Improving reliability in environmental DNA detection surveys through enhanced quality control

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    8 Citations (Scopus)

    Abstract

    Species-specific environmentalDNA(eDNA) surveys are increasingly being used to infer species presence in an environment. Current inadequacies in quality control increase concern for false negatives, which can have serious ramifications for both the management of invasive species and the conservation of native species. eDNA surveys involve a multi-step process to sample, capture, extract and amplify target DNA from the environment. We outline various positive control options and show that many of the commonly used controls are capable of detecting false negatives arising during the amplification stage only. We suggest a secondary, generic primer, designed to co-amplify endogenous DNA sampled during species-specific eDNA surveys, constitutes a superior positive control to monitor method success throughout all stages ofeDNAanalysis.Wedevelop a species-specific European carp (Cyprinus carpio) assay and a generic fish assay for use as an endogenous control for eDNA surveys in Australian freshwater systems where fish are known to be abundant.We use these assays in a multiplex on eDNA samples that are simultaneously sampled, captured, extracted and amplified. This positive control allows us to distinguish method error from informative non-amplification results, improving reliability in eDNA surveys, which will ultimately lead to better informed conservation management decisions. Journal compilation.

    Original languageEnglish
    Pages (from-to)388-395
    Number of pages8
    JournalMarine and Freshwater Research
    Volume68
    Issue number2
    DOIs
    Publication statusPublished - 2017

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    quality control
    DNA
    assay
    assays
    conservation management
    fish
    Cyprinus carpio
    carp
    invasive species
    native species
    amplification
    indigenous species
    detection
    sampling
    monitoring
    extracts
    methodology
    method

    Cite this

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    title = "Improving reliability in environmental DNA detection surveys through enhanced quality control",
    abstract = "Species-specific environmentalDNA(eDNA) surveys are increasingly being used to infer species presence in an environment. Current inadequacies in quality control increase concern for false negatives, which can have serious ramifications for both the management of invasive species and the conservation of native species. eDNA surveys involve a multi-step process to sample, capture, extract and amplify target DNA from the environment. We outline various positive control options and show that many of the commonly used controls are capable of detecting false negatives arising during the amplification stage only. We suggest a secondary, generic primer, designed to co-amplify endogenous DNA sampled during species-specific eDNA surveys, constitutes a superior positive control to monitor method success throughout all stages ofeDNAanalysis.Wedevelop a species-specific European carp (Cyprinus carpio) assay and a generic fish assay for use as an endogenous control for eDNA surveys in Australian freshwater systems where fish are known to be abundant.We use these assays in a multiplex on eDNA samples that are simultaneously sampled, captured, extracted and amplified. This positive control allows us to distinguish method error from informative non-amplification results, improving reliability in eDNA surveys, which will ultimately lead to better informed conservation management decisions. Journal compilation.",
    keywords = "Detection, False negative, Positive control, Sensitivity, Type II error",
    author = "Elise FURLAN and Dianne GLEESON",
    year = "2017",
    doi = "10.1071/MF15349",
    language = "English",
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    pages = "388--395",
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    T1 - Improving reliability in environmental DNA detection surveys through enhanced quality control

    AU - FURLAN, Elise

    AU - GLEESON, Dianne

    PY - 2017

    Y1 - 2017

    N2 - Species-specific environmentalDNA(eDNA) surveys are increasingly being used to infer species presence in an environment. Current inadequacies in quality control increase concern for false negatives, which can have serious ramifications for both the management of invasive species and the conservation of native species. eDNA surveys involve a multi-step process to sample, capture, extract and amplify target DNA from the environment. We outline various positive control options and show that many of the commonly used controls are capable of detecting false negatives arising during the amplification stage only. We suggest a secondary, generic primer, designed to co-amplify endogenous DNA sampled during species-specific eDNA surveys, constitutes a superior positive control to monitor method success throughout all stages ofeDNAanalysis.Wedevelop a species-specific European carp (Cyprinus carpio) assay and a generic fish assay for use as an endogenous control for eDNA surveys in Australian freshwater systems where fish are known to be abundant.We use these assays in a multiplex on eDNA samples that are simultaneously sampled, captured, extracted and amplified. This positive control allows us to distinguish method error from informative non-amplification results, improving reliability in eDNA surveys, which will ultimately lead to better informed conservation management decisions. Journal compilation.

    AB - Species-specific environmentalDNA(eDNA) surveys are increasingly being used to infer species presence in an environment. Current inadequacies in quality control increase concern for false negatives, which can have serious ramifications for both the management of invasive species and the conservation of native species. eDNA surveys involve a multi-step process to sample, capture, extract and amplify target DNA from the environment. We outline various positive control options and show that many of the commonly used controls are capable of detecting false negatives arising during the amplification stage only. We suggest a secondary, generic primer, designed to co-amplify endogenous DNA sampled during species-specific eDNA surveys, constitutes a superior positive control to monitor method success throughout all stages ofeDNAanalysis.Wedevelop a species-specific European carp (Cyprinus carpio) assay and a generic fish assay for use as an endogenous control for eDNA surveys in Australian freshwater systems where fish are known to be abundant.We use these assays in a multiplex on eDNA samples that are simultaneously sampled, captured, extracted and amplified. This positive control allows us to distinguish method error from informative non-amplification results, improving reliability in eDNA surveys, which will ultimately lead to better informed conservation management decisions. Journal compilation.

    KW - Detection

    KW - False negative

    KW - Positive control

    KW - Sensitivity

    KW - Type II error

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    UR - http://www.mendeley.com/research/improving-reliability-environmental-dna-detection-surveys-through-enhanced-quality-control

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    DO - 10.1071/MF15349

    M3 - Article

    VL - 68

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    EP - 395

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    SN - 0067-1940

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