San Francisco Estuary and Watershed Science

Accurate species identification is critical to monitoring programs because mis-identifications can lead to incorrect assessments of population status and trends. In the San Francisco Estuary, efforts to monitor the imperiled osmerid Delta Smelt (Hypomesus transpacificus) using morphology can be challenging because of the presence of the similar-looking non-native osmerid Wakasagi (Hypomesus nipponensis). In 2017, the US Fish and Wildlife Service’s field office in Lodi implemented a two-stage verification process for Wakasagi to help prevent Delta Smelt from being mis-identified as Wakasagi. Under this process, Wakasagi are initially identified in the field, independently identified a second time by an experienced staff member in the laboratory, then stored on-site where they can be made available for future studies. Using the recently developed Specific High-sensitivity Enzymatic Reporter un-LOCKing (SHERLOCK) assay for Wakasagi, we evaluated how well verification protocols performed by genetically identifying a subset of Wakasagi collected during routine sampling between 2017 and 2021. Through this study, we found that the protocols have served as an effective quality control measure for over 4 years and across multiple surveys. With the development of field-deployable genetics tools such as SHERLOCK, genetic identification will likely play an increasingly important role in ecological monitoring. We expect that hybrid approaches that combine morphological identifications by trained field crew with application of field-based genetic tools may offer an effective and efficient approach to ensuring data accuracy in the future.