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Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: a case study on a threatened amphibian

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/aqc.748openalex-snapshot

Ponds and pools as model systems in conservation biology, ecology and evolutionary biology

inferredcites →https://doi.org/10.1002/aqc.853openalex-snapshot

Conservation of newt guilds in an agricultural landscape of Belgium: the importance of aquatic and terrestrial habitats

inferredcites →https://doi.org/10.1002/ece3.2186openalex-snapshot

Estimating species richness using environmental DNA

inferredcites →https://doi.org/10.1002/ece3.4013openalex-snapshot

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt ( Triturus cristatus )

inferredcites →https://doi.org/10.1002/ecs2.2500openalex-snapshot

Fine‐scale environmental DNA sampling reveals climate‐mediated interactions between native and invasive trout species

inferredcites →https://doi.org/10.1002/edn3.24openalex-snapshot

Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding

inferredcites →https://doi.org/10.1002/edn3.5openalex-snapshot

Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake

inferredcites →https://doi.org/10.1007/978-0-387-87458-6openalex-snapshot

Mixed effects models and extensions in ecology with R

inferredcites →https://doi.org/10.1007/978-0-387-98141-3openalex-snapshot

ggplot2: Elegant Graphics for Data Analysis

inferredcites →https://doi.org/10.1007/978-94-011-5648-6_26openalex-snapshot

Interactions between coot (Fulica atra) and submerged macrophytes: the role of birds in the restoration process

inferredcites →https://doi.org/10.1007/s00442-018-4267-3openalex-snapshot

Context-dependent dispersal, public information, and heterospecific attraction in newts

inferredcites →https://doi.org/10.1007/s10211-010-0082-5openalex-snapshot

Behaviour of the Common Moorhen in Rio Grande do Sul, Brazil

inferredcites →https://doi.org/10.1007/s10592-015-0775-4openalex-snapshot

The ecology of environmental DNA and implications for conservation genetics

inferredcites →https://doi.org/10.1007/s10750-009-9884-8openalex-snapshot

Restoring ponds for amphibians: a success story

inferredcites →https://doi.org/10.1007/s10750-016-3007-0openalex-snapshot

The importance of small waterbodies for biodiversity and ecosystem services: implications for policy makers

inferredcites →https://doi.org/10.1007/s10750-018-3750-5openalex-snapshot

Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds

inferredcites →https://doi.org/10.1016/0304-3770(93)90061-zopenalex-snapshot

Colonization of submerged macrophytes in shallow fish manipulated Lake Væng: impact of sediment composition and waterfowl grazing

inferredcites →https://doi.org/10.1016/j.biocon.2014.11.029openalex-snapshot

Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus)

inferredcites →https://doi.org/10.1016/j.biocon.2017.06.002openalex-snapshot

Dramatic impact of alien carp Cyprinus carpio on globally threatened diving ducks and other waterbirds in Mediterranean shallow lakes

inferredcites →https://doi.org/10.1016/j.watres.2018.03.003openalex-snapshot

Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive

inferredcites →https://doi.org/10.1016/s0304-3770(01)00182-6openalex-snapshot

Interaction between coot (Fulica atra) and waterlily (Nymphaea alba) in a lake: the indirect impact of foraging

inferredcites →https://doi.org/10.1021/acs.est.8b03869openalex-snapshot

Application of Environmental DNA Metabarcoding for Predicting Anthropogenic Pollution in Rivers

inferredcites →https://doi.org/10.1051/limn/2007017openalex-snapshot

Monitoring status, habitat features and amphibian species richness of Crested newt (Triturus cristatus superspecies) ponds at the edge of the species range (Salzburg, Austria)

inferredcites →https://doi.org/10.1089/10665270050081478openalex-snapshot

A Greedy Algorithm for Aligning DNA Sequences

inferredcites →https://doi.org/10.1093/bioinformatics/btr381openalex-snapshot

UCHIME improves sensitivity and speed of chimera detection

inferredcites →https://doi.org/10.1093/bioinformatics/btr507openalex-snapshot

FLASH: fast length adjustment of short reads to improve genome assemblies

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/biomet/60.2.255openalex-snapshot

Maximum Likelihood Identification of Gaussian Autoregressive Moving Average Models

inferredcites →https://doi.org/10.1093/nar/gkr732openalex-snapshot

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

inferredcites →https://doi.org/10.1111/1365-2664.12306openalex-snapshot

REVIEW: The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology

inferredcites →https://doi.org/10.1111/1365-2664.13352openalex-snapshot

Ground‐truthing of a fish‐based environmental DNA metabarcoding method for assessing the quality of lakes

inferredcites →https://doi.org/10.1111/1755-0998.12338openalex-snapshot

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

inferredcites →https://doi.org/10.1111/1755-0998.12690openalex-snapshot

Environmental DNA enables detection of terrestrial mammals from forest pond water

inferredcites →https://doi.org/10.1111/1755-0998.12735openalex-snapshot

ednaoccupancy : An r package for multiscale occupancy modelling of environmental DNA data

inferredcites →https://doi.org/10.1111/1755-0998.12934openalex-snapshot

Accuracy, limitations and cost efficiency of eDNA‐based community survey in tropical frogs

inferredcites →https://doi.org/10.1111/1755-0998.12940openalex-snapshot

Comparison of environmental DNA and bulk‐sample metabarcoding using highly degenerate cytochrome c oxidase I primers

inferredcites →https://doi.org/10.1111/bij.12516openalex-snapshot

How will the ‘molecular revolution’ contribute to biological recording?

inferredcites →https://doi.org/10.1111/conl.12447openalex-snapshot

New policy directions for global pond conservation

inferredcites →https://doi.org/10.1111/ddi.12829openalex-snapshot

Individual‐based models forecast the spread and inform the management of an emerging riverine invader

inferredcites →https://doi.org/10.1111/fwb.13094openalex-snapshot

Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods

inferredcites →https://doi.org/10.1111/j.1472-4642.2009.00575.xopenalex-snapshot

Niche position, but not niche breadth, differs in two coexisting amphibians having contrasting trends in Europe

inferredcites →https://doi.org/10.1111/j.1523-1739.2001.99200.xopenalex-snapshot

Habitat Matrix Effects on Pond Occupancy in Newts

inferredcites →https://doi.org/10.1111/mec.13428openalex-snapshot

Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

inferredcites →https://doi.org/10.1111/mec.13660openalex-snapshot

Environmental DNA metabarcoding of lake fish communities reflects long‐term data from established survey methods

inferredcites →https://doi.org/10.1111/mec.14350openalex-snapshot

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

inferredcites →https://doi.org/10.1127/fal/2017/1004openalex-snapshot

Consequences of fish for cladoceran, water beetle and macrophyte communities in a farmland pond landscape: implications for conservation

inferredcites →https://doi.org/10.1139/cjfas-2016-0306openalex-snapshot

Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering

inferredcites →https://doi.org/10.1163/156853806778189972openalex-snapshot

Habitat use during the aquatic phase of the newts Triturus vulgaris (L.) and T. cristatus (Laurenti) in central Norway: proposition for a conservation and monitoring area

inferredcites →https://doi.org/10.1163/15685381-00003040openalex-snapshot

Environmental factors associated with amphibian breeding in streams and springs: effects of habitat and fish occurrence

inferredcites →https://doi.org/10.1163/15685381-00003108openalex-snapshot

Testing the validity of a commonly-used habitat suitability index at the edge of a species’ range: great crested newt Triturus cristatus in Scotland

inferredcites →https://doi.org/10.1186/1471-2164-11-434openalex-snapshot

An In silico approach for the evaluation of DNA barcodes

inferredcites →https://doi.org/10.1186/s12983-015-0103-3openalex-snapshot

Linking habitat suitability to demography in a pond-breeding amphibian

inferredcites →https://doi.org/10.1371/journal.pone.0062727openalex-snapshot

Similar Local and Landscape Processes Affect Both a Common and a Rare Newt Species

inferredcites →https://doi.org/10.18637/jss.v069.c02openalex-snapshot

cooccur : Probabilistic Species Co-Occurrence Analysis in R

inferredcites →https://doi.org/10.32614/cran.package.aiccmodavgopenalex-snapshot

AICcmodavg: Model Selection and Multimodel Inference Based on (Q)AIC(c)

inferredcites →https://doi.org/10.32614/cran.package.resourceselectionopenalex-snapshot

ResourceSelection: Resource Selection (Probability) Functions for Use-Availability Data

inferredcites →https://doi.org/10.3390/d9040054openalex-snapshot

Metabarcoding of Environmental DNA Samples to Explore the Use of Uranium Mine Containment Ponds as a Water Source for Wildlife

inferredcites →https://doi.org/10.3897/mbmg.2.24262openalex-snapshot

Estimating fish alpha- and beta-diversity along a small stream with environmental DNA metabarcoding

inferredcites →https://doi.org/10.3929/ethz-b-000105397openalex-snapshot

Fitting Linear Mixed-Effects Models Using lme4

inferredcites →https://doi.org/10.5735/086.048.0504openalex-snapshot

Terrestrial Habitat Predicts use of Aquatic Habitat for Breeding Purposes — A Study on the Great Crested Newt (Triturus cristatus)

inferredcites →https://doi.org/10.5735/086.050.0303openalex-snapshot

Breeding Success of the Threatened Great Crested Newt in Boreal Forest Ponds

inferredcites →https://doi.org/10.7717/peerj.2444openalex-snapshot

Genetic signatures of ecological diversity along an urbanization gradient

inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot

VSEARCH: a versatile open source tool for metagenomics

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/aqc.3208openalex-snapshot

Taxonomic and geographical representation of freshwater environmental DNA research in aquatic conservation

inferred← citeshttps://doi.org/10.1002/edn3.41openalex-snapshot

A performance evaluation of targeted eDNA and eDNA metabarcoding analyses for freshwater fishes

inferred← citeshttps://doi.org/10.1002/edn3.80openalex-snapshot

Parallel, targeted analysis of environmental samples via high‐throughput quantitative PCR

inferred← citeshttps://doi.org/10.1007/s10750-018-3750-5openalex-snapshot

Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds

inferred← citeshttps://doi.org/10.1016/j.biocon.2019.108225openalex-snapshot

Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals

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