Stomach Content DNA from Predatory Fishes: Environmental Sampling of Trophic Relationships

Piscivore stomach contents represent naturally filtered environmental samples. Here we use DNA recovered from the stomach contents of predatory fish species to genetically identify prey species providing a method to characterize predator diets, trophic relationships, and assess the presence of non-native species. First we evaluated the number of stomachs required to provide a representative snapshot of a predator’s diet, and then sampled four predatory fishes (walleye, yellow perch, white bass, white perch) across three years (2006, 2007, 2008) in Western Lake Erie to provide a spatial and temporal context to our analysis. Next-generation sequencing of targeted species-specific and universal mtDNA primer sets was performed to identify prey items to species-level. Our results not only confirm the presence/absence of non-native species in Lake Erie, but suggest that those present are of sufficient numbers to influence trophic ecology.