Data from: eDNA metabarcoding bioassessment of endangered fairy shrimp (Branchinecta spp.) - Part B

Fairy shrimp are integral components of vernal pool ecosystems, providing key food resources for migratory birds and amphibians. However, habitat degradation and land use change severely threaten the health of both vernal pools and the survival of fairy shrimp species. Branchinecta sandiegonensis  Fugate, 1993 has been particularly affected by urban and agricultural development in its small native range within San Diego County, California, USA. It is listed as an endangered species under federal laws and is actively managed for its conservation. However, despite its legal protections, current methods of population assessment require the capture and sacrifice of individuals of B. sandiegonensis in order to identify specimens to species level through microscopy. Furthermore, accurate species-level identification is especially important given the overlap of B. sandiegonensis with a common (non-threatened) sister species, B. lindahli Packard, 1883. Thus non-invasive methods to definitively distinguish these species are desirable. Here we demonstrate that eDNA metabarcoding methods are an effective non-invasive technique for monitoring fairy shrimp. We sampled a series of vernal pools with both eDNA and traditional dip net methods, finding that eDNA metabarcoding with 16S rDNA provides species-level resolution.

eDNA metabarcoding for B. sandiegonensis had a sensitivity of 99% and a specificity of 99% while dip net sampling had a sensitivity of 98.8% and a specificity of 89.2%.

We found that the two methods were concordant within the early hydroperiod of pools. Additionally, the eDNA method detected fairy shrimp in vernal pools up to 2 months after dip nets detected any adult individuals, suggesting eDNA methods detect fairy shrimp eggs, newly hatched larvae, or decaying individuals. Together these results provide resource managers a simple, cost effective, and non-invasive method for biomonitoring endangered fairy shrimp species.