Refining Environmental DNA Protocols Developed for the Endangered James Spinymussel (Pleurobema collina)

Report No: 21-R14

Published in 2021

About the report:

Molecular genetic techniques provide tools that may be used to locate, monitor, and survey the presence of cryptic aquatic species such as the endangered James Spinymussel (Pleurobema collina).  Previous work on this species developed protocols that—across a range of conditions—were at least as accurate for detecting the presence of P. collina as currently deployed physical sampling approaches.  This project builds on those findings in three different ways.  First, the limits of detection for realistic field conditions were examined and showed that formative populations whose census sizes are on the order of 10 to 20 known individuals, environmental (eDNA) approaches can similarly provide positive evidence of P. collina presence.  Second, alternative approaches for both DNA extraction and post-extraction cleanup were tested to identify the most effective combination that reduces the negative effects of inhibition on successful PCR amplification. Tests revealed two viable options that recover up to 56% of samples previously yielding no PCR product due to environmental inhibition.  Third, in situ transect sampling was performed at two different locations to evaluate the extent to which eDNA template concentration can be used to model downstream concentration gradients. Across two sites and repeated sampling sessions, we were not able to construct well supported diffusion approximations for eDNA template concentrations for distances extending up to 500 meters downstream of known populations. The results of this work show that the eDNA approach for P. collina surveys is a viable addition to the suite of tools available to agencies for monitoring and management of this cryptic aquatic species.  The study recommends that the Virginia Department of Transportation’s Environmental Division meet with the U.S. Fish and Wildlife Service and the Virginia Department of Wildlife Resources to discuss whether there are circumstances under which eDNA can be an acceptable replacement for in-person surveys.

Disclaimer Statement:The contents of this report reflect the views of the author(s), who is responsible for the facts and the accuracy of the data presented herein. The contents do not necessarily reflect the official views or policies of the Virginia Department of Transportation, the Commonwealth Transportation Board, or the Federal Highway Administration. This report does not constitute a standard, specification, or regulation. Any inclusion of manufacturer names, trade names, or trademarks is for identification purposes only and is not to be considered an endorsement.


Other Authors

Rodney J. Dyer, Bonnie A. Roderique, M. Charis Deadwyler

Last updated: November 9, 2023

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