Examination of Predation on Early Life Stage Delta Smelt in the San Francisco Estuary Using DNA Diet Analysis

AbstractWe examined predation by nonnative Mississippi Silversides Menidia audens, other small fishes, and invertebrates on the early life stages of the endangered Delta Smelt Hypomesus transpacificus, which is endemic to the Sacramento–San Joaquin Delta in California. Mississippi Silversides and other putative predators were collected primarily via boat electrofishing in the northern reaches of the upper San Francisco Estuary, an area targeted for substantial tidal wetland restoration to enhance habitat for Delta Smelt and other endangered fishes. Predators’ digestive tracts were removed and analyzed for the presence of Delta Smelt DNA by using quantitative PCR TaqMan assays. Across all sites, 69 of 550 Mississippi Silversides tested positive for Delta Smelt DNA. The number of sampled Mississippi Silversides that were positive for Delta Smelt DNA was significantly greater in offshore habitats than in nearshore habitats. Delta Smelt DNA detection data indicated that a wide variety of other species were al...