Combining molecular datasets with strongly heterogeneous taxon coverage enlightens the peculiar biogeographic history of stoneflies (Insecta: Plecoptera)

Phylogenomics of the North American Plecoptera

(2020) Eric J. South et al.   SYSTEMATIC ENTOMOLOGY

Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects

(2019) Benjamin Wipfler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

(2019) Dominic A. Evangelista et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error

(2019) Alexandros Vasilikopoulos et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The contribution of temperature and continental fragmentation to amphibian diversification

(2019) Jonathan Rolland et al.   JOURNAL OF BIOGEOGRAPHY

The phylogeny and evolutionary timescale of stoneflies (Insecta: Plecoptera) inferred from mitochondrial genomes

(2019) Shuangmei Ding et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life

(2018) Rosa Fernández et al.   CURRENT BIOLOGY

Conceptual and statistical problems with the DEC+J model of founder-event speciation and its comparison with DEC via model selection

(2018) Richard H. Ree et al.   JOURNAL OF BIOGEOGRAPHY

The Pangean journey of ‘south forestflies’ (Insecta: Plecoptera) revealed by their first fossils

(2018) Yingying Cui et al.   JOURNAL OF SYSTEMATIC PALAEONTOLOGY

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

A time-calibrated phylogeny of southern hemisphere stoneflies: Testing for Gondwanan origins

(2016) Graham A. McCulloch et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction

(2016) Rosa Fernández et al.   SYSTEMATIC BIOLOGY

AMAS: a fast tool for alignment manipulation and computing of summary statistics

(2016) Marek L. Borowiec   PeerJ

Global warming and the end-Permian extinction event: Proxy and modeling perspectives

(2015) Ying Cui et al.   EARTH-SCIENCE REVIEWS

Comment on "Phylogenomics resolves the timing and pattern of insect evolution"

(2015) K. J. Tong et al.   SCIENCE

Ephemeroptera, Plecoptera, and Trichoptera on Isle Royale National Park, USA, compared to mainland species pool and size distribution

(2015) R. DeWalt et al.   ZooKeys

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

L.U.St: a tool for approximated maximum likelihood supertree reconstruction

(2014) Wasiu A Akanni et al.   BMC BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

(2014) Adam D. Leaché et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees

(2014) Daniel L. Rabosky   PLoS One

Tectonic-driven climate change and the diversification of angiosperms

(2014) Anne-Claire Chaboureau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

The Unsolved Challenge to Phylogenetic Correlation Tests for Categorical Characters

(2014) Wayne P. Maddison et al.   SYSTEMATIC BIOLOGY

Character state-based taxa erected to accommodate fossil and extant needle stoneflies (Leuctridae -Leuctrida tax.n.) and close relatives

(2014) OLIVIER BÉTHOUX et al.   SYSTEMATIC ENTOMOLOGY

BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

(2014) Daniel L. Rabosky et al.   Methods in Ecology and Evolution

Refugia and postglacial expansion of Acroneuria frisoni Stark & Brown (Plecoptera:Perlidae) in North America

(2014) Massimo Pessino et al.   Freshwater Science

Selecting informative subsets of sparse supermatrices increases the chance to find correct trees

(2013) Bernhard Misof et al.   BMC BIOINFORMATICS

Exploring power and parameter estimation of the BiSSE method for analyzing species diversification

(2013) Matthew P Davis et al.   BMC EVOLUTIONARY BIOLOGY

Two plates — Many subduction zones: The Variscan orogeny reconsidered

(2013) U. Kroner et al.   GONDWANA RESEARCH

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   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

BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions

(2013) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Bayesian Analysis of Biogeography when the Number of Areas is Large

(2013) Michael J. Landis et al.   SYSTEMATIC BIOLOGY

Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

(2013) Daniel L. Rabosky et al.   Nature Communications

Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data

(2012) Sabrina Simon et al.   Genome Biology and Evolution

Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

(2012) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

At last, a Pennsylvanian stem-stonefly (Plecoptera) discovered

(2011) Olivier Béthoux et al.   BMC EVOLUTIONARY BIOLOGY

Detecting the symplesiomorphy trap: a multigene phylogenetic analysis of terebelliform annelids

(2011) Min Zhong et al.   BMC EVOLUTIONARY BIOLOGY

Split-based computation of majority-rule supertrees

(2011) Anne Kupczok   BMC EVOLUTIONARY BIOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Do insects lose flight before they lose their wings? Population genetic structure in subalpine stoneflies

(2009) GRAHAM A. McCULLOCH et al.   MOLECULAR ECOLOGY

A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion

(2009) Bernhard Misof et al.   SYSTEMATIC BIOLOGY

Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis

(2008) Richard H. Ree et al.   SYSTEMATIC BIOLOGY

Ancient Rapid Radiations of Insects: Challenges for Phylogenetic Analysis

(2007) James B. Whitfield et al.   Annual Review of Entomology