Assessing the performance of DNA barcoding using posterior predictive simulations

The Effects of Partitioning on Phylogenetic Inference

(2015) David Kainer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa

(2015) S. Geisen et al.   MOLECULAR ECOLOGY

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

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

(2015) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mass extinction in poorly known taxa

(2015) Claire Régnier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deflating Trees: Improving Bayesian Branch-Length Estimates using Informed Priors

(2015) Bradley J. Nelson et al.   SYSTEMATIC BIOLOGY

Phenotypic plasticity raises questions for taxonomically important traits: a remarkable new Andean rainfrog (Pristimantis) with the ability to change skin texture

(2015) Juan M. Guayasamin et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

(2015) Jullien M. Flynn et al.   Ecology and Evolution

Natural History's Place in Science and Society

(2014) Joshua J. Tewksbury et al.   BIOSCIENCE

Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

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

Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?

(2014) Diana M. Percy et al.   MOLECULAR ECOLOGY

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

(2014) Klemen Čandek et al.   Molecular Ecology Resources

DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago

(2014) Takema Saitoh et al.   Molecular Ecology Resources

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

(2014) Mari Kekkonen et al.   Molecular Ecology Resources

Global Biodiversity Assessment and Hyper-Cryptic Species Complexes: More Than One Species of Elephant in the Room?

(2014) Mark Adams et al.   SYSTEMATIC BIOLOGY

Genetic Distance for a General Non-Stationary Markov Substitution Process

(2014) Benjamin D. Kaehler et al.   SYSTEMATIC BIOLOGY

Predictive Approaches to Assessing the Fit of Evolutionary Models

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

A Preliminary Framework for DNA Barcoding, Incorporating the Multispecies Coalescent

(2014) Mark Dowton et al.   SYSTEMATIC BIOLOGY

Mixture Models of Nucleotide Sequence Evolution that Account for Heterogeneity in the Substitution Process Across Sites and Across Lineages

(2014) Vivek Jayaswal et al.   SYSTEMATIC BIOLOGY

Doomed before they are described? The need for conservation assessments of cryptic species complexes using an amblyopsid cavefish (Amblyopsidae: Typhlichthys) as a case study

(2013) Matthew L. Niemiller et al.   BIODIVERSITY AND CONSERVATION

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Multilocus phylogeny of talpine moles (Talpini, Talpidae, Eulipotyphla) and its implications for systematics

(2013) Kai He et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2013) Sujeevan Ratnasingham et al.   PLoS One

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

(2013) C. Mora et al.   SCIENCE

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

Evolutionary Biology for the 21st Century

(2013) Jonathan B. Losos et al.   PLOS BIOLOGY

Efficient Selection of Branch-Specific Models of Sequence Evolution

(2012) Julien Y. Dutheil 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

The future of environmental DNA in ecology

(2012) NIGEL G. YOCCOZ   MOLECULAR ECOLOGY

Bioinformatic challenges for DNA metabarcoding of plants and animals

(2012) ERIC COISSAC et al.   MOLECULAR ECOLOGY

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

First Large-Scale DNA Barcoding Assessment of Reptiles in the Biodiversity Hotspot of Madagascar, Based on Newly Designed COI Primers

(2012) Zoltán T. Nagy et al.   PLoS One

Robustness of Compound Dirichlet Priors for Bayesian Inference of Branch Lengths

(2012) Chi Zhang 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

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

What we know and don’t know about Earth's missing biodiversity

(2012) Brett R. Scheffers 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

Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification

(2012) Rupert A. Collins et al.   Methods in Ecology and Evolution

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

(2011) Amrita Srivathsan et al.   CLADISTICS

Tail Paradox, Partial Identifiability, and Influential Priors in Bayesian Branch Length Inference

(2011) B. Rannala et al.   MOLECULAR BIOLOGY AND EVOLUTION

Who is eating what: diet assessment using next generation sequencing

(2011) FRANCOIS POMPANON et al.   MOLECULAR ECOLOGY

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

(2011) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

Pitfalls in comparisons of genetic distances: A case study of the avian family Acrocephalidae

(2011) Silke Fregin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Predicting Total Global Species Richness Using Rates of Species Description and Estimates of Taxonomic Effort

(2011) Mark J. Costello et al.   SYSTEMATIC BIOLOGY

How Many Species Are There on Earth and in the Ocean?

(2011) Camilo Mora et al.   PLOS BIOLOGY

Quantifying Uncertainty in Estimation of Tropical Arthropod Species Richness

(2010) Andrew J. Hamilton et al.   AMERICAN NATURALIST

A Global Assessment of Amphibian Taxonomic Effort and Expertise

(2010) Ana S. L. Rodrigues et al.   BIOSCIENCE

Choosing among Partition Models in Bayesian Phylogenetics

(2010) Y. Fan et al.   MOLECULAR BIOLOGY AND EVOLUTION

The roles of time and ecology in the continental radiation of the Old World leaf warblers (Phylloscopus and Seicercus)

(2010) T. D. Price   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Exploring the Use of Cytochrome Oxidase c Subunit 1 (COI) for DNA Barcoding of Free-Living Marine Nematodes

(2010) Sofie Derycke et al.   PLoS One

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

(2010) N. Rodrigue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

(2009) Yijun Sun et al.   NUCLEIC ACIDS RESEARCH

A DNA barcode for land plants

(2009) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

When Trees Grow Too Long: Investigating the Causes of Highly Inaccurate Bayesian Branch-Length Estimates

(2009) Jeremy M. Brown et al.   SYSTEMATIC BIOLOGY

Cryptic Failure of Partitioned Bayesian Phylogenetic Analyses: Lost in the Land of Long Trees

(2009) David C. Marshall   SYSTEMATIC BIOLOGY

PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy

(2008) J. M. Brown et al.   BIOINFORMATICS