Detecting endangered pinto abalone (<i>Haliotis kamtschatkana</i>) using environmental <scp>DNA</scp>: Comparison of <scp>ddPCR</scp>, <scp>qPCR</scp>, and conventional diver surveys

Dimond, James L.; Gathright, Benjamin Ryder; Bouma, Joshua V.; Carson, Henry S.; Sowul, Kathleen

doi:10.1002/edn3.351

Cited by 9 publications

(4 citation statements)

References 44 publications

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“…abundance and age structure) and dispersal of the translocated fish that must combine various monitoring methods (such as those implemented in the present study) depending on the cost‐effectiveness in both economic and human resources. Species‐specific eDNA monitoring is increasingly used for assessing the distribution of rare or scarce species and has been shown to be more sensitive than conventional electrofishing and optical methods (Beng & Corlett, 2020; Brys et al, 2020; Dimond et al, 2022; Goldberg, Strickler & Fremier, 2018; Meulenbroek et al, 2022; Rojahn et al, 2021; Sepulveda et al, 2019). It should be noted that the presence of the Corfu killifish was confirmed with underwater footage and electrofishing only in the spring area, which was the release site, but these two methods did not detect the species in the mid‐section or lower section of the stream, indicating poor dispersal.…”

Section: Discussionmentioning

confidence: 99%

Designing, implementing and monitoring the translocation of a highly threatened freshwater fish

Kalogianni,

Leris,

Vardakas

et al. 2024

Aquatic Conservation

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Conservation translocations are increasingly applied for the protection of threatened species, but their success depends strongly on pre‐release preparatory work and strict implementation methodology, followed by post‐release monitoring. The aim of this work was to implement a conservation translocation that involved (a) the design and application of a pre‐release feasibility assessment tool for the selection of the translocation water bodies; (b) the translocation of 77 individuals of the highly threatened freshwater Corfu killifish Valencia letourneuxi in 2015, 2016 and 2017; and (c) a 5‐year post‐release monitoring with multiple methods. After initial pre‐screening, a feasibility assessment was conducted on two potential release water bodies (R‐WBs) and on four potential source water bodies (S‐WBs), using a custom‐made feasibility assessment tool that incorporated 14 criteria for the potential R‐WBs, related to the species' habitat requirements, human pressures and technical issues. Two criteria were applied to the potential S‐WBs, on source population availability and on its genetic compatibility to the release area. Post‐release monitoring (2017–2022) was conducted with fish sampling methods, underwater video recording and/or using environmental DNA (eDNA). The feasibility assessment tool gave one R‐WB high, positive score, and one S‐WB met both criteria, thus these selected as the translocation water bodies. Despite the low number of founders, the establishment of a self‐reproducing population was finally confirmed in 2022 in the R‐WB, initially with video recording and subsequently by fish sampling and eDNA. This study highlights the importance of pre‐release feasibility assessment, the use of multiple post‐release monitoring methods and actions to secure the long‐term viability of the translocated population. The feasibility assessment tool and the methodological protocol can easily be modified for successful application to other freshwater fish species, with different habitat requirements, current and future human pressures and genetic constraints.

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Section: Discussionmentioning

confidence: 99%

Designing, implementing and monitoring the translocation of a highly threatened freshwater fish

Kalogianni,

Leris,

Vardakas

et al. 2024

Aquatic Conservation

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“…Thus, the eDNA from the frass or other debris may provide a clue about the target species 35,36,37,38 . For the detection of eDNA, the ddPCR has higher sensitivity over the real-time quantitative PCR, LAMP, and conventional PCR 29,30,39,40 . In this study, the ddPCR method can detect the DNA of C. pomonella at a minimum concentration of 1.43×10 − 2 ng/uL, which provides a potential tool to detect the eDNA of C. pomonella in the eld.…”

Section: Discussionmentioning

confidence: 99%

“…Until now, the LAMP assays have successfully been used to diagnose other plant pests [23][24][25][26][27][28] . For the detection of eDNA, the droplet digital PCR (ddPCR) has the advantage over real-time quantitative PCR, LAMP, and conventional PCR, especially in the detection sensitivity 29,30 .…”

Section: Introductionmentioning

confidence: 99%

Development of LAMP and droplet digital PCR methods for differentiation between Cydia pomonella (L.) and Grapholita molesta (Busck)

yang,

Zhang,

Zhang

et al. 2024

Preprint

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The codling moth, Cydia pomonella (L.), is an economically important key fruit pest worldwide. In China, C. pomonella was first discovered in 1953 and has since been introduced into at least eight provinces. The monitoring of C. pomonella using sex pheromones is essential for controlling this destructive pest and preventing its spread from infested areas. However, the sex pheromone of C. pomonella also has strong attractive effects on Grapholita molesta (Busck), which results in the mixture of the two pest insects. Furthermore, capturing individuals, especially during the early phase of spread, is challenging due to the limited number of introductions. Thus, it is crucial to provide an accurate and rapid diagnostic method to differentiate them. To develop such a method for distinguishing between C. pomonella and G. molesta, we initially selected a set of C. pomonella specific-LAMP primers from seven designed sets of candidate primers and its sensitivity was evaluated using DNA. Finally, the effectiveness of the method was proven using insect tissue and a temperature-controlled, insulated cup. Additionally, the optimal reaction temperature, specificity, and sensitivity of the C. pomonella ddPCR-primer were determined. The development of the C. pomonella LAMP and ddPCR methods provide tools for the monitoring of C. pomonella in China.

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“…Species‐specific assays require the development of specific markers (Klymus et al., 2020 ), and are generally amplified using quantitative PCR (qPCR) or digital droplet PCR (ddPCR), either with or without probes to increase specificity (Brys et al., 2021 ). Some studies suggest that ddPCR is more sensitive than qPCR to detect rare species with low abundances in the environment (Dimond et al., 2022 ; Mauvisseau et al., 2019 , but see Johnsen et al., 2020 ). Additional advantages of ddPCR include a better tolerance to PCR inhibitors present in plants, soil, water, and food (Morisset et al., 2013 ; Rački et al., 2014 ) and the access to DNA absolute quantification without relying on a standard curve (Hunter et al., 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Optimizing detectability of the endangered fan mussel using eDNA and ddPCR

Marques,

Loot,

Blanchet

et al. 2024

Ecology and Evolution

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Spatial and temporal monitoring of species threatened with extinction is of critical importance for conservation and ecosystem management. In the Mediterranean coast, the fan mussel (Pinna nobilis) is listed as critically endangered after suffering from a mass mortality event since 2016, leading to 100% mortality in most marine populations. Conventional monitoring for this macroinvertebrate is done using scuba, which is challenging in dense meadows or with low visibility. Here we developed an environmental DNA assay targeting the fan mussel and assessed the influence of several environmental parameters on the species detectability in situ. We developed and tested an eDNA molecular marker and collected 48 water samples in two sites at the Thau lagoon (France) with distinct fan mussel density, depths and during two seasons (summer and autumn). Our marker can amplify fan mussel DNA but lacks specificity since it also amplifies a conspecific species (Pinna rudis). We successfully amplified fan mussel DNA from in situ samples with 46 positive samples (out of 48) using ddPCR, although the DNA concentrations measured were low over almost all samples. Deeper sampling depth slightly increased DNA concentrations, but no seasonal effect was found. We highlight a putative spawning event on a single summer day with much higher DNA concentration compared to all other samples. We present an eDNA molecular assay able to detect the endangered fan mussel and provide guidelines to optimize the sampling protocol to maximize detectability. Effective and non‐invasive monitoring tools for endangered species are promising to monitor remaining populations and have the potential of ecological restoration or habitat recolonization following a mass mortality event.

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Detecting endangered pinto abalone (Haliotis kamtschatkana) using environmental DNA: Comparison of ddPCR, qPCR, and conventional diver surveys

Cited by 9 publications

References 44 publications

Designing, implementing and monitoring the translocation of a highly threatened freshwater fish

Designing, implementing and monitoring the translocation of a highly threatened freshwater fish

Development of LAMP and droplet digital PCR methods for differentiation between Cydia pomonella (L.) and Grapholita molesta (Busck)

Optimizing detectability of the endangered fan mussel using eDNA and ddPCR

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