Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers

The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera

(2020) Sonia Ferreira et al.   Biodiversity Data Journal

Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding

(2020) Gentile Francesco Ficetola et al.   MOLECULAR ECOLOGY

Have the cake and eat it: Optimising non‐destructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring

(2019) Filipa M.S. Martins et al.   Molecular Ecology Resources

Using molecular diet analysis to inform invasive species management: A case study of introduced rats consuming endemic New Zealand frogs

(2019) Bastian Egeter et al.   Ecology and Evolution

Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

(2019) Joeselle M. Serrana et al.   ECOLOGICAL INDICATORS

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

Advancing the integration of multi‐marker metabarcoding data in dietary analysis of trophic generalists

(2019) Luís P. da Silva et al.   Molecular Ecology Resources

Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches

(2019) Daniel Marquina et al.   Molecular Ecology Resources

Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol

(2019) Mailys Gauthier et al.   Molecular Ecology Resources

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

Applicability of DNA metabarcoding approach in the bioassessment of Portuguese rivers using diatoms

(2019) Andreia Mortágua et al.   ECOLOGICAL INDICATORS

Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates

(2019) Alex Bush et al.   Frontiers in Ecology and Evolution

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

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

(2018) Owen S. Wangensteen et al.   PeerJ

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

(2018) Melissa E. Carew et al.   PeerJ

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

Slippage of degenerate primers can cause variation in amplicon length

(2018) Vasco Elbrecht et al.   Scientific Reports

Multi-marker metabarcoding approach to study mesozooplankton at basin scale

(2018) Sergio Stefanni et al.   Scientific Reports

Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring

(2018) Vasco Elbrecht et al.   FRESHWATER BIOLOGY

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

(2018) Vera M A Zizka et al.   GENOME

Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring

(2018) Tristan Cordier et al.   TRENDS IN MICROBIOLOGY

Using beta diversity to inform agricultural policies and conservation actions on Mediterranean farmland

(2017) Joana Santana et al.   JOURNAL OF APPLIED ECOLOGY

A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies

(2017) Emmanuel Corse et al.   Molecular Ecology Resources

Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring

(2017) Laure Apothéloz-Perret-Gentil 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

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

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

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

(2017) Zachary S. L. Foster et al.   PLoS Computational Biology

DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient

(2017) Caroline E. Emilson 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

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

(2016) Vasco Elbrecht 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

Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

(2015) Joana Amorim Visco et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

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

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

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

(2015) Magdalena Guardiola 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

Comparing alternatives for combining invertebrate and diatom assessment in stream quality classification

(2014) T�nia Mendes et al.   MARINE AND FRESHWATER RESEARCH

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

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

Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities

(2014) Aibin Zhan et al.   Molecular Ecology Resources

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

(2013) Marie-Theres Gansauge et al.   Nature Protocols

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

(2012) DONALD J. BAIRD et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol

(2012) Mehrdad Hajibabaei et al.   BMC ECOLOGY

Direct PCR amplification and sequencing of specimens' DNA from preservative ethanol

(2010) Shadi Shokralla et al.   BIOTECHNIQUES

An In silico approach for the evaluation of DNA barcodes

(2010) Gentile Ficetola et al.   BMC GENOMICS