A Systematic Review of Sources of Variability and Uncertainty in eDNA Data for Environmental Monitoring

Optimizing environmental DNA sampling effort for fish inventories in tropical streams and rivers

(2019) Isabel Cantera et al.   Scientific Reports

Joint species distribution models with species correlations and imperfect detection

(2019) Mathias W. Tobler et al.   ECOLOGY

DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

(2019) Lucie Zinger et al.   MOLECULAR ECOLOGY

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types

(2018) Syrie M. Hermans et al.   Molecular Ecology Resources

Towards robust and repeatable sampling methods in eDNA-based studies

(2018) Ian A. Dickie et al.   Molecular Ecology Resources

Macroecology to Unite All Life, Large and Small

(2018) Ashley Shade et al.   TRENDS IN ECOLOGY & EVOLUTION

Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity

(2018) Andrew Dopheide et al.   Methods in Ecology and Evolution

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

(2018) Jacob T. Nearing et al.   PeerJ

Using environmental DNA and occupancy modelling to identify drivers of eastern hellbender (Cryptobranchus alleganiensis alleganiensis ) extirpation

(2018) Sean M. Wineland et al.   FRESHWATER BIOLOGY

Accounting for observation processes across multiple levels of uncertainty improves inference of species distributions and guides adaptive sampling of environmental DNA

(2018) Amy J. Davis et al.   Ecology and Evolution

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Green alder (Alnus viridis ) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently

(2017) G. Schwob et al.   ENVIRONMENTAL MICROBIOLOGY

Improving reliability in environmental DNA detection surveys through enhanced quality control

(2017) Elise M. Furlan et al.   MARINE AND FRESHWATER RESEARCH

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities

(2017) Hirotoshi Sato et al.   Scientific Reports

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

(2017) Laurence J. Clarke et al.   Ecology and Evolution

An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples

(2017) Laura Clusa et al.   PeerJ

Surveying Europe’s Only Cave-Dwelling Chordate Species (Proteus anguinus) Using Environmental DNA

(2017) Judit Vörös et al.   PLoS One

Application of environmental DNA to detect an endangered marine skate species in the wild

(2017) Kay Weltz et al.   PLoS One

Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

(2017) Xavier Pochon et al.   PLoS One

The power of monitoring: optimizing survey designs to detect occupancy changes in a rare amphibian population

(2017) Izabela M. Barata et al.   Scientific Reports

Early detection of aquatic invaders using metabarcoding reveals a high number of non-indigenous species in Canadian ports

(2016) Emily A. Brown et al.   DIVERSITY AND DISTRIBUTIONS

Modelling of species distributions, range dynamics and communities under imperfect detection: advances, challenges and opportunities

(2016) Gurutzeta Guillera-Arroita   ECOGRAPHY

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

(2016) Katharina Dulias et al.   JOURNAL OF PALEOLIMNOLOGY

Residual eDNA detection sensitivity assessed by quantitative real-time PCR in a river ecosystem

(2016) Katherine D. Balasingham et al.   Molecular Ecology Resources

Detecting the movement and spawning activity of bigheaded carps with environmental DNA

(2016) Richard A. Erickson et al.   Molecular Ecology Resources

The ecology and biogeochemistry of stream biofilms

(2016) Tom J. Battin et al.   NATURE REVIEWS MICROBIOLOGY

Environmental DNA reveals that rivers are conveyer belts of biodiversity information

(2016) Kristy Deiner et al.   Nature Communications

Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed filter

(2016) Johan Spens et al.   Methods in Ecology and Evolution

boral - Bayesian Ordination and Regression Analysis of Multivariate Abundance Data in r

(2016) Francis K.C. Hui   Methods in Ecology and Evolution

Critical considerations for the application of environmental DNA methods to detect aquatic species

(2016) Caren S. Goldberg et al.   Methods in Ecology and Evolution

Diversity Takes Shape: Understanding the Mechanistic and Adaptive Basis of Bacterial Morphology

(2016) David T. Kysela et al.   PLOS BIOLOGY

Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary

(2016) Thomas C. Jeffries et al.   Frontiers in Microbiology

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

(2016) Magdalena Guardiola et al.   PeerJ

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

(2016) Paul Carini et al.   Nature Microbiology

Implementation of Novel Design Features for qPCR-Based eDNA Assessment

(2016) Nik Veldhoen et al.   PLoS One

Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA

(2015) Kristy Deiner et al.   BIOLOGICAL CONSERVATION

Effects of sample processing on the detection rate of environmental DNA from the Common Carp (Cyprinus carpio)

(2015) Teruhiko Takahara et al.   BIOLOGICAL CONSERVATION

Environmental DNA as an effective tool for detection of imperiled fishes

(2015) Alexis M. Janosik et al.   ENVIRONMENTAL BIOLOGY OF FISHES

Fishing in the Water: Effect of Sampled Water Volume on Environmental DNA-Based Detection of Macroinvertebrates

(2015) Elvira Mächler et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Techniques for the practical collection of environmental DNA: filter selection, preservation, and extraction

(2015) Toshifumi Minamoto et al.   LIMNOLOGY

Statistical approaches to account for false-positive errors in environmental DNA samples

(2015) José J. Lahoz-Monfort et al.   Molecular Ecology Resources

A framework for estimating the sensitivity of eDNA surveys

(2015) Elise M. Furlan et al.   Molecular Ecology Resources

Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

(2015) Ida Baerholm Schnell et al.   Molecular Ecology Resources

Microbial ecology of Antarctic aquatic systems

(2015) Ricardo Cavicchioli   NATURE REVIEWS MICROBIOLOGY

Microbial ecology of the cryosphere: sea ice and glacial habitats

(2015) Antje Boetius et al.   NATURE REVIEWS MICROBIOLOGY

rSPACE: Spatially based power analysis for conservation and ecology

(2015) Martha M. Ellis et al.   Methods in Ecology and Evolution

Estimating abundance of unmarked animal populations: accounting for imperfect detection and other sources of zero inflation

(2015) Francisco V. Dénes et al.   Methods in Ecology and Evolution

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

(2015) Emily A. Brown et al.   Ecology and Evolution

Stream microbial diversity in response to environmental changes: review and synthesis of existing research

(2015) Lydia H. Zeglin   Frontiers in Microbiology

Functional Gene Composition, Diversity and Redundancy in Microbial Stream Biofilm Communities

(2015) Andrew Dopheide et al.   PLoS One

Estimating the Effects of Habitat and Biological Interactions in an Avian Community

(2015) Robert M. Dorazio et al.   PLoS One

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes

(2015) Kathryn M. Docherty et al.   PLoS One

Multi-causality and spatial non-stationarity in the determinants of groundwater crustacean diversity in Europe

(2014) David Eme et al.   ECOGRAPHY

Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

(2014) Gavin Lear et al.   ISME Journal

Environmental metabarcodes for insects:in silicoPCR reveals potential for taxonomic bias

(2014) Laurence J. Clarke et al.   Molecular Ecology Resources

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

(2014) Gentile F. Ficetola et al.   Molecular Ecology Resources

The microbial ecology of permafrost

(2014) Janet K. Jansson et al.   NATURE REVIEWS MICROBIOLOGY

Accounting for Imperfect Detection in Ecology: A Quantitative Review

(2014) Kenneth F. Kellner et al.   PLoS One

The Relationship between the Distribution of Common Carp and Their Environmental DNA in a Small Lake

(2014) Jessica J. Eichmiller et al.   PLoS One

The application of eDNA for monitoring of the Great Crested Newt in the UK

(2014) Helen C. Rees et al.   Ecology and Evolution

Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

(2014) Sebastien Terrat et al.   Microbial Biotechnology

The problem of pattern and scale in ecology: what have we learned in 20 years?

(2013) Jérôme Chave   ECOLOGY LETTERS

Imperfect detection is the rule rather than the exception in plant distribution studies

(2013) Guoke Chen et al.   JOURNAL OF ECOLOGY

Diversity, Abundance, and Spatial Distribution of Ammonia-Oxidizing β-Proteobacteria in Sediments from Changjiang Estuary and Its Adjacent Area in East China Sea

(2013) Yangyang Chen et al.   MICROBIAL ECOLOGY

Factors influencing detection of eDNA from a stream-dwelling amphibian

(2013) David S. Pilliod et al.   Molecular Ecology Resources

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Detecting diversity: emerging methods to estimate species diversity

(2013) Kelly J. Iknayan et al.   TRENDS IN ECOLOGY & EVOLUTION

Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen

(2013) Benedikt R. Schmidt et al.   Methods in Ecology and Evolution

Biodiversity of man-made open habitats in an underused country: a class of multispecies abundance models for count data

(2012) Yuichi Yamaura et al.   BIODIVERSITY AND CONSERVATION

Bioinformatic challenges for DNA metabarcoding of plants and animals

(2012) ERIC COISSAC et al.   MOLECULAR ECOLOGY

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

From molecules to management: Adopting DNA-based methods for monitoring biological invasions in aquatic environments

(2011) John A. Darling et al.   ENVIRONMENTAL RESEARCH

Measuring biodiversity to explain community assembly: a unified approach

(2010) S. Pavoine et al.   BIOLOGICAL REVIEWS

The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies

(2010) Patrick D. Schloss   PLoS Computational Biology

Trend estimation in populations with imperfect detection

(2009) Marc Kéry et al.   JOURNAL OF APPLIED ECOLOGY

Scale as a lurking factor: incorporating scale-dependence in experimental ecology

(2009) Brody Sandel et al.   OIKOS

Environmental rRNA inventories miss over half of protistan diversity

(2008) Sunok Jeon et al.   BMC MICROBIOLOGY