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

Molecular taxonomic tools provide more accurate estimates of species richness at less cost than traditional morphology-based taxonomic practices in a vegetation survey

(2014) Ken A. Thompson et al.   BIODIVERSITY AND CONSERVATION

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

(2014) Laurence J. Clarke 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

A metagenetic approach for revealing community structure of marine planktonic copepods

(2014) J. Hirai et al.   Molecular Ecology Resources

Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)

(2014) Amrita Srivathsan et al.   Molecular Ecology Resources

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

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

Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications

(2014) John K. Jackson et al.   Freshwater Science

The tiny mayfly in the room: implications of size-dependent invertebrate taxonomic identification for biomonitoring data properties

(2013) Jessica M. Orlofske et al.   AQUATIC ECOLOGY

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. 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

Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

(2013) Melissa E Carew et al.   Frontiers in Zoology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modular tagging of amplicons using a single PCR for high-throughput sequencing

(2013) Laurence J. Clarke et al.   Molecular Ecology Resources

Redesign of PCR primers for mitochondrial cytochromecoxidase subunit I for marine invertebrates and application in all-taxa biotic surveys

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

Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets

(2013) Tomochika Fujisawa et al.   SYSTEMATIC BIOLOGY

A plea for digital reference collections and other science-based digitization initiatives in taxonomy: Sepsidnet as exemplar

(2013) YUCHEN ANG et al.   SYSTEMATIC ENTOMOLOGY

Using seemingly unnecessary illustrations to improve the diagnostic usefulness of descriptions in taxonomy–a case study on Perochaeta orientalis (Diptera, Sepsidae)

(2013) Rudolf Meier et al.   ZooKeys

SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons

(2013) Shanlin Liu et al.   Methods in Ecology and Evolution

Insights into biodiversity sampling strategies for freshwater microinvertebrate faunas through bioblitz campaigns and DNA barcoding

(2013) Brandon J Laforest et al.   BMC ECOLOGY

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

(2013) Xin Zhou et al.   GigaScience

A multi-marker DNA barcoding approach to save time and resources in vegetation surveys

(2012) FABRIZIO DE MATTIA et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

An update on DNA barcoding: low species coverage and numerous unidentified sequences

(2012) Shiyang Kwong et al.   CLADISTICS

An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding

(2012) H. R. TAYLOR et al.   Molecular Ecology Resources

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

DNA Barcoding for Community Ecology - How to Tackle a Hyperdiverse, Mostly Undescribed Melanesian Fauna

(2012) Rene Tänzler et al.   PLoS One

Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples

(2012) Maxime Galan et al.   PLoS One

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

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

Comparison of intraspecific genetic structure among related chironomids (Diptera) from New Zealand and Patagonia: disparity between potential and realized dispersal

(2012) Matt N. Krosch et al.   Freshwater Science

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

The seven impediments in invertebrate conservation and how to overcome them

(2011) Pedro Cardoso et al.   BIOLOGICAL CONSERVATION

On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature

(2011) Amrita Srivathsan et al.   CLADISTICS

Determining Species Boundaries in a World Full of Rarity: Singletons, Species Delimitation Methods

(2011) Gwynne S. Lim et al.   SYSTEMATIC BIOLOGY

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

(2010) M. J. T. N. Timmermans et al.   NUCLEIC ACIDS RESEARCH

Females do count: Documenting Chironomidae (Diptera) species diversity using DNA barcoding

(2010) Torbjørn Ekrem et al.   ORGANISMS DIVERSITY & EVOLUTION

Mitochondrial Cox1 Sequence Data Reliably Uncover Patterns of Insect Diversity But Suffer from High Lineage-Idiosyncratic Error Rates

(2010) Lars Hendrich et al.   PLoS One

Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation

(2009) Michael T. Monaghan et al.   SYSTEMATIC BIOLOGY

From ‘cryptic species’ to integrative taxonomy: an iterative process involving DNA sequences, morphology, and behaviour leads to the resurrection ofSepsis pyrrhosoma(Sepsidae: Diptera)

(2009) Denise S. H. Tan et al.   ZOOLOGICA SCRIPTA

Conflict, Convergent Evolution, and the Relative Importance of Immature and Adult Characters in Endopterygote Phylogenetics

(2008) Rudolf Meier et al.   Annual Review of Entomology

Phylogeography and genetic diversity of a widespread Old World butterfly, Lampides boeticus (Lepidoptera: Lycaenidae)

(2008) David J Lohman et al.   BMC EVOLUTIONARY BIOLOGY

Discrimination of Cricotopus species (Diptera: Chironomidae) by DNA barcoding

(2008) C.S. Sinclair et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

Monitoring arthropods in a tropical landscape: relative effects of sampling methods and habitat types on trap catches

(2008) Olivier Missa et al.   JOURNAL OF INSECT CONSERVATION

Data quality, performance, and uncertainty in taxonomic identification for biological assessments

(2008) James B. Stribling et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

The need for specifying species concepts: How many species of silvered langurs (Trachypithecus cristatus group) should be recognized?

(2008) Tan Siew Hoong Denise et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Use of Mean Instead of Smallest Interspecific Distances Exaggerates the Size of the “Barcoding Gap” and Leads to Misidentification

(2008) Rudolf Meier et al.   SYSTEMATIC BIOLOGY