A framework for estimating the sensitivity of <scp>eDNA</scp> surveys

Furlan, Elise M.; Gleeson, Dianne; Hardy, Christopher M.; Duncan, Richard P.

doi:10.1111/1755-0998.12483

Cited by 178 publications

(235 citation statements)

References 51 publications

(99 reference statements)

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“…This is a critical consideration in locations where no positive detections were recorded and where there was a limited sampling effort (locations with fewer than 30 samples collected). The results from our re-screening are consistent with other eDNA studies that highlight the importance of PCR replication and the potential for high prevalence of false negatives from eDNA samples when detection probabilities are low (Ficetola et al 2015;Furlan et al 2015).…”

Section: Discussionsupporting

confidence: 88%

A sensitive environmental DNA (eDNA) assay leads to new insights on Ruffe (Gymnocephalus cernua) spread in North America

et al. 2016

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Detection of invasive species before or soon after they establish in novel environments is critical to prevent widespread ecological and economic impacts. Environmental DNA (eDNA) surveillance and monitoring is an approach to improve early detection efforts. Here we describe a large-scale conservation application of a quantitative polymerase chain reaction assay with a case study for surveillance of a federally listed nuisance species (Ruffe, Gymnocephalus cernua) in the Laurentian Great Lakes. Using current Ruffe distribution data and predictions of future Ruffe spread derived from a recently developed model of ballast-mediated dispersal in US waters of the Great Lakes, we designed an eDNA surveillance study to target Ruffe at the putative leading edge of the invasion. We report a much more advanced invasion front for Ruffe than has been indicated by conventional surveillance methods and we quantify rates of false negative detections (i.e. failure to detect DNA when it is present in a sample). Our results highlight the important role of eDNA surveillance as a sensitive tool to improve early detection efforts for aquatic invasive species and draw attention to the need for an improved understanding of detection errors. Based on axes that reflect the weight of eDNA evidence of species presence and the likelihood of secondary

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Section: Discussionsupporting

confidence: 88%

A sensitive environmental DNA (eDNA) assay leads to new insights on Ruffe (Gymnocephalus cernua) spread in North America

et al. 2016

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“…In one example, eastern hellbenders (Cryptobranchus a. alleganiensis) were successfully detected using environmental DNA at densities approaching the lowest reported natural population densities (Olson et al 2012). In many cases, the likelihood of false positive detection is reported to be low; potential biases for the incomplete detection of DNA can be quantified by formal estimation of DNA detection probabilities under occupancy modelling frameworks, as used by Moyer et al (2014) and more recently by Furlan et al (2016).…”

Section: Studies Conducted On Rare Organismsmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

107

112

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

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“…To now benefit from the rich information DNA metabarcoding can provide, robust sampling designs are needed, built on a quantitative understanding of spatial variability among samples, detection probabilities (e.g. Furlan et al 2016), repeatability by field teams, and uncertainty and statistical power to determine effect sizes that can be interpreted ecologically. Most current metabarcoding studies lack these design elements (e.g.…”

Section: Methodological Uncertainties Associated With Dna Metabarcodingmentioning

confidence: 99%

“…For example, taxonomic classifications and the coverage and depth of reference databases are continually improving (Ratnasingham & Hebert 2013), and the quantification of uncertainty in sampling, molecular and bioinformatics methods is well underway (e.g. Furlan et al 2016;Lindgreen et al 2016). Furthermore, an increasing uptake of metabarcoding approaches by ecological researchers (Bohmann et al 2014;Creer et al 2016) is likely to improve the design and ecological interpretation of DNA metabarcoding data sets.…”

Section: Methodological Uncertainties Associated With Dna Metabarcodingmentioning

confidence: 99%

“…Application of DNA metabarcoding alongside conventional methods of assessment, coupled with a quantitative understanding of the detection probabilities and biases of different methods (e.g. Furlan et al 2016), could lead to greater overall detection probabilities for target taxa. Further, conventional monitoring techniques provide additional information that cannot be obtained from metabarcoding.…”

Section: General Benefits Of Dna Metabarcoding and Its Integration Wimentioning

confidence: 99%

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Using DNA meta barcoding to assess New Zealand's terrestrial biodiversity

Holdaway¹,

Wood²,

Dickie³

et al. 2017

NZ J Ecol

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High throughput DNA sequencing technology has enabled entire biological communities to be characterised from DNA derived from pools of organisms, such as bulk-collected invertebrates, or DNA extracted from environmental samples (e.g. soil). These DNA-based techniques have the potential to revolutionise biodiversity monitoring. One approach in particular, DNA metabarcoding, can provide unprecedented taxonomic breadth at a scale not practically achievable through the morphological identification of individual organisms. Here, we assess the current strengths and weaknesses of DNA metabarcoding techniques for biodiversity assessment. We argue that it is essential to integrate conventional monitoring methods with novel DNA methods, to validate methods, and to better use and interpret data. We present a conceptual framework for how this might be done, explore potential applications within national biodiversity assessment frameworks, Maori biodiversity monitoring and the primary sector, and highlight areas of current uncertainty and future research directions. Rapid developments in DNA sequencing technology and bioinformatics will make DNA-based community data increasingly accessible to ecologists, and there needs to be a corresponding shift in research focus from DNA metabarcoding method development and evaluation to real-world applications that provide rich information for a range of purposes, including conservation planning and land management decisions.

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A framework for estimating the sensitivity of eDNA surveys

Cited by 178 publications

References 51 publications

A sensitive environmental DNA (eDNA) assay leads to new insights on Ruffe (Gymnocephalus cernua) spread in North America

A sensitive environmental DNA (eDNA) assay leads to new insights on Ruffe (Gymnocephalus cernua) spread in North America

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Using DNA meta barcoding to assess New Zealand's terrestrial biodiversity

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