Considerations for metabarcoding‐based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments

Species-level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization

(2019) Gert-Jan Jeunen et al.   Ecology and Evolution

Non‐specific amplification compromises environmental DNA metabarcoding with COI

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

Assessing biological invasions in European Seas: Biological traits of the most widespread non-indigenous species

(2018) Alice Cardeccia et al.   ESTUARINE COASTAL AND SHELF SCIENCE

The challenges and promises of genetic approaches for ballast water management

(2018) Anaïs Rey et al.   JOURNAL OF SEA RESEARCH

Evaluation of marine zooplankton community structure through environmental DNA metabarcoding

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

Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys

(2018) Erin K. Grey et al.   Scientific Reports

Presence-absence of marine macrozoobenthos does not generally predict abundance and biomass

(2018) Allert I. Bijleveld et al.   Scientific Reports

eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity

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

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

(2018) Eva Aylagas et al.   ECOLOGICAL INDICATORS

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

(2018) Jan-Niklas Macher et al.   Molecular Ecology Resources

Strategy of port baseline surveys (PBS) in the Adriatic Sea

(2018) Romina Kraus et al.   MARINE POLLUTION BULLETIN

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

Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity

(2017) Iliana Bista et al.   Nature Communications

Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding

(2017) Vasco Elbrecht et al.   Ecology and Evolution

Spatial distribution of environmental DNA in a nearshore marine habitat

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

Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes

(2017) Katy E. Klymus et al.   PLoS One

DNA in a bottle—Rapid metabarcoding survey for early alerts of invasive species in ports

(2017) Yaisel J. Borrell et al.   PLoS One

Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management

(2016) Anastasija Zaiko et al.   BIOFOULING

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

Using environmental (e)DNA sequencing for aquatic biodiversity surveys: a beginner’s guide

(2016) Jennifer L. A. Shaw et al.   MARINE AND FRESHWATER RESEARCH

Early detection of invasive species in marine ecosystems using high-throughput sequencing: technical challenges and possible solutions

(2016) Wei Xiong et al.   MARINE BIOLOGY

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

The ecologist's field guide to sequence-based identification of biodiversity

(2016) Simon Creer et al.   Methods in Ecology and Evolution

First record of the non-indigenous Melita nitida Smith, 1873 (Crustacea: Amphipoda: Melitidae) in the Bay of Biscay (NE Atlantic)

(2016) Benoit Gouillieux et al.   BioInvasions Records

DNA (meta)barcoding of biological invasions: a powerful tool to elucidate invasion processes and help managing aliens

(2015) Thierry Comtet et al.   BIOLOGICAL INVASIONS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

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

(2014) Frédéric Mahé et al.   PeerJ

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

The risk of marine bioinvasion caused by global shipping

(2013) H. Seebens et al.   ECOLOGY LETTERS

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

Spatial distribution and temporal trends of soft-bottom marine benthic alien species collected during the period 1989–2008 in the Nervión estuary (southeastern Bay of Biscay)

(2013) Izaskun Zorita et al.   JOURNAL OF SEA RESEARCH

Evaluating Detection Limits of Next-Generation Sequencing for the Surveillance and Monitoring of International Marine Pests

(2013) Xavier Pochon et al.   PLoS One

Hitting the right target: taxonomic challenges for, and of, plant invasions

(2013) P. Pysek et al.   AoB Plants

Global ballast water management and the “same location” concept: a clear term or a clear issue?

(2012) Matej David et al.   ECOLOGICAL APPLICATIONS

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Potential risk of harmful algae transport by ballast waters: The case of Bilbao Harbour

(2011) Ainhize Butrón et al.   MARINE POLLUTION BULLETIN

A new conceptual and methodological framework for exploring and explaining pattern in presence - absence data

(2011) János Podani et al.   OIKOS

Cost-efficiency of biodiversity indicators for Mediterranean ecosystems and the effects of socio-economic factors

(2010) Yael Mandelik et al.   JOURNAL OF APPLIED ECOLOGY

How useful are port surveys focused on target pest identification for exotic species management?

(2010) M.J. Bishop et al.   MARINE POLLUTION BULLETIN

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One