Environmental DNA (eDNA) has opened up opportunities in many systems to non-invasively monitor both general biodiversity and specific organisms of interest. California’s delicate vernal pool ecosystems contain more than a dozen endangered and endemic plants and animals. These ecosystems feed, water, and house migrating waterfowl, breeding amphibians and larval insects, in addition to supporting California’s grass diversity. Vernal pool branchiopods are small freshwater crustaceans that are specially adapted for these temporary wetlands. Currently, monitoring for vernal pool branchiopods is done by hand, using dip-net surveys and visual species identifications. This process is expensive, potentially destructive to the ecosystem, and susceptible to human error in identification.
This project aims to determine if species-specific environmental DNA assays perform comparably to the current dip-net method of monitoring vernal pools. The project developed a series of species-specific Taq-Man Probe-based qPCR assays for monitoring five vernal pool branchiopod species and the endangered California Tiger Salamander Ambystoma californiense. We then developed a protocol for filtering vernal pool water to obtain environmental DNA samples, and compared the results of simultaneous eDNA and traditional dip-net surveys in 82 vernal pools during the 2016 and 2017 wet seasons.
Initial results from this project have found that in general, environmental DNA assays fare comparably to dip-net assays with concordance between the two methods >90%. In some cases, populations were detected in the molecular assays when no branchiopods were detected in the ponds. However, in each of these cases, a population was found to either have been in the pond earlier in the same season, or would be found later in the season, suggesting that these detections were biologically real, and detecting either juveniles or the remains of deceased organisms.
These early results suggest that molecular, environmental methods for monitoring vernal pool inhabitants may provide an alternative for managers, landowners, and conservation professionals wishing to reduce or supplement their dip-net surveys. The protocols developed could potentially be used in other lentic ecosystems for other targets.