Cooperative Fish and Wildlife Research Units Program: New York
Education, Research and Technical Assistance for Managing Our Natural Resources

Dick, C., Larson, W.A., Karpan, K., Baetscher, D.S., Shi, Y., Sethi, S., Fangue, N.A., Henderson, M.J. Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding. Submitted to Molecular Ecology Resources.


Diet analysis is a vital tool for understanding trophic interactions and is frequently used to inform conservation and management. Molecular approaches can identify diet items that are impossible to distinguish using more traditional visual-based methods. Yet, our understanding of how different variables, such as predator species or prey ration size, influence molecular diet analysis is still incomplete. Here, we conducted a large feeding trial to assess the impact that ration size, predator species, and temperature had on digestion rates estimated with visual identification, qPCR, and metabarcoding. Our trial was conducted by feeding two different rations of Chinook salmon (Oncorhynchus tshawytscha) to two piscivorous fish species (striped bass [Morone saxatilis] and channel catfish [Ictalurus punctatus]) held at two different temperatures (15.5°C and 18.5°C) and sacrificed at regular intervals up to 120 hours from the time of ingestion to quantify digestive tract contents. We found that ration size had the largest influence on digestion rate followed by prey species and temperature. DNA based analyses were able to identify salmon smolt prey in predator gut samples for much longer than visual analysis (~6 hours for visual analysis versus ~72 hours for molecular analyses). Notably, metabarcoding results had substantially less variance than qPCR results and produced better quantitative estimates of evacuation rates that could be more confidently integrated into modeling efforts. Our study provides evidence that modeling the persistence of prey DNA in predator guts for molecular diet analyses may be feasible using a small set of controlling variables for many fish systems.