The evolution of insect biodiversity

Systematic errors in phylogenetic trees

(2021) Paschalia Kapli et al.   CURRENT BIOLOGY

Systematic errors in orthology inference and their effects on evolutionary analyses

(2021) Paschalis Natsidis et al.   iScience

Phylogenomic subsampling and the search for phylogenetically reliable loci

(2021) Nicolás Mongiardino Koch   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding

(2021) Anthony K. Redmond et al.   Nature Communications

Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing

(2021) Scott Hotaling et al.   Genome Biology and Evolution

Phylogenomics

(2021) David A. Duchêne   CURRENT BIOLOGY

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Impact of Cross-Species Gene Flow on Species Tree Estimation

(2020) Xiyun Jiao et al.   SYSTEMATIC BIOLOGY

Morphological phylogenetics evaluated using novel evolutionary simulations

(2020) Joseph N Keating et al.   SYSTEMATIC BIOLOGY

Data curation and modeling of compositional heterogeneity in insect phylogenomics: A case study of the phylogeny of Dytiscoidea (Coleoptera: Adephaga)

(2020) Chenyang Cai et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha

(2020) Paschalia Kapli et al.   Science Advances

A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans

(2019) Ferdinand Marlétaz et al.   CURRENT BIOLOGY

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

Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics.

(2019) Karen Siu-Ting et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content

(2019) Walker Pett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data

(2019) Yuyu Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Palaeodictyopterida

(2019) Jakub Prokop et al.   CURRENT BIOLOGY

The Relative Importance of Modeling Site Pattern Heterogeneity Versus Partition-Wise Heterotachy in Phylogenomic Inference

(2019) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

The Phylogeny and Evolutionary History of Arthropods

(2019) Gonzalo Giribet et al.   CURRENT BIOLOGY

Pancrustacean evolution illuminated by taxon-rich genomic-scale data sets with an expanded remipede sampling

(2019) Jesus Lozano-Fernandez et al.   Genome Biology and Evolution

Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida

(2019) Jesus Lozano-Fernandez et al.   Nature Communications

The Prevalence and Impact of Model Violations in Phylogenetic Analysis

(2019) Suha Naser-Khdour et al.   Genome Biology and Evolution

Distinct genotypes and phenotypes in European and American strains of Drosophila suzukii: implications for biology and management of an invasive organism

(2019) Omar Rota-Stabelli et al.   JOURNAL OF PEST SCIENCE

The evolution and genomic basis of beetle diversity

(2019) Duane D. McKenna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

(2019) Tomáš Flouri et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Cretaceous peak in family-level insect diversity estimated with mark–recapture methodology

(2019) Sandra R. Schachat et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The phylogeny of insects in the data‐driven era

(2019) Douglas Chesters   SYSTEMATIC ENTOMOLOGY

Putting the genome in insect phylogenomics

(2019) Kevin P Johnson   Current Opinion in Insect Science

Phylogenomics provides robust support for a two-domains tree of life

(2019) Tom A. Williams et al.   Nature Ecology & Evolution

Reanalyzing the Palaeoptera problem – The origin of insect flight remains obscure

(2018) Sabrina Simon et al.   ARTHROPOD STRUCTURE & DEVELOPMENT

Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics

(2018) Thomas Bourguignon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Compositional heterogeneity in true bug mitochondrial phylogenomics

(2018) Yingqi Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The timescale of early land plant evolution

(2018) Jennifer L. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of metazoan morphological disparity

(2018) Bradley Deline et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The phylogeny of Coleopterida (Hexapoda) - morphological characters and molecular phylogenies

(2018) Rolf G. Beutel et al.   SYSTEMATIC ENTOMOLOGY

A general theory of genital homologies for the Hexapoda (Pancrustacea) derived from skeletomuscular correspondences, with emphasis on the Endopterygota

(2018) Brendon E. Boudinot   ARTHROPOD STRUCTURE & DEVELOPMENT

Phylogenomics and the evolution of hemipteroid insects

(2018) Kevin P. Johnson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mitochondrial phylogenomics of the Hymenoptera

(2018) Pu Tang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models

(2016) Fan Song et al.   Genome Biology and Evolution

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

(2016) James E. Tarver et al.   Genome Biology and Evolution

Progress, pitfalls and parallel universes: a history of insect phylogenetics

(2016) Karl M. Kjer et al.   Journal of the Royal Society Interface

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases

(2016) Daria Esyunina et al.   NUCLEIC ACIDS RESEARCH

A molecular palaeobiological exploration of arthropod terrestrialization

(2016) Jesus Lozano-Fernandez et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

(2016) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

Power, resolution and bias: recent advances in insect phylogeny driven by the genomic revolution

(2016) David K Yeates et al.   Current Opinion in Insect Science

A review of methods for analysing insect structures — the role of morphology in the age of phylogenomics

(2016) Benjamin Wipfler et al.   Current Opinion in Insect Science

Embryonic development of a collembolan, Tomocerus cuspidatus Börner, 1909: With special reference to the development and developmental potential of serosa (Hexapoda: Collembola, Tomoceridae)

(2015) Shigekazu Tomizuka et al.   ARTHROPOD STRUCTURE & DEVELOPMENT

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera)

(2015) Maria Heikkilä et al.   BMC EVOLUTIONARY BIOLOGY

Insect evolution

(2015) Michael S. Engel   CURRENT BIOLOGY

Total-Evidence Dating under the Fossilized Birth–Death Process

(2015) Chi Zhang et al.   SYSTEMATIC BIOLOGY

Coalescent methods for estimating species trees from phylogenomic data

(2015) Liang Liu et al.   Journal of Systematics and Evolution

Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences

(2015) Hu Li et al.   Scientific Reports

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

(2014) Prashant P. Sharma et al.   MOLECULAR BIOLOGY AND EVOLUTION

The hybrid nature of the Eukaryota and a consilient view of life on Earth

(2014) James O. McInerney et al.   NATURE REVIEWS MICROBIOLOGY

Strepsiptera, Phylogenomics and the Long Branch Attraction Problem

(2014) Bastien Boussau et al.   PLoS One

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

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

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

A History of Entomological Classification

(2013) Michael S. Engel et al.   Annual Review of Entomology

Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny

(2013) Stephen L. Cameron   Annual Review of Entomology

ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

(2013) Scott C. Clark et al.   BIOINFORMATICS

Agalma: an automated phylogenomics workflow

(2013) Casey W Dunn et al.   BMC BIOINFORMATICS

Molecular phylogenetic analyses support the monophyly of Hexapoda and suggest the paraphyly of Entognatha

(2013) Go Sasaki et al.   BMC EVOLUTIONARY BIOLOGY

Molecular Timetrees Reveal a Cambrian Colonization of Land and a New Scenario for Ecdysozoan Evolution

(2013) Omar Rota-Stabelli et al.   CURRENT BIOLOGY

Changes in base composition bias of nuclear and mitochondrial genes in lice (Insecta: Psocodea)

(2013) Kazunori Yoshizawa et al.   GENETICA

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

Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

(2013) Claire C. Morgan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

(2013) Emiliano Dell’Ampio et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

(2013) M. Groussin et al.   SYSTEMATIC BIOLOGY

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

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Insect phylogenomics: new insights on the relationships of lower neopteran orders (Polyneoptera)

(2013) HARALD LETSCH et al.   SYSTEMATIC ENTOMOLOGY

Arthropod fossil data increase congruence of morphological and molecular phylogenies

(2013) David A. Legg et al.   Nature Communications

Revival of Palaeoptera-head characters support a monophyletic origin of Odonata and Ephemeroptera (Insecta)

(2012) Alexander Blanke et al.   CLADISTICS

Genomic and Morphological Evidence Converge to Resolve the Enigma of Strepsiptera

(2012) Oliver Niehuis et al.   CURRENT BIOLOGY

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

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

Diverse transitional giant fleas from the Mesozoic era of China

(2012) Diying Huang et al.   NATURE

Metazoan opsin evolution reveals a simple route to animal vision

(2012) R. Feuda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study

(2012) Omar Rota-Stabelli et al.   SYSTEMATIC BIOLOGY

A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

(2012) Fredrik Ronquist 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

Relaxed Phylogenetics and the Palaeoptera Problem: Resolving Deep Ancestral Splits in the Insect Phylogeny

(2012) Jessica A. Thomas et al.   SYSTEMATIC BIOLOGY

Phylogeny of the Coleoptera Based on Morphological Characters of Adults and Larvae

(2011) John F. Lawrence et al.   ANNALES ZOOLOGICI

Advances in Insect Phylogeny at the Dawn of the Postgenomic Era

(2011) Michelle D. Trautwein et al.   Annual Review of Entomology

Reevaluating the Arthropod Tree of Life

(2011) Gonzalo Giribet et al.   Annual Review of Entomology

Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates

(2011) P. J. Wagner   Biology Letters

What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny

(2011) Gerard Talavera et al.   BMC EVOLUTIONARY BIOLOGY

Pancrustacean Phylogeny in the Light of New Phylogenomic Data: Support for Remipedia as the Possible Sister Group of Hexapoda

(2011) B. M. von Reumont et al.   MOLECULAR BIOLOGY AND EVOLUTION

MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda

(2011) L. I. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Morphological and molecular evidence converge upon a robust phylogeny of the megadiverse Holometabola

(2010) Rolf G. Beutel et al.   CLADISTICS

Deep Genomic-Scale Analyses of the Metazoa Reject Coelomata: Evidence from Single- and Multigene Families Analyzed Under a Supertree and Supermatrix Paradigm

(2010) Thérèse A. Holton et al.   Genome Biology and Evolution

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic relationships among insect orders based on three nuclear protein-coding gene sequences

(2010) Keisuke Ishiwata et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

(2010) Jerome C. Regier et al.   NATURE

A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata

(2010) O. Rota-Stabelli et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogeny and classification of the Psocodea, with particular reference to the lice (Psocodea: Phthiraptera)

(2010) C. H. C. Lyal   SYSTEMATIC ENTOMOLOGY

Palaeomorphology: fossils and the inference of cladistic relationships

(2009) Gregory D. Edgecombe   ACTA ZOOLOGICA

Bayesian Phylogenetics and Its Influence on Insect Systematics

(2009) Fredrik Ronquist et al.   Annual Review of Entomology

Characterizing phylogenetically decisive taxon coverage

(2009) Mike Steel et al.   APPLIED MATHEMATICS LETTERS

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

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

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Phylogenetic Signal, Evolutionary Process, and Rate

(2008) Liam J. Revell et al.   SYSTEMATIC BIOLOGY