Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences

30% land conservation and climate action reduces tropical extinction risk by more than 50%

(2020) Lee Hannah et al.   ECOGRAPHY

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

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

Fishing for mammals: Landscape‐level monitoring of terrestrial and semi‐aquatic communities using eDNA from riverine systems

(2020) Naiara Guimarães Sales et al.   JOURNAL OF APPLIED ECOLOGY

Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events

(2019) Tina E. Berry et al.   PLoS Genetics

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

(2019) Isabel Cantera et al.   Scientific Reports

More is less: net gain in species richness, but biotic homogenization over 140 years

(2019) Tora Finderup Nielsen et al.   ECOLOGY LETTERS

The marine fish food web is globally connected

(2019) Camille Albouy et al.   Nature Ecology & Evolution

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

(2019) Hannah Weigand et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Non‐specific amplification compromises environmental DNA metabarcoding with COI

(2019) Rupert A. Collins et al.   Methods in Ecology and Evolution

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

The geography of biodiversity change in marine and terrestrial assemblages

(2019) Shane A. Blowes et al.   SCIENCE

The commonness of rarity: Global and future distribution of rarity across land plants

(2019) Brian J. Enquist et al.   Science Advances

Deficits of biodiversity and productivity linger a century after agricultural abandonment

(2019) Forest Isbell et al.   Nature Ecology & Evolution

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

(2018) Robert C Edgar   BIOINFORMATICS

The hidden half: ecology and evolution of cryptobenthic fishes on coral reefs

(2018) Simon J. Brandl et al.   BIOLOGICAL REVIEWS

The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar

(2018) Salvador Lladó Fernández et al.   FOLIA MICROBIOLOGICA

Unlocking biodiversity and conservation studies in high-diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes

(2018) Kévin Cilleros et al.   Molecular Ecology Resources

Divergent biodiversity change within ecosystems

(2018) Anne E. Magurran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Environmental DNA illuminates the dark diversity of sharks

(2018) Germain Boussarie et al.   Science Advances

The value of environmental DNA biobanking for long-term biomonitoring

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

Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation

(2018) Didier Pont et al.   Scientific Reports

Toward an ecoregion scale evaluation of eDNA metabarcoding primers: A case study for the freshwater fish biodiversity of the Murray-Darling Basin (Australia)

(2018) Jonas Bylemans et al.   Ecology and Evolution

How to protect half of Earth to ensure it protects sufficient biodiversity

(2018) Stuart L. Pimm et al.   Science Advances

Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring

(2018) Andjin Siegenthaler et al.   Molecular Ecology Resources

GenBank

(2018) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Mapping knowledge gaps in marine diversity reveals a latitudinal gradient of missing species richness

(2018) André Menegotto et al.   Nature Communications

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Coral reefs in the Anthropocene

(2017) Terry P. Hughes et al.   NATURE

Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

(2017) Léa Siegwald et al.   PLoS One

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

A global database on freshwater fish species occurrence in drainage basins

(2017) Pablo A. Tedesco et al.   Scientific Data

Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding

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

Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact

(2017) Judith Bakker et al.   Scientific Reports

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

(2016) Alice Valentini et al.   MOLECULAR ECOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers

(2016) Nicole A. Fahner et al.   PLoS One

Invasive predators and global biodiversity loss

(2016) Tim S. Doherty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System

(2016) Raphaël Civade et al.   PLoS One

Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes

(2016) Philip Francis Thomsen et al.   PLoS One

Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity

(2015) Joaquín Hortal et al.   Annual Review of Ecology Evolution and Systematics

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

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

(2015) Thierry Chambert et al.   ECOLOGY

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer 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

Marine defaunation: Animal loss in the global ocean

(2015) D. J. McCauley et al.   SCIENCE

Fifteen forms of biodiversity trend in the Anthropocene

(2015) Brian J. McGill et al.   TRENDS IN ECOLOGY & EVOLUTION

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

(2015) Jullien M. Flynn et al.   Ecology and Evolution

Swarm v2: highly-scalable and high-resolution amplicon clustering

(2015) Frédéric Mahé et al.   PeerJ

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

DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match

(2014) B. E. Deagle et al.   Biology Letters

Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

Defaunation in the Anthropocene

(2014) R. Dirzo et al.   SCIENCE

Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss

(2014) M. Dornelas et al.   SCIENCE

Environmental DNA for wildlife biology and biodiversity monitoring

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

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

Global meta-analysis reveals no net change in local-scale plant biodiversity over time

(2013) M. Vellend et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Illumina metabarcoding of a soil fungal community

(2013) Philipp-André Schmidt et al.   SOIL BIOLOGY & BIOCHEMISTRY

betapart: an R package for the study of beta diversity

(2012) Andrés Baselga et al.   Methods in Ecology and Evolution

Evidence for morphological and adaptive genetic divergence between lake and stream habitats in European minnows (Phoxinus phoxinus, Cyprinidae)

(2011) HÉLÈNE COLLIN et al.   MOLECULAR ECOLOGY

Persistence of Environmental DNA in Freshwater Ecosystems

(2011) Tony Dejean et al.   PLoS One

Global Human Footprint on the Linkage between Biodiversity and Ecosystem Functioning in Reef Fishes

(2011) Camilo Mora et al.   PLOS BIOLOGY

How Many Species Are There on Earth and in the Ocean?

(2011) Camilo Mora et al.   PLOS BIOLOGY

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

The completeness of taxonomic inventories for describing the global diversity and distribution of marine fishes

(2007) C. Mora et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES