Capture enrichment of aquatic environmental DNA: A first proof of concept

Wilcox, Taylor M.; Zarn, Katherine E.; Piggott, Maxine P.; Young, Michael K.; McKelvey, Kevin S.; Schwartz, Michael K.

doi:10.1111/1755-0998.12928

Cited by 53 publications

(63 citation statements)

References 65 publications

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“…In previous studies on eDNA isolated from water samples, large volumes of water (e.g. 5 L; Wilcox et al, ) were used for filtration, and a study using a comparable volume of water (250 ml water for filtration) obtained variable results (Grey et al, ). It would thus seem advisable, based on our results and those of Grey et al () that a large volume of water be utilized.…”

Section: Discussionmentioning

confidence: 99%

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Seeber

McEwen

Löber

et al. 2019

Molecular Ecology Resources

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Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA‐based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water‐limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus‐specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non‐African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over‐representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100‐fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.

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Section: Discussionmentioning

confidence: 99%

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Seeber

McEwen

Löber

et al. 2019

Molecular Ecology Resources

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“…We also detected ecologically important PCR as a method for assessing a large number of diverse taxa relevant to stream and riparian communities. This highly multiplexed approach significantly extends the reach of traditional "metabarcoding" (Cilleros et al, 2019;e.g., Deiner et al, 2016;Thomsen, Kielgast, Iversen, Møller, et al, 2012;Valentini et al, 2016), and it offers a high degree of specificity that exceeds early results from hybridization-based enrichment (Wilcox et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…Originally developed for characterizing microbial (Venter et al, 2004) and fungal (Anderson and Cairney, 2004) communities, eDNA analysis has expanded to include diverse eukaryotes, including plants (Willerslev et al, 2003), invertebrates (Hajibabaei et al, 2011;Thomsen, Kielgast, Iversen, Wiuf, et al, 2012), and vertebrates (Andersen et al, 2012;Thomsen, Kielgast, Iversen, Møller, et al, 2012). Methods for eDNA analysis have evolved from assays targeting one to a few well-characterized taxa (e.g., qPCR, digital PCR; Nathan et al, 2014), to "metabarcoding" assays that identify scores of taxonomic targets per sample (Deiner et al, 2016;Thomsen, Kielgast, Iversen, Møller, et al, 2012;Valentini et al, 2016;Wilcox et al, 2018). Metabarcoding approaches have been shown to provide detection accuracies equivalent or better than traditional sampling methods (Deiner et al, 2016;Thomsen, Kielgast, Iversen, Møller, et al, 2012;Valentini et al, 2016; but see Cilleros et al, 2019), and a much larger taxonomic spectrum per assay.…”

Section: Introductionmentioning

confidence: 99%

Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from diverse taxonomic targets

et al. 2019

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Environmental DNA (eDNA) assays for single‐ and multi‐species detection show promise for providing standardized assessment methods for diverse taxa, but techniques for evaluating multiple taxonomically divergent assemblages are in their infancy. We evaluated whether microfluidic multiplex metabarcoding on the Fluidigm Access Array™ platform and high‐throughput sequencing could identify diverse stream and riparian assemblages from 48 taxon‐general and taxon‐specific metabarcode primers. eDNA screening was paired with electrofishing along a stream continuum to evaluate congruence between methods. A fish hatchery located midway along the stream continuum provided a dispersal barrier, and a point source for non‐native White Sturgeon (Acipencer transmontanus). Microfluidic metabarcoding had 87% accuracy with respect to electrofishing and detected all 13 species electrofishing observed. Taxon‐specific barcoding primers were more successful than taxon‐general universal metabarcoding primers at classifying sequences to species. Both types of markers detected a transition from downstream sites dominated by multiple fish species, to upstream sites dominated by a single species; however, we failed to detect a complementary transition in amphibian occupancy. White Sturgeon was only detected at the hatchery outflow, indicating eDNA transport was not detectable ~2.4 km from its source. Overall, we identified 878 predicted taxa. Most sequences (50.1%) derived from fish (Actinopteri, Petromyzontidae), oomycetes (21.3%), arthropoda (classes Insecta, Decapoda; 16.5%), and apicomplexan parasites (3.8%). Taxa accounting for ~1% or less of sequences included freshwater red algae, diatoms, amphibians, and beaver. Our work shows that microfluidic metabarcoding can survey multiple phyla per assay, providing fine discrimination required to resolve closely related species, and enable data‐driven prioritization for multiple forest health objectives.

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“…, Wilcox et al. ). The implication is that analysis of water samples may be used to demonstrate whether mink are present, or not present, in a particular river (upstream of the sampling site) or lake.…”

Section: What Has Changed?mentioning

confidence: 99%

A mink‐free GB: perspectives on eradicating American minkNeovison visonfrom Great Britain and its islands

Martin

Lea²

2020

Mammal Review

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This paper examines the case for, and plausibility of, eradicating American mink Neovison vison from mainland Great Britain and its associated offshore islands. This invasive species causes extensive damage to native fauna throughout Europe, and the UK Government is obliged to eradicate it, if feasible, under the Bern Convention. Current mink control buys time, but is patchy and dependent on substantial funding in perpetuity. If enacted, eradication would be cheaper in the long term and much more effective in preserving native wildlife. The methodology of an eradication campaign is explored, together with risks, challenges, and a tentative timeline and cost. We judge that mink eradication is now logistically feasible, due to technological developments and experience gained from landscape‐scale control. Using live traps fitted with electronic sensors – ‘smart’ traps – as the primary means of catching mink would render the campaign efficient, humane and free of non‐target mortality and negative environmental impacts. The ecological benefits of mink eradication would be profound, including greatly improving prospects for water vole Arvicola amphibius populations. Reinvasion is highly unlikely. The greatest logistical challenge is probably removing mink from Scottish west coast islands. Eradication might take around a decade and be dependent on co‐ordination between many conservation, fishing, farming, and water‐related organisations, together with the consent of landowners. By adding alarms to existing mink traps, land and water managers can pave the way to eradication now. A mink‐free Great Britain would plausibly cost tens of millions of pounds, against which could be set the limitless future costs of mink control. Such a campaign would be by far the world's largest invasive predator eradication project by geographical area and would set a precedent for citizen‐led conservation action globally. Regional trials would be extremely valuable in determining the costs and practicality of a GB‐wide campaign.

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Capture enrichment of aquatic environmental DNA: A first proof of concept

Cited by 53 publications

References 65 publications

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from diverse taxonomic targets

A mink‐free GB: perspectives on eradicating American minkNeovison visonfrom Great Britain and its islands

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