Guidelines for DNA taxonomy, with a focus on the meiofauna

Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA

(2015) Kristy Deiner et al.   BIOLOGICAL CONSERVATION

Species are hypotheses: avoid connectivity assessments based on pillars of sand

(2015) Eric Pante et al.   MOLECULAR ECOLOGY

Cryptic diversity within the Anatololacerta species complex (Squamata: Lacertidae) in the Anatolian Peninsula: Evidence from a multi-locus approach

(2015) Adriana Bellati et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC

(2015) Simon Dellicour et al.   SYSTEMATIC BIOLOGY

DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent

(2014) Graham Jones et al.   BIOINFORMATICS

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives

(2014) Aibin Zhan et al.   CONSERVATION GENETICS

SEXUAL SPECIES ARE SEPARATED BY LARGER GENETIC GAPS THAN ASEXUAL SPECIES IN ROTIFERS

(2014) Cuong Q. Tang et al.   EVOLUTION

Cryptic diversity within the rotiferPolyarthra dolichopteraalong an altitudinal gradient

(2014) Ulrike Obertegger et al.   FRESHWATER BIOLOGY

Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida)

(2014) Astrid Cornils et al.   Frontiers in Zoology

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes

(2014) Vera G. Fonseca et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Molecular phylogenies as a tool to understand diversity in rotifers

(2014) Diego Fontaneto   INTERNATIONAL REVIEW OF HYDROBIOLOGY

REVIEW: The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology

(2014) Helen C. Rees et al.   JOURNAL OF APPLIED ECOLOGY

Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

(2014) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

DNA barcode-based delineation of putative species: efficient start for taxonomic workflows

(2014) Mari Kekkonen et al.   Molecular Ecology Resources

The incidence of species-level paraphyly in animals: A re-assessment

(2014) Howard A. Ross   MOLECULAR PHYLOGENETICS AND EVOLUTION

Hyper-Cryptic Marine Meiofauna: Species Complexes in Nemertodermatida

(2014) Inga Meyer-Wachsmuth et al.   PLoS One

The Necessity of DNA Taxonomy to Reveal Cryptic Diversity and Spatial Distribution of Meiofauna, with a Focus on Nemertea

(2014) Francesca Leasi et al.   PLoS One

Current noise-removal methods can create false signals in ecogenomic data

(2014) A. G. Rossberg et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A critique of Rossberg et al.: noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets

(2014) M. J. Morgan et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Preliminary Framework for DNA Barcoding, Incorporating the Multispecies Coalescent

(2014) Mark Dowton et al.   SYSTEMATIC BIOLOGY

Known Knowns, Known Unknowns, Unknown Unknowns and Unknown Knowns in DNA Barcoding: A Comment on Dowton et al.

(2014) Rupert A. Collins et al.   SYSTEMATIC BIOLOGY

Species Delimitation using Genome-Wide SNP Data

(2014) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Diversity of the rotiferBrachionus plicatilisspecies complex (Rotifera: Monogononta) in Iran through integrative taxonomy

(2014) Reza Malekzadeh-Viayeh et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

With eyes wide open: a revision of species within and closely related to thePocillopora damicornisspecies complex (Scleractinia; Pocilloporidae) using morphology and genetics

(2014) Sebastian Schmidt-Roach et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

(2014) Cuong Q. Tang et al.   Methods in Ecology and Evolution

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

Improved Reversible Jump Algorithms for Bayesian Species Delimitation

(2013) Bruce Rannala et al.   GENETICS

Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system

(2013) Mehdi Adjeroud et al.   MARINE BIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Niphargus-Thiothrixassociations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania

(2013) Jean-François Flot et al.   MOLECULAR ECOLOGY

How to fail at species delimitation

(2013) Bryan C. Carstens et al.   MOLECULAR ECOLOGY

Species Detection and Identification in Sexual Organisms Using Population Genetic Theory and DNA Sequences

(2013) C. William Birky   PLoS One

A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

(2013) Sujeevan Ratnasingham et al.   PLoS One

Are there species smaller than 1 mm?

(2013) A. G. Rossberg et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Species Delimitation Using Bayes Factors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae)

(2013) Jared A. Grummer et al.   SYSTEMATIC BIOLOGY

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

Otostephanos(Rotifera, Bdelloidea, Habrotrochidae) with the description of two new species

(2013) Nataliia S. Iakovenko et al.   SYSTEMATICS AND BIODIVERSITY

Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification

(2013) Gontran Sonet et al.   ZooKeys

Cryptic diversity with wide salinity tolerance in the putative euryhalineTestudinella clypeata(Rotifera, Monogononta)

(2013) Francesca Leasi et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Integrative delineation of species of Mediterranean freshwater planarians (Platyhelminthes: Tricladida: Dugesiidae)

(2013) Ronald Sluys et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen

(2013) Benedikt R. Schmidt et al.   Methods in Ecology and Evolution

Factors affecting species delimitations with the GMYC model: insights from a butterfly survey

(2013) Gerard Talavera et al.   Methods in Ecology and Evolution

Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs

(2012) Katharina M Jörger et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model

(2012) Noah M Reid et al.   BMC EVOLUTIONARY BIOLOGY

SPECIES DELIMITATION WITH ABC AND OTHER COALESCENT-BASED METHODS: A TEST OF ACCURACY WITH SIMULATIONS AND AN EMPIRICAL EXAMPLE WITH LIZARDS OF THE LIOLAEMUS DARWINII COMPLEX (SQUAMATA: LIOLAEMIDAE)

(2012) Arley Camargo et al.   EVOLUTION

Using DNA taxonomy to investigate the ecological determinants of plankton diversity: explaining the occurrence of Synchaeta spp. (Rotifera, Monogononta) in mountain lakes

(2012) ULRIKE OBERTEGGER et al.   FRESHWATER BIOLOGY

The ITS region of groundwater amphipods: length, secondary structure and phylogenetic information content in Crangonyctoids and Niphargids

(2012) Etienne Kornobis et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Comparison of commercial kits for the extraction of DNA from paddy soils

(2012) S. Knauth et al.   LETTERS IN APPLIED MICROBIOLOGY

Spatially structured populations with a low level of cryptic diversity in European marine Gastrotricha

(2012) ALEXANDER KIENEKE et al.   MOLECULAR ECOLOGY

Large-scale species delimitation method for hyperdiverse groups

(2012) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Overlooked cryptic endemism in copepods: Systematics and natural history of the calanoid subgenus Occidodiaptomus Borutzky 1991 (Copepoda, Calanoida, Diaptomidae)

(2012) Federico Marrone et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Patterns of Diversity in Soft-Bodied Meiofauna: Dispersal Ability and Body Size Matter

(2012) Marco Curini-Galletti et al.   PLoS One

Cryptic Species in Putative Ancient Asexual Darwinulids (Crustacea, Ostracoda)

(2012) Isa Schön et al.   PLoS One

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

(2012) C. Q. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-locus species delimitation: a test of the mixed Yule-coalescent model, with an empirical application to Philippine round-leaf bats

(2012) J. A. Esselstyn et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Effect of Geographical Scale of Sampling on DNA Barcoding

(2012) J. Bergsten et al.   SYSTEMATIC BIOLOGY

Coalescent-based species delimitation in an integrative taxonomy

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

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

SPECIATION AND DISPERSAL ALONG CONTINENTAL COASTLINES AND ISLAND ARCS IN THE INDO-WEST PACIFIC TURBINID GASTROPOD GENUSLUNELLA

(2011) Suzanne Williams et al.   EVOLUTION

Structurama: Bayesian Inference of Population Structure

(2011) John P. Huelsenbeck et al.   Evolutionary Bioinformatics

A phylogenetic approach to species delimitation in freshwater Gastrotricha from Sweden

(2011) Tobias Kånneby et al.   HYDROBIOLOGIA

Application of an inexpensive and high-throughput genomic DNA extraction method for the molecular ecology of zooplanktonic diapausing eggs

(2011) Javier Montero-Pau et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Phylogeography of the marine interstitial nemertean Ototyphlonemertes parmula (Nemertea, Hoplonemertea) reveals cryptic diversity and high dispersal potential

(2011) Alexander Y. Tulchinsky et al.   MARINE BIOLOGY

Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

(2011) HOLLY M. BIK et al.   MOLECULAR ECOLOGY

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

(2011) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

jMOTU and Taxonerator: Turning DNA Barcode Sequences into Annotated Operational Taxonomic Units

(2011) Martin Jones et al.   PLoS One

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

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

Integrating DNA and morphological taxonomy to describe diversity in poorly studied microscopic animals: new species of the genus Abrochtha Bryce, 1910 (Rotifera: Bdelloidea: Philodinavidae)

(2011) C. WILLIAM BIRKY JR et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Accounting for uncertainty in species delineation during the analysis of environmental DNA sequence data

(2011) Jeff R. Powell   Methods in Ecology and Evolution

Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization?

(2011) Jean-François Flot et al.   BMC ECOLOGY

High-throughput DNA sequencing - concepts and limitations

(2010) Martin Kircher et al.   BIOESSAYS

Haplowebs as a graphical tool for delimiting species: a revival of Doyle's "field for recombination" approach and its application to the coral genus Pocillopora in Clipperton

(2010) Jean-François Flot et al.   BMC EVOLUTIONARY BIOLOGY

DNA barcoding: a six-question tour to improve users' awareness about the method

(2010) M. Casiraghi et al.   BRIEFINGS IN BIOINFORMATICS

The integrative future of taxonomy

(2010) Jose M. Padial et al.   Frontiers in Zoology

Molecular evidence for the presence of cryptic evolutionary lineages in the freshwater copepod genus Hemidiaptomus G.O. Sars, 1903 (Calanoida, Diaptomidae)

(2010) Federico Marrone et al.   HYDROBIOLOGIA

Cryptic diversity in the genus Adineta Hudson & Gosse, 1886 (Rotifera: Bdelloidea: Adinetidae): a DNA taxonomy approach

(2010) Diego Fontaneto et al.   HYDROBIOLOGIA

Molecular taxonomy confirms morphological classification of deep-sea hydrothermal vent copepods (Dirivultidae) and suggests broad physiological tolerance of species and frequent dispersal along ridges

(2010) Sabine Gollner et al.   MARINE BIOLOGY

Preventing the pollution of mitochondrial datasets with nuclear mitochondrial paralogs (numts)

(2010) Sébastien Calvignac et al.   MITOCHONDRION

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

SpedeSTEM: a rapid and accurate method for species delimitation

(2010) DANIEL D. ENCE et al.   Molecular Ecology Resources

Circumantarctic distribution in Southern Ocean benthos? A genetic test using the genus Macroscapha (Crustacea, Ostracoda) as a model

(2010) Simone N. Brandão et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

New insights into diversity and evolution of deep-sea Mytilidae (Mollusca: Bivalvia)

(2010) Julien Lorion et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Using Population Genetic Theory and DNA Sequences for Species Detection and Identification in Asexual Organisms

(2010) C. William Birky et al.   PLoS One

Bayesian species delimitation using multilocus sequence data

(2010) Z. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species Delimitation Using Dominant and Codominant Multilocus Markers

(2010) Bernhard Hausdorf et al.   SYSTEMATIC BIOLOGY

Second-generation environmental sequencing unmasks marine metazoan biodiversity

(2010) Vera G. Fonseca et al.   Nature Communications

Integrative Taxonomy: A Multisource Approach to Exploring Biodiversity

(2009) Birgit C. Schlick-Steiner et al.   Annual Review of Entomology

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

EVALUATION OF ELEVATED PLOIDY AND ASEXUAL REPRODUCTION AS ALTERNATIVE EXPLANATIONS FOR GEOGRAPHIC PARTHENOGENESIS IN EUCYPRIS VIRENS OSTRACODS

(2009) Sofia Adolfsson et al.   EVOLUTION

DNA Barcoding of Commercially Important Salmon and Trout Species (Oncorhynchus and Salmo) from North America

(2009) Rosalee S. Rasmussen et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

seqphase: a web tool for interconverting phase input/output files and fasta sequence alignments

(2009) J-F. FLOT   Molecular Ecology Resources

Extreme levels of hidden diversity in microscopic animals (Rotifera) revealed by DNA taxonomy

(2009) Diego Fontaneto et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Exceptional cryptic diversity and multiple origins of parthenogenesis in a freshwater ostracod

(2009) S.N.S. Bode et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Microdroplet-based PCR enrichment for large-scale targeted sequencing

(2009) Ryan Tewhey et al.   NATURE BIOTECHNOLOGY

Can mtDNA Barcodes Be Used to Delimit Species? A Response to Pons et al. (2006)

(2009) Konrad Lohse   SYSTEMATIC BIOLOGY

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

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

New Heuristic Methods for Joint Species Delimitation and Species Tree Inference

(2009) Brian C. O'Meara   SYSTEMATIC BIOLOGY

Morphological plasticity in scleractinian corals

(2008) Peter A. Todd   BIOLOGICAL REVIEWS

Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology

(2008) Jean-François Flot et al.   COMPTES RENDUS BIOLOGIES

ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA

(2008) Liang Liu et al.   EVOLUTION

Slow Mitochondrial COI Sequence Evolution at the Base of the Metazoan Tree and Its Implications for DNA Barcoding

(2008) Danwei Huang et al.   JOURNAL OF MOLECULAR EVOLUTION

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS

Parallel tagged sequencing on the 454 platform

(2008) Matthias Meyer et al.   Nature Protocols

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters

(2008) A. Papadopoulou et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified

(2008) H. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA BARCODING: Barcoding corals: limited by interspecific divergence, not intraspecific variation

(2007) T. L. SHEARER et al.   Molecular Ecology Resources