Evaluating monitoring options for conservation: comparing traditional and environmental DNA tools for a critically endangered mammal

Abstract

While conservation management has made tremendous strides to date, deciding where, when and how to invest limited monitoring budgets is a central concern for impactful decision-making. New analytical tools, such as environmental DNA (eDNA), are now facilitating broader biodiversity monitoring at unprecedented scales, in part, due to time, and presumably cost, of methodological efficiency. Genetic approaches vary from conventional PCR (cPCR; species presence), to metabarcoding (community structure), and qPCR (relative DNA abundance, detection sensitivity). Knowing when to employ these techniques over traditional protocols could enable practitioners to make more informed choices concerning data collection. Using 12 species-specific primers designed for cPCR, eDNA analysis of the Yangtze finless porpoise (YFP; Neophocaena asiaeorientalis asiaeorientalis), a critically endangered aquatic mammal within the Yangtze River, we validated and optimized these primers for use in qPCR. We tested repeatability and sensitivity to detect YFP eDNA and subsequently compared the cost of traditional (visual and capture) sampling to eDNA tools. Our results suggest cPCR as the least expensive sampling option but the lack of PCR sensitivity suggests it may not be the most robust method for this taxon, predominately useful as a supplementary tool or with large expected populations. Alternatively, qPCR remained less expensive than traditional surveys, representing a highly repeatable and sensitive method for this behaviorally elusive species. Cost comparisons of surveying practices have scarcely been discussed; however, given budgetary constraints particularly for developing countries with limited local oversight but high endemism, we encourage managers to carefully consider the trade-offs among accuracy, cost, coverage, and speed for biodiversity monitoring.

Field application of an improved protocol for environmental DNA extraction, purification, and measurement using Sterivex filter

“…Depends on assays, the qualitative method may have limited resolution to species diversity and are sometimes sensitive up to family level 20,21 . On the other hand, quantitative methods using qPCR on certain species not only can detect the presence of the target species, but also infers the relative abundance of the species in the environment, which complements the limitation of metabarcoding analysis 5,22 . In open oceans, the eDNA concentrations are often low, and filtering large volumes of water is required to accumulate sufficient amounts of eDNA.…”

Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

“…Detection and monitoring of rare, cryptic, and endangered species using conventional techniques is a difficult task that often involves huge amounts of time and effort (Qu & Stewart 2019b).…”

“…Studies that have quantitatively assessed the cost-efficiency of eDNA relative to traditional methods suggest that eDNA sampling is relatively cheaper than traditional surveys (Biggs et al 2015;Davy et al 2015;Huver et al 2015;Sigsgaard et al 2015a;Qu & Stewart 2019a), although this can depend on the target taxa, site-specific detection rates, budgets, and other considerations (Smart et al 2016). For instance, Qu & Stewart (2019) found that the cost of detecting and quantifying Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) populations using visual surveys was 1.41-1.88 times (monthly cost) and 4.22-5.64 times (seasonal cost) higher than using eDNA.…”

Using Environmental DNA to Monitor the Reintroduction Success of the Rhine Sculpin (Cottus rhenanus) in a Restored Stream

“…We did not have the option for more sensitive qPCR or ddPCR, yet our applied end-point nPCR approach is known to lead to reliable detections (Nathan et al, 2014;Davison et al, 2019). Furthermore, end-point PCRs can have low detection limits (e.g., Qu and Stewart, 2017), which is why we considered that our results were more impacted by low detection rates than cross-contamination.…”