Development of quantitative PCR primers and probes for environmental DNA detection of amphibians in Ontario

Beauclerc, Kaela B.; Wozney, Kristyne M.; Smith, Caleigh M.; Wilson, Chris C.

doi:10.1007/s12686-017-0962-3

Cited by 13 publications

(9 citation statements)

References 9 publications

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“…This DNA is then used to characterize the taxa present within the community and/or to identify particular species within that community (Comtet et al 2015 ). There are now multiple species-specific assays available for use, including assays for numerous amphibians (Beauclerc et al 2018 ), fish (Thomsen et al 2012 ), plants (Scriver et al 2015 ), and mammals (Andersen et al 2012 ), and more assays are continually being developed (Thomsen and Willerslev 2015 , see Washington State University’s eDNA toolbox: https://labs.wsu.edu/edna/edna-assays/ ).…”

Section: Introductionmentioning

confidence: 99%

Matching a snail’s pace: successful use of environmental DNA techniques to detect early stages of invasion by the destructive New Zealand mud snail

2021

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Early detection of invasive species allows for a more rapid and effective response. Restoration of the native ecosystem after an invasive population has established is expensive and difficult but more likely to succeed when invasions are detected early in the invasion process. Containment efforts to prevent the spread of known invasions also benefit from earlier knowledge of invaded sites. Environmental DNA (eDNA) techniques have emerged as a tool that can identify invasive species at a distinctly earlier time point than traditional methods of detection. Here, we focus on whether eDNA techniques can be successfully applied to detect new invasions by the destructive New Zealand Mud Snail Potamopyrgus antipodarum (NZMS). It is an opportune time to apply eDNA-based detection in P. antipodarum , which is currently expanding its invasive range across eastern North America. We collected water samples from eight sites in central Pennsylvania that prior evidence indicated were not yet invaded by the NZMS but were part of the same watershed as other previously documented invaded sites. We found evidence for NZMS invasion at five of the eight sites, with subsequent physical confirmation of mud snails at one of these sites. This study is the first example of successful application of eDNA to detect a previously unidentified invasive population of NZMS, setting the stage for further monitoring of at-risk sites to detect and control new invasions of this destructive snail. This study also shows potential opportunities for invasion monitoring offered by using low-cost efforts and methods that are adaptable for citizen science.

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Section: Introductionmentioning

confidence: 99%

Matching a snail’s pace: successful use of environmental DNA techniques to detect early stages of invasion by the destructive New Zealand mud snail

2021

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“…All samples were assayed within 6 h of extraction, with 3 test replicates run per sample. Each qPCR was run with 20 μl of the following cocktail: 10 μl of TaqMan® Environmental PCR Master Mix 2.0 (Applied Biosystems), 0.2 μM reverse primer, 0.2 μM forward primer, 0.2 μM species‐specific probe (Beauclerc et al, 2019), 0.2 μM synthetic control probe, 3.4 μl ddH 2 O, and 5 μl of undiluted DNA. Primer pairs and probes developed by Beauclerc et al (2019) were shown to be species‐specific, with reported efficiencies of 96.8% and 102.5% for R. sylvatica and R. pipiens , respectively.…”

Section: Methodsmentioning

confidence: 99%

Testing the effectiveness of environmental DNA (eDNA) to quantify larval amphibian abundance

et al. 2022

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Environmental DNA (eDNA) monitoring is rapidly becoming an established approach for detecting the presence of aquatic organisms and may also be useful for indexing or estimating species abundance. However, the link between eDNA concentration and abundance of individuals (i.e., density or biomass) remains tenuous and may vary widely across species and environmental conditions. We investigated the relationship between eDNA concentration and abundance in two common and closely related amphibians in eastern North America, the wood frog (Rana sylvatica), and northern leopard frog (R. pipiens). We manipulated tadpole density in 80-L mesocosms and documented the relationship between tadpole density and biomass and eDNA concentration through time. The two species differed in the amount of detectible genetic material produced, despite having comparable biomass. Concentration of eDNA increased with tadpole numbers and was primarily correlated with tadpole density in wood frogs and biomass in leopard frogs. eDNA degradation rates were rapid and comparable between species, with tadpoles becoming indetectable within 5 days post-removal from the mesocosm, irrespective of tadpole density. Overall, our findings support that eDNA concentration has potential for tracking amphibian abundance in wetlands, but that indices of abundance are likely to be coarse and speciesspecific calibration will be required. Future research should address how biotic and abiotic factors influence eDNA production, degradation, and recovery across species and through time before relying on eDNA for monitoring amphibian abundance in nature.

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“…Several studies have evaluated the methodological efficiency of eDNA versus conventional surveys in detecting rare, cryptic, and endangered species, and demonstrated that the probability of eDNA accurately detecting a target species is relatively higher than or comparable to that of conventional surveys (Deiner et al 2017). However, most eDNA-based studies have focused on aquatic taxa, especially fishes and amphibians (Beauclerc et al 2019;Deutschmann et al 2019). Studies on other taxa and in terrestrial environments are scarce.…”

Section: Detecting Rare Cryptic or Endangered Speciesmentioning

confidence: 99%

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

2020

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Development of quantitative PCR primers and probes for environmental DNA detection of amphibians in Ontario

Cited by 13 publications

References 9 publications

Matching a snail’s pace: successful use of environmental DNA techniques to detect early stages of invasion by the destructive New Zealand mud snail

Matching a snail’s pace: successful use of environmental DNA techniques to detect early stages of invasion by the destructive New Zealand mud snail

Testing the effectiveness of environmental DNA (eDNA) to quantify larval amphibian abundance

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

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