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

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

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

The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

(2018) Frederic Rimet et al.   Fottea

Insights into global planktonic diatom diversity: The importance of comparisons between phylogenetically equivalent units that account for time

(2018) Teofil Nakov et al.   ISME Journal

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

(2018) Teresita M. Porter et al.   MOLECULAR ECOLOGY

Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring

(2018) Tristan Cordier et al.   Molecular Ecology Resources

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

Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive

(2018) Daniel Hering et al.   WATER RESEARCH

Automated high throughput animal CO1 metabarcode classification

(2018) Teresita M. Porter et al.   Scientific Reports

Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

(2018) Colin J. Curry et al.   Freshwater Science

Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

(2018) Colin J. Curry et al.   Freshwater Science

Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation

(2018) Melania E. Cristescu et al.   Annual Review of Ecology Evolution and Systematics

Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities

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

Over 2.5 million COI sequences in GenBank and growing

(2018) Teresita M. Porter et al.   PLoS One

Microbiomes as Metacommunities: Understanding Host-Associated Microbes through Metacommunity Ecology

(2018) Elizabeth Theresa Miller et al.   TRENDS IN ECOLOGY & EVOLUTION

DNA metabarcoding reveals the complex and hidden responses of chironomids to multiple stressors

(2018) Arne J. Beermann et al.   Environmental Sciences Europe

Researchers launch plan to sequence 66,000 species in the United Kingdom. But that’s just a start

(2018) Erik Stokstad   SCIENCE

Accounting for observation processes across multiple levels of uncertainty improves inference of species distributions and guides adaptive sampling of environmental DNA

(2018) Amy J. Davis et al.   Ecology and Evolution

Freshwater biomonitoring in the Information Age

(2017) François Keck et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

The EU Water Framework Directive: From great expectations to problems with implementation

(2017) Nikolaos Voulvoulis et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Next-Generation Global Biomonitoring: Large-scale, Automated Reconstruction of Ecological Networks

(2017) David A. Bohan et al.   TRENDS IN ECOLOGY & EVOLUTION

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

Connecting Earth observation to high-throughput biodiversity data

(2017) Alex Bush et al.   Nature Ecology & Evolution

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

Modelling of species distributions, range dynamics and communities under imperfect detection: advances, challenges and opportunities

(2016) Gurutzeta Guillera-Arroita   ECOGRAPHY

Confidence in ecological indicators: A framework for quantifying uncertainty components from monitoring data

(2016) Jacob Carstensen et al.   ECOLOGICAL INDICATORS

Multiple-stressor effects on stream invertebrates: DNA barcoding reveals contrasting responses of cryptic mayfly species

(2016) Jan N. Macher et al.   ECOLOGICAL INDICATORS

Global patterns and drivers of species and trait composition in diatoms

(2016) Janne Soininen et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Causes and consequences of biotic homogenization in freshwater ecosystems

(2016) Danielle Katharine Petsch   INTERNATIONAL REVIEW OF HYDROBIOLOGY

Forecasting pollination declines through DNA barcoding: the potential contributions of macroecological and macroevolutionary scales of inquiry

(2016) Jana C. Vamosi et al.   NEW PHYTOLOGIST

Turning Up the Heat on a Hotspot: DNA Barcodes Reveal 80% More Species of Geometrid Moths along an Andean Elevational Gradient

(2016) Gunnar Brehm et al.   PLoS One

Taxonomic resolution based on DNA barcoding affects environmental signal in metacommunity structure

(2016) Gillian K. Martin et al.   Freshwater Science

Taxonomic resolution based on DNA barcoding affects environmental signal in metacommunity structure

(2016) Gillian K. Martin et al.   Freshwater Science

Global effects of land use on local terrestrial biodiversity

(2015) Tim Newbold et al.   NATURE

Molecular Barcoding of Aquatic Oligochaetes: Implications for Biomonitoring

(2015) Régis Vivien 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

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing

(2015) Joel F. Gibson et al.   PLoS One

Stream biomonitoring using macroinvertebrates around the globe: a comparison of large-scale programs

(2014) Daniel F. Buss et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

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

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

Population densities and density–area relationships in a community with advective dispersal and variable mosaics of resource patches

(2014) Jill Lancaster et al.   OECOLOGIA

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

(2014) J. Gibson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sensing biodiversity

(2014) W. Turner   SCIENCE

Performance of the standard CABIN method: comparison of BEAST models and error rates to detect simulated degradation from multiple data sets

(2014) Stephanie A. Strachan et al.   Freshwater Science

Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications

(2014) John K. Jackson et al.   Freshwater Science

The tiny mayfly in the room: implications of size-dependent invertebrate taxonomic identification for biomonitoring data properties

(2013) Jessica M. Orlofske et al.   AQUATIC ECOLOGY

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Global meta-analysis reveals no net change in local-scale plant biodiversity over time

(2013) M. Vellend et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards generalised reference condition models for environmental assessment: a case study on rivers in Atlantic Canada

(2012) D. G. Armanini et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

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

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

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Biodiversity loss and its impact on humanity

(2012) Bradley J. Cardinale et al.   NATURE

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

(2012) Douglas W. Yu et al.   Methods in Ecology and Evolution

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

Three hundred ways to assess Europe's surface waters: An almost complete overview of biological methods to implement the Water Framework Directive

(2011) Sebastian Birk et al.   ECOLOGICAL INDICATORS

Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality?

(2011) Bernard W. Sweeney et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

(2011) Mehrdad Hajibabaei et al.   PLoS One

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

(2010) David B. Lindenmayer et al.   ECOSYSTEMS

First audit of macroinvertebrate samples from an EU Water Framework Directive monitoring program: human error greatly lowers precision of assessment results

(2010) Peter Haase et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

Effect of fixed-fraction subsampling on macroinvertebrate bioassessment of rivers

(2009) Vesna Petkovska et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

Taxonomic sufficiency: The influence of taxonomic resolution on freshwater bioassessments using benthic macroinvertebrates

(2009) F. Chris Jones   ENVIRONMENTAL REVIEWS

Taxonomic structure and the effectiveness of surrogates in environmental monitoring: a lesson from polychaetes

(2009) L Musco et al.   MARINE ECOLOGY PROGRESS SERIES

The effect of excluding diatom taxa and reducing taxonomic resolution on multivariate analyses and stream bioassessment

(2008) Isabelle Lavoie et al.   ECOLOGICAL INDICATORS