Mitochondrial phylogenomics, the origin of swallowtail butterflies, and the impact of the number of clocks in Bayesian molecular dating

The latitudinal diversity gradient in New World swallowtail butterflies is caused by contrasting patterns of out-of- and into-the-tropics dispersal

(2017) Hannah L. Owens et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics

(2017) Jesse W. Breinholt et al.   SYSTEMATIC BIOLOGY

An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times

(2017) Konstantinos Angelis et al.   SYSTEMATIC BIOLOGY

Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)

(2017) RIENK DE JONG   ZOOTAXA

Reconstructing a 55-million-year-old butterfly (Lepidoptera: Hesperiidae)

(2016) Rienk DE JONG   EUROPEAN JOURNAL OF ENTOMOLOGY

Hybrid dynamics in a species group of swallowtail butterflies

(2016) J. R. Dupuis et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves

(2016) Alexander Suh   ZOOLOGICA SCRIPTA

Reconstructing a 55-million-year-old butterfly (Lepidoptera: Hesperiidae)

(2016) Rienk DE JONG   EUROPEAN JOURNAL OF ENTOMOLOGY

To what extent do new fossil discoveries change our understanding of clade evolution? A cautionary tale from burying beetles (Coleoptera:Nicrophorus)

(2015) Emmanuel F. A. Toussaint et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Rapid assembly of taxonomically validated mitochondrial genomes from historical insect collections

(2015) Martijn J. T. N. Timmermans et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

The fossil record and taphonomy of butterflies and moths (Insecta, Lepidoptera): implications for evolutionary diversity and divergence-time estimates

(2015) Jae-Cheon Sohn et al.   BMC EVOLUTIONARY BIOLOGY

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway

(2015) Mark A. Miller et al.   Evolutionary Bioinformatics

The Effects of Partitioning on Phylogenetic Inference

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

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity

(2015) Susana Magallón et al.   NEW PHYTOLOGIST

Deciphering the evolution of birdwing butterflies 150 years after Alfred Russel Wallace

(2015) Fabien L. Condamine et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

The Evolutionary History of Termites as Inferred from 66 Mitochondrial Genomes

(2014) Thomas Bourguignon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Towards a mitogenomic phylogeny of Lepidoptera

(2014) Martijn J.T.N. Timmermans et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

doublesex is a mimicry supergene

(2014) K. Kunte et al.   NATURE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research

(2014) STEPHEN L. CAMERON   SYSTEMATIC ENTOMOLOGY

Molecular phylogeny of Parnassiinae butterflies (Lepidoptera: Papilionidae) based on the sequences of four mitochondrial DNA segments

(2013) François Michel et al.   ANNALES DE LA SOCIETE ENTOMOLOGIQUE DE FRANCE

The Fossil Record of Plant-Insect Dynamics

(2013) Conrad C. Labandeira et al.   Annual Review of Earth and Planetary Sciences

Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny

(2013) Stephen L. Cameron   Annual Review of Entomology

Phylotranscriptomics: Saturated Third Codon Positions Radically Influence the Estimation of Trees Based on Next-Gen Data

(2013) Jesse W. Breinholt et al.   Genome Biology and Evolution

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

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

Mitogenome sequences stabilize the phylogenetics of weevils (Curculionoidea) and establish the monophyly of larval ectophagy

(2013) Julien Haran et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A comparative analysis of complete mitochondrial genomes among Hexapoda

(2013) Sabrina Simon et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

Timing and Patterns in the Taxonomic Diversification of Lepidoptera (Butterflies and Moths)

(2013) Niklas Wahlberg et al.   PLoS One

Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study

(2013) Adam L. Bazinet et al.   PLoS One

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

What causes latitudinal gradients in species diversity? Evolutionary processes and ecological constraints on swallowtail biodiversity

(2012) Fabien L. Condamine et al.   ECOLOGY LETTERS

Global biogeographical pattern of swallowtail diversification demonstrates alternative colonization routes in the Northern and Southern hemispheres

(2012) Fabien L. Condamine et al.   JOURNAL OF BIOGEOGRAPHY

Efficient Selection of Branch-Specific Models of Sequence Evolution

(2012) Julien Y. Dutheil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

High Levels of Gene Expression Explain the Strong Evolutionary Constraint of Mitochondrial Protein-Coding Genes

(2012) B. Nabholz et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast and Robust Characterization of Time-Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping

(2012) Jonathan Romiguier et al.   PLoS One

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Cretaceous origin and repeated tertiary diversification of the redefined butterflies

(2011) M. Heikkila et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

(2011) Daniel L. Ayres et al.   SYSTEMATIC BIOLOGY

Phylogenetics and divergence times of Papilioninae (Lepidoptera) with special reference to the enigmatic genera Teinopalpus and Meandrusa

(2010) Thomas J. Simonsen et al.   CLADISTICS

Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies

(2010) M. Mutanen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study

(2009) Jerome C Regier et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeny of snout butterflies (Lepidoptera: Nymphalidae: Libytheinae): combining evidence from the morphology of extant, fossil, and recently extinct taxa

(2009) Akito Y. Kawahara   CLADISTICS

THE DIVERSITY AND EVOLUTION OF BATESIAN MIMICRY INPAPILIOSWALLOWTAIL BUTTERFLIES

(2009) Krushnamegh Kunte   EVOLUTION

Revised classification of the family Hesperiidae (Lepidoptera: Hesperioidea) based on combined molecular and morphological data

(2009) ANDREW D. WARREN et al.   SYSTEMATIC ENTOMOLOGY

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

(2008) Julien Dutheil et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic relationships of subfamilies and circumscription of tribes in the family Hesperiidae (Lepidoptera: Hesperioidea)

(2008) Andrew D. Warren et al.   CLADISTICS

The conditioned reconstructed process

(2008) Tanja Gernhard   JOURNAL OF THEORETICAL BIOLOGY

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION