AUTHORS: Tariq Tajjioui, U.S. Geological Survey; Daniel Kelner, U.S. Army Corps of Engineers; Stephen F. Spear, U.S. Geological Survey; Diane L. Waller, U.S. Geological Survey; Trevor W. Cyphers, U.S. Army Corps of Engineers; Joseph W. Jordan, U.S. Army Corps of Engineers; Christopher M. Merkes, U.S. Geological Survey; Colin C. Moratz, U.S. Army Corps of Engineers; Theresa M. Schreier, U.S. Geological Survey; Bernard E. Sietman, Minnesota Department of Natural Resources; Sarah A. Douglass, Illinois Natural History Survey
ABSTRACT: The Spectaclecase mussel (Cumberlandia monodonta) is an endangered freshwater species native to the large rivers of the Mississippi River basin in the Midwest and Southeast United States. To support the conservation of Spectaclecase populations, organizations such as the U.S. Army Corps of Engineers, Minnesota Department of Natural Resources, and Wisconsin Department of Natural Resources are implementing habitat restoration initiatives along the upper Mississippi River (UMR). However, there are few known populations of Spectaclecase in the UMR, and gathering more occurrence data is crucial for effective restoration efforts. Traditional diving methods are typically used for surveying Spectaclecase, but this species’ preference for sheltered habitats, such as large interstitial spaces and crevices, makes these methods risky, costly, and time-consuming. Environmental DNA (eDNA) presents a promising alternative for monitoring aquatic species, although freshwater mussels often yield low detection rates. A quantitative PCR (qPCR) assay for Spectaclecase has previously been developed to detect known populations. Our study aimed to build on this foundation by conducting eDNA surveys throughout the UMR to assess detection rates and locate unknown populations. Between 2020 and 2024, we collected eDNA samples from over 250 sites across 23 pools in the UMR. DNA from the samples was extracted and analyzed using the established Spectaclecase eDNA marker. We also performed dive surveys at any new positive eDNA detection site to confirm the presence of this species. Our findings indicate that eDNA can successfully identify previously unknown populations of Spectaclecase, although locations with documented populations of Spectaclecase sometimes failed to produce positive eDNA detections. Dive surveys revealed that even weak positive eDNA detections were sufficient to locate Spectaclecase mussels. This research highlights the effectiveness of eDNA as a monitoring tool for this endangered species while also addressing the challenges of detecting declining mussel populations in expansive river systems.
