Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation

Cristescu, Melania E.; Hebert, Paul D. N.

doi:10.1146/annurev-ecolsys-110617-062306

Cited by 267 publications

(255 citation statements)

References 127 publications

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“…For that, we need multiscale measures of ecosystem processes (Soranno et al 2019) and biodiversity change (Barnes et al 2016;Chase et al 2019). For measuring biodiversity change at different scales, BEF research must harness current methodological developments (Bush et al 2017), like metagenomics, eDNA (Cristescu & Hebert 2018), remote sensing (Pau & Dee 2016;Rocchini et al 2018) and multi-site monitoring networks and experiments. Scale-explicit analyses will require multiscale statistical methods, such as generalised dissimilarity modelling (Ferrier et al 2007), that can be used to predict spatial patterns of turnover in diversity that are crucial to understanding how the BEF relationship will change across large spatial and temporal extents (Leibold et al 2017;Hu et al 2018;Mori et al 2018).…”

Section: Linking Theory To New Observational Data On Biodiversity Chamentioning

confidence: 99%

Scaling‐up biodiversity‐ecosystem functioning research

et al. 2020

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A rich body of knowledge links biodiversity to ecosystem functioning (BEF), but it is primarily focused on small scales. We review the current theory and identify six expectations for scale dependence in the BEF relationship: (1) a nonlinear change in the slope of the BEF relationship with spatial scale; (2) a scale‐dependent relationship between ecosystem stability and spatial extent; (3) coexistence within and among sites will result in a positive BEF relationship at larger scales; (4) temporal autocorrelation in environmental variability affects species turnover and thus the change in BEF slope with scale; (5) connectivity in metacommunities generates nonlinear BEF and stability relationships by affecting population synchrony at local and regional scales; (6) spatial scaling in food web structure and diversity will generate scale dependence in ecosystem functioning. We suggest directions for synthesis that combine approaches in metaecosystem and metacommunity ecology and integrate cross‐scale feedbacks. Tests of this theory may combine remote sensing with a generation of networked experiments that assess effects at multiple scales. We also show how anthropogenic land cover change may alter the scaling of the BEF relationship. New research on the role of scale in BEF will guide policy linking the goals of managing biodiversity and ecosystems.

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Section: Linking Theory To New Observational Data On Biodiversity Chamentioning

confidence: 99%

Scaling‐up biodiversity‐ecosystem functioning research

et al. 2020

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“…Fieldwork requires only the collection of water samples and thus lowers the effort and cost of species detection compared with traditional organismal surveys, such as netting, snorkeling, or electrofishing (Smart et al 2016, Wilcox et al 2016. Methods involving eDNA are gaining widespread use in monitoring and conservation applications (Cristescu and Hebert 2018), but questions remain about how to best implement regional, multi-watershed eDNA monitoring that is effective and efficient, especially for aquatic invasive species (e.g., Darling and Mahon 2011, De Ventura et al 2017, Gingera et al 2017. Methods involving eDNA are gaining widespread use in monitoring and conservation applications (Cristescu and Hebert 2018), but questions remain about how to best implement regional, multi-watershed eDNA monitoring that is effective and efficient, especially for aquatic invasive species (e.g., Darling and Mahon 2011, De Ventura et al 2017, Gingera et al 2017.…”

Section: Introductionmentioning

confidence: 99%

“…Even some of the first studies demonstrated the sensitivity of eDNA analysis for detection of rare and cryptic species, as well as providing crucial early detection for invasive species (Ficetola et al 2008, Goldberg et al 2011, Jerde et al 2011, Thomsen et al 2011. Methods involving eDNA are gaining widespread use in monitoring and conservation applications (Cristescu and Hebert 2018), but questions remain about how to best implement regional, multi-watershed eDNA monitoring that is effective and efficient, especially for aquatic invasive species (e.g., Darling and Mahon 2011, De Ventura et al 2017, Gingera et al 2017.…”

Section: Introductionmentioning

confidence: 99%

Adding invasive species biosurveillance to the U.S. Geological Survey streamgage network

et al. 2019

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The costs of invasive species in the United States alone are estimated to exceed US$100 billion per year, so a critical tactic in minimizing the costs of invasive species is the development of effective, early-detection systems. To this end, we evaluated the efficacy of adding environmental (e)DNA surveillance to the U.S. Geological Survey (USGS) streamgage network, which consists of >8200 streamgages nationwide systemically visited by USGS hydrologic technicians. Incorporating strategic eDNA sample collection during routine streamgage visits could provide early-detection surveillance of aquatic invasive species with minimal additional cost. For this evaluation, USGS hydrologic technicians collected monthly eDNA water samples, May-September 2018, from streamgages downstream of reservoirs in the Columbia River Basin thought to be vulnerable to invasive dreissenid mussel (Dreissenidae spp.) establishment. We tested water samples for dreissenid mussel DNA and also for kokanee (Oncorhynchus nerka) and yellow perch (Perca flavescens) DNA; the two fishes were used to assess if streamgages are adequately located to provide early-detection eDNA surveillance of taxa known to be present in upstream reservoirs. No Columbia River Basin streamgage samples met our criteria for being scored as positive for dreissenid DNA. We did detect kokanee and yellow perch DNA at all streamgages downstream of reservoirs where these species are known to occur. Field collection, laboratory analyses, and personnel time required for collection of four eDNA samples at a streamgage site cost US$500-US$600 (net). Given these results, incorporating eDNA biosurveillance into routine streamgage visits might decrease costs associated with an invasion since early detection maximizes the potential for eradication, containment, and mitigation.

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“…While both targeted and community-wide characterization methods have now been applied widely in a range of habitats (Dowle, Pochon, Banks, Shearer, & Wood, 2016;Evans et al, 2017;Laroche et al, 2016), few studies have directly compared the sensitivity of techniques (Pochon, Bott, Smith, & Wood, 2013). This is particularly important when these methods are applied with the aim of detecting rare or invasive species (Cristescu & Hebert, 2018;Goldberg et al, 2016).…”

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confidence: 99%

A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA

Wood

Pochon

Laroche

et al. 2019

Molecular Ecology Resources

100

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Targeted species‐specific and community‐wide molecular diagnostics tools are being used with increasing frequency to detect invasive or rare species. Few studies have compared the sensitivity and specificity of these approaches. In the present study environmental DNA from 90 filtered seawater and 120 biofouling samples was analyzed with quantitative PCR (qPCR), droplet digital PCR (ddPCR) and metabarcoding targeting the cytochrome c oxidase I (COI) and 18S rRNA genes for the Mediterranean fanworm Sabella spallanzanii. The qPCR analyses detected S. spallanzanii in 53% of water and 85% of biofouling samples. Using ddPCR S. spallanzanii was detected in 61% of water of water and 95% of biofouling samples. There were strong relationships between COI copy numbers determined via qPCR and ddPCR (water R2 = 0.81, p < .001, biofouling R2 = 0.68, p < .001); however, qPCR copy numbers were on average 125‐fold lower than those measured using ddPCR. Using metabarcoding there was higher detection in water samples when targeting the COI (40%) compared to 18S rRNA (5.4%). The difference was less pronounced in biofouling samples (25% COI, 29% 18S rRNA). Occupancy modelling showed that although the occupancy estimate was higher for biofouling samples (ψ = 1.0), higher probabilities of detection were derived for water samples. Detection probabilities of ddPCR (1.0) and qPCR (0.93) were nearly double metabarcoding (0.57 to 0.27 marker dependent). Studies that aim to detect specific invasive or rare species in environmental samples should consider using targeted approaches until a detailed understanding of how community and matrix complexity, and primer biases affect metabarcoding data.

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Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation

Cited by 267 publications

References 127 publications

Scaling‐up biodiversity‐ecosystem functioning research

Scaling‐up biodiversity‐ecosystem functioning research

Adding invasive species biosurveillance to the U.S. Geological Survey streamgage network

A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA

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