The importance of including imperfect detection models in eDNA experimental design

Abstract

Environmental DNA (eDNA) is DNA that has been isolated from field samples, and it is increasingly used to infer the presence or absence of particular species in an ecosystem. However, the combination of sampling procedures and subsequent molecular amplification of eDNA can lead to spurious results. As such, it is imperative that eDNA studies include a statistical framework for interpreting eDNA presence/absence data. We reviewed published literature for studies that utilized eDNA where the species density was known and compared the probability of detecting the focal species to the sampling and analysis protocols. Although biomass of the target species and the volume per sample did not impact detectability, the number of field replicates and number of samples from each replicate were positively related to detection. Additionally, increased number of PCR replicates and increased primer specificity significantly increased detectability. Accordingly, we advocate for increased use of occupancy modelling as a method to incorporate effects of sampling effort and PCR sensitivity in eDNA study design. Based on simulation results and the hierarchical nature of occupancy models, we suggest that field replicates, as opposed to molecular replicates, result in better detection probabilities of target species.

Sampling Designs for Landscape‐level eDNA Monitoring Programs

“…These probability calculations can then be used to calculate the minimum sample size necessary to detect a species during a visit to a site. These probability calculations are similar to the calculations presented by Hunter et al (), Lacoursière‐Roussel et al (), and Willoughby et al (). We assumed eDNA is present at a site (i.e., Z i,v = 1 for all i and v ).…”

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

“…This can occur even in those studies that use more sensitive methods such as the digital droplet (dd)PCR used by Baker et al (2018). and the number of field replicates is advised in order to achieve a reliable result (Leray & Knowlton, 2015;Piggott, 2016;Schultz & Lance, 2015;Taberlet et al, 1996;Willoughby, Wijayawardena, Sundaram, Swihart, & DeWoody, 2016). and the number of field replicates is advised in order to achieve a reliable result (Leray & Knowlton, 2015;Piggott, 2016;Schultz & Lance, 2015;Taberlet et al, 1996;Willoughby, Wijayawardena, Sundaram, Swihart, & DeWoody, 2016).…”

Living quarters of a living fossil—Uncovering the current distribution pattern of the rediscovered Hula painted frog (Latonia nigriventer) using environmental DNA

“…The qPCR cycling protocol began with 2 min at 95°C followed by 40 cycles of 95°C for 5 s and 60°C for 25 s. All samples were run in duplicates with both positive and negative controls. Six independent qPCR replications were performed for each of the four field sample replicates (24 PCR for each sampling site) to increase detection probability (Willoughby et al., ). A sample was considered as positive if at least two of its six amplification repeats came up positive.…”