Reliable Discrimination of 10 Ungulate Species Using High Resolution Melting Analysis of Faecal DNA

Ana Ramón-Laca, Dianne GLEESON, Ivor Yockney, Mike Perry, Graham Nugent, David M. Forsyth

    Research output: Contribution to journalArticle

    25 Citations (Scopus)
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    Abstract

    Identifying species occupying an area is essential for many ecological and conservation studies. Faecal DNA is a potentially powerful method for identifying cryptic mammalian species. In New Zealand, 10 species of ungulate (Order: Artiodactyla) have established wild populations and are managed as pests because of their impacts on native ecosystems. However, identifying the ungulate species present within a management area based on pellet morphology is unreliable. We present a method that enables reliable identification of 10 ungulate species (red deer, sika deer, rusa deer, fallow deer, sambar deer, white-tailed deer, Himalayan tahr, Alpine chamois, feral sheep, and feral goat) from swabs of faecal pellets. A high resolution melting (HRM) assay, targeting a fragment of the 12S rRNA gene, was developed. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behaviour for each species. The method was developed using tissue from each of the 10 species, and was validated in blind trials. Our protocol enabled species to be determined for 94% of faecal pellet swabs collected during routine monitoring by the New Zealand Department of Conservation. Our HRM method enables high-throughput and cost-effective species identification from low DNA template samples, and could readily be adapted to discriminate other mammalian species from faecal DNA.
    Original languageEnglish
    Pages (from-to)1-8
    Number of pages8
    JournalPLoS One
    Volume9
    Issue number3
    DOIs
    Publication statusPublished - 2014

    Fingerprint

    Deer
    ungulates
    melting
    Freezing
    Melting
    pellets
    DNA
    Conservation
    Alpine (goat breed)
    New Zealand
    chamois
    Artiodactyla
    Cervus nippon
    Ecosystems
    Cervus dama
    Assays
    Rupicapra
    Odocoileus virginianus
    Cervus elaphus
    Genes

    Cite this

    Ramón-Laca, Ana ; GLEESON, Dianne ; Yockney, Ivor ; Perry, Mike ; Nugent, Graham ; Forsyth, David M. / Reliable Discrimination of 10 Ungulate Species Using High Resolution Melting Analysis of Faecal DNA. In: PLoS One. 2014 ; Vol. 9, No. 3. pp. 1-8.
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    abstract = "Identifying species occupying an area is essential for many ecological and conservation studies. Faecal DNA is a potentially powerful method for identifying cryptic mammalian species. In New Zealand, 10 species of ungulate (Order: Artiodactyla) have established wild populations and are managed as pests because of their impacts on native ecosystems. However, identifying the ungulate species present within a management area based on pellet morphology is unreliable. We present a method that enables reliable identification of 10 ungulate species (red deer, sika deer, rusa deer, fallow deer, sambar deer, white-tailed deer, Himalayan tahr, Alpine chamois, feral sheep, and feral goat) from swabs of faecal pellets. A high resolution melting (HRM) assay, targeting a fragment of the 12S rRNA gene, was developed. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behaviour for each species. The method was developed using tissue from each of the 10 species, and was validated in blind trials. Our protocol enabled species to be determined for 94{\%} of faecal pellet swabs collected during routine monitoring by the New Zealand Department of Conservation. Our HRM method enables high-throughput and cost-effective species identification from low DNA template samples, and could readily be adapted to discriminate other mammalian species from faecal DNA.",
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    Reliable Discrimination of 10 Ungulate Species Using High Resolution Melting Analysis of Faecal DNA. / Ramón-Laca, Ana; GLEESON, Dianne; Yockney, Ivor; Perry, Mike; Nugent, Graham; Forsyth, David M.

    In: PLoS One, Vol. 9, No. 3, 2014, p. 1-8.

    Research output: Contribution to journalArticle

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    AU - Ramón-Laca, Ana

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    AU - Perry, Mike

    AU - Nugent, Graham

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