Elisabeth Lutz, Philipp Hirsch, Karen Bussmann, Joschka Wiegleb, Hans-Peter Jermann, Roxane Muller, Patricia Burkhardt-Holm, Irene Adrian-Kalchhauser

1. Conservation of riverine fish typically aims at improving access to spawning grounds and the restoration of longitudinal connectivity requires substantial investments. However, the removal of migration barriers also enables the upstream invasion of non-native species into spawning areas, with potential negative effects on recruitment of threatened freshwater fish through egg or fry predation.

2. Detecting egg predation is often challenging. Visual gut inspections are thought to underestimate predation on soft material such as eggs and fry, which hampers the discovery of predators preying upon these life-stages. For soft materials, molecular approaches may therefore offer a more sensitive tool for detection.

3. Here, we uncover such a macroscopically invisible conservation issue caused by predation of invasive round goby (Neogobius melanostomus) predation on eggs or fry of threatened common nase (Chondrostoma nasus) in Switzerland.

4. In addition, this manuscript presents species-specific molecular assays for five more valuable native fish, including endangered salmonid and cyprinid river spawners, and confirms the applicability of the assays in a series of laboratory and field feeding experiments involving eggs and fish tissue. The manuscript also provides a guiding tool for conservation managers regarding the use and applicability of different molecular approaches in gut-content analysis.

5. Our results inspire recommendations for local conservation measures such as a temporary reduction of round goby densities at the spawning site prior to the spawning period, and demonstrate how the targeted application of species-specific molecular markers can inform freshwater fish management.