate a target species can be used to evaluate many other species with no additional field costs and can serve as a multi-species baseline for future biodiversity assessments.

Detection probability of a single trout in 100 m of stream exceeds 85%, an efficiency several-fold better than one-pass electrofishing.
Detection probability of a single trout in 100 m of stream exceeds 85%, an efficiency several-fold better than one-pass electrofishing.

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
Wilcox, Taylor M. ; McKelvey, Kevin S. ; Young, Michael K. ; Jane, Stephen F. ; Lowe, Winsor H. ; Whiteley, Andrew R. ; Schwartz, Michael K. , 2013


Project Contact: 

Principal Investigators:
Co-Investigators:
Collaborators:
Nevada Department of Wildlife
Oregon Department of Fish & Wildlife
Utah Division of Wildlife Resources
Wild Fish Conservancy
Wildlife Conservation Society
Snoqualmie Tribe
U.S. Fish & Wildlife Service
U.S. Geological Survey
Arizona Game & Fish Department
California Department of Fish & Game
Idaho Department of Fish & Game
Montana Fish Wildlife & Parks