Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies

Metabarcoding a Diverse Arthropod Mock Community

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

Environmental DNA provides quantitative estimates of a threatened salmon species

(2019) Andrew Olaf Shelton et al.   BIOLOGICAL CONSERVATION

Concentrations of environmental DNA (eDNA) reflect spawning salmon abundance at fine spatial and temporal scales

(2018) Michael D. Tillotson et al.   BIOLOGICAL CONSERVATION

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

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

(2018) Bruce E. Deagle et al.   MOLECULAR ECOLOGY

Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea

(2018) Steen Wilhelm Knudsen et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Comparative Cost and Effort of Fish Distribution Detection via Environmental DNA Analysis and Electrofishing

(2017) Nathan T. Evans et al.   FISHERIES

Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

(2017) Michael Stat et al.   Scientific Reports

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

(2017) Satoshi Yamamoto et al.   Scientific Reports

Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis

(2016) Taylor M. Wilcox et al.   BIOLOGICAL CONSERVATION

A framework for inferring biological communities from environmental DNA

(2016) Andrew Olaf Shelton et al.   ECOLOGICAL APPLICATIONS

Quantification of Environmental DNA (eDNA) Shedding and Decay Rates for Three Marine Fish

(2016) Lauren M. Sassoubre et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Quantifying relative fish abundance with eDNA: a promising tool for fisheries management

(2016) Anaïs Lacoursière-Roussel et al.   JOURNAL OF APPLIED ECOLOGY

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

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

(2016) James L. O’Donnell et al.   PLoS One

Environmental DNA reveals that rivers are conveyer belts of biodiversity information

(2016) Kristy Deiner et al.   Nature Communications

Estimating species richness using environmental DNA

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

Genetic signatures of ecological diversity along an urbanization gradient

(2016) Ryan P. Kelly et al.   PeerJ

Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces

(2016) Michael J. Ford et al.   PLoS One

Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples

(2015) Marta Pawluczyk et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

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

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

NGS metabarcoding proves successful for quantitative assessment of symbiont abundance: the case of feather mites on birds

(2015) J. Diaz-Real et al.   EXPERIMENTAL AND APPLIED ACAROLOGY

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

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

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

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

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

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

Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers

(2014) Anne Chao et al.   Annual Review of Ecology Evolution and Systematics

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

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

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

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

Measuring copepod naupliar abundance in a subtropical bay using quantitative PCR

(2013) Michelle J. Jungbluth et al.   MARINE BIOLOGY

Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

(2013) Bruce E. Deagle et al.   Molecular Ecology Resources

Estimation of Fish Biomass Using Environmental DNA

(2012) Teruhiko Takahara 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

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

(2011) Tiayyba Riaz et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data

(2009) J. M. Ruijter et al.   NUCLEIC ACIDS RESEARCH