Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Non‐specific amplification compromises environmental DNA metabarcoding with COI

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

Evaluation of marine zooplankton community structure through environmental DNA metabarcoding

(2018) Anni Djurhuus et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula

(2018) Dominique A. Cowart et al.   Marine Genomics

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

(2018) Owen S. Wangensteen et al.   MARINE POLLUTION BULLETIN

Large-scale ocean connectivity and planktonic body size

(2018) Ernesto Villarino et al.   Nature Communications

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity

(2018) David López-Escardó et al.   Scientific Reports

eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity

(2018) Anaïs Lacoursière-Roussel et al.   Ecology and Evolution

DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers

(2018) Owen S. Wangensteen et al.   PeerJ

The effect of tides on nearshore environmental DNA

(2018) Ryan P. Kelly et al.   PeerJ

Environmental DNA illuminates the dark diversity of sharks

(2018) Germain Boussarie et al.   Science Advances

Why the COI barcode should be the community DNA metabarcode for the metazoa

(2018) Carmelo Andújar et al.   MOLECULAR ECOLOGY

Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes

(2018) Babett Günther et al.   Scientific Reports

Bats as potential suppressors of multiple agricultural pests: A case study from Madagascar

(2018) James Kemp et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

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

(2018) Andjin Siegenthaler et al.   Molecular Ecology Resources

Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning

(2017) Tristan Cordier et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

18S V9 metabarcoding correctly depicts plankton estuarine community drivers

(2017) D Abad et al.   MARINE ECOLOGY PROGRESS SERIES

DNA metabarcoding reveals that 200-μ m-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes

(2017) Lemian Liu et al.   Molecular Ecology Resources

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

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

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

(2017) Michael Stat 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

18S V9 metabarcoding correctly depicts plankton estuarine community drivers

(2017) D Abad et al.   MARINE ECOLOGY PROGRESS SERIES

Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding

(2017) Matthieu Leray et al.   PeerJ

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

(2017) Judith Bakker et al.   Scientific Reports

Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities among marine and freshwater ports

(2016) Frédéric J. J. Chain et al.   DIVERSITY AND DISTRIBUTIONS

A framework for inferring biological communities from environmental DNA

(2016) Andrew Olaf Shelton et al.   ECOLOGICAL APPLICATIONS

Metabarcoding of marine zooplankton: prospects, progress and pitfalls

(2016) Ann Bucklin et al.   JOURNAL OF PLANKTON RESEARCH

Censusing marine eukaryotic diversity in the twenty-first century

(2016) Matthieu Leray et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genetic signatures of ecological diversity along an urbanization gradient

(2016) Ryan P. Kelly et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

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

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

(2015) Massimo C Pernice et al.   ISME Journal

Metabarcoding approach for nonindigenous species surveillance in marine coastal waters

(2015) Anastasija Zaiko et al.   MARINE POLLUTION BULLETIN

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

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

(2015) Frédéric Mahé et al.   PeerJ

Evaluating a multigene environmental DNA approach for biodiversity assessment

(2015) Alexei J. Drummond et al.   GigaScience

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

Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons

(2015) Magdalena Guardiola et al.   PLoS One

High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems

(2015) Franck Lejzerowicz et al.   Scientific Reports

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

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

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

(2014) Helen C. Rees et al.   JOURNAL OF APPLIED ECOLOGY

A metagenetic approach for revealing community structure of marine planktonic copepods

(2014) J. Hirai et al.   Molecular Ecology Resources

Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

(2014) Jan Pawlowski et al.   Molecular Ecology Resources

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

Genomics in marine monitoring: New opportunities for assessing marine health status

(2013) Sarah J. Bourlat et al.   MARINE POLLUTION BULLETIN

Redesign of PCR primers for mitochondrial cytochromecoxidase subunit I for marine invertebrates and application in all-taxa biotic surveys

(2013) J. Geller et al.   Molecular Ecology Resources

Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

(2013) Penelope K. Lindeque et al.   PLoS One

The Magnitude of Global Marine Species Diversity

(2012) Ward Appeltans et al.   CURRENT BIOLOGY

Bioinformatic challenges for DNA metabarcoding of plants and animals

(2012) ERIC COISSAC et al.   MOLECULAR ECOLOGY

Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill

(2012) Holly M. Bik et al.   PLoS One

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

(2012) C. Q. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Status and Solutions for the World's Unassessed Fisheries

(2012) C. Costello et al.   SCIENCE

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

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

(2011) Tiayyba Riaz et al.   NUCLEIC ACIDS RESEARCH

Biodiversity and ecosystem services: a multilayered relationship

(2011) Georgina M. Mace et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2011) Camilo Mora et al.   PLOS BIOLOGY

Oomycetes and fungi: important parasites on marine algae

(2010) Wei Li et al.   ACTA OCEANOLOGICA SINICA

DNA Barcoding of Marine Metazoa

(2010) Ann Bucklin et al.   Annual Review of Marine Science

Direct Measurement Versus Surrogate Indicator Species for Evaluating Environmental Change and Biodiversity Loss

(2010) David B. Lindenmayer et al.   ECOSYSTEMS

Second-generation environmental sequencing unmasks marine metazoan biodiversity

(2010) Vera G. Fonseca et al.   Nature Communications

Comparisons of zooplankton time series

(2009) David L. Mackas et al.   JOURNAL OF MARINE SYSTEMS