Molecular Star Gazing: Development and Validation of an Environmental DNA Assay for the Imperiled Sunflower Sea Star (Pycnopodia helianthoides)

Abstract

The sunflower sea star (Pycnopodia helianthoides) suffered a catastrophic population decline across its range from 2013 to 2017 due to the devastating Vibrio pectenicida FHCF-3 driven sea star wasting disease (SSWD) pandemic with minimal signs of population recovery. The functional extinction of this apex predator across substantial parts of its range has created a need to identify and track the remaining intact populations. Environmental DNA (eDNA) approaches provide a simple, cost-effective, and non-destructive method for monitoring occurrences, and in some cases abundances, of marine species, consistently outperforming visual occurrence monitoring efforts in sensitivity, speed, and cost. Here, we designed, developed, and validated a P. helianthoides-specific eDNA assay to identify refugia, using both quantitative and digital droplet PCR approaches. We first generated the most comprehensive sea star mitochondrial genome reference database to date (n=93 taxa, n= 15 novel). We then used unikseq and Geneious bioinformatics software to identify the unique nad5 gene region and design a highly specific hydrolysis probe-based PCR assay. We validated the performance of this assay through laboratory, mesocosm, and field testing, demonstrating a highly specific and sensitive assay. In a field application of the new assay across regions in British Columbia, Canada, we found a positive correlation between P. helianthoides eDNA concentrations and biomass density, especially when appropriately accounting for spatiotemporal integration scales (R2=0.67). The eDNA assay provides a rapid and scalable tool for monitoring the sunflower sea star which has been proposed for listing as threatened under the U.S. Endangered Species Act of 1973. Molecular tools like the one presented here enhance management and recovery efforts not only by identification and monitoring of remnant wild populations, but also by helping to assess population level response and recovery following reintroduction efforts.