Exploring species boundaries with multiple genetic loci using empirical data from non-biting midges

Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses

(2017) Ziheng Yang et al.   MOLECULAR ECOLOGY

DNA Barcoding of an Assembly of Montane Andean Butterflies (Satyrinae): Geographical Scale and Identification Performance

(2017) M A Marín et al.   NEOTROPICAL ENTOMOLOGY

The importance of naming cryptic species and the conservation of endemic subterranean amphipods

(2017) Teo Delić et al.   Scientific Reports

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Algorithmic single-locus species delimitation: effects of sampling effort, variation and nonmonophyly in four methods and 1870 species of beetles

(2016) Mikko Pentinsaari et al.   Molecular Ecology Resources

Bayesian inference of species diffusion in the West African Agama agama species group (Reptilia, Agamidae)

(2016) Adam D. Leaché et al.   SYSTEMATICS AND BIODIVERSITY

Species delimitation in northern European water scavenger beetles of the genus Hydrobius (Coleoptera, Hydrophilidae)

(2016) Erlend Fossen et al.   ZooKeys

Delineating taxonomic boundaries in the largest species complex of black flies (Simuliidae) in the Oriental Region

(2016) Van Lun Low et al.   Scientific Reports

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

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

(2015) Simon Dellicour et al.   SYSTEMATIC BIOLOGY

DNA barcodes for ecology, evolution, and conservation

(2015) W. John Kress et al.   TRENDS IN ECOLOGY & EVOLUTION

popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

Guidelines for DNA taxonomy, with a focus on the meiofauna

(2015) Diego Fontaneto et al.   Marine Biodiversity

Exploring Genetic Divergence in a Species-Rich Insect Genus Using 2790 DNA Barcodes

(2015) Xiaolong Lin et al.   PLoS One

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Cryptic species diversity: an overlooked factor in environmental management?

(2014) Alexander Feckler et al.   JOURNAL OF APPLIED ECOLOGY

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

(2014) Klemen Čandek et al.   Molecular Ecology Resources

Multilocus approach to clarify species status and the divergence history of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex

(2014) Chia-Hung Hsieh et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Testing DNA Barcode Performance in 1000 Species of European Lepidoptera: Large Geographic Distances Have Small Genetic Impacts

(2014) Peter Huemer et al.   PLoS One

The biodiversity of species and their rates of extinction, distribution, and protection

(2014) S. L. Pimm et al.   SCIENCE

One and the same: integrative taxonomic evidence thatBactrocera invadens(Diptera: Tephritidae) is the same species as the Oriental fruit flyBactrocera dorsalis

(2014) MARK K. SCHUTZE et al.   SYSTEMATIC ENTOMOLOGY

Species delimitation in theAleochara fucicolaspecies complex (Coleoptera: Staphylinidae: Aleocharinae) and its phylogenetic relationships

(2014) Jeong-Hun Song et al.   ZOOLOGICA SCRIPTA

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

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

Multi-gene phylogenetic analysis of south-east Asian pest members of theBactrocera dorsalisspecies complex (Diptera: Tephritidae) does not support current taxonomy

(2013) L. M. Boykin et al.   JOURNAL OF APPLIED ENTOMOLOGY

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

(2013) Sujeevan Ratnasingham et al.   PLoS One

Can We Name Earth's Species Before They Go Extinct?

(2013) M. J. Costello et al.   SCIENCE

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

Cryptic species in the cosmopolitanBugula neritinacomplex (Bryozoa, Cheilostomata)

(2013) Karin H. Fehlauer-Ale et al.   ZOOLOGICA SCRIPTA

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

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

Molecular and morphological methods reveal cryptic diversity and three new species of Nearctic Micropsectra (Diptera:Chironomidae)

(2013) Alyssa M. Anderson et al.   Freshwater Science

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

The Magnitude of Global Marine Species Diversity

(2012) Ward Appeltans et al.   CURRENT 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

Molecular-based rapid inventories of sympatric diversity: A comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians

(2012) Andrea Paz et al.   JOURNAL OF BIOSCIENCES

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Coalescent-based species delimitation in an integrative taxonomy

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

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

(2011) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

raxmlGUI: a graphical front-end for RAxML

(2011) Daniele Silvestro et al.   ORGANISMS DIVERSITY & EVOLUTION

Unexpected layers of cryptic diversity in wood white Leptidea butterflies

(2011) Vlad Dincă et al.   Nature Communications

SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

(2010) Gaurav Vaidya et al.   CLADISTICS

DNA markers to disentangle complexes of cryptic taxa in mealybugs (Hemiptera: Pseudococcidae)

(2010) T. Malausa et al.   JOURNAL OF APPLIED ENTOMOLOGY

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

Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus)

(2010) A. D. Leache et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Towards a comprehensive barcode library for arctic life - Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada

(2009) Xin Zhou et al.   Frontiers in Zoology

Reticulate evolution and incomplete lineage sorting among the ponderosa pines

(2009) Ann Willyard et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Morphology versus molecules: the phylogenetic relationships of Sepsidae (Diptera: Cyclorrhapha) based on morphology and DNA sequence data from ten genes

(2008) Kathy Feng-Yi Su et al.   CLADISTICS

Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence

(2008) Jerome C. Regier et al.   SYSTEMATIC BIOLOGY