The ecology of environmental DNA and implications for conservation genetics

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

(2015) Kristy Deiner et al.   BIOLOGICAL CONSERVATION

Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix

(2015) Katy E. Klymus et al.   BIOLOGICAL CONSERVATION

Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms

(2015) Katherine M. Strickler 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

Fish environmental DNA is more concentrated in aquatic sediments than surface water

(2015) Cameron R. Turner 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

Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus)

(2015) Jeremy Biggs et al.   BIOLOGICAL CONSERVATION

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

Genomics and the challenging translation into conservation practice

(2015) Aaron B.A. Shafer et al.   TRENDS IN ECOLOGY & EVOLUTION

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

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

Modern Methods for Delineating Metagenomic Complexity

(2015) Ebrahim Afshinnekoo et al.   Cell Systems

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

(2015) Ebrahim Afshinnekoo et al.   Cell Systems

Of Paleo-Genes and Perch: What if an “Alien” Is Actually a Native?

(2015) J. Curt Stager 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

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows

(2015) Dáithí C. Murray 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

Genetic studies of aquatic biological invasions: closing the gap between research and management

(2014) John A. Darling   BIOLOGICAL INVASIONS

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

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

Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

(2014) Chenxue Yang et al.   ECOLOGICAL INDICATORS

Sequencing Human Mitochondrial Hypervariable Region II as a Molecular Fingerprint for Environmental Waters

(2014) Vikram Kapoor et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Environmental Conditions Influence eDNA Persistence in Aquatic Systems

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

How many16S-based studies should be included in a metagenomic conference? It may be a matter of etymology

(2014) Alfonso Esposito et al.   FEMS MICROBIOLOGY LETTERS

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

Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing

(2014) Ken Kraaijeveld et al.   Molecular Ecology Resources

Parsing ecological signal from noise in next generation amplicon sequencing

(2014) Nhu H. Nguyen et al.   NEW PHYTOLOGIST

Ancient and modern environmental DNA

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

Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization

(2014) Xiaoquan Su et al.   PLoS One

Transport Distance of Invertebrate Environmental DNA in a Natural River

(2014) Kristy Deiner et al.   PLoS One

Using Environmental DNA to Census Marine Fishes in a Large Mesocosm

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

Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods: Results from a Survey of Freshwater Bioassessment Efforts in the United States?

(2014) Eric D. Stein et al.   PLoS One

Assessing Environmental DNA Detection in Controlled Lentic Systems

(2014) Gregory R. Moyer et al.   PLoS One

Persistence of DNA in Carcasses, Slime and Avian Feces May Affect Interpretation of Environmental DNA Data

(2014) Christopher M. Merkes et al.   PLoS One

Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data

(2014) Richard W. Lusk   PLoS One

The Relationship between the Distribution of Common Carp and Their Environmental DNA in a Small Lake

(2014) Jessica J. Eichmiller 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

The Release Rate of Environmental DNA from Juvenile and Adult Fish

(2014) Atsushi Maruyama et al.   PLoS One

Current noise-removal methods can create false signals in ecogenomic data

(2014) A. G. Rossberg et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Harnessing DNA to improve environmental management

(2014) R. P. Kelly et al.   SCIENCE

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

Meta-genomic surveillance of invasive species in the bait trade

(2014) Andrew R. Mahon 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

The application of eDNA for monitoring of the Great Crested Newt in the UK

(2014) Helen C. Rees et al.   Ecology and Evolution

Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species

(2014) Elvira Mächler et al.   Freshwater Science

Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples

(2013) David S. Pilliod et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity

(2013) Sébastien Calvignac-Spencer et al.   MOLECULAR ECOLOGY

Factors influencing detection of eDNA from a stream-dwelling amphibian

(2013) David S. Pilliod et al.   Molecular Ecology Resources

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

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

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces

(2013) William Orsi et al.   PLoS One

Deep Sequencing of RNA from Ancient Maize Kernels

(2013) Sarah L. Fordyce et al.   PLoS One

Validation of eDNA Surveillance Sensitivity for Detection of Asian Carps in Controlled and Field Experiments

(2013) Andrew R. Mahon 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

An eDNA approach to detect eastern hellbenders (Cryptobranchus a. alleganiensis) using samples of water

(2013) Zachary H. Olson et al.   WILDLIFE RESEARCH

Rapid Invasive Species Detection by Combining Environmental DNA with Light Transmission Spectroscopy

(2013) Scott P. Egan et al.   Conservation Letters

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

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

Conservation Genomics of Threatened Animal Species

(2013) Cynthia C. Steiner et al.   Annual Review of Animal Biosciences

Something in the water: biosecurity monitoring of ornamental fish imports using environmental DNA

(2012) Rupert A. Collins et al.   BIOLOGICAL INVASIONS

Emerging prion disease drives host selection in a wildlife population

(2012) Stacie J. Robinson et al.   ECOLOGICAL APPLICATIONS

The use of molecular tools in invasion biology: an emphasis on freshwater ecosystems

(2012) S. BLANCHET   FISHERIES MANAGEMENT AND ECOLOGY

DNA-based species detection capabilities using laser transmission spectroscopy

(2012) A. R. Mahon et al.   Journal of the Royal Society Interface

The future of environmental DNA in ecology

(2012) NIGEL G. YOCCOZ   MOLECULAR 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

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

(2012) DAVID M. LODGE et al.   MOLECULAR ECOLOGY

DNA from soil mirrors plant taxonomic and growth form diversity

(2012) N. G. YOCCOZ 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

Estimation of Fish Biomass Using Environmental DNA

(2012) Teruhiko Takahara et al.   PLoS One

Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals

(2012) Andrew D. Foote et al.   PLoS One

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

(2012) Philip Francis Thomsen et al.   PLoS One

SSU Ribosomal DNA-Based Monitoring of Nematode Assemblages Reveals Distinct Seasonal Fluctuations within Evolutionary Heterogeneous Feeding Guilds

(2012) Mariëtte T. W. Vervoort et al.   PLoS One

‘Ecosystomics’: ecology by sequencer

(2012) Anthony M. Poole et al.   TRENDS IN ECOLOGY & EVOLUTION

A horizon scan of global conservation issues for 2013

(2012) William J. Sutherland et al.   TRENDS IN ECOLOGY & EVOLUTION

Fecal source tracking in water using a mitochondrial DNA microarray

(2012) Nguyet-Minh Vuong et al.   WATER RESEARCH

Development of 134 novel polynucleotide-repeat microsatellite markers in silver carp (Hypophthalmichthys molitrix)

(2012) Wenjie Guo et al.   Conservation Genetics Resources

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

Biodiversity assessment: State-of-the-art techniques in phylogenomics and species identification

(2011) P. R. Steele et al.   AMERICAN JOURNAL OF BOTANY

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

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

Forensic quest for age determination of bloodstains

(2011) Rolf H. Bremmer et al.   FORENSIC SCIENCE INTERNATIONAL

Surveillance of fish species composition using environmental DNA

(2011) Toshifumi Minamoto et al.   LIMNOLOGY

A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability

(2011) TINA JØRGENSEN 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

Underwater Application of Quantitative PCR on an Ocean Mooring

(2011) Christina M. Preston et al.   PLoS One

Persistence of Environmental DNA in Freshwater Ecosystems

(2011) Tony Dejean et al.   PLoS One

Quantitative and Rapid DNA Detection by Laser Transmission Spectroscopy

(2011) Frank Li et al.   PLoS One

Subjectivity and bias in forensic DNA mixture interpretation

(2011) Itiel E. Dror et al.   SCIENCE & JUSTICE

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

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

Microbial Metagenomics: Beyond the Genome

(2010) Jack A. Gilbert et al.   Annual Review of Marine Science

Use of DNA barcoding to detect invertebrate invasive species from diapausing eggs

(2010) Elizabeta Briski et al.   BIOLOGICAL INVASIONS

The Functional Genomics of Inbreeding Depression: A New Approach to an Old Problem

(2010) Ken N. Paige   BIOSCIENCE

mRNA profiling in forensic genetics I: Possibilities and limitations

(2010) Marielle Vennemann et al.   FORENSIC SCIENCE INTERNATIONAL

Recovery of Environmental Human DNA by Insects*,†

(2010) Karen M. Kester et al.   JOURNAL OF FORENSIC SCIENCES

Ecometagenetics confirm high tropical rainforest nematode diversity

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

Strategy for Extracting DNA from Clay Soil and Detecting a Specific Target Sequence via Selective Enrichment and Real-Time (Quantitative) PCR Amplification

(2009) K. K. Yankson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Extracellular plant DNA in Geneva groundwater and traditional artesian drinking water fountains

(2009) John Poté et al.   CHEMOSPHERE

Plant leaf mass loss and DNA release in freshwater sediments

(2009) John Poté et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Improving the sensitivity of negative controls in ancient DNA extractions

(2009) Zhi Xu et al.   ELECTROPHORESIS

Detection of microbial biomass by intact polar membrane lipid analysis in the water column and surface sediments of the Black Sea

(2009) Florence Schubotz et al.   ENVIRONMENTAL MICROBIOLOGY

Advancing ecological understandings through technological transformations in noninvasive genetics

(2009) ALBANO BEJA-PEREIRA et al.   Molecular Ecology Resources

Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column

(2009) Yanmei Shi et al.   NATURE

Non-Destructive Sampling of Ancient Insect DNA

(2009) Philip Francis Thomsen et al.   PLoS One

Ancient DNA reveals late survival of mammoth and horse in interior Alaska

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

Species detection using environmental DNA from water samples

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

Characterization of human DNA in environmental samples

(2008) Mary H. Toothman et al.   FORENSIC SCIENCE INTERNATIONAL

Molecular detection of native and invasive marine invertebrate larvae present in ballast and open water environmental samples collected in Puget Sound

(2008) Julio B.J. Harvey et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Recovery of DNA and pollen from New Zealand lake sediments

(2007) Elizabeth Matisoo-Smith et al.   QUATERNARY INTERNATIONAL