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Resolving management uncertainty: Detecting rare fish with environmental DNA

Date: January 14, 2021

A novel environmental DNA tool allows biologists to efficiently and accurately detect mountain suckers at new locations in the Upper Missouri River Basin.


Arm reaching into stream water with sampling cup
A researcher uses a portable pump with a filter attachment to collect an eDNA sample from a stream. (Photo by Thomas Franklin)
Freshwater ecosystems are among the most threatened in the world, and conserving rare native species is a critical priority. By their very nature, rare fish are difficult to locate and monitor, and management programs often struggle to overcome the effects of false positive and false negative observations without requiring extremely large levels of resource commitment. Environmental DNA (eDNA) approaches offer a solution to this issue by providing species-specific and highly sensitive methods to determine the presence of the targeted organism. Our previous research has demonstrated the reliability of this technology, so we designed an eDNA tool to apply to a cold-water fish of conservation concern, the mountain sucker (Pantosteus jordani).

Close examination of the evolutionary history of suckers in the streams of the Rocky Mountains indicates that the Upper Missouri River Basin contains its own distinct lineage of fish, designated as Pantosteus jordani. Due to their apparently low population densities and disappearance from several headwater streams, these fish are receiving careful attention from Forest Service biologists. To survey for mountain suckers across large areas, we needed a more efficient and more sensitive approach than was previously available.

Using new genetic data, we located a section of mountain sucker DNA that is completely unique to the species and created a molecular tool to detect this DNA fragment from stream water, even when it is only present at extremely low levels. This new eDNA tool reliably and accurately detected P. Jordani at sites where its presence or absence was previously known. It also detected mountain suckers at ten locations where they had not been previously observed. In the future, our method will allow biologists to monitor mountain sucker populations at many locations simultaneously, at less expense than was previously possible.

Key Findings

  • Detecting mountain suckers via DNA in water samples was extremely reliable and accurate.
  • This method has already located mountain suckers at new locations in Wyoming and South Dakota.
  • Accurate and cost-effective surveys can now monitor mountain suckers at many locations simultaneously.
    A mountain sucker (Pantosteus jordani)
    A mountain sucker (Pantosteus jordani) (Photo by Doug Watkinson)

Featured Publications

Mason, Daniel ; Dysthe, Joseph ; Franklin, Thomas W. ; Williams, Chris L. ; Young, Michael K. ; McKelvey, Kevin S. ; Schwartz, Michael K. , 2020


Forest Service Partners: 
Chris L. Williams - Bighorn National Forest