High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities

Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing

(2020) Guillemette A. de Kerdrel et al.   Scientific Reports

Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

(2019) Henrik Krehenwinkel et al.   GigaScience

One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

(2019) Emmanuel Corse et al.   Ecology and Evolution

Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods

(2019) Philip Francis Thomsen et al.   Ecology and Evolution

Multiplex PCR targeting lineage specific SNP s ‐ A highly efficient and simple approach to block out predator sequences in molecular gut content analysis

(2019) Henrik Krehenwinkel et al.   Methods in Ecology and Evolution

A new cost-effective and fast direct PCR protocol for insects based on PBS buffer

(2019) Kantima Thongjued et al.   Molecular Ecology Resources

Have the cake and eat it: Optimising non‐destructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring

(2019) Filipa M.S. Martins et al.   Molecular Ecology Resources

An integrated model of population genetics and community ecology

(2019) Isaac Overcast et al.   JOURNAL OF BIOGEOGRAPHY

Estimating the biodiversity of terrestrial invertebrates on a forested island using DNA barcodes and metabarcoding data

(2019) Andrew Dopheide et al.   ECOLOGICAL APPLICATIONS

Spider webs, stable isotopes and molecular gut content analysis: Multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders

(2019) Susan Kennedy et al.   FUNCTIONAL ECOLOGY

A revolutionary protocol to describe understudied hyperdiverse taxa and overcome the taxonomic impediment

(2019) Sarah Meierotto et al.   DEUTSCHE ENTOMOLOGISCHE ZEITSCHRIFT

Tarantula phylogenomics: A robust phylogeny of deep theraphosid clades inferred from transcriptome data sheds light on the prickly issue of urticating setae evolution

(2019) Stephen Foley et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

(2019) Benjamin J Callahan et al.   NUCLEIC ACIDS RESEARCH

Towards PacBio‐based pan‐eukaryote metabarcoding using full‐length ITS sequences

(2019) Leho Tedersoo et al.   Environmental Microbiology Reports

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

(2019) Alexander M Piper et al.   GigaScience

Understanding the effect of competition during evolutionary radiations: an integrated model of phenotypic and species diversification

(2019) Leandro Aristide et al.   ECOLOGY LETTERS

Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches

(2019) Daniel Marquina et al.   Molecular Ecology Resources

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

(2019) Amrita Srivathsan et al.   BMC BIOLOGY

Spider‐specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae)

(2019) Siddharth Kulkarni et al.   Molecular Ecology Resources

Identifying models of trait‐mediated community assembly using random forests and approximate Bayesian computation

(2019) Megan Ruffley et al.   Ecology and Evolution

Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

(2019) Krehenwinkel et al.   Genes

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

High resistance towards herbivore-induced habitat change in a high Arctic arthropod community

(2018) Niels M. Schmidt et al.   Biology Letters

A Sequel to Sanger: amplicon sequencing that scales

(2018) Paul D. N. Hebert et al.   BMC GENOMICS

Repeated Diversification of Ecomorphs in Hawaiian Stick Spiders

(2018) Rosemary G. Gillespie et al.   CURRENT BIOLOGY

Selectivity underlies the dissociation between seasonal prey availability and prey consumption in a generalist predator

(2018) Thomas D. Whitney et al.   MOLECULAR ECOLOGY

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

Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: Validating a reverse workflow for specimen processing

(2018) Wendy Y. Wang et al.   Molecular Ecology Resources

Comparing three types of dietary samples for prey DNA decay in an insect generalist predator

(2018) Stefaniya Kamenova et al.   Molecular Ecology Resources

Minimizing polymerase biases in metabarcoding

(2018) Ruth V. Nichols et al.   Molecular Ecology Resources

Insectivorous birds consume an estimated 400–500 million tons of prey annually

(2018) Martin Nyffeler et al.   NATURWISSENSCHAFTEN

Molecular gut content analysis of different spider body parts

(2018) Nuria Macías-Hernández et al.   PLoS One

Towards holomorphology in entomology: rapid and cost-effective adult-larva matching using NGS barcodes

(2018) Darren Yeo et al.   SYSTEMATIC ENTOMOLOGY

Scaling up DNA barcoding - Primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing

(2018) Henrik Krehenwinkel et al.   Methods in Ecology and Evolution

Estimating intraspecific genetic diversity from community DNA metabarcoding data

(2018) Vasco Elbrecht et al.   PeerJ

Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?

(2018) Melissa E. Carew et al.   PeerJ

Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building

(2018) Aaron Pomerantz et al.   GigaScience

Insectivorous birds consume an estimated 400–500 million tons of prey annually

(2018) Martin Nyffeler et al.   Science of Nature

DNA metabarcoding of spiders, insects, and springtails for exploring potential linkage between above- and below-ground food webs

(2018) Hirokazu Toju et al.   Zoological Letters

Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities

(2018) Guang K. Zhang et al.   Evolutionary Applications

Resolving the predator first paradox: Arthropod predator food webs in pioneer sites of glacier forelands

(2018) Daniela Sint et al.   MOLECULAR ECOLOGY

Seasonally varying marine influences on the coastal ecosystem detected through molecular gut analysis

(2018) Vasiliki Verschut et al.   MOLECULAR ECOLOGY

Assessing changes in arthropod predator-prey interactions through DNA-based gut content analysis - variable environment, stable diet

(2018) Bernhard Eitzinger et al.   MOLECULAR ECOLOGY

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

(2018) Ryan R. Wick et al.   PLoS Computational Biology

NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform.

(2018) Szymon T Calus et al.   GigaScience

MinION as part of a biomedical rapidly deployable laboratory

(2017) Mathias C. Walter et al.   JOURNAL OF BIOTECHNOLOGY

An estimated 400–800 million tons of prey are annually killed by the global spider community

(2017) Martin Nyffeler et al.   NATURWISSENSCHAFTEN

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

On site DNA barcoding by nanopore sequencing

(2017) Michele Menegon et al.   PLoS One

Evolution in a Community Context: On Integrating Ecological Interactions and Macroevolution

(2017) Marjorie G. Weber et al.   TRENDS IN ECOLOGY & EVOLUTION

Mitonuclear discordance as a confounding factor in the DNA taxonomy of monogonont rotifers

(2017) Ulrike Obertegger et al.   ZOOLOGICA SCRIPTA

Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

(2017) Henrik Krehenwinkel et al.   Scientific Reports

Capture efficiency and trophic adaptations of a specialist and generalist predator: A comparison

(2017) Ondřej Michálek et al.   Ecology and Evolution

Ancient DNA Resolves the History of Tetragnatha (Araneae, Tetragnathidae) Spiders on Rapa Nui

(2017) Darko Cotoras et al.   Genes

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation

(2017) Peter R. Sternes et al.   GigaScience

An estimated 400–800 million tons of prey are annually killed by the global spider community

(2017) Martin Nyffeler et al.   Science of Nature

Molecular phylogenetic analysis of “pirate spiders” (Araneae, Mimetidae) with the description of a new African genus and the first report of maternal care in the family

(2016) Ligia R. Benavides et al.   CLADISTICS

A quantitative protocol for DNA metabarcoding of springtails (Collembola)

(2016) Seikoh Saitoh et al.   GENOME

Plant-eating by spiders

(2016) Martin Nyffeler et al.   JOURNAL OF ARACHNOLOGY

A phylogeographical survey of a highly dispersive spider reveals eastern Asia as a major glacial refugium for Palaearctic fauna

(2016) Henrik Krehenwinkel et al.   JOURNAL OF BIOGEOGRAPHY

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

(2016) Alice Valentini et al.   MOLECULAR ECOLOGY

A combined field survey and molecular identification protocol for comparing forest arthropod biodiversity across spatial scales

(2016) Brent C. Emerson et al.   Molecular Ecology Resources

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

meteR: anrpackage for testing the maximum entropy theory of ecology

(2016) Andrew J. Rominger et al.   Methods in Ecology and Evolution

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

Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes

(2016) Peter A. Hambäck et al.   Ecology and Evolution

Mitochondrial metagenomics: letting the genes out of the bottle

(2016) Alex Crampton-Platt et al.   GigaScience

Towards a DNA Barcode Reference Database for Spiders and Harvestmen of Germany

(2016) Jonas J. Astrin et al.   PLoS One

$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples

(2015) Rudolf Meier et al.   CLADISTICS

Phylogenies support out-of-equilibrium models of biodiversity

(2015) Marc Manceau et al.   ECOLOGY LETTERS

Sparing spiders: faeces as a non-invasive source of DNA

(2015) Daniela Sint et al.   Frontiers in Zoology

Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research

(2015) Anna Papadopoulou et al.   MOLECULAR ECOLOGY

Untangling taxonomy: a DNA barcode reference library for Canadian spiders

(2015) Gergin A. Blagoev et al.   Molecular Ecology Resources

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

Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae)

(2015) Dean H. Leavitt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Library preparation methodology can influence genomic and functional predictions in human microbiome research

(2015) Marcus B. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of a monophagous true predator, a specialist termite-eating spider (Araneae: Ammoxenidae)

(2015) Lenka Petráková et al.   Scientific Reports

An Analysis of Factors Affecting Genotyping Success from Museum Specimens Reveals an Increase of Genetic and Morphological Variation during a Historical Range Expansion of a European Spider

(2015) Henrik Krehenwinkel 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

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

(2015) Shadi Shokralla et al.   Scientific Reports

Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing

(2014) Vinzenz Lange et al.   BMC GENOMICS

Phylogenetic approaches for studying diversification

(2014) Hélène Morlon   ECOLOGY LETTERS

Intraguild predation in pioneer predator communities of alpine glacier forelands

(2014) Lorna Raso et al.   MOLECULAR ECOLOGY

Drawing ecological inferences from coincident patterns of population- and community-level biodiversity

(2014) Mark Vellend et al.   MOLECULAR ECOLOGY

Predator-prey trophic relationships in response to organic management practices

(2014) Jason M. Schmidt et al.   MOLECULAR ECOLOGY

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

DNA barcoding gap: reliable species identification over morphological and geographical scales

(2014) Klemen Čandek et al.   Molecular Ecology Resources

‘Direct PCR’ optimization yields a rapid, cost-effective, nondestructive and efficient method for obtaining DNA barcodes without DNA extraction

(2014) Wing Hing Wong et al.   Molecular Ecology Resources

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

(2014) J. Gibson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity

(2014) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

Maximum information entropy: a foundation for ecological theory

(2014) John Harte et al.   TRENDS IN ECOLOGY & EVOLUTION

Environmental DNA for wildlife biology and biodiversity monitoring

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

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

(2014) Douglas W Fadrosh et al.   Microbiome

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

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

Northern range expansion of European populations of the wasp spiderArgiope bruennichiis associated with global warming-correlated genetic admixture and population-specific temperature adaptations

(2013) Henrik Krehenwinkel et al.   MOLECULAR ECOLOGY

A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes

(2013) J. Piñol et al.   Molecular Ecology Resources

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Multilocus Species Delimitation in a Complex of Morphologically Conserved Trapdoor Spiders (Mygalomorphae, Antrodiaetidae, Aliatypus)

(2013) Jordan D. Satler et al.   SYSTEMATIC BIOLOGY

Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol

(2013) Jeremy Miller et al.   ZooKeys

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

(2013) Xin Zhou et al.   GigaScience

Phylogenetic placement of pelican spiders (Archaeidae, Araneae), with insight into evolution of the “neck” and predatory behaviours of the superfamily Palpimanoidea

(2012) Hannah Marie Wood et al.   CLADISTICS

Multi-locus species delimitation in closely related animals and fungi: one marker is not enough

(2012) JULIAN R. DUPUIS et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Removing external DNA contamination from arthropod predators destined for molecular gut-content analysis

(2012) MATTHEW H. GREENSTONE et al.   Molecular Ecology Resources

DNA Extraction from Museum Specimens of Parasitic Hymenoptera

(2012) Jeremy C. Andersen et al.   PLoS One

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

Coalescent-based species delimitation in an integrative taxonomy

(2012) Matthew K. Fujita et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

Analyzing Tropical Forest Tree Species Abundance Distributions Using a Nonneutral Model and through Approximate Bayesian Inference

(2011) Franck Jabot et al.   AMERICAN NATURALIST

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

(2011) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

Global Patterns of Guild Composition and Functional Diversity of Spiders

(2011) Pedro Cardoso et al.   PLoS One

Coupling non-destructive DNA extraction and voucher retrieval for small soft-bodied Arthropods in a high-throughput context: the example of Collembola

(2010) DAVID PORCO et al.   Molecular Ecology Resources

Multiplex reactions for the molecular detection of predation on pest and nonpest invertebrates in agroecosystems

(2010) R. ANDREW KING et al.   Molecular Ecology Resources

Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces

(2010) MATT R. K. ZEALE et al.   Molecular Ecology Resources

Natural enemy responses and pest control: Importance of local vegetation

(2009) Linda J. Thomson et al.   BIOLOGICAL CONTROL

Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes)

(2009) DARREN E. IRWIN et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Herbivory in a spider through exploitation of an ant–plant mutualism

(2009) Christopher J. Meehan et al.   CURRENT BIOLOGY

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

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

Prospects for using DNA barcoding to identify spiders in species-rich genera

(2009) Gergin Blagoev et al.   ZooKeys

Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation

(2008) GARY M. BARKER   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogenetic analysis of community assembly and structure over space and time

(2008) Brent C. Emerson et al.   TRENDS IN ECOLOGY & EVOLUTION