Integrative Taxonomy Recognizes Evolutionary Units Despite Widespread Mitonuclear Discordance: Evidence from a Rotifer Cryptic Species Complex

Rapid adaptation of herbivore consumers to nutrient limitation: eco-evolutionary feedbacks to population demography and resource control

(2015) Steven A. J. Declerck et al.   ECOLOGY LETTERS

Coalescent Times and Patterns of Genetic Diversity in Species with Facultative Sex: Effects of Gene Conversion, Population Structure, and Heterogeneity

(2015) M. Hartfield et al.   GENETICS

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes

(2015) David J. Krause et al.   SYSTEMATIC BIOLOGY

Species Delimitation's Coming of Age: Figure 1.

(2015) Jean-François Flot   SYSTEMATIC BIOLOGY

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

(2015) Simon Dellicour et al.   SYSTEMATIC BIOLOGY

Guidelines for DNA taxonomy, with a focus on the meiofauna

(2015) Diego Fontaneto et al.   Marine Biodiversity

Molecular phylogenies as a tool to understand diversity in rotifers

(2014) Diego Fontaneto   INTERNATIONAL REVIEW OF HYDROBIOLOGY

Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation ofMesocarabus(Coleoptera: Carabidae)

(2014) C. Andújar et al.   MOLECULAR ECOLOGY

Take up the challenge! Opportunities for evolution research from resolving conflict in integrative taxonomy

(2014) Birgit C. Schlick-Steiner et al.   MOLECULAR ECOLOGY

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Exploring the Effect of Asymmetric Mitochondrial DNA Introgression on Estimating Niche Divergence in Morphologically Cryptic Species

(2014) Ben Wielstra et al.   PLoS One

Updating the description and taxonomic status of Brachionus sessilis Varga, 1951 (Rotifera: Brachionidae) based on detailed morphological analysis and molecular data

(2014) KONSTANTINOS PROIOS et al.   ZOOTAXA

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

Simulating gene trees under the multispecies coalescent and time-dependent migration

(2013) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution

(2013) Xuhua Xia   MOLECULAR BIOLOGY AND EVOLUTION

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

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

The role of hybridization in the origin and spread of asexuality inDaphnia

(2013) Sen Xu et al.   MOLECULAR ECOLOGY

How to fail at species delimitation

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

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

(2013) Jean-François Flot et al.   NATURE

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

Allochronic divergence and clonal succession: two microevolutionary processes sculpturing population structure of Brachionus rotifers

(2012) Spiros Papakostas et al.   HYDROBIOLOGIA

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

Speciation with gene flow and the genetics of habitat transitions

(2012) MELANIA E. CRISTESCU et al.   MOLECULAR ECOLOGY

The biogeography of mitochondrial and nuclear discordance in animals

(2012) DAVID P. L. TOEWS et al.   MOLECULAR ECOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

(2012) S. Will et al.   RNA

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Genome size evolution at the speciation level: The cryptic species complex Brachionus plicatilis(Rotifera)

(2011) Claus-Peter Stelzer et al.   BMC EVOLUTIONARY BIOLOGY

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

A framework for comparing processes of speciation in the presence of gene flow

(2011) CAROLE M. SMADJA et al.   MOLECULAR ECOLOGY

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

(2011) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

JML: testing hybridization from species trees

(2011) SIMON JOLY   Molecular Ecology Resources

Patterns and processes in the genetic differentiation of the Brachionus calyciflorus complex, a passively dispersing freshwater zooplankton

(2011) Xian-ling Xiang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Magic traits in speciation: ‘magic’ but not rare?

(2011) Maria R. Servedio et al.   TRENDS IN ECOLOGY & 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

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

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

The integrative future of taxonomy

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

Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species

(2010) M A F Noor et al.   HEREDITY

Validating the systematic position of Plationus Segers, Murugan & Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase

(2010) Miriam E. Reyna-Fabián et al.   HYDROBIOLOGIA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

Integrative Taxonomy: A Multisource Approach to Exploring Biodiversity

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

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

(2009) P. Librado et al.   BIOINFORMATICS

Bayesian Inference of Species Trees from Multilocus Data

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

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

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

Tinamous and Moa Flock Together: Mitochondrial Genome Sequence Analysis Reveals Independent Losses of Flight among Ratites

(2009) Matthew J. Phillips et al.   SYSTEMATIC BIOLOGY

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

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

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

(2009) David C. Marshall   SYSTEMATIC BIOLOGY

Gene flow and species delimitation

(2009) Rémy J. Petit et al.   TRENDS IN ECOLOGY & EVOLUTION

Generalized linear mixed models: a practical guide for ecology and evolution

(2009) Benjamin M. Bolker et al.   TRENDS IN ECOLOGY & EVOLUTION

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

(2009) Rob J. Kulathinal et al.   PLoS Genetics

TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

(2008) I. Milne et al.   BIOINFORMATICS

A Multiplex PCR Method for Rapid Identification of Brachionus Rotifers

(2008) Kalliopi Vasileiadou et al.   MARINE BIOTECHNOLOGY

Mitochondrial DNA under siege in avian phylogeography

(2008) ROBERT M. ZINK et al.   MOLECULAR ECOLOGY

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

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY

The role of hybridization in evolution

(2003) N. H. Barton   MOLECULAR ECOLOGY