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).
Highlights
Assessing the distribution, abundance, and dynamics of populations or species frequently requires the collection and identification of individuals from sample locations
1-L environmental DNA (eDNA) water samples were taken from each pond 15 days before the introduction of the fish to check for any potential contamination
A total of 28 detections of African jewelfish eDNA were made across 324 individual 1-L water samples collected from the four experimental ponds (Table 1)
Summary
Abundance, and dynamics of populations or species frequently requires the collection and identification of individuals from sample locations. Defined as short DNA fragments that an organism leaves behind in non-living components of the ecosystem (i.e., water, air or sediments) [7,8], eDNA can be used to detect the presence (or absence) of a species through cells or tissues found in the environment containing the genetic material. Genetic material can be collected via water filtration through a micron screen and tested for presence of the target species using specific genetic markers via polymerase chain reaction (PCR), quantitative PCR (qPCR) or direct sequencing of the PCR product. EDNA has garnered increased attention for use with endangered aquatic organisms [2,6] and aquatic invasive species [1,9,10]
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