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

Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding

(2018) Ostaizka Aizpurua et al.   MOLECULAR ECOLOGY

Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring

(2018) Valentin Vasselon et al.   Methods in Ecology and Evolution

Puffins reveal contrasting relationships between forage fish and ocean climate in the North Pacific

(2017) William J. Sydeman et al.   FISHERIES OCEANOGRAPHY

Assessing the trophic ecology of top predators across a recolonisation frontier using DNA metabarcoding of diets

(2017) N Hardy et al.   MARINE ECOLOGY PROGRESS SERIES

High occurrence of jellyfish predation by black-browed and Campbell albatross identified by DNA metabarcoding

(2017) Julie C. McInnes et al.   MOLECULAR ECOLOGY

A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies

(2017) Emmanuel Corse et al.   Molecular Ecology Resources

Reference standards for next-generation sequencing

(2017) Simon A. Hardwick et al.   NATURE REVIEWS GENETICS

Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

(2017) Henrik Krehenwinkel et al.   Scientific Reports

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

(2017) Michael Stat et al.   Scientific Reports

Reconstructing a herbivore’s diet using a novel rbcL DNA mini-barcode for plants

(2017) David L. Erickson et al.   AoB Plants

Assessing the trophic ecology of top predators across a recolonisation frontier using DNA metabarcoding of diets

(2017) N Hardy et al.   MARINE ECOLOGY PROGRESS SERIES

Quantitative species-level ecology of reef fish larvae via metabarcoding

(2017) Naama Kimmerling et al.   Nature Ecology & Evolution

Molecular dietary analysis of two sympatric felids in the Mountains of Southwest China biodiversity hotspot and conservation implications

(2017) Mengyin Xiong et al.   Scientific Reports

Competing tradeoffs between increasing marine mammal predation and fisheries harvest of Chinook salmon

(2017) Brandon E. Chasco et al.   Scientific Reports

Diet reconstruction using next-generation sequencing increases the known ecosystem usage by a shorebird

(2016) Travis G. Gerwing et al.   AUK

Dietary preferences of Hawaiian tree snails to inform culture for conservation

(2016) Richard O'Rorke et al.   BIOLOGICAL CONSERVATION

Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate

(2016) Amrita Srivathsan et al.   Frontiers in Zoology

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

(2016) Tomas Roslin et al.   GENOME

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

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

What you need is what you eat? Prey selection by the bat Myotis daubentonii

(2016) Eero J. Vesterinen et al.   MOLECULAR ECOLOGY

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

A cost-efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large-scale gut content analysis by Illumina sequencing

(2016) Henrik Krehenwinkel et al.   Methods in Ecology and Evolution

Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates

(2016) Julie C. McInnes et al.   Methods in Ecology and Evolution

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

DNA Metabarcoding Reveals Diet Overlap between the Endangered Walia Ibex and Domestic Goats - Implications for Conservation

(2016) Berihun Gebremedhin et al.   PLoS One

Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes

(2016) Philip Francis Thomsen et al.   PLoS One

Using metabarcoding to reveal and quantify plant-pollinator interactions

(2016) André Pornon et al.   Scientific Reports

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

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

Organellar genome copy number variation and integrity during moderate maturation of roots and leaves of maize seedlings

(2015) Jin Ma et al.   CURRENT GENETICS

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

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

Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material

(2015) Austen C. Thomas 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

DNA metabarcoding illuminates dietary niche partitioning by African large herbivores

(2015) Tyler R. Kartzinel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EpiRADseq: scalable analysis of genomewide patterns of methylation using next-generation sequencing

(2015) Drew R. Schield et al.   Methods in Ecology and Evolution

Climatic warming and the future of bison as grazers

(2015) Joseph M. Craine et al.   Scientific Reports

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

Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis

(2014) F. Finotello et al.   Briefings in Functional Genomics

Molecular detection of trophic interactions: emerging trends, distinct advantages, significant considerations and conservation applications

(2014) Elizabeth L. Clare   Evolutionary Applications

Special issue on molecular detection of trophic interactions: Unpicking the tangled bank

(2014) William O. C. Symondson et al.   MOLECULAR 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

Fifty thousand years of Arctic vegetation and megafaunal diet

(2014) Eske Willerslev et al.   NATURE

Parsing ecological signal from noise in next generation amplicon sequencing

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

Pyrosequencing of prey DNA in faeces of carnivorous land snails to facilitate ecological restoration and relocation programmes

(2014) Benjamin R. Waterhouse et al.   OECOLOGIA

The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics

(2014) Federico M. Ibarbalz et al.   PLoS One

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

(2014) Florent E Angly et al.   Microbiome

Who's for dinner? High-throughput sequencing reveals bat dietary differentiation in a biodiversity hotspot where prey taxonomy is largely undescribed

(2013) Joanna M. Burgar et al.   MOLECULAR ECOLOGY

Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias

(2013) Austen C. Thomas et al.   MOLECULAR ECOLOGY

The detectability half-life in arthropod predator-prey research: what it is, why we need it, how to measure it, and how to use it

(2013) Matthew H. Greenstone et al.   MOLECULAR ECOLOGY

An inordinate fondness for beetles? Variation in seasonal dietary preferences of night-roosting big brown bats (Eptesicus fuscus)

(2013) Elizabeth L. Clare et al.   MOLECULAR ECOLOGY

DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

(2013) M. De Barba et al.   Molecular Ecology Resources

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

A DNA Metabarcoding Study of a Primate Dietary Diversity and Plasticity across Its Entire Fragmented Range

(2013) Erwan Quéméré et al.   PLoS One

Adélie Penguin Population Diet Monitoring by Analysis of Food DNA in Scats

(2013) Simon N. Jarman et al.   PLoS One

From Puffins to Plankton: A DNA-Based Analysis of a Seabird Food Chain in the Northern Gulf of Maine

(2013) A. Kirsten Bowser et al.   PLoS One

Diet analysis by next-generation sequencing indicates the frequent consumption of introduced plants by the critically endangered red-headed wood pigeon (Columba janthina nitens) in oceanic island habitats

(2013) Haruko Ando et al.   Ecology and Evolution

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

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

Who is eating what: diet assessment using next generation sequencing

(2011) FRANCOIS POMPANON et al.   MOLECULAR ECOLOGY

Proportion of prey consumed can be determined from faecal DNA using real-time PCR

(2011) ELLA BOWLES et al.   Molecular Ecology Resources

Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?

(2010) Bruce E. Deagle et al.   CONSERVATION GENETICS

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

Complexity in quantitative food webs

(2009) Carolin Banašek-Richter et al.   ECOLOGY

Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

(2009) Eeva M Soininen et al.   Frontiers in Zoology

Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

(2009) BRUCE E. DEAGLE et al.   MOLECULAR ECOLOGY

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: thetrnL approach

(2009) ALICE VALENTINI et al.   Molecular Ecology Resources

INVITED REVIEW: Molecular analysis of predation: a review of best practice for DNA-based approaches

(2008) R. A. KING et al.   MOLECULAR ECOLOGY