Phylogenomic analyses clarify the pattern of evolution of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming

The enduring value of reciprocal illumination in the era of insect phylogenomics: a response to Cai et al . (2020)

(2021) Grey T. Gustafson et al.   SYSTEMATIC ENTOMOLOGY

Adding leaves to the Lepidoptera tree: capturing hundreds of nuclear genes from old museum specimens

(2021) Christoph Mayer et al.   SYSTEMATIC ENTOMOLOGY

Rooting the Animal Tree of Life

(2021) Yuanning Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Phylogenetic tree building in the genomic age

(2020) Paschalia Kapli et al.   NATURE REVIEWS GENETICS

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

Resolving the phylogenetic position of Hygrobiidae (Coleoptera: Adephaga) requires objective statistical tests and exhaustive phylogenetic methodology: a response to Cai et al. (2020)

(2020) Alexandros Vasilikopoulos et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Validation of tiger beetles as distinct family (Coleoptera: Cicindelidae), review and reclassification of tribal relationships

(2020) Daniel P. Duran et al.   SYSTEMATIC ENTOMOLOGY

More is needed—Thousands of loci are required to elucidate the relationships of the ‘flowers of the sea’ (Sabellida, Annelida)

(2020) Ekin Tilic et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?

(2020) Daniel M Portik et al.   SYSTEMATIC BIOLOGY

A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data

(2020) Nicolás Mongiardino Koch et al.   SYSTEMATIC BIOLOGY

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

(2020) Jacob L. Steenwyk et al.   PLOS BIOLOGY

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

(2020) Paschalia Kapli et al.   Science Advances

A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error

(2019) Jesús A Ballesteros et al.   SYSTEMATIC BIOLOGY

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

Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

(2019) Alison Cloutier et al.   SYSTEMATIC BIOLOGY

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

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

Phylogenomics of the longitarsal Colossendeidae: The evolutionary history of an Antarctic sea spider radiation

(2019) Lars Dietz et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Revisiting metazoan phylogeny with genomic sampling of all phyla

(2019) Christopher E. Laumer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization

(2019) Grey T. Gustafson et al.   Ecology and Evolution

The Prevalence and Impact of Model Violations in Phylogenetic Analysis

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

Divergence and support among slightly suboptimal likelihood gene trees

(2019) Mark P. Simmons et al.   CLADISTICS

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

(2019) Benjamin R Karin et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Transcriptomics illuminate the phylogenetic backbone of tiger beetles

(2019) Harlan M Gough et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogenomic analysis of the beetle suborder Adephaga with comparison of tailored and generalized ultraconserved element probe performance

(2019) Grey T. Gustafson et al.   SYSTEMATIC ENTOMOLOGY

The morphological evolution of the Adephaga (Coleoptera)

(2019) Rolf Georg Beutel et al.   SYSTEMATIC ENTOMOLOGY

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

(2019) Andrew D. Young et al.   SYSTEMATIC ENTOMOLOGY

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

(2018) James B. Pease et al.   AMERICAN JOURNAL OF BOTANY

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

A software tool ‘CroCo’ detects pervasive cross-species contamination in next generation sequencing data

(2018) Paul Simion et al.   BMC BIOLOGY

Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

(2018) Manuela Sann et al.   BMC EVOLUTIONARY BIOLOGY

Early burst in body size evolution is uncoupled from species diversification in diving beetles (Dytiscidae)

(2018) Aurélie Désamoré et al.   MOLECULAR ECOLOGY

DiscoVista: Interpretable visualizations of gene tree discordance

(2018) Erfan Sayyari et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary history of Coleoptera revealed by extensive sampling of genes and species

(2018) Shao-Qian Zhang et al.   Nature Communications

MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

(2018) Vincent Ranwez et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the thoracic anatomy of the Madagascan Heterogyrus milloti and the phylogeny of Gyrinidae (Coleoptera)

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

A comprehensive molecular phylogeny of tiger beetles (Coleoptera, Carabidae, Cicindelinae)

(2018) Harlan M. Gough et al.   SYSTEMATIC ENTOMOLOGY

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

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

Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

(2017) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

The mitogenome phylogeny of Adephaga (Coleoptera)

(2017) Alejandro López-López et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular phylogeny of the aquatic beetle family Noteridae (Coleoptera: Adephaga) with an emphasis on data partitioning strategies

(2017) Stephen M. Baca et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae)

(2017) Sarah Bank et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

More on the Best Evolutionary Rate for Phylogenetic Analysis

(2017) Seraina Klopfstein et al.   SYSTEMATIC BIOLOGY

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Higher-level phylogeny of diving beetles (Coleoptera: Dytiscidae) based on larval characters

(2017) MARIANO C. MICHAT et al.   SYSTEMATIC ENTOMOLOGY

Systematics of aquatic beetles (Coleoptera): current state and future directions

(2017) ANDREW EDWARD Z. SHORT   SYSTEMATIC ENTOMOLOGY

Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’

(2017) STEPHEN M. BACA et al.   SYSTEMATIC ENTOMOLOGY

Tip-dated phylogeny of whirligig beetles reveals ancient lineage surviving on Madagascar

(2017) Grey T. Gustafson et al.   Scientific Reports

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

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

BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design

(2016) Christoph Mayer et al.   MOLECULAR BIOLOGY AND EVOLUTION

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

(2016) Charles W. Linkem et al.   SYSTEMATIC BIOLOGY

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes

(2016) Iker Irisarri et al.   SYSTEMATIC BIOLOGY

The peril of dating beetles

(2016) EMMANUEL F. A. TOUSSAINT et al.   SYSTEMATIC ENTOMOLOGY

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exon capture phylogenomics: efficacy across scales of divergence

(2015) Jason G. Bragg et al.   Molecular Ecology Resources

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

(2015) Ge Tan et al.   SYSTEMATIC BIOLOGY

The beetle tree of life reveals that Coleoptera survived end-Permian mass extinction to diversify during the Cretaceous terrestrial revolution

(2015) DUANE D. MCKENNA et al.   SYSTEMATIC ENTOMOLOGY

Molecular phylogeny of the highly disjunct cliff water beetles from South Africa and China (Coleoptera: Aspidytidae)

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

A priori assessment of data quality in molecular phylogenetics

(2014) Bernhard Misof et al.   Algorithms for Molecular Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

AliGROOVE – visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support

(2014) Patrick Kück et al.   BMC BIOINFORMATICS

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

(2014) Patrick Kück et al.   Frontiers in Zoology

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

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

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

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

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

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

(2013) Bernhard Misof et al.   BMC BIOINFORMATICS

Deep metazoan phylogeny: When different genes tell different stories

(2013) Tetyana Nosenko et al.   MOLECULAR PHYLOGENETICS 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

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

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

On the phylogeny and evolution of Mesozoic and extant lineages of Adephaga (Coleoptera, Insecta)

(2012) Rolf G. Beutel et al.   CLADISTICS

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Phylogeny and classification of whirligig beetles (Coleoptera: Gyrinidae): relaxed-clock model outperforms parsimony and time-free Bayesian analyses

(2012) KELLY B. MILLER et al.   SYSTEMATIC ENTOMOLOGY

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

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

Molecular phylogeny of the squeak beetles, a family with disjunct Palearctic-Australian range

(2011) Oliver Hawlitschek et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

(2010) Patrick Kück et al.   Frontiers in Zoology

On the systematic position of the family Gyrinidae (Coleoptera: Adephaga)

(2010) R. G. Beutel et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Phylogenetic analysis of thoracic structures of Carabidae (Coleoptera: Adephaga)

(2010) R. G.Beutel   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics

(2010) HOJUN SONG et al.   SYSTEMATIC ENTOMOLOGY

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

The structure of the defence glands of the Cicindelidae, Amphizoidae, and Hygrobiidae (Insecta: Coleoptera)

(2009) D. J. Forsyth   JOURNAL OF ZOOLOGY

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

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

(2009) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

On the systematics of Noteridae (Coleoptera: Adephaga: Hydradephaga): Phylogeny, description of a new tribe, genus and species, and survey of female genital morphology

(2009) Kelly B. Miller   SYSTEMATICS AND BIODIVERSITY

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

Phylogeny and diversification of diving beetles (Coleoptera: Dytiscidae)

(2008) Ignacio Ribera et al.   CLADISTICS

Systematic placement of the recently discovered beetle family Meruidae (Coleoptera: Dytiscoidea) based on molecular data

(2008) Michael Balke et al.   ZOOLOGICA SCRIPTA

Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae)

(2008) David R. Maddison et al.   ZOOLOGICA SCRIPTA