Environmental DNA metabarcoding for fish diversity assessment in a macrotidal estuary: A comparison with established fish survey methods

Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries

(2022) Raman P. Nagarajan et al.   Estuaries and Coasts

The use of environmental DNA to monitor impacted coastal estuaries

(2022) Joseph D. DiBattista et al.   MARINE POLLUTION BULLETIN

Reproduction influences seasonal eDNA variation in a temperate marine fish community

(2022) Rupert A. Collins et al.   Limnology and Oceanography Letters

Improving the reliability of eDNA data interpretation

(2021) Alfred Burian et al.   Molecular Ecology Resources

Meta‐Fish‐Lib : A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes

(2021) Rupert A. Collins et al.   JOURNAL OF FISH BIOLOGY

Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data

(2020) Lucas Czech et al.   BIOINFORMATICS

Environmental DNA effectively captures functional diversity of coastal fish communities

(2020) Giorgio Aglieri et al.   MOLECULAR ECOLOGY

Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding

(2020) Hyojin Ahn et al.   PLoS One

A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish

(2020) Shan Zhang et al.   Methods in Ecology and Evolution

The Elephant in the Lab (and Field): Contamination in Aquatic Environmental DNA Studies

(2020) Adam J. Sepulveda et al.   Frontiers in Ecology and Evolution

Debunking paradigms in estuarine fish species richness

(2019) A Waugh et al.   MARINE ECOLOGY PROGRESS SERIES

Temperate airborne grass pollen defined by spatio-temporal shifts in community composition

(2019) Georgina L. Brennan et al.   Nature Ecology & Evolution

Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples

(2019) Lucas Czech et al.   PLoS One

Non‐specific amplification compromises environmental DNA metabarcoding with COI

(2019) Rupert A. Collins et al.   Methods in Ecology and Evolution

gllvm ‐ Fast analysis of multivariate abundance data with generalized linear latent variable models in R

(2019) Jenni Niku et al.   Methods in Ecology and Evolution

Can we manage fisheries with the inherent uncertainty from eDNA?

(2019) Christopher L. Jerde   JOURNAL OF FISH BIOLOGY

eDNA metabarcoding as a promising conservation tool for monitoring fish diversity in a coastal wetland of the Pearl River Estuary compared to bottom trawling

(2019) Keshu Zou et al.   SCIENCE OF THE TOTAL ENVIRONMENT

OUP accepted manuscript

(2018)   BIOINFORMATICS

The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries

(2018) Brian Klitgaard Hansen et al.   FISH AND FISHERIES

Freshwater fisheries assessment using environmental DNA: A primer on the method, its potential, and shortcomings as a conservation tool

(2018) Nathan T. Evans et al.   FISHERIES RESEARCH

Comparing local- and regional-scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods

(2018) Hikaru Nakagawa et al.   FRESHWATER BIOLOGY

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

(2018) Daniel Hering et al.   WATER RESEARCH

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

(2018) Pierre Barbera et al.   SYSTEMATIC BIOLOGY

How quantitative is metabarcoding: A meta‐analytical approach

(2018) Philip D. Lamb et al.   MOLECULAR ECOLOGY

Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement

(2018) Gert-Jan Jeunen et al.   Molecular Ecology Resources

Environmental drivers of taxonomic, functional and phylogenetic diversity (alpha, beta and gamma components) in estuarine fish communities

(2017) Nils Teichert et al.   JOURNAL OF BIOGEOGRAPHY

Seawater environmental DNA reflects seasonality of a coastal fish community

(2017) Eva Egelyng Sigsgaard et al.   MARINE BIOLOGY

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary

(2017) Mark Y. Stoeckle et al.   PLoS One

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

(2017) Satoshi Yamamoto et al.   Scientific Reports

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

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

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Restoring fish ecological quality in estuaries: Implication of interactive and cumulative effects among anthropogenic stressors

(2016) Nils Teichert et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed filter

(2016) Johan Spens et al.   Methods in Ecology and Evolution

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   Methods in Ecology and Evolution

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

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

How will the ‘molecular revolution’ contribute to biological recording?

(2015) Lori Lawson Handley   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

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

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

Transport Distance of Invertebrate Environmental DNA in a Natural River

(2014) Kristy Deiner et al.   PLoS One

Development of an estuarine multi-metric fish index and its application to Irish transitional waters

(2013) Trevor D. Harrison et al.   ECOLOGICAL INDICATORS

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

Influence of sampling effort on metrics of fish-based indices for the assessment of estuarine ecological quality

(2012) Rita Gamito et al.   ECOLOGICAL INDICATORS

Seasonal succession of estuarine fish, shrimps, macrozoobenthos and plankton: Physico-chemical and trophic influence. The Gironde estuary as a case study

(2012) Jonathan Selleslagh et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Tidal, Riverine, and Wind Influences on the Circulation of a Macrotidal Estuary

(2012) Rodolfo Bolaños et al.   JOURNAL OF PHYSICAL OCEANOGRAPHY

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

mvabund- anRpackage for model-based analysis of multivariate abundance data

(2012) Yi Wang et al.   Methods in Ecology and Evolution

Paradigms in estuarine ecology – A review of the Remane diagram with a suggested revised model for estuaries

(2011) A.K. Whitfield et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Functional diversity in European estuaries: Relating the composition of fish assemblages to the abiotic environment

(2010) D. Nicolas et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Fish and macro-crustacean communities and their dynamics in the Severn Estuary

(2010) P.A. Henderson et al.   MARINE POLLUTION BULLETIN

Development of a fish-based index to assess the ecological quality of transitional waters: The case of French estuaries

(2010) C. Delpech et al.   MARINE POLLUTION BULLETIN

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Environmental factors structuring fish composition and assemblages in a small macrotidal estuary (eastern English Channel)

(2008) Jonathan Selleslagh et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Fish composition and assemblage structure in three Eastern English Channel macrotidal estuaries: A comparison with other French estuaries

(2008) Jonathan Selleslagh et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage

(2008) K. Robert Clarke et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Life strategies of fishes in European estuaries: the functional guild approach

(2008) A Franco et al.   MARINE ECOLOGY PROGRESS SERIES