A practical guide to DNA metabarcoding for entomological ecologists

Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

(2019) Henrik Krehenwinkel et al.   GigaScience

Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?

(2019) Clare I.M. Adams et al.   Genes

Invasion genetics from eDNA and thousands of larvae: A targeted metabarcoding assay that distinguishes species and population variation of zebra and quagga mussels

(2019) Nathaniel T. Marshall et al.   Ecology and Evolution

Toward accurate species‐level metabarcoding of arthropod communities from the tropical forest canopy

(2019) Thomas J. Creedy et al.   Ecology and Evolution

Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods

(2019) Philip Francis Thomsen et al.   Ecology and Evolution

Metabarcoding a Diverse Arthropod Mock Community

(2019) Thomas W. A. Braukmann et al.   Molecular Ecology Resources

Estimating the biodiversity of terrestrial invertebrates on a forested island using DNA barcodes and metabarcoding data

(2019) Andrew Dopheide et al.   ECOLOGICAL APPLICATIONS

SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data

(2019) Yoann Dufresne et al.   BMC BIOINFORMATICS

Mechanisms structuring host–parasitoid networks in a global warming context: a review

(2019) Mélanie Thierry et al.   ECOLOGICAL ENTOMOLOGY

DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

(2019) Lucie Zinger et al.   MOLECULAR ECOLOGY

The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data

(2019) Marc A. Sze et al.   mSphere

Metabarcoding of storage ethanol vs. conventional morphometric identification in relation to the use of stream macroinvertebrates as ecological indicators in forest management

(2019) Maitane Erdozain et al.   ECOLOGICAL INDICATORS

The devil is in the detail: Metabarcoding of arthropods provides a sensitive measure of biodiversity response to forest stand composition compared with surrogate measures of biodiversity

(2019) N. Barsoum et al.   ECOLOGICAL INDICATORS

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

The effects of spatial and temporal replicate sampling on eDNA metabarcoding

(2019) Kevin K. Beentjes et al.   PeerJ

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

(2019) Alexander M Piper et al.   GigaScience

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

(2019) Jeremiah J. Minich et al.   mSystems

Field Evaluation of DNA Based Biodiversity Monitoring of Caribbean Mosquitoes

(2019) Sam P. Boerlijst et al.   Frontiers in Ecology and 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

Validation of COI metabarcoding primers for terrestrial arthropods

(2019) Vasco Elbrecht et al.   PeerJ

High resistance towards herbivore-induced habitat change in a high Arctic arthropod community

(2018) Niels M. Schmidt et al.   Biology Letters

Locality or habitat? Exploring predictors of biodiversity in Amazonia

(2018) Camila D. Ritter et al.   ECOGRAPHY

Host-plant dissections reveal contrasting distributions of Crematogaster ants and their symbionts in two myrmecophytic Macaranga species

(2018) Mickal Y.I. Houadria et al.   ECOLOGICAL ENTOMOLOGY

eDNA-based bioassessment of coastal sediments impacted by an oil spill

(2018) Yuwei Xie et al.   ENVIRONMENTAL POLLUTION

Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding

(2018) Ostaizka Aizpurua et al.   MOLECULAR ECOLOGY

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

Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis

(2018) Teresita M. Porter 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

Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: Validating a reverse workflow for specimen processing

(2018) Wendy Y. Wang et al.   Molecular Ecology Resources

Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples

(2018) Iliana Bista et al.   Molecular Ecology Resources

Minimizing polymerase biases in metabarcoding

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

Towards robust and repeatable sampling methods in eDNA-based studies

(2018) Ian A. Dickie et al.   Molecular Ecology Resources

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Diet shifts by adult flightless dung beetles Circellium bacchus, revealed using DNA metabarcoding, reflect complex life histories

(2018) Graham I. H. Kerley et al.   OECOLOGIA

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

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

eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity

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

Estimating intraspecific genetic diversity from community DNA metabarcoding data

(2018) Vasco Elbrecht et al.   PeerJ

Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?

(2018) Melissa E. Carew et al.   PeerJ

Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building

(2018) Aaron Pomerantz et al.   GigaScience

Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities

(2018) Guang K. Zhang et al.   Evolutionary Applications

Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds

(2018) Lynsey R. Harper et al.   HYDROBIOLOGIA

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

(2018) Carmelo Andújar et al.   MOLECULAR ECOLOGY

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

New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods

(2018) Daniel Marquina et al.   Molecular Ecology Resources

Evaluating freshwater macroinvertebrates from eDNA metabarcoding: A river Nalón case study

(2018) Sara Fernández et al.   PLoS One

Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity

(2018) Andrew Dopheide et al.   Methods in Ecology and Evolution

Ecological influence of sediment bypass tunnels on macroinvertebrates in dam-fragmented rivers by DNA metabarcoding

(2018) Joeselle M. Serrana et al.   Scientific Reports

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

DNA metabarcoding from sample fixative as a quick and voucher-preserving biodiversity assessment method

(2018) Vera M A Zizka et al.   GENOME

Body size determines soil community assembly in a tropical forest

(2018) Lucie Zinger et al.   MOLECULAR ECOLOGY

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

Environmental DNA Time Series in Ecology

(2018) Miklós Bálint et al.   TRENDS IN ECOLOGY & EVOLUTION

A broadly applicable COI primer pair and an efficient single‐tube amplicon library preparation protocol for metabarcoding

(2018) Oskar Rennstam Rubbmark et al.   Ecology and Evolution

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

(2017) Benjamin J Callahan et al.   ISME Journal

Spatial and temporal variation of intertidal nematodes in the northern Gulf of Mexico after the Deepwater Horizon oil spill

(2017) Pamela M. Brannock et al.   MARINE ENVIRONMENTAL RESEARCH

Documenting DNA in the dust

(2017) M. T. P. Gilbert   MOLECULAR ECOLOGY

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Genetic monitoring of open ocean biodiversity: An evaluation of DNA metabarcoding for processing continuous plankton recorder samples

(2017) Bruce E. Deagle et al.   Molecular Ecology Resources

Molecular approaches for blood meal analysis and species identification of mosquitoes (Insecta: Diptera: Culicidae) in rural locations in southern England, United Kingdom

(2017) LUIS MIGUEL HERNÁNDEZ-TRIANA et al.   ZOOTAXA

DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

(2017) Jorge Lobo et al.   Scientific Reports

Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

(2017) Henrik Krehenwinkel et al.   Scientific Reports

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

(2017) Vasco Elbrecht et al.   Ecology and Evolution

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

(2017) Laurence J. Clarke et al.   Ecology and Evolution

No single driver of biodiversity: divergent responses of multiple taxa across land use types

(2017) Jamie R. Wood et al.   Ecosphere

Filling reference gaps via assembling DNA barcodes using high-throughput sequencing—moving toward barcoding the world

(2017) Shanlin Liu et al.   GigaScience

Cooled Propylene Glycol as a Pragmatic Choice for Preservation of DNA From Remote Field-Collected Diptera for Next-Generation Sequence Analysis

(2016) H. J. H. Patrick et al.   JOURNAL OF ECONOMIC ENTOMOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

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

PrimerMiner : an r package for development and in silico validation of DNA metabarcoding primers

(2016) Vasco Elbrecht 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

Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects

(2016) Vasco Elbrecht et al.   PeerJ

Detection of Invasive Mosquito Vectors Using Environmental DNA (eDNA) from Water Samples

(2016) Judith Schneider et al.   PLoS One

Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA

(2015) Kristy Deiner 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

DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

(2015) G.-J. Brandon-Mong et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

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

Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

(2015) Ida Baerholm Schnell et al.   Molecular Ecology Resources

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

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

DNA polymerase preference determines PCR priming efficiency

(2014) Wenjing Pan et al.   BMC BIOTECHNOLOGY

Effect of Propylene Glycol Concentration on Mid-Term DNA Preservation of Coleoptera

(2014) Michael L. Ferro et al.   COLEOPTERISTS BULLETIN

Environmental metabarcodes for insects:in silicoPCR reveals potential for taxonomic bias

(2014) Laurence J. Clarke et al.   Molecular Ecology Resources

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

(2014) Gentile F. Ficetola et al.   Molecular Ecology Resources

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

DNA preservation: a test of commonly used preservatives for insects

(2013) Corrie S. Moreau et al.   INVERTEBRATE SYSTEMATICS

Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol

(2013) Jeremy Miller et al.   ZooKeys

Bioinformatic challenges for DNA metabarcoding of plants and animals

(2012) ERIC COISSAC et al.   MOLECULAR ECOLOGY

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

(2012) LAURA S. EPP et al.   MOLECULAR ECOLOGY

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

Current progress in DNA barcoding and future implications for entomology

(2011) Utsugi JINBO et al.   ENTOMOLOGICAL SCIENCE

Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces

(2010) MATT R. K. ZEALE et al.   Molecular Ecology Resources

Second-generation environmental sequencing unmasks marine metazoan biodiversity

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

Non-Destructive Sampling of Ancient Insect DNA

(2009) Philip Francis Thomsen et al.   PLoS One

Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified

(2008) H. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA