Fish composition in a complex freshwater estuary: Environmental DNA metabarcoding versus capture surveys
A comparison of eDNA metabarcoding and multigear capture surveys in the St. Louis River estuary shows that eDNA detects more species and at higher frequencies, including unexpected taxa with no prior basin records. However, eDNA signals were spatially homogenized and often mismatched with capture‑based distributions, indicating limited ability to resolve fine‑scale patterns in a complex estuary. The study concludes that eDNA is powerful for system‑wide species detection, while capture surveys remain essential for spatially explicit fisheries and habitat management.
Subject Tags
- Wildlife
- Conservation Technology
- Estuary
Abstract
Objective
The potential for environmental DNA (eDNA) to disperse widely from source organisms enables high detection efficiency but raises questions about eDNA's ability to differentiate fine-scale spatial patterns relative to conventional fish capture data.
Methods
We evaluate these questions in the St. Louis River estuary—a hydrologically and spatially complex coastal system within Lake Superior that supports a diverse assemblage of resident and migratory fish species—via comparison of eDNA metabarcoding (12S and 16S loci) to multigear capture survey data from 2 years and two seasons.
Results
The eDNA and capture surveys collectively yielded 68 fish species: 2 species detected only by capture, 27 detected only by eDNA, and 39 shared across both survey types but having generally higher occurrence frequencies with eDNA than capture. Six species detected only by eDNA were unexpected, having no prior records in the Lake Superior basin. Data from paired eDNA and capture stations showed little relationship between the two survey types, with capture yielding species at stations that eDNA did not, eDNA detecting species in different habitats and distant locations from any captures, and assemblage patterns homogenized in eDNA surveys relative to capture surveys.
Conclusions
Our study finds that eDNA is a sensitive tool for assessing species presence at the system scale but that capture surveys may better yield the fine-scale spatial distribution information of interest to fisheries and habitat managers, especially in spatially and hydrologically complex systems.
Citation
Trebitz, A. S., Hoffman, J. C., Peterson, G. S., Hatzenbuhler, C., Pilgrim, E., Okum, S., ... & Myers, J. T. (2025). Fish composition in a complex freshwater estuary: Environmental DNA metabarcoding versus capture surveys. Transactions of the American Fisheries Society, 154(6), 657-674. https://doi.org/10.1093/tafafs/vnaf036
TNC Authors
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Lindsay Chadderton
Program Director, AIS, Wisconsin
The Nature Conservancy
Email: lchadderton@tnc.org -
Andrew Tucker
Conservation Scientist, Wisconsin
The Nature Conservancy
Email: atucker@tnc.org