Refining the use of environmental DNA (eDNA) as a method to detect presence of the endangered Topeka Shiner (Notropis topeka)

Topeka Shiner (Notropis topeka) is an endangered fish species that inhabits oxbows, floodplains, and small headwater streams throughout the central United States. Habitat loss and alterations represent the main threats to this species and conservation actions have included restoring oxbows that were historically occupied. Information on species occupancy is critical for evaluating the success of habitat restoration efforts, however, collection efforts can be difficult. Traditionally, sampling for Topeka Shiners has relied on seining. The effectiveness of seine surveys depends largely on habitat characteristics including oxbow size, depth, and substrate. Environmental DNA surveys have emerged as a method to effectively survey across broad landscapes and collect data on species occupancy. In this study our objectives were to: 1) Refine eDNA laboratory methods for Topeka Shiner (specifically increase the sensitivity of existing methods); and 2) Evaluate multiple eDNA field collection methods in order to make recommendations for future Topeka Shiner monitoring efforts. We modified an existing eDNA assay by adding a hydrolysis probe, which resulted in a highly sensitive tool for Topeka Shiner eDNA detection. From 2021 to 2022, we compared three different eDNA collection methods to evaluate their effectiveness: surface water grabs with centrifugation, surface water grabs with vacuum manifold filtration, and on-site surface water filtration using Smith Root filter packs. eDNA sampling at oxbows was followed by seine surveys to confirm species presence/absence. At each site where Topeka Shiners were collected in seine surveys, we also detected Topeka Shiner eDNA. Control sites where Topeka Shiners were presumed absent and no individuals were collected in seine surveys, had no eDNA detections. At one site with unknown Topeka Shiner status, no individuals were collected via seine surveys, but we did detect eDNA. Logistic regression showed that sampling method (i.e., centrifuge, vacuum filtration, Smith Root filtration) was a significant factor predicting detection rate, with centrifugation and Smith Root filtration having higher overall detection rates compared to vacuum filtration. We used linear regression to evaluate which sampling method collected the greatest amount of eDNA. Once again, collection method did have a significant effect on the number of copies per liter collected. At sites sampled in 2021, centrifugation had much higher copies detected than vacuum filtration. In 2022, there was much greater variability in the number of copies detected, and the comparison between vacuum filtration and Smith Root filtration was much more site dependent. For future sampling events, we suggest using Smith Root filters as the most efficient and economical means for collecting eDNA samples for Topeka Shiners.

Author(s)
Fws staff at desk
Fish Biologist
Fish and Aquatic Conservation
Expertise
Ecological Modeling,
Statistical Data Analysis,
Data Harmonization,
Science Communication,
Aquatic Invasive Species,
Native Species Restoration,
Historical Fish Survey Data,
Comparative Morphology
Onalaska,WI
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Report
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PCR machine with blue strand of DNA
The Whitney Genetics Laboratory specializes in high-throughput environmental DNA processing for monitoring aquatic invasive species through its Invasive Carp eDNA Monitoring and Genetic Surveillance of Invasive Species programs. Lab staff participate in development of new scientific methods to help...
A blue sky with clouds as the sun shines on the upper Mississippi River with green bluffs in the distance.
The Midwest Fisheries Center is the region’s Fish Technology Center for the U.S. Fish and Wildlife Service. Fish Technology Centers provide leadership in science-based management of trust aquatic resources through applied research and the development of new concepts, strategies and techniques to...
Woman on boat with fish net in hand on Mississippi river.
La Crosse Fish and Wildlife Conservation Office was established in 1981 and works to monitor and control the spread of invasive species such as invasive carp and round goby as well as restore threatened and endangered freshwater mussels and fish like the Topeka shiner and  inter-jurisdictional ...
The Fish Technology Center brown and white entrance sign welcomes visitors to the facility.
Warm Springs Fish Technology Center provides leadership in the science-based management of aquatic resources through the development of new concepts, strategies, technologies, and techniques to solve problems and develop innovative efficiencies for hatchery operations and for aquatic resources...
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A man is fishing in a boat with three young girls. The kids are excitedly pulling a fish out of the water.
The Fish and Aquatic Conservation programs work together to deliver resilient habitats, healthy fish, connected people, and strong partnerships. From habitat restoration to aquatic invasive species prevention, captive breeding to population assessment and monitoring, our programs are driven by the...
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FWS and DOI Region(s)