Imperfect sensitivity, or imperfect detection, is a feature of all survey methods that needs to be accounted for when interpreting survey results. Detection of environmental DNA (eDNA) is increasingly being used to infer species distributions, yet the sensitivity of the technique has not been fully evaluated. Sensitivity, or the probability of detecting target DNA given it is present at a site, will depend on both the survey method and the concentration and dispersion of target DNA molecules at a site. We present a model to estimate target DNA concentration and dispersion at survey sites and to estimate the sensitivity of an eDNA survey method. We fitted this model to data from a species-specific eDNA survey for Oriental weatherloach, Misgurnus anguillicaudatus, at three sites sampled in both autumn and spring. The concentration of target DNA molecules was similar at all three sites in autumn but much higher at two sites in spring. Our analysis showed the survey method had ≥95% sensitivity at sites where target DNA concentrations were ≥11 molecules per litre. We show how these data can be used to compare sampling schemes that differ in the number of field samples collected per site and number of PCR replicates per sample to achieve ≥95% sensitivity at a given target DNA concentration. These models allow researchers to quantify the sensitivity of eDNA survey methods to optimize the probability of detecting target species, and to compare DNA concentrations spatially and temporarily.

The environmental DNA (eDNA) method is a detection technique that is rapidly gaining credibility as a sensitive tool useful in the surveillance and monitoring of invasive and threatened species. Because eDNA analysis often deals with small quantities of short and degraded DNA fragments, methods that maximize eDNA recovery are required to increase detectability. In this study, we performed experiments at different stages of the eDNA analysis to show which combinations of methods give the best recovery rate for eDNA. Using Oriental weatherloach (Misgurnus anguillicaudatus) as a study species, we show that various combinations of DNA capture, preservation and extraction methods can significantly affect DNA yield. Filtration using cellulose nitrate filter paper preserved in ethanol or stored in a -20°C freezer and extracted with the Qiagen DNeasy kit outperformed other combinations in terms of cost and efficiency of DNA recovery. Our results support the recommendation to filter water samples within 24hours but if this is not possible, our results suggest that refrigeration may be a better option than freezing for short-term storage (i.e., 3–5 days). This information is useful in designing eDNA detection of low-density invasive or threatened species, where small variations in DNA recovery can signify the difference between detection success or failure.

Environmental DNA (eDNA) has revolutionized our ability to identify the presence and distributions of terrestrial and aquatic organisms. Recent evidence suggests the concentration of eDNA could also provide a rapid, cost-effective indicator of abundance and/or biomass for fisheries stock assessments. Globally, fisheries resources are under immense pressure, and their sustainable harvest requires accurate information on the sizes of fished stocks. However, in many cases the required information remains elusive because of a reliance on imprecise or costly fishery-dependent and independent data. Here, we review the literature describing relationships between eDNA concentrations and fish abundance and/or biomass, as well as key influencing factors, as a precursor to determining the broader utility of eDNA for monitoring fish populations.We reviewed 63 studies published between 2012 and 2020 and found 90% identified positive relationships between eDNA concentrations and the abundance and/or biomass of focal species. Key influencing biotic factors included the taxon examined as well as their body size, distribution, reproduction, and migration. Key abiotic factors mostly comprised hydrological processes affecting the dispersal and persistence of eDNA, especially water flow and temperature, although eDNA collection methods were also influential. The cumulative influence of these different factors likely explains the substantial variability observed in eDNA concentrations, both within and among studies. Nevertheless, there is considerable evidence to support using eDNA as an ancillary tool for assessing fish population abundance and/or biomass across discrete spatio-temporal scales, following preliminary investigations to determine speciesand context-specific factors influencing the eDNA abundance/biomass relationship.Advantages of eDNA monitoring relative to other approaches include reduced costs, increased efficiencies, and nonlethal sampling.

Summary1. Determining the timing and location of reproductive events is critical for efficient management of species. However, methods currently used for aquatic species are costly, time intensive, biased and often require destructive or injurious sampling. Hence, developing a non-invasive sampling method to accurately determine the timing and location of reproduction for aquatic species would be extremely valuable. 2. We conducted an experimental and field study to determine the influence of spawning, and the mass release of spermatozoa in particular, on environmental DNA (eDNA) concentrations. Using a quantitative PCR approach we monitored changes in nuclear and mitochondrial eDNA concentrations over time. 3. The data from the experimental study and the field survey supported our hypothesis that spawning events are characterized by higher concentrations of nuclear relative to mitochondrial eDNA. Outside of the reproductive period, we find that nuclear and mitochondrial DNA fragments are equally abundant in environmental water samples. 4. We have shown that changes in the relative abundance of nuclear and mitochondrial eDNA can be used to monitor spawning activity of the endangered Macquarie perch. Our method is likely to be transferrable to other aquatic species and can be particularly useful to increase our understanding of the spawning biology of cryptic, rare or threatened species as well as design and evaluate environmental management actions and determine species establishment.

Environmental DNA (eDNA) is increasingly used to monitor aquatic macrofauna. Typically, short mitochondrial DNA fragments are targeted because these should be relatively more abundant in the environment as longer fragments will break into smaller fragments over time. However, longer fragments may permit more flexible primer design and increase taxonomic resolution for eDNA metabarcoding analyses, and recent studies have shown that long mitochondrial eDNA fragments can be extracted from environmental water samples. Nuclear eDNA fragments have also been proposed as targets, but little is known about their persistence in the aquatic environment. Here we measure the abundance of mitochondrial eDNA fragments of different lengths and of short nuclear eDNA fragments, originating from captive fish in experimental tanks, and we test whether longer mitochondrial and short nuclear fragments decay faster than short mitochondrial fragments following fish removal. We show that when fish are present, shorter mitochondrial fragments are more abundant in water samples than both longer mitochondrial fragments and short nuclear eDNA fragments. However, the rate of decay following fish removal was similar for all fragment types, suggesting that the differences in abundance resulted from differences in the rates at which different fragment types were produced rather than differences in their decay rates.