Validation of eDNA Surveillance Sensitivity for Detection of Asian Carps in Controlled and Field Experiments

Mahon, Andrew R.; Jerde, Christopher L.; Galaska, Matthew P.; Bergner, Jennifer L.; Chadderton, W. Lindsay; Lodge, David M.; Hunter, Margaret E.; Nico, Leo G.

doi:10.1371/journal.pone.0058316

Cited by 155 publications

(139 citation statements)

References 11 publications

(36 reference statements)

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“…One implication is studies targeting a small number of known taxa-for example, invasive or endangered species-are more likely to have success with qPCR assays than with large-scale eDNA sequencing. Consistent with this idea, the most high-profile uses of eDNA to date have targeted particular taxa using qPCR Mahon et al, 2013;Eichmiller et al, 2014;Laramie et al, 2015).…”

Section: Occupancy Modelingmentioning

confidence: 94%

“…While qPCR techniques have focused on single species detections to good effect (Mahon et al, 2013;Eichmiller et al, 2014), high-throughput sequencing using generalized PCR primers offers the promise of a more holistic view of an ecosystem, revealing hundreds or thousands of taxa present and potentially their abundance via cheap and relatively easy-to-collect environmental samples (e.g., Leray and Knowlton, 2015). Nevertheless, questions remain about sequence-based eDNA surveys, even as the technique becomes more common in the field.…”

Section: Introductionmentioning

confidence: 99%

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Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem

et al. 2017

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Given the rapid rise of environmental DNA (eDNA) surveys in ecology and environmental science, it is important to be able to compare the results of these surveys to traditional methods of measuring biodiversity. Here we compare samples from a traditional method (a manual tow-net) to companion eDNA samples sequenced at three different genetic loci. We find only partial taxonomic overlap among the resulting datasets, with each reflecting a portion of the larger suite of taxa present in the sampled nearshore marine environment. In the larger context of eDNA sequencing surveys, our results suggest that primer amplification bias drives much of the taxonomic bias in eDNA detection, and that the baseline probability of detecting any given taxon with a broad-spectrum primer set is likely to be low. Whether catching fish with different nets or using different PCR primer sets, multiple data types can provide complementary views of a common ecosystem. However, it remains difficult to cross-validate eDNA sequencing techniques in the field, either for presence/absence or for abundance, particularly for primer sets that target very wide taxonomic ranges. Finally, our results highlight the breadth of diversity in a single habitat, and although eDNA does capture a richer sample of the community than traditional methods of sampling, a large number of eDNA primer sets focusing on different subsets of the biota would be necessary to survey any ecological community in a reasonably comprehensive way.

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Section: Occupancy Modelingmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem

et al. 2017

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“…Distributions of organisms and biomass in freshwater systems have been correlated with eDNA concentration (Takahara et al, , 2013. Thus eDNA concentration has been used as a proxy for population distribution in amphibians (Ficetola et al, 2008;Goldberg et al, 2011), fishes (Mahon, Jerde, Galaska, Bergner, Chadderton, Lodge, Hunter, & Nico, 2012;Minamoto, Yamanaka, Takahara, Honjo, & Kawabata, 2012) and reptiles species (Piaggio et al, 2013). In marine species no studies have been conducted to determine the relationship between eDNA concentration and species distribution, abundance and biomass.…”

Section: Edna Applications In Ecology and Conservationmentioning

confidence: 99%

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

Díaz-Ferguson

Moyer

2014

RBT

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Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980's and phytoplankton communities in the water column since the early-1990's. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist with an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments. Rev. Biol. Trop. 62 (4): 1273-1284. Epub 2014 December 01.Key words: environmental DNA (eDNA), detection probability, occupancy models, persistence, metabarcode, minibarcode.In order to understand distributions, patterns, and abundances for populations or species, the collection (detection) and identification of individuals from their physical origins must be undertaken. Thus, species detection is fundamental to scientific disciplines such as phylogenetics, conservation biology, and ecology. However, species detection is sometimes extremely difficult especially in marine and aquatic environments where organisms have complex life cycles, and direct observation of early development stages is almost impossible (Ficetola, Miaud, Pompanon, & Taberlet, 2008). Species detection in these environments has been conducted using traditional direct observation methods (visual or acoustic) (Thomsen et al., 2012a). Nonetheless, traditional detection methods can have logistic limitations, be time consuming, expensive, and in some cases, harmful to the environment (e.g., marine bottom trawls, electrofishing and rotenone poisoning) (Thomsen et al., 2012b). The advent of novel molecular and forensic methods have provided innovative tools for detecting marine and aquatic organisms that may circumvent the aforementioned limitations (Darling & Blum, 2007;valentini, Pompano, & Taberlet, 2009;Lodge et al., 2012).One such tool is the detection of an organism's environmental DNA (eDNA). Defined as short DNA fragments that an organism leaves behind in non-living components of the ecosystem (i.e., water, air or sediments), eDNA is derived from either cellular DNA present in epithelial cells released by organisms to the environment through skin, urine, feces or mucus or extracellular DNA that is the DNA in the environment resulting from cell death and subsequent destruction of cell structure (Foote, Thomsen, Sveegaard, Wahlberg, Kielgast, Kyhn, Salling, Galatius, Orlando, & Gilbert, 2012;Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012a). Methodologically, eDNA d...

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“…Thus, one of the first demonstrations of macrobial eDNA surveillance targeted invasive American bullfrogs (Rana catesbeiana) in French wetlands (Ficetola et al 2008). The high-profile invasion of bigheaded carps Hypophthalmichthys molitrix and H. nobilis into waters of the midwestern United States (USA) has also represented a frequent target of eDNA surveillance efforts (Jerde et al 2011;Mahon et al 2013;Turner et al 2014b). Other eDNA surveillance targets in natural waters have included Bluegill Sunfish (Lepomis macrochirus) invading ponds in Japan (Takahara and Minamoto 2013), New Zealand mudsnails (Potamopyrgus antipodarum) in streams of Idaho, USA , PontoCaspian zebra mussels (Dreissena polymorpha) in the midwestern USA (Egan et al 2013), Louisiana crayfish (Procambarus clarkii) in France (Tréguier et al 2014), and African Jewelfish (Hemichromis letourneuxi) and Burmese pythons (Python bivittatus) in Florida, USA's ponds ) and wetlands (Piaggio et al 2014), respectively.…”

Section: Introductionmentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

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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 biomolecules 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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Validation of eDNA Surveillance Sensitivity for Detection of Asian Carps in Controlled and Field Experiments

Cited by 155 publications

References 11 publications

Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem

Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

The ecology of environmental DNA and implications for conservation genetics

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