Analysis of environmental DNA (eDNA) offers an unprecedented ability to accurately survey biodiversity from aquatic ecosystems. Although eDNA methods have been applied to myriad taxa, scientists are now moving away from proof-of-concept work, ultimately evaluating the limits and opportunities of this technology to detect and quantify abundance across organisms and environments. Important considerations enabling such methodology to be used for aquatic conservation contexts includes understanding both the effects of (1) the amount of eDNA released from focal taxa-sources, and (2) the removal of eDNA in the environment-sinks. I review publications on aquatic macroorganism eDNA that have evaluated or considered the effect of sources on signal detection (or quantification) and find few studies acknowledge, and fewer still evaluate, the impact of eDNA production on genomic signal recovery. In this review, I encourage readers to carefully consider source dynamics, and using previously published literature, dissect what roles biotic (e.g. lifehistory traits, species interactions including stressors) and abiotic (e.g. temperature, salinity) factors likely play in eDNA deposition and recovery, and how this impacts detection, abundance, biomass estimation, and ultimately informed signal interpretation. I further explore the physical sources of eDNA and propose other methods (spatial and temporal) and markers to assist in identifying eDNA origins in aquatic systems. Understanding how these parameters influence variation in eDNA sources will allow for a more comprehensive survey tool, and potentially give insights into environment-population responses.

In a recent paper, "Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring," Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view. However, we are concerned that their proposed two-level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived.This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

1demonstrates no significant amplicon size effects on primer sensitivity or longevity. We summarize the impact primer design may have on eDNA applications in general and suggest future considerations for conservation efforts with the Yangtze finless porpoise.

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.