Integrative phylogenomics reveals a Permian origin of Adephaga beetles

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

HyRAD-X exome capture museomics unravels giant ground beetle evolution

(2021) Emmanuel F A Toussaint et al.   Genome Biology and Evolution

Habitat preference and diversification rates in a speciose lineage of diving beetles

(2021) Adrián Villastrigo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

New methods to calculate concordance factors for phylogenomic datasets

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

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

Phylogenomics indicates Amazonia as the major source of Neotropical swarm-founding social wasp diversity

(2020) Rodolpho S. T. Menezes et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Protein‐encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera: Calyptratae)

(2020) Eliana Buenaventura et al.   SYSTEMATIC ENTOMOLOGY

Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera)

(2020) James M. Pflug et al.   G3-Genes Genomes Genetics

Interrogating genomic-scale data to resolve recalcitrant nodes in the Spider Tree of Life

(2020) Siddharth Kulkarni et al.   MOLECULAR BIOLOGY AND EVOLUTION

Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana)

(2020) Kin Onn Chan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

(2020) Matthew H Van Dam et al.   SYSTEMATIC BIOLOGY

Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

(2020) Bonnie B. Blaimer et al.   BMC EVOLUTIONARY BIOLOGY

UCE data reveal multiple origins of rose gallers in North America: Global phylogeny of Diplolepis Geoffroy (Hymenoptera: Cynipidae)

(2020) Y. Miles Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Baltic amber species of the diving beetle genus Coptotomus Say, 1830 (Coleoptera: Dytiscidae: Coptotominae)

(2020) LARS HENDRICH et al.   ZOOTAXA

Water Beetles as Models in Ecology and Evolution

(2019) David T. Bilton et al.   Annual Review of Entomology

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

Ambarticus myanmaricus gen. et sp. nov., the first diving beetle from mid-Cretaceous amber of northern Myanmar (Coleoptera, Dytiscidae, Dytiscinae)

(2019) Qiang Yang et al.   CRETACEOUS RESEARCH

Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci

(2019) Marshal Hedin et al.   PeerJ

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

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

Reliable placement of beetle fossils via phylogenetic analyses – Triassic Leehermania as a case study (Staphylinidae or Myxophaga?)

(2019) Martin Fikáček et al.   SYSTEMATIC ENTOMOLOGY

Kryzhanovskiana olegi gen. et sp. nov., a remarkable eyeless representative of the tribe Metriini (Coleoptera: Carabidae: Paussinae) from Upper Cretaceous amber of northern Myanmar

(2019) Boris M. Kataev et al.   CRETACEOUS RESEARCH

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

Cretodineutus rotundus gen. et sp. nov., the oldest adult whirligig beetle from the Upper Cretaceous of Myanmar (Coleoptera, Gyrinidae, Gyrininae)

(2019) Zulong Liang et al.   CRETACEOUS RESEARCH

Burmapseudomorphus planus gen. et sp. nov. – a Late Cretaceous stem group member of the specialized Pseudomorphini (Carabidae, Coleoptera) from northern Myanmar

(2019) Rolf Georg Beutel et al.   CRETACEOUS RESEARCH

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

OUP accepted manuscript

(2018)   BIOINFORMATICS

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Whirling in the late Permian: ancestral Gyrinidae show early radiation of beetles before Permian-Triassic mass extinction

(2018) Evgeny V. Yan et al.   BMC EVOLUTIONARY BIOLOGY

Estimating Improved Partitioning Schemes for Ultraconserved Elements

(2018) Victor A Tagliacollo et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2018) Aurélie Désamoré et al.   MOLECULAR ECOLOGY

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

(2018) Stephen A. Smith et al.   PLoS One

Structural absorption by barbule microstructures of super black bird of paradise feathers

(2018) Dakota E. McCoy et al.   Nature Communications

On the universality of target-enrichment baits for phylogenomic research

(2018) Silas Bossert et al.   Methods in Ecology and Evolution

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

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

Middle-Late Triassic insect radiation revealed by diverse fossils and isotopic ages from China

(2018) Daran Zheng et al.   Science Advances

Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae

(2018) Silas Bossert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources

(2018) Troy J. Kieran et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The earliest tiger beetle from the Lower Cretaceous of China (Coleoptera: Cicindelinae)

(2018) Xiangdong Zhao et al.   CRETACEOUS RESEARCH

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

Speciation below ground: Tempo and mode of diversification in a radiation of endogean ground beetles

(2017) Carmelo Andújar et al.   MOLECULAR ECOLOGY

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

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

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

Evolution of salinity tolerance in the diving beetle tribe Hygrotini (Coleoptera, Dytiscidae)

(2017) Adrián Villastrigo et al.   ZOOLOGICA SCRIPTA

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

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

Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils

(2017) Matthew H. Van Dam et al.   PLoS One

Evolution of Pacific Rim diving beetles sheds light on Amphi-Pacific biogeography

(2016) Emmanuel F. A. Toussaint et al.   ECOGRAPHY

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gondwanian relicts and oceanic dispersal in a cosmopolitan radiation of euedaphic ground beetles

(2016) Carmelo Andújar et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Colorful patterns indicate common ancestry in diverged tiger beetle taxa: Molecular phylogeny, biogeography, and evolution of elytral coloration of the genus Cicindela subgenus Sophiodela and its allies

(2016) Kaoru Tsuji et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Islands in the desert: Species delimitation and evolutionary history of Pseudotetracha tiger beetles (Coleoptera: Cicindelidae: Megacephalini) from Australian salt lakes

(2016) Alejandro López-López et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Bitterfeld amber is not Baltic amber: Three geochemical tests and further constraints on the botanical affinities of succinite

(2016) Alexander P. Wolfe et al.   REVIEW OF PALAEOBOTANY AND PALYNOLOGY

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

The peril of dating beetles

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

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

(2016) Marek L. Borowiec   PeerJ

Phylogenetic niche conservatism explains an inverse latitudinal diversity gradient in freshwater arthropods

(2016) Jérôme Morinière et al.   Scientific Reports

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

The first record of Cretaceous ground beetle (Coleoptera: Carabidae: Oodini) from Burmese amber

(2015) Ye Liu et al.   CRETACEOUS RESEARCH

Review of paleontological data on the evolution of aquatic beetles (Coleoptera)

(2015) A. G. Ponomarenko et al.   PALEONTOLOGICAL JOURNAL

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

(2015) K. J. Tong et al.   SCIENCE

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

In or Out-of-Madagascar?—Colonization Patterns for Large-Bodied Diving Beetles (Coleoptera: Dytiscidae)

(2015) Rasa Bukontaite et al.   PLoS One

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

The utility of CAD in recovering Gondwanan vicariance events and the evolutionary history of Aciliini (Coleoptera: Dytiscidae)

(2014) Rasa Bukontaite et al.   BMC EVOLUTIONARY BIOLOGY

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Explosive Adaptive Radiation and Extreme Phenotypic Diversity within Ant-Nest Beetles

(2014) Wendy Moore et al.   CURRENT BIOLOGY

Late Miocene origin of an Ibero-Maghrebian clade of ground beetles with multiple colonizations of the subterranean environment

(2014) Arnaud Faille et al.   JOURNAL OF BIOGEOGRAPHY

A rare diving beetle from Baltic amber: Hydrotrupes prometheus new species reveals former widespread distribution of the genus (Coleoptera, Dytiscidae)

(2014) R. Antonio Gómez et al.   JOURNAL OF PALEONTOLOGY

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer 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 Distribution of Extant Richness Suggests Metamorphosis Is a Key Innovation Driving Diversification in Insects

(2014) James L. Rainford et al.   PLoS One

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Unveiling the Diversification Dynamics of Australasian Predaceous Diving Beetles in the Cenozoic

(2014) Emmanuel F.A. Toussaint et al.   SYSTEMATIC BIOLOGY

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

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

A molecular phylogeny of Alpine subterranean Trechini (Coleoptera: Carabidae)

(2013) Arnaud Faille et al.   BMC EVOLUTIONARY BIOLOGY

Macroinvertebrate communities as bioindicators of water quality in conventional and organic irrigated rice fields in Guanacaste, Costa Rica

(2013) Federico Rizo-Patrón V. et al.   ECOLOGICAL INDICATORS

Evolution of the elytral venation and structural adaptations in the oldest Palaeozoic beetles (Insecta: Coleoptera: Tshekardocoleidae)

(2013) Alexander G. Kirejtshuk et al.   JOURNAL OF SYSTEMATIC PALAEONTOLOGY

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

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

The first record of crawling water beetles (Coleoptera, Haliplidae) in the Lower Cretaceous of Mongolia

(2013) A. A. Prokin et al.   PALEONTOLOGICAL JOURNAL

New fossil taxa and notes on the Mesozoic evolution of Liadytidae and Dytiscidae (Coleoptera)

(2013) ALEXANDER A. PROKIN et al.   ZOOTAXA

Leehermania prorova, the Earliest Staphyliniform Beetle, from the Late Triassic of Virginia (Coleoptera: Staphylinidae)

(2012) Stylianos Chatzimanolis et al.   AMERICAN MUSEUM NOVITATES

Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation

(2012) Carmelo Andújar et al.   BMC EVOLUTIONARY BIOLOGY

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

(2012) Rolf G. Beutel et al.   CLADISTICS

Age constraint on Burmese amber based on U–Pb dating of zircons

(2012) Guanghai Shi et al.   CRETACEOUS RESEARCH

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Glypholomatine Rove Beetles (Coleoptera: Staphylinidae): a Southern Hemisphere Recent Group Recorded from the Middle Jurassic of China

(2012) Chenyang Cai et al.   JOURNAL OF THE KANSAS ENTOMOLOGICAL SOCIETY

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

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

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

Catalogue of Geadephaga (Coleoptera: Adephaga) of America, north of Mexico

(2012) Yves Bousquet   ZooKeys

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

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

The first skiff beetle (Coleoptera: Myxophaga: Hydroscaphidae) from Early Cretaceous Jehol Biota

(2011) Chenyang Cai et al.   JOURNAL OF PALEONTOLOGY

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

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

IsMerua specialized noterid (Coleoptera, Adephaga)?

(2011) CARINA DRESSLER et al.   SYSTEMATIC ENTOMOLOGY

Forty years of carabid beetle research in Europe – from taxonomy, biology, ecology and population studies to bioindication, habitat assessment and conservation

(2011) D. Johan Kotze et al.   ZooKeys

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae)

(2010) Karen A Ober et al.   BMC EVOLUTIONARY BIOLOGY

Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships

(2010) Jeffrey P. Townsend et al.   SYSTEMATIC BIOLOGY

Late Cenozoic insects of northern Eurasia

(2009) S. V. Kiselev et al.   PALEONTOLOGICAL JOURNAL

Phylogeny and diversification of diving beetles (Coleoptera: Dytiscidae)

(2008) Ignacio Ribera et al.   CLADISTICS

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION

The genome of the model beetle and pest Tribolium castaneum

(2008) Stephen Richards et al.   NATURE

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