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: 3.25). 09/2008; 4(4):423-5. DOI: 10.1098/rsbl.2008.0118
Source: PubMed


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, Oct 01, 2015
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    • "One of the earliest studies to target detection of vertebrate eDNA collected terrestrial mammal mitochondrial eDNA from aquatic environments, implicating fecal origins of such material (Martellini et al. 2005). Although feces remains a probable source of eDNA from a wide range of taxa targeted in aquatic (Thomsen et al. 2012a) and terrestrial environments (Andersen et al. 2012), high rates of success detecting taxa which produce slimy coatings such as amphibians (Ficetola et al. 2008) and fish (Jerde et al. 2011) suggest that other bodily fluids also act as a source of eDNA. Still other studies have demonstrated that dead carcasses and predator feces may also serve as an eDNA source in some cases (Merkes et al. 2014). "
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    ABSTRACT: Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the ''ecology'' of eDNA—myriad interactions between extraorganismal genetic material and its environment—and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomole-cules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.
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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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    ABSTRACT: Surrogate concepts are used in all sub-disciplines of environmental science. However, controversy remains regarding the extent to which surrogates are useful for resolving environmental problems. Here, we argue that conflicts about the utility of surrogates (and the related concepts of indicators and proxies) often reflect context-specific differences in trade-offs between measurement accuracy and practical constraints. By examining different approaches for selecting and applying surrogates, we identify five trade-offs that correspond to key points of contention in the application of surrogates. We then present an 8-step Adaptive Surrogacy Framework that incorporates cross-disciplinary perspectives from a wide spectrum of the environmental sciences, aiming to unify surrogate concepts across disciplines and applications. Our synthesis of the science of surrogates is intended as a first step towards fully leveraging knowledge accumulated across disciplines, thus consolidating lessons learned so that they may be accessible to all those operating in different fields, yet facing similar hurdles. Copyright © 2015 Elsevier B.V. All rights reserved.
    Science of The Total Environment 08/2015; DOI:10.1016/j.scitotenv.2015.08.056 · 4.10 Impact Factor
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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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    ABSTRACT: 1. There is a growing literature on the detection of species-specific DNA fragments in water to reveal animals' presence in aquatic environments. 2. Analysis of Rees et al. (Journal of Applied Ecology, 2014, 51, 1450) and additional publications highlight the downside of the method and suggest that some conclusions have to be toned down. 3. Non-detection of species-specific DNA fragments in a water sample does not automatically imply the absence of the target species. A positive signal does not necessarily mean the species is present because the environmental DNA (eDNA) could have been transported or preserved after an animal's death. Detection of aquatic invertebrates is weakly documented. The effect of species abundance on detection efficiency is not always established. 4. Synthesis and applications. Before successfully becoming an efficient tool to assist proper management policies for monitoring of aquatic species, eDNA surveys must implement sampling strategies that allow estimating detection rates and scaling up information from water samples to larger spatial areas. The effects of discharge variations and dendritic organization in running waters require particular consideration.
    Journal of Applied Ecology 08/2015; 52:823-826. DOI:10.1111/1365-2664.12428 · 4.56 Impact Factor
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