Towards robust and repeatable sampling methods in eDNA-based studies

Ian A. Dickie, Stephane Boyer, Hannah L. Buckley, Richard P. Duncan, Paul P. Gardner, Ian D. Hogg, Robert J. Holdaway, Gavin Lear, Andreas Makiola, Sergio E. Morales, Jeff R. Powell, Louise Weaver

    Research output: Contribution to journalArticle

    11 Citations (Scopus)

    Abstract

    DNA-based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. We reviewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three-year period (n = 75). We found that 95% (n = 71) of these studies used subjective sampling methods and inappropriate field methods and/or failed to provide critical methodological information. It would be possible for researchers to replicate only 5% of the metabarcoding studies in our sample, a poorer level of reproducibility than for ecological studies in general. Our findings suggest greater attention to field sampling methods, and reporting is necessary in eDNA-based studies of biodiversity to ensure robust outcomes and future reproducibility. Methods must be fully and accurately reported, and protocols developed that minimize subjectivity. Standardization of sampling protocols would be one way to help to improve reproducibility and have additional benefits in allowing compilation and comparison of data from across studies.

    Original languageEnglish
    Pages (from-to)940-952
    Number of pages13
    JournalMolecular Ecology Resources
    Volume18
    Issue number5
    DOIs
    Publication statusPublished - 1 Sep 2018

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    sampling
    Biodiversity
    reproducibility
    biodiversity
    terrestrial ecosystem
    Ecosystem
    methodology
    bioinformatics
    field method
    freshwater ecosystem
    standardization
    aquatic ecosystem
    community composition
    method
    Computational Biology
    Fresh Water
    DNA
    Research Personnel
    researchers
    protocol

    Cite this

    Dickie, I. A., Boyer, S., Buckley, H. L., Duncan, R. P., Gardner, P. P., Hogg, I. D., ... Weaver, L. (2018). Towards robust and repeatable sampling methods in eDNA-based studies. Molecular Ecology Resources, 18(5), 940-952. https://doi.org/10.1111/1755-0998.12907
    Dickie, Ian A. ; Boyer, Stephane ; Buckley, Hannah L. ; Duncan, Richard P. ; Gardner, Paul P. ; Hogg, Ian D. ; Holdaway, Robert J. ; Lear, Gavin ; Makiola, Andreas ; Morales, Sergio E. ; Powell, Jeff R. ; Weaver, Louise. / Towards robust and repeatable sampling methods in eDNA-based studies. In: Molecular Ecology Resources. 2018 ; Vol. 18, No. 5. pp. 940-952.
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    abstract = "DNA-based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. We reviewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three-year period (n = 75). We found that 95{\%} (n = 71) of these studies used subjective sampling methods and inappropriate field methods and/or failed to provide critical methodological information. It would be possible for researchers to replicate only 5{\%} of the metabarcoding studies in our sample, a poorer level of reproducibility than for ecological studies in general. Our findings suggest greater attention to field sampling methods, and reporting is necessary in eDNA-based studies of biodiversity to ensure robust outcomes and future reproducibility. Methods must be fully and accurately reported, and protocols developed that minimize subjectivity. Standardization of sampling protocols would be one way to help to improve reproducibility and have additional benefits in allowing compilation and comparison of data from across studies.",
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    Dickie, IA, Boyer, S, Buckley, HL, Duncan, RP, Gardner, PP, Hogg, ID, Holdaway, RJ, Lear, G, Makiola, A, Morales, SE, Powell, JR & Weaver, L 2018, 'Towards robust and repeatable sampling methods in eDNA-based studies', Molecular Ecology Resources, vol. 18, no. 5, pp. 940-952. https://doi.org/10.1111/1755-0998.12907

    Towards robust and repeatable sampling methods in eDNA-based studies. / Dickie, Ian A.; Boyer, Stephane; Buckley, Hannah L.; Duncan, Richard P.; Gardner, Paul P.; Hogg, Ian D.; Holdaway, Robert J.; Lear, Gavin; Makiola, Andreas; Morales, Sergio E.; Powell, Jeff R.; Weaver, Louise.

    In: Molecular Ecology Resources, Vol. 18, No. 5, 01.09.2018, p. 940-952.

    Research output: Contribution to journalArticle

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    UR - http://www.mendeley.com/research/towards-robust-repeatable-sampling-methods-ednabased-studies

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