Assessing Environmental DNA Detection in Controlled Lentic Systems

Abstract

Little consideration has been given to environmental DNA (eDNA) sampling strategies for rare species. The certainty of species detection relies on understanding false positive and false negative error rates. We used artificial ponds together with logistic regression models to assess the detection of African jewelfish eDNA at varying fish densities (0, 0.32, 1.75, and 5.25 fish/m3). Our objectives were to determine the most effective water stratum for eDNA detection, estimate true and false positive eDNA detection rates, and assess the number of water samples necessary to minimize the risk of false negatives. There were 28 eDNA detections in 324, 1-L, water samples collected from four experimental ponds. The best-approximating model indicated that the per-L-sample probability of eDNA detection was 4.86 times more likely for every 2.53 fish/m3 (1 SD) increase in fish density and 1.67 times less likely for every 1.02 C (1 SD) increase in water temperature. The best section of the water column to detect eDNA was the surface and to a lesser extent the bottom. Although no false positives were detected, the estimated likely number of false positives in samples from ponds that contained fish averaged 3.62. At high densities of African jewelfish, 3–5 L of water provided a >95% probability for the presence/absence of its eDNA. Conversely, at moderate and low densities, the number of water samples necessary to achieve a >95% probability of eDNA detection approximated 42–73 and >100 L, respectively. Potential biases associated with incomplete detection of eDNA could be alleviated via formal estimation of eDNA detection probabilities under an occupancy modeling framework; alternatively, the filtration of hundreds of liters of water may be required to achieve a high (e.g., 95%) level of certainty that African jewelfish eDNA will be detected at low densities (i.e., <0.32 fish/m3 or 1.75 g/m3).

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

“…of citrus (Hu et al 2014), all investigations were undertaken in aquatic environments. A majority of these studies investigated the presence of exotic fish such as common carp (Cyprinus carpio; Eichmiller et al 2014;Takahara et al 2015), silver and bighead carp (Hypophthalmichthys molitrix and nobilis; Jerde et al 2013;Farrington et al 2015), African jewelfish (Hemichromis lifalili; Moyer et al 2014), bluegill sunfish (Lepomis macrochirus; Takahara & Minimoto 2013) and zebrafish (Danio rerio; Collins et al 2013).…”

“…In one example, eastern hellbenders (Cryptobranchus a. alleganiensis) were successfully detected using environmental DNA at densities approaching the lowest reported natural population densities (Olson et al 2012). In many cases, the likelihood of false positive detection is reported to be low; potential biases for the incomplete detection of DNA can be quantified by formal estimation of DNA detection probabilities under occupancy modelling frameworks, as used by Moyer et al (2014) and more recently by Furlan et al (2016).…”

Using Environmental DNA to Improve Species Distribution Models for Freshwater Invaders

“…Small-scale freshwater lentic bodies provide an excellent opportunity to study eDNA characteristics related to degradation, which can affect successful detectability of species. Recent studies have tried to underline degradation rates in correlation to abiotic factors, such as, (i) most effective water stratum for eDNA detection (Moyer et al, 2014), (ii) pH, UV-B (Strickler et al, 2015), (iii) effects of temperature on eDNA degradation (Strickler et al, 2015;Eichmiller et al, 2016), and (iv) temporal effects (Dejean et al, 2011). Freshwater lotic bodies can provide important information due to their longitudinal downstream dynamics, such as, (i) eDNA persistence in the environment Wilcox et al, 2016), (ii) residence time of eDNA , and (iii) the ecology of eDNA (Barnes and Turner, 2016).…”

“…In terms of IAS certainty of existence in a non-native environment, false-positive and false-negative are crucial points for management and environmental policies (Moyer et al, 2014;Lahoz-Monfort et al, 2016). Even low rate false-positives pose a bias toward species specific occupancy (Lahoz-Monfort et al, 2016).…”

“…It can be applied for the detection of a number of specific IAS (barcoding), or detecting multiple IAS as part of whole communities (metabarcoding). New revolutionary techniques for eDNA are being developed on a daily basis with the aim to provide a number of useful information such as, presence or absence of the species (Ficetola et al, 2008), density assessments (Moyer et al, 2014), population dynamics (Sigsgaard et al, 2016), sex (Nichols and Spong, 2017), hybridization process between subspecies, (Uchii et al, 2016;Goricki et al, 2017), spatial representativeness (Civade et al, 2016;Bista et al, 2017) and ability to amplify whole mitochondrial genome (Deiner et al, 2017b). A wide range of eDNA detection possibilities is currently limited.…”