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

Exploring the evolution and terrestrialization of scorpions (Arachnida: Scorpiones) with rocks and clocks

(2019) Richard J. Howard et al.   ORGANISMS DIVERSITY & EVOLUTION

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

Optimised DNA extraction and library preparation for minute arthropods: application to target enrichment in chalcid wasps used for biocontrol

(2019) Astrid Cruaud et al.   Molecular Ecology Resources

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

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

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

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

Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds ( Pachyramphus )

(2018) Lukas J. Musher 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

On the universality of target-enrichment baits for phylogenomic research

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

Advancing mite phylogenomics: Designing ultraconserved elements for acari phylogeny

(2018) Matthew H. Van Dam et al.   Molecular Ecology Resources

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

Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements

(2017) Jacob A. Esselstyn et al.   Genome Biology and Evolution

Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems

(2017) Andrea M. Quattrini et al.   Molecular Ecology Resources

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

The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism

(2017) Philip S. Ward et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

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

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

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

High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

(2016) James Starrett et al.   Molecular Ecology Resources

Mammal madness: is the mammal tree of life not yet resolved?

(2016) Nicole M. Foley et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus:Piranga)

(2016) Joseph D. Manthey et al.   SYSTEMATIC BIOLOGY

The peril of dating beetles

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

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

Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

(2015) Bonnie B. Blaimer et al.   BMC EVOLUTIONARY BIOLOGY

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

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

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

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

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

(2014) Brant C. Faircloth et al.   Molecular Ecology Resources

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

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

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

Ademosynoides asiaticus Martynov, 1936, the earliest known member of an extant beetle family (Insecta, Coleoptera, Trachypachidae)

(2013) A. G. Ponomarenko et al.   PALEONTOLOGICAL JOURNAL

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

(2013) John E. McCormack et al.   PLoS One

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

(2012) N. G. Crawford et al.   Biology Letters

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

(2012) Ylenia Chiari et al.   BMC BIOLOGY

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

(2012) Rolf G. Beutel et al.   CLADISTICS

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

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

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

(2012) Fredrik Ronquist 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

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 impact of taxon sampling on phylogenetic inference: a review of two decades of controversy

(2011) A. R. Nabhan et al.   BRIEFINGS IN BIOINFORMATICS

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

(2011) J. E. McCormack et al.   GENOME RESEARCH

Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles

(2011) X.-X. Shen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

IsMerua specialized noterid (Coleoptera, Adephaga)?

(2011) CARINA DRESSLER et al.   SYSTEMATIC ENTOMOLOGY

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

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

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

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

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

A genus-level supertree of Adephaga (Coleoptera)

(2007) R BEUTEL et al.   ORGANISMS DIVERSITY & EVOLUTION