The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA

Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system

(2016) Jennifer L.A. Shaw et al.   BIOLOGICAL CONSERVATION

Active and passive environmental DNA surveillance of aquatic invasive species

(2016) Megan Simmons et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

The use of environmental DNA of fishes as an efficient method of determining habitat connectivity

(2016) Hiroki Yamanaka et al.   ECOLOGICAL INDICATORS

Development of species-specific primers with potential for amplifying eDNA from imperilled freshwater unionid mussels

(2016) Anna Cho et al.   GENOME

Pollen DNA barcoding: current applications and future prospects

(2016) Karen L. Bell et al.   GENOME

Improving herpetological surveys in eastern North America using the environmental DNA method

(2016) Anaïs Lacoursière-Roussel et al.   GENOME

Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea

(2016) Mamoon M.D. Al-Rshaidat et al.   GENOME

Sampling large geographic areas for rare species using environmental DNA: a study of bull troutSalvelinus confluentusoccupancy in western Montana

(2016) K. S. McKelvey et al.   JOURNAL OF FISH BIOLOGY

Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods

(2016) Bernd Hänfling et al.   MOLECULAR ECOLOGY

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

(2016) Alice Valentini et al.   MOLECULAR ECOLOGY

Using occupancy modelling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species

(2016) Molly C. Schmelzle et al.   Molecular Ecology Resources

Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers

(2016) Nicole A. Fahner et al.   PLoS One

Critical considerations for the application of environmental DNA methods to detect aquatic species

(2016) Caren S. Goldberg et al.   Methods in Ecology and Evolution

In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River

(2016) M. V. Cannon et al.   Scientific Reports

Estimating species richness using environmental DNA

(2016) Brett P. Olds et al.   Ecology and Evolution

Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds

(2016) Ayaka Fujiwara et al.   Freshwater Science

Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds

(2016) Ayaka Fujiwara et al.   Freshwater Science

Environmental DNA as a ‘Snapshot’ of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan

(2016) Satoshi Yamamoto et al.   PLoS One

An eDNA Assay to Monitor a Globally Invasive Fish Species from Flowing Freshwater

(2016) Irene Adrian-Kalchhauser et al.   PLoS One

Development of species-specific environmental DNA (eDNA) markers for invasive aquatic plants

(2015) Michelle Scriver et al.   AQUATIC BOTANY

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

(2015) Kristy Deiner et al.   BIOLOGICAL CONSERVATION

Characterizing the distribution of an endangered salmonid using environmental DNA analysis

(2015) Matthew B. Laramie et al.   BIOLOGICAL CONSERVATION

Using environmental DNA methods to improve detectability in a hellbender (Cryptobranchus alleganiensis) monitoring program

(2015) Stephen F. Spear et al.   BIOLOGICAL CONSERVATION

Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples

(2015) Eva Egelyng Sigsgaard 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

The ecology of environmental DNA and implications for conservation genetics

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

Environmental DNA sampling is more sensitive than a traditional survey technique for detecting an aquatic invader

(2015) Adam S. Smart et al.   ECOLOGICAL APPLICATIONS

Environmental DNA as an effective tool for detection of imperiled fishes

(2015) Alexis M. Janosik et al.   ENVIRONMENTAL BIOLOGY OF FISHES

Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

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

Fishing in the Water: Effect of Sampled Water Volume on Environmental DNA-Based Detection of Macroinvertebrates

(2015) Elvira Mächler et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Next generation sequencing for characterizing biodiversity: promises and challenges

(2015) François Pompanon et al.   GENETICA

Applications and limitations of measuring environmental DNA as indicators of the presence of aquatic animals

(2015) Helen C. Rees et al.   JOURNAL OF APPLIED ECOLOGY

The downside of eDNA as a survey tool in water bodies

(2015) Jean-Marc Roussel et al.   JOURNAL OF APPLIED ECOLOGY

A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan

(2015) Sou Fukumoto et al.   JOURNAL OF APPLIED ECOLOGY

An eDNA assay for IrishPetromyzon marinusandSalmo truttaand field validation in running water

(2015) M. S. Gustavson et al.   JOURNAL OF FISH BIOLOGY

Improving efficiency and reliability of environmental DNA analysis for silver carp

(2015) Jon J. Amberg et al.   JOURNAL OF GREAT LAKES RESEARCH

Environmental DNA evidence of transfer of North Sea molluscs across tropical waters through ballast water

(2015) Alba Ardura et al.   JOURNAL OF MOLLUSCAN STUDIES

Techniques for the practical collection of environmental DNA: filter selection, preservation, and extraction

(2015) Toshifumi Minamoto et al.   LIMNOLOGY

Targeted capture in evolutionary and ecological genomics

(2015) Matthew R. Jones et al.   MOLECULAR ECOLOGY

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

(2015) Jesse A. Port et al.   MOLECULAR ECOLOGY

Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish

(2015) Jessica J. Eichmiller et al.   Molecular Ecology Resources

Comparative study of the validity of three regions of the 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community

(2015) Akifumi S. Tanabe et al.   Molecular Ecology Resources

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

(2015) Nathan T. Evans et al.   Molecular Ecology Resources

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

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

Unveiling the Biodiversity of Deep-Sea Nematodes through Metabarcoding: Are We Ready to Bypass the Classical Taxonomy?

(2015) Antonio Dell’Anno et al.   PLoS One

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

(2015) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An evaluation of target specificity and sensitivity of three qPCR assays for detecting environmental DNA from Northern Pike (Esox lucius)

(2015) Jeffrey B. Olsen et al.   Conservation Genetics Resources

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

(2015) Emily A. Brown et al.   Ecology and Evolution

Assessment of Environmental DNA for Detecting Presence of Imperiled Aquatic Amphibian Species in Isolated Wetlands

(2015) Anna M. McKee et al.   Journal of Fish and Wildlife Management

Application of ITS2 Metabarcoding to Determine the Provenance of Pollen Collected by Honey Bees in an Agroecosystem

(2015) Rodney T. Richardson et al.   Applications in Plant Sciences

Evaluating a multigene environmental DNA approach for biodiversity assessment

(2015) Alexei J. Drummond et al.   GigaScience

MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

(2015) M. Miya et al.   Royal Society Open Science

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

Use of Droplet Digital PCR for Estimation of Fish Abundance and Biomass in Environmental DNA Surveys

(2015) Hideyuki Doi et al.   PLoS One

Environmental DNA (eDNA) Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons

(2015) Margaret E. Hunter et al.   PLoS One

Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences

(2015) Jennifer Hawkins et al.   PLoS One

The Dual Challenges of Generality and Specificity When Developing Environmental DNA Markers for Species and Subspecies of Oncorhynchus

(2015) Taylor M. Wilcox et al.   PLoS One

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

(2015) Edgardo E. Díaz-Ferguson et al.   REVISTA DE BIOLOGIA TROPICAL

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

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

The use of environmental DNA in invasive species surveillance of the Great Lakes commercial bait trade

(2014) Lucas R. Nathan et al.   CONSERVATION BIOLOGY

Quantifying Environmental DNA Signals for Aquatic Invasive Species Across Multiple Detection Platforms

(2014) Lucas M. Nathan et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Environmental Conditions Influence eDNA Persistence in Aquatic Systems

(2014) Matthew A. Barnes et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfishProcambarus clarkiiin freshwater ponds

(2014) Anne Tréguier et al.   JOURNAL OF APPLIED ECOLOGY

REVIEW: The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology

(2014) Helen C. Rees et al.   JOURNAL OF APPLIED ECOLOGY

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

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

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

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

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

Ancient and modern environmental DNA

(2014) Mikkel Winther Pedersen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Using Environmental DNA to Census Marine Fishes in a Large Mesocosm

(2014) Ryan P. Kelly et al.   PLoS One

Improved Methods for Capture, Extraction, and Quantitative Assay of Environmental DNA from Asian Bigheaded Carp (Hypophthalmichthys spp.)

(2014) Cameron R. Turner et al.   PLoS One

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

A blocking primer increases specificity in environmental DNA detection of bull trout (Salvelinus confluentus)

(2014) Taylor M. Wilcox et al.   Conservation Genetics Resources

Particle size distribution and optimal capture of aqueous macrobial eDNA

(2014) Cameron R. Turner et al.   Methods in Ecology and Evolution

Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species

(2014) Elvira Mächler et al.   Freshwater Science

The evolutionary history and conservation value of disjunct Bartonia paniculata subsp. paniculata (Branched Bartonia) populations in Canada

(2013) Claudia Ciotir et al.   Botany

Detection of Asian carp DNA as part of a Great Lakes basin-wide surveillance program

(2013) Christopher L. Jerde et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Single-Nucleotide Polymorphisms and Other Mismatches Reduce Performance of Quantitative PCR Assays

(2013) S. Lefever et al.   CLINICAL CHEMISTRY

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates

(2013) Erik S. Wright et al.   ENVIRONMENTAL MICROBIOLOGY

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

20 years since the introduction of DNA barcoding: from theory to application

(2013) Živa Fišer Pečnikar et al.   JOURNAL OF APPLIED GENETICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia

(2013) Laura Parducci et al.   MOLECULAR ECOLOGY

Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA

(2013) Antoinette J. Piaggio et al.   Molecular Ecology Resources

DNA barcoding at riverscape scales: assessing biodiversity among fishes of the genusCottus(Teleostei) in northern Rocky Mountain streams

(2013) Michael K. Young et al.   Molecular Ecology Resources

Using Environmental DNA to Estimate the Distribution of an Invasive Fish Species in Ponds

(2013) Teruhiko Takahara et al.   PLoS One

Robust Detection of Rare Species Using Environmental DNA: The Importance of Primer Specificity

(2013) Taylor M. Wilcox et al.   PLoS One

A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

(2013) Mikkel Winther Pedersen et al.   QUATERNARY SCIENCE REVIEWS

Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum)

(2013) Caren S. Goldberg et al.   Freshwater Science

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Screening mammal biodiversity using DNA from leeches

(2012) Ida Bærholm Schnell et al.   CURRENT BIOLOGY

Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrogLithobates catesbeianus

(2012) Tony Dejean et al.   JOURNAL OF APPLIED ECOLOGY

Tracking earthworm communities from soil DNA

(2012) FRIEDERIKE BIENERT et al.   MOLECULAR ECOLOGY

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Browsed twig environmental DNA: diagnostic PCR to identify ungulate species

(2012) RUTH V. NICHOLS et al.   Molecular Ecology Resources

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples

(2012) Philip Francis Thomsen et al.   PLoS One

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

(2012) C. Q. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glacial Survival of Boreal Trees in Northern Scandinavia

(2012) L. Parducci et al.   SCIENCE

Sequencing our way towards understanding global eukaryotic biodiversity

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

Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics

(2011) Lynn L Anderson-Carpenter et al.   BMC EVOLUTIONARY BIOLOGY

Surveillance of fish species composition using environmental DNA

(2011) Toshifumi Minamoto et al.   LIMNOLOGY

Significant genetic boundaries and spatial dynamics of giant pandas occupying fragmented habitat across southwest China

(2011) LIFENG ZHU et al.   MOLECULAR ECOLOGY

Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity

(2011) KENNETH ANDERSEN et al.   MOLECULAR ECOLOGY

Monitoring endangered freshwater biodiversity using environmental DNA

(2011) PHILIP FRANCIS THOMSEN et al.   MOLECULAR ECOLOGY

A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding

(2011) A.-B. ZHANG et al.   MOLECULAR ECOLOGY

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

(2011) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

(2011) Tiayyba Riaz et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Mehrdad Hajibabaei et al.   PLoS One

Molecular Detection of Vertebrates in Stream Water: A Demonstration Using Rocky Mountain Tailed Frogs and Idaho Giant Salamanders

(2011) Caren S. Goldberg et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

“Sight-unseen” detection of rare aquatic species using environmental DNA

(2011) Christopher L. Jerde et al.   Conservation Letters

Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode

(2011) Kevin S. Burgess et al.   Methods in Ecology and Evolution

Characterisation of insect and plant origins using DNA extracted from small volumes of bee honey

(2010) Ida Bærholm Schnell et al.   Arthropod-Plant Interactions

An In silico approach for the evaluation of DNA barcodes

(2010) Gentile Ficetola et al.   BMC GENOMICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

(2010) Anthony A Chariton et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

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

Population genetics reveals origin and number of founders in a biological invasion

(2010) GENTILE FRANCESCO FICETOLA et al.   MOLECULAR ECOLOGY

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

Ecometagenetics confirm high tropical rainforest nematode diversity

(2010) DOROTA L. PORAZINSKA et al.   MOLECULAR ECOLOGY

Phylogeographic inferences from chloroplast DNA: quantifying the effects of mutations in repetitive and non-repetitive sequences

(2010) NICOLE VACHON et al.   Molecular Ecology Resources

Design of phylum-specific hybrid primers for DNA barcoding: addressing the need for efficient COI amplification in the Echinodermata

(2010) T. B. HOAREAU et al.   Molecular Ecology Resources

Evaluation of the impact of single nucleotide polymorphisms and primer mismatches on quantitative PCR

(2009) Brian Boyle et al.   BMC BIOTECHNOLOGY

The ITS region as a target for characterization of fungal communities using emerging sequencing technologies

(2009) Rolf Henrik Nilsson et al.   FEMS MICROBIOLOGY LETTERS

A DNA barcode for land plants

(2009) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Barcoding of Plants and Fungi

(2009) M. W. Chase et al.   SCIENCE

Species detection using environmental DNA from water samples

(2008) G. F. Ficetola et al.   Biology Letters

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS

Identifying the source of species invasions: sampling intensity vs. genetic diversity

(2008) JIM R. MUIRHEAD et al.   MOLECULAR ECOLOGY