Quantification of marine benthic communities with metabarcoding

Half a century of monitoring macrobenthic animals on tidal flats in the Dutch Wadden Sea

(2020) JJ Beukema et al.   MARINE ECOLOGY PROGRESS SERIES

Understanding the effects of biotic and abiotic factors on sources of aquatic environmental DNA

(2019) Kathryn A. Stewart   BIODIVERSITY AND CONSERVATION

A field guide for the compositional analysis of any-omics data

(2019) Thomas P Quinn et al.   GigaScience

Diversity of Wadden Sea macrofauna and meiofauna communities highest in DNA from extractions preceded by cell lysis

(2019) Lise Klunder et al.   JOURNAL OF SEA RESEARCH

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

Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies

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

The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative

(2018) Josep Piñol et al.   MOLECULAR ECOLOGY

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

(2018) Bruce E. Deagle et al.   MOLECULAR ECOLOGY

Minimizing polymerase biases in metabarcoding

(2018) Ruth V. Nichols et al.   Molecular Ecology Resources

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

The effect of tides on nearshore environmental DNA

(2018) Ryan P. Kelly et al.   PeerJ

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

(2018) Eva Aylagas et al.   ECOLOGICAL INDICATORS

A comparative analysis of metabarcoding and morphology-based identification of benthic communities across different regional seas

(2018) Abigail E. Cahill et al.   Ecology and Evolution

How quantitative is metabarcoding: A meta‐analytical approach

(2018) Philip D. Lamb et al.   MOLECULAR ECOLOGY

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

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

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

(2017) Vasco Elbrecht et al.   Ecology and Evolution

DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea )

(2017) Tina E. Berry et al.   Ecology and Evolution

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments

(2017) Anders Lanzén et al.   PLoS One

High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities

(2016) Anders Lanzén et al.   MOLECULAR ECOLOGY

Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data

(2016) Rodney T. Richardson et al.   Molecular Ecology Resources

Censusing marine eukaryotic diversity in the twenty-first century

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

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

(2016) Magdalena Guardiola et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

The ecology of environmental DNA and implications for conservation genetics

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

Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

(2015) Anthony A. Chariton et al.   ENVIRONMENTAL POLLUTION

Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods

(2015) Pamela M. Brannock et al.   Marine Genomics

Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities

(2015) Dominique A. Cowart et al.   PLoS One

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

(2015) Vasco Elbrecht et al.   PLoS One

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

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

Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods

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

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

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

Distinctly variable mudscapes: Distribution gradients of intertidal macrofauna across the Dutch Wadden Sea

(2013) Tanya J. Compton et al.   JOURNAL OF SEA RESEARCH

DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

(2013) M. De Barba et al.   Molecular Ecology Resources

Effect of a physical disturbance event on deep-sea nematode community structure and ecosystem function

(2012) Daniel Leduc et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

The seven impediments in invertebrate conservation and how to overcome them

(2011) Pedro Cardoso et al.   BIOLOGICAL CONSERVATION

Who is eating what: diet assessment using next generation sequencing

(2011) FRANCOIS POMPANON et al.   MOLECULAR ECOLOGY

DNA Barcoding of Marine Metazoa

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The robustness of ecological indicators to detect long-term changes in the macrobenthos of estuarine systems

(2009) Joana Patrício et al.   MARINE ENVIRONMENTAL RESEARCH

Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

Quantification of Extinction Risk: IUCN's System for Classifying Threatened Species

(2008) GEORGINA M. MACE et al.   CONSERVATION BIOLOGY

Exponential Decline of Deep-Sea Ecosystem Functioning Linked to Benthic Biodiversity Loss

(2008) Roberto Danovaro et al.   CURRENT BIOLOGY

Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences

(2008) C. CORINALDESI et al.   MOLECULAR ECOLOGY