Monitoring Delta Smelt Environmental DNA (eDNA)
Carlton

The Delta Smelt (Hypomesus transpacificus, McAllister) is a small pelagic fish (120 mm maximum length) endemic to the San Francisco Estuary that has experienced a significant decline in population abundance over the past few decades.  Dramatic alterations of the estuary have been ongoing since the Gold Rush (mid 19th century), with the current ecosystem inhospitable to native species.  The inadequacy of existing habitat to sustain Delta Smelt is exemplified by decreasing population abundance observed in long term monitoring programs, with declines becoming particularly acute in the early 2000’s.  The low encounter rates (high frequency of zero catches) results in survey estimate imprecision, although measurement precision is not reported for abundance indices.  Additionally, low population abundance restricts “take” under the State and Federal Endangered Species Act, which limits activities permitted to target Delta Smelt.  Current monitoring is insufficient to associate species occurrence with relevant habitat attributes; however, monitoring enhancements needed to evaluate population recovery cannot be implemented due to perceived impacts.  Therefore, alternative approaches are needed to obtain biological information on rare, cryptic species that do not require “take” authorization.  One of the most compelling approaches likely applies molecular diagnostic methods that detect species-specific DNA in the environment (Environmental DNA; eDNA).

Environmental DNA methods provide a means to address limitations of visual surveys, because they are 1) cost effective and feasible to deploy over a large survey area 2) unambiguously identify target organisms and 3) are sensitive, capable of detecting trace amounts of DNA in sampled material. The eDNA approach differs from traditional sampling in that a given survey does not capture the target organisms themselves, but the biological material those organisms leave in their environment.  To use Delta Smelt eDNA information effectively in a regulatory context, a mathematical model is required that describes the relationship between DNA detection (positives, negatives) and the three main variables (volume, distance and biomass) influencing detection of DNA particles within an aquatic unidirectional or tidally-influences system.  The relationship is needed to reliably determine that when a positive detection for Delta Smelt occurs one can estimate how far away the DNA could have traveled (given a biomass).  Focused experiments have been designed to fill in the most pressing gaps in our current knowledge needed to inform our existing models and test performance under realistic field conditions.