Diversity and distribution assessment of elasmobranchs in a shallow estuarine lagoon using environmental DNA

Shinnecock Bay is a small, shallow lagoon and barrier beach estuary located in southeastern Long Island, New York, which has undergone a successful restoration effort in recent years. Anecdotal observations, benthic trawl surveys, and baited remote underwater videos indicate the presence of multiple elasmobranch species in the bay. However, these methodologies are highly selective and likely underestimate the diversity of elasmobranch species. To improve the characterization of elasmobranch diversity and better inform ecosystem modeling and bay research, restoration, and management efforts, we utilized environmental DNA (eDNA), a powerful, non-invasive tool for detecting rare, seasonal, and highly mobile nektonic species. This study reports on elasmobranch-targeted eDNA surveys conducted in Shinnecock Bay in 2021 and 2023. eDNA libraries, generated using an elasmobranch-specific primer set, indicated the presence of 12 unique elasmobranch species over the two sampling years, whereas traditional benthic trawling methods previously identified only 4 species. eDNA results also suggested spatiotemporal distributions for frequently observed elasmobranch species within the bay. This study thus demonstrates the improved efficacy of eDNA in detecting species of a largely threatened, often difficult to assess taxonomic group, offering a scalable tool to enhance ecosystem assessments and inform management of threatened elasmobranch populations.