FraGen: eDNA-based methods for assessing the genetic fragmentation of fish populations in federal waterways
Details
Dams, weirs and other hydraulic structures fragment rivers and drive biodiversity loss in freshwater ecosystems. By restricting fish migration, these barriers reduce gene flow, increase genetic isolation and compromise the long-term resilience of populations. Fishways are commonly installed to restore connectivity, but their effectiveness is usually assessed with telemetry or capture-based surveys, which say little about genetic exchange. Traditional tissue-based genetic studies can fill this gap, but they are invasive, costly and impractical for large-scale monitoring.
FraGen aims to develop and validate a non-invasive framework based on environmental DNA (eDNA), the traces of DNA that fish shed into the water, for assessing the genetic diversity and population fragmentation of indigenous key fish species in German federal waterways. The project comprises five integrated work packages:
- Target species. Select species by ecological relevance, genetic tractability and suitability for controlled trials.
- Genetic markers. Identify and validate the best markers (mitochondrial DNA, microsatellites and SNPs) for eDNA-based population genetics, using tissue-derived reference datasets.
- Controlled experiments. Use artificial fish populations of known genetic composition (indoor flumes) to test whether eDNA captures genetic variation under varying species, density, age class, exposure time and suspended solids.
- Field validation. Compare parallel eDNA and tissue samples from free-flowing and dam-regulated river sections.
- Connectivity. Correlate the observed genetic patterns with historical fragmentation data to quantify ecological connectivity.
Once implemented, FraGen should provide a scalable framework for evaluating fish passage, monitoring genetic recovery and supporting evidence-based waterway management. We presented the conceptual design as a poster at an early stage of the project, to discuss the approach and exchange experience on eDNA-based population genetics in freshwater conservation.
Project team at the BfG: Dr. Shaolin Xu, Dr. Sascha Krenek, Dr. David Nijssen, Saskia Schmidt, Dr. Christian Burberg and Dr. Nicole Scheifhacken. PIs: Dr. Nicole Scheifhacken and Dr. Sascha Krenek. I work on the project in department U4.
