Article

Species detection using environmental DNA from water samples. Biol Lett 4:423-425

Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble Cedex 09, France.
Biology letters (Impact Factor: 3.43). 09/2008; 4(4):423-5. DOI: 10.1098/rsbl.2008.0118
Source: PubMed

ABSTRACT The assessment of species distribution is a first critical phase of biodiversity studies and is necessary to many disciplines such as biogeography, conservation biology and ecology. However, several species are difficult to detect, especially during particular time periods or developmental stages, potentially biasing study outcomes. Here we present a novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water. We used specific primers that amplify short mitochondrial DNA sequences to track the presence of a frog (Rana catesbeiana) in controlled environments and natural wetlands. A multi-sampling approach allowed for species detection in all environments where it was present, even at low densities. The reliability of the results was demonstrated by the identification of amplified DNA fragments, using traditional sequencing and parallel pyrosequencing techniques. As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples.

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Available from: Gentile Francesco Ficetola, Aug 29, 2015
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    • "Non-invasive genetic methods also allow measurement of demographic features such as population size (Luikart et al., 2010) and population immigration (De Barba et al., 2010). As ecological surrogates, genetic metrics can fill a wide niche as they can be a surrogate for traditional occupancy (Ficetola et al., 2008), population threats such as fragmentation (England et al., 2010), spread of invasive species (Hohenlohe et al., 2011), changes in resilience (Schindler et al., 2010), and population declines (Luikart et al., 1998). Another technological advancement that will change the cost and usefulness of potential surrogates is the suite of remote sensing technologies (Pettorelli et al., 2014). "
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    • "In this work, eDNA detection efficiency was poor when crayfish abundance – estimated by conventional trapping – was estimated to be low, perhaps because DNA was too sparse to be detected. As initially indicated by Ficetola et al. (2008), the detection of eDNA in water samples is 'useful for studying secretive aquatic or semi-aquatic species , which release DNA into the environment through mucus, faeces, urine and remains'. If detection efficiency varies between aquatic species, notably between vertebrates and invertebrates, then preliminary tests to estimate the detectability of DNA of a new target species under a range of semi-natural conditions should be a prerequisite for surveying. "
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    • "In this work, eDNA detection efficiency was poor when crayfish abundance – estimated by conventional trapping – was estimated to be low, perhaps because DNA was too sparse to be detected. As initially indicated by Ficetola et al. (2008), the detection of eDNA in water samples is 'useful for studying secretive aquatic or semi-aquatic species , which release DNA into the environment through mucus, faeces, urine and remains'. If detection efficiency varies between aquatic species, notably between vertebrates and invertebrates, then preliminary tests to estimate the detectability of DNA of a new target species under a range of semi-natural conditions should be a prerequisite for surveying. "
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