A manager’s guide to using eDNA metabarcoding in marine ecosystems

Airborne environmental DNA for terrestrial vertebrate community monitoring

(2022) Christina Lynggaard et al.   CURRENT BIOLOGY

Tracking an invasion front with environmental DNA

(2022) Abigail G. Keller et al.   ECOLOGICAL APPLICATIONS

Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries

(2022) Raman P. Nagarajan et al.   Estuaries and Coasts

Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm

(2021) Pedro M. Martins et al.   BMC BIOINFORMATICS

Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia

(2021) Katrina West et al.   DIVERSITY AND DISTRIBUTIONS

The CALeDNA program: Citizen scientists and researchers inventory California's biodiversity

(2021) Rachel S. Meyer et al.   CALIFORNIA AGRICULTURE

eDNA metabarcoding as a biomonitoring tool for marine protected areas

(2021) Zachary Gold et al.   PLoS One

Animals, protists and bacteria share marine biogeographic patterns

(2021) Luke E. Holman et al.   Nature Ecology & Evolution

eDNA metabarcoding illuminates species diversity and composition of three phyla (chordata, mollusca and echinodermata) across Indonesian coral reefs

(2021) Hawis Madduppa et al.   BIODIVERSITY AND CONSERVATION

Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA

(2021) Andrea Polanco F. et al.   BIOTROPICA

Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California

(2021) Meixi Lin et al.   ECOLOGICAL APPLICATIONS

Strategies for sample labelling and library preparation in DNA metabarcoding studies

(2021) Kristine Bohmann et al.   Molecular Ecology Resources

Towards reproducible metabarcoding data: Lessons from an international cross‐laboratory experiment

(2021) Anastasija Zaiko et al.   Molecular Ecology Resources

Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

(2021) Zachary Gold et al.   Molecular Ecology Resources

Short-lived detection of an introduced vertebrate eDNA signal in a nearshore rocky reef environment

(2021) Taylor Ely et al.   PLoS One

MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes)

(2021) Markus A. Min et al.   Conservation Genetics Resources

Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities

(2021) Thomas Lamy et al.   Scientific Reports

Measuring and mitigating PCR bias in microbiota datasets

(2021) Justin D. Silverman et al.   PLoS Computational Biology

Current laboratory protocols for detecting fish species with environmental DNA optimize sensitivity and reproducibility, especially for more abundant populations

(2021) Mark Y Stoeckle et al.   ICES JOURNAL OF MARINE SCIENCE

eDNA captures depth partitioning in a kelp forest ecosystem

(2021) Keira Monuki et al.   PLoS One

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

(2021) J. Pawlowski et al.   SCIENCE OF THE TOTAL ENVIRONMENT

From eDNA to citizen science: emerging tools for the early detection of invasive species

(2020) Eric R Larson et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

eDNA metabarcoding survey reveals fine‐scale coral reef community variation across a remote, tropical island ecosystem

(2020) Katrina M. West et al.   MOLECULAR ECOLOGY

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

(2020) Tamara Schenekar et al.   RIVER RESEARCH AND APPLICATIONS

Environmental DNA reveals seasonal shifts and potential interactions in a marine community

(2020) Anni Djurhuus et al.   Nature Communications

Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

(2020) Kingsly C. Beng et al.   BIODIVERSITY AND CONSERVATION

At Palmyra Atoll, the fish‐community environmental DNA signal changes across habitats but not with tides

(2020) Kevin D. Lafferty et al.   JOURNAL OF FISH BIOLOGY

Identifying error and accurately interpreting eDNA metabarcoding results: A case study to detect vertebrates at arid zone waterholes

(2020) Elise M. Furlan et al.   Molecular Ecology Resources

Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA

(2020) Beverly McClenaghan et al.   PLoS One

Optimizing an eDNA protocol for estuarine environments: Balancing sensitivity, cost and time

(2020) Thiago M. Sanches et al.   PLoS One

Zooplankton biogeographic boundaries in the California Current System as determined from metabarcoding

(2020) Kathleen J. Pitz et al.   PLoS One

Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle

(2020) Jean-Baptiste Juhel et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Environmental DNA detection tracks established seasonal occurrence of blacktip sharks (Carcharhinus limbatus) in a semi-enclosed subtropical bay

(2020) Bautisse D. Postaire et al.   Scientific Reports

Improved Environmental DNA Reference Library Detects Overlooked Marine Fishes in New Jersey, United States

(2020) Mark Y. Stoeckle et al.   Frontiers in Marine Science

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

(2020) Masaki Miya et al.   FISHERIES SCIENCE

DNA Barcoding and geographical scale effect: The problems of undersampling genetic diversity hotspots

(2020) Álvaro Gaytán et al.   Ecology and Evolution

Environmental DNA metabarcoding reveals winners and losers of global change in coastal waters

(2020) Ramón Gallego et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Anacapa Toolkit : an environmental DNA toolkit for processing multilocus metabarcode datasets

(2019) Emily E. Curd et al.   Methods in Ecology and Evolution

Stream Transport and Retention of Environmental DNA Pulse Releases in Relation to Hydrogeomorphic Scaling Factors

(2019) Alexander K. Fremier et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater

(2019) G. A. C. Singer et al.   Scientific Reports

Environmental DNA provides quantitative estimates of a threatened salmon species

(2019) Andrew Olaf Shelton et al.   BIOLOGICAL CONSERVATION

Consistent and correctable bias in metagenomic sequencing experiments

(2019) Michael R McLaren et al.   eLife

Gaps in DNA-Based Biomonitoring Across the Globe

(2019) Katie M. McGee et al.   Frontiers in Ecology and Evolution

GenBank is a reliable resource for 21st century biodiversity research

(2019) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting the fate of eDNA in the environment and implications for studying biodiversity

(2019) Jori B. Harrison et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

(2019) Luke E. Holman et al.   Scientific Reports

Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies

(2019) Ryan P. Kelly et al.   Scientific Reports

Successful molecular detection studies require clear communication among diverse research partners

(2019) Brittany A Mosher et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

(2019) Jeremy R. deWaard et al.   Scientific Data

Concentrations of environmental DNA (eDNA) reflect spawning salmon abundance at fine spatial and temporal scales

(2018) Michael D. Tillotson et al.   BIOLOGICAL CONSERVATION

Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

(2018) Michal Stat et al.   CONSERVATION BIOLOGY

Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles

(2018) François Keck et al.   Molecular Ecology Resources

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

(2018) Jan Pawlowski et al.   SCIENCE OF THE TOTAL ENVIRONMENT

An analytical framework for estimating aquatic species density from environmental DNA

(2018) Thierry Chambert et al.   Ecology and Evolution

Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

(2018) Colin J. Curry et al.   Freshwater Science

Correcting for batch effects in case-control microbiome studies

(2018) Sean M. Gibbons et al.   PLoS Computational Biology

Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

(2018) Colin J. Curry et al.   Freshwater Science

The effect of tides on nearshore environmental DNA

(2018) Ryan P. Kelly et al.   PeerJ

Taxonomy annotation and guide tree errors in 16S rRNA databases

(2018) Robert Edgar   PeerJ

Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

(2018) Robert C. Edgar   PeerJ

The value of environmental DNA biobanking for long-term biomonitoring

(2018) Simon N. Jarman et al.   Nature Ecology & Evolution

Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks

(2018) Eva Aylagas et al.   ECOLOGICAL INDICATORS

Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement

(2018) Gert-Jan Jeunen et al.   Molecular Ecology Resources

Environmental DNA metabarcoding studies are critically affected by substrate selection

(2018) Adam Koziol et al.   Molecular Ecology Resources

Comparative Cost and Effort of Fish Distribution Detection via Environmental DNA Analysis and Electrofishing

(2017) Nathan T. Evans et al.   FISHERIES

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

GenBank

(2017) Dennis A Benson et al.   NUCLEIC ACIDS RESEARCH

Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

(2017) Michael Stat et al.   Scientific Reports

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples

(2017) John Deck et al.   PLOS BIOLOGY

Spatial distribution of environmental DNA in a nearshore marine habitat

(2017) James L. O’Donnell et al.   PeerJ

Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples

(2017) Alfred J. Arulandhu et al.   GigaScience

Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary

(2017) Mark Y. Stoeckle et al.   PLoS One

Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding

(2017) Elizabeth A. Andruszkiewicz et al.   PLoS One

Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp.

(2017) Maggie R. Williams et al.   PLoS One

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

(2017) Satoshi Yamamoto et al.   Scientific Reports

Controls on eDNA movement in streams: Transport, Retention, and Resuspension

(2017) Arial J. Shogren et al.   Scientific Reports

From barcodes to genomes: extending the concept of DNA barcoding

(2016) Eric Coissac et al.   MOLECULAR ECOLOGY

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

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   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

Genetic signatures of ecological diversity along an urbanization gradient

(2016) Ryan P. Kelly et al.   PeerJ

Environmental DNA as a ‘Snapshot’ of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan

(2016) Satoshi Yamamoto et al.   PLoS One

Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples

(2015) Marta Pawluczyk et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms

(2015) Katherine M. Strickler et al.   BIOLOGICAL CONSERVATION

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

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

(2015) Jeremy Biggs et al.   BIOLOGICAL CONSERVATION

The ecology of environmental DNA and implications for conservation genetics

(2015) Matthew A. Barnes et al.   CONSERVATION GENETICS

Modeling false positive detections in species occurrence data under different study designs

(2015) Thierry Chambert et al.   ECOLOGY

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

(2015) Jesse A. Port et al.   MOLECULAR ECOLOGY

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

(2015) Nathan T. Evans et al.   Molecular Ecology Resources

MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

(2015) M. Miya et al.   Royal Society Open Science

Environmental Conditions Influence eDNA Persistence in Aquatic Systems

(2014) Matthew A. Barnes et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Ancient and modern environmental DNA

(2014) Mikkel Winther Pedersen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Environmental Status Assessment Using DNA Metabarcoding: Towards a Genetics Based Marine Biotic Index (gAMBI)

(2014) Eva Aylagas et al.   PLoS One

Harnessing DNA to improve environmental management

(2014) R. P. Kelly et al.   SCIENCE

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

Particle size distribution and optimal capture of aqueous macrobial eDNA

(2014) Cameron R. Turner et al.   Methods in Ecology and Evolution

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

(2013) Matthieu Leray et al.   Frontiers in Zoology

Robust Detection of Rare Species Using Environmental DNA: The Importance of Primer Specificity

(2013) Taylor M. Wilcox et al.   PLoS One

Validation of eDNA Surveillance Sensitivity for Detection of Asian Carps in Controlled and Field Experiments

(2013) Andrew R. Mahon et al.   PLoS One

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

PCR inhibitors - occurrence, properties and removal

(2012) C. Schrader et al.   JOURNAL OF APPLIED MICROBIOLOGY

Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples

(2012) Philip Francis Thomsen et al.   PLoS One

The Effect of Geographical Scale of Sampling on DNA Barcoding

(2012) J. Bergsten et al.   SYSTEMATIC BIOLOGY

Moorea BIOCODE barcode library as a tool for understanding predator–prey interactions: insights into the diet of common predatory coral reef fishes

(2011) M. Leray et al.   CORAL REEFS

“Sight-unseen” detection of rare aquatic species using environmental DNA

(2011) Christopher L. Jerde et al.   Conservation Letters

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The campaign to DNA barcode all fishes, FISH-BOL

(2009) R. D. Ward et al.   JOURNAL OF FISH BIOLOGY

Barcode of Life

(2009) Mark Y. Stockle et al.   SCIENTIFIC AMERICAN