DNA-based identification of anadromous fishes (Alosa spp., Family Clupeidae) in stomach contents of marine groundfish.

Using DNA techniques for prey identification is an emerging approach for enhancing the precision and accuracy of trophic information. We evaluated the effectiveness of DNA-based prey identification in conjunction with visual stomach content analysis of commercially important groundfish in the nearshore Gulf of Maine, with a focus on distinguishing consumed anadromous (Alosa spp.) and closely related marine prey (Atlantic herring Clupea harengus, Atlantic menhaden Brevoortia tyrannus). DNA barcoding of 179 consumed prey specimens provided species- or genus-level identification in 122 cases (68.2%), including 104 improvements to taxonomic resolution and three conflicting results compared to visual identifications. Combining DNA-based identifications of partially or well-digested prey with the broader visual analysis substantially improved quantification of a diet metric, frequency occurrence, as a proxy for the relative diet contributions of anadromous and marine clupeids. Body size measurements of consumed Alosa spp. identified using DNA were consistent with year-0 or year-1 juvenile life stages. Possible limitations to success rates of DNA assignment included the quality of sample preservation (ethanol), reference database quality (accuracy of voucher specimen identification) and sequencing errors (miscalling of nucleotide bases). Despite this, the integration of molecular methods substantially improved the interpretability of trophic interactions involving morphologically similar prey with ecologically important differences in life history. These results highlight how the targeted application of DNA-based prey identification can complement conventional diet analyses by improving the quantification of trophic interactions that ultimately govern ecosystem processes.