Detecting endangered pinto abalone (Haliotis kamtschatkana) using environmental DNA: Comparison of ddPCR, qPCR, and conventional diver surveys

Abalone populations along the Pacific Coast of North America are threatened. In the Salish Sea (Washington, USA), pinto abalone (Haliotis kamtschatkana) have failed to recover from intensive harvest after over 25 years of fishery closure, prompting a growing restoration effort. As these efforts expand, a persistent challenge is simply locating this rare and highly cryptic species in the field, limiting the ability to identify critical habitat and locate wild adults to serve as restoration broodstock. Here, we tested the use of environmental DNA (eDNA) to detect pinto abalone. Using a quantitative PCR (qPCR) assay previously developed for larval pinto abalone, we first evaluated its sensitivity to abalone eDNA in aquaria settings, finding a positive relationship between abalone biomass and the concentration of abalone DNA. We then tested abalone eDNA detection in the field by collecting replicate water samples from abalone restoration sites, using an occupancy model to estimate detection probability in relation to abalone biomass estimated via diver surveys. Both eDNA concentration and detection probability were positively associated with diver-estimated abalone biomass. By modifying the assay for droplet digital PCR (ddPCR), detection probability increased by 32%-89% over qPCR. eDNA surveys using ddPCR had higher error (CV = 96.9%) than diver surveys (CV = 29.4%) but were more efficient, taking approximately 1/10th of the person-hours per site of a diver survey. For the final phase of the study, we collected water samples at 80 sites throughout the region, obtaining positive abalone eDNA detections at 11 sites with qPCR and 19 additional sites with ddPCR. Our results provide novel survey data on abalone populations within the Salish Sea and show that eDNA is a viable tool for cost-effective, efficient, and non-invasive abalone detection.