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The case for eDNA archiving: Case study in re-analyzing samples for the western pearlshell mussel

Date: March 05, 2018

Can an environmental DNA sample (eDNA) be used to detect the presence of multiple species that are not closely related? A study of western pearlshell demonstrated that it can

A western pearlshell sits next to a data reader. Photo by John Csoka, US Forest Service.
A western pearlshell sits next to a data reader. Photo by John Csoka, US Forest Service.


Effective conservation and management decisions for habitats require information about the distribution of multiple species but such data is expensive to obtain; this often limits data collection to just a few, high-profile species. Environmental DNA (eDNA) sampling can be more sensitive, and less expensive, than traditional sampling for aquatic species, and a single sample potentially contains DNA from all species present in a water body. Cost-savings accrue if eDNA collected for detecting a particular species can be re-purposed to detect additional species. This study tested the feasibility of re-purposing and re-analyzing already collected samples. 

Freshwater mussel populations provide valuable information about the status of aquatic habitats. Mussels are tied to water quality and can indicate changes in the fish communities that they need for reproduction and dispersal. Specifically, researchers looked at the western pearlshell(Margaritifera falcata), a widely distributed and declining mussel, to determine whether archived eDNA samples collected for fish could be re-purposed to confirm the presence of western pearlshell at historic locations.

A western pearlshell sits in a streambed. Photo by John Csoka, US Forest Service
A western pearlshell sits in a streambed. Photo by John Csoka, US Forest Service.


A western pearlshell assay was successfully developed and its efficacy was tested on DNA extracted directly from western pearlshell tissue, and from control samples of non-target mussel and fish species. The assay also detected western pearlshell in re-purposed, archived eDNA samples originally collected to detect bull trout. The re-purposed eDNA was collected in historically overlapping habitat for western pearlshell and bull trout. 

Key Findings

  • An eDNA assay for western pearlshell was successfully developed.

  • The assay was used successfully on re-purposed DNA samples originally collected for detection of bull trout, a species with a very different life history.

  • Sample sites used for eDNA detection for one species might not be ideal sample sites for detection of other species due to incomplete range and habitat overlap but the original purpose of the sample is relatively unimportant.

  • New data from additional sampling sites might be needed to supplement a re-purposed sample, using existing eDNA sample databases as a valuable and cost effective first step.

  • Careful archiving of samples is critical, including location and collection data, and storage that prevents degradation.



Forest Service Partners: 
Scott Spaulding, Regional Fisheries Biologist, Northern Region
External Partners: 
Torrey Rodgers, Utah State University
Karen E. Mock, Utah State University
Research Location: