Origin and higher-level diversification of acariform mites – evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment

Comparative genomics and transcriptomics in ants provide new insights into the evolution and function of odorant binding and chemosensory proteins

(2014) Sean K McKenzie et al.   BMC GENOMICS

The role of the integument with respect to different modes of locomotion in the Nematalycidae (Endeostigmata)

(2014) Samuel J. Bolton et al.   EXPERIMENTAL AND APPLIED ACAROLOGY

ITS2, 18S, 16S or any other RNA — simply aligning sequences and their individual secondary structures simultaneously by an automatic approach

(2014) Matthias Wolf et al.   GENE

A new genus and species of Nematalycidae (Acari: Endeostigmata)

(2014) Samuel J. Bolton et al.   JOURNAL OF NATURAL HISTORY

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

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

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

An opilioacarid mite in Cretaceous Burmese amber

(2014) Jason A. Dunlop et al.   NATURWISSENSCHAFTEN

Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

(2014) Daniele Salvi et al.   PLoS One

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

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

The blood alga: phylogeny of Haematococcus (Chlorophyceae) inferred from ribosomal RNA gene sequence data

(2013) Mark A. Buchheim et al.   EUROPEAN JOURNAL OF PHYCOLOGY

Secondary structure prediction for complete rDNA sequences (18S, 5.8S, and 28S rDNA) of Demodex folliculorum, and comparison of divergent domains structures across Acari

(2013) Ya-E. Zhao et al.   EXPERIMENTAL PARASITOLOGY

DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution

(2013) Xuhua Xia   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Nucleotide Composition of CO1 Sequences in Chelicerata (Arthropoda): Detecting New Mitogenomic Rearrangements

(2012) Juliette Arabi et al.   JOURNAL OF MOLECULAR EVOLUTION

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

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

Convergent evolution of defense mechanisms in oribatid mites (Acari, Oribatida) shows no “ghosts of predation past”

(2012) Patrick Pachl et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Nearly complete rRNA genes from 371 Animalia: Updated structure-based alignment and detailed phylogenetic analysis

(2012) Jon Mallatt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: Evidence from case studies in the Metazoa

(2011) Harald O Letsch et al.   BMC EVOLUTIONARY BIOLOGY

Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae)

(2011) LACEY L. KNOWLES et al.   PARASITOLOGY

Sources of Signal in 62 Protein-Coding Nuclear Genes for Higher-Level Phylogenetics of Arthropods

(2011) Jerome C. Regier et al.   PLoS One

Compluriscutula vetulum (Acari: Ixodida: Ixodidae), A New Genus And Species of Hard Tick from Lower Cretaceous Burmese Amber

(2011) George O. Poinar et al.   PROCEEDINGS OF THE ENTOMOLOGICAL SOCIETY OF WASHINGTON

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

(2010) Alexander Keller et al.   Biology Direct

Phylogenetic position of the acariform mites: sensitivity to homology assessment under total evidence

(2010) Almir R Pepato 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

Untersuchungen zur Morphologie, Taxonomie und Phylogenie der Chelicerata1 II. Cladogramme und die Entfaltung der Chelicerata

(2010) P. Weygoldt et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

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

Arthropod colonization of land – Linking molecules and fossils in oribatid mites (Acari, Oribatida)

(2010) Ina Schaefer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

FASconCAT: Convenient handling of data matrices

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

Molecular phylogeny of acariform mites (Acari, Arachnida): Strong conflict between phylogenetic signal and long-branch attraction artifacts

(2010) Miroslawa Dabert 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

Direct optimization overly optimizes data

(2010) KAZUNORI YOSHIZAWA   SYSTEMATIC ENTOMOLOGY

ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus )

(2009) Martin Wiemers et al.   BMC EVOLUTIONARY BIOLOGY

Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships

(2009) Björn M von Reumont et al.   BMC EVOLUTIONARY BIOLOGY

POY version 4: phylogenetic analysis using dynamic homologies

(2009) Andrés Varón et al.   CLADISTICS

Calibrating the chelicerate clock: a paleontological reply to Jeyaprakash and Hoy

(2009) Jason A. Dunlop et al.   EXPERIMENTAL AND APPLIED ACAROLOGY

Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy

(2009) K. Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species, Rhizoctonia solani

(2009) Paavo Ahvenniemi et al.   JOURNAL OF MOLECULAR EVOLUTION

ITS2 sequence–structure analysis in phylogenetics: A how-to manual for molecular systematics

(2009) Jörg Schultz et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction

(2009) Jon Mallatt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Accurate and efficient reconstruction of deep phylogenies from structured RNAs

(2009) Roman R. Stocsits et al.   NUCLEIC ACIDS RESEARCH

When Trees Grow Too Long: Investigating the Causes of Highly Inaccurate Bayesian Branch-Length Estimates

(2009) Jeremy M. Brown et al.   SYSTEMATIC BIOLOGY

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

Cryptic Failure of Partitioned Bayesian Phylogenetic Analyses: Lost in the Land of Long Trees

(2009) David C. Marshall   SYSTEMATIC BIOLOGY

The thoracic morphology of Archostemata and the relationships of the extant suborders of Coleoptera (Hexapoda)

(2008) Frank Friedrich et al.   CLADISTICS

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

A multi criterion approach for the selection of optimal outgroups in phylogeny: Recovering some support for Mandibulata over Myriochelata using mitogenomics

(2008) Omar Rota-Stabelli et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION