Maximizing eDNA detections of rare marine organisms: A case study of a delphinid species

Environmental DNA (eDNA) is an emerging tool for surveying marine organisms. Advances in molecular assay designs and bioinformatic methods provide new opportunities for detecting rare species; however, overcoming methodological challenges of rare species detection remains an important obstacle for the widespread deployment of eDNA methods for biomonitoring. Here, we provide a rigorous evaluation of eDNA sampling and processing methods to optimize eDNA capture and detection of a rare delphinid species. We applied a hierarchical Bayesian occupancy model to separate the effects of presence, capture and detection of target eDNA from Delphinus delphis and its two associated subspecies. We used a highly replicated sampling effort in the California Current Ecosystem to assess (1) the effect of water depth on the probability of D. delphis eDNA presence, (2) the effects of filtered water volume and filtration method on the likelihood of capturing D. delphis eDNA given its presence and (3) the effect of primer choice on the probability of D. delphis eDNA detection given its capture. Our results show that D. delphis eDNA is most likely to occur in surface (0–10 m) waters, and that large volume (>4 L) sampling increased the probability of capturing D. delphis eDNA on a filter. Moreover, the use of primers designed for cetaceans increased detection probabilities relative to more general primers designed for vertebrates. Our intensive replication in field sampling and laboratory assays and subsequent hierarchical modelling indicates that D. delphis eDNA was present in 90% of surface samples. Yet, since it makes up a tiny fraction of the ambient DNA pool, reliable detection requires optimized experimental design at both the sampling and processing stages. The modelling approach applied here provides an experimental design framework for eDNA studies focused on capturing rare targets. We use the results of this application to provide specific guidance on optimal experimental design for detection of delphinid eDNA.