Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

Evaluating Topological Conflict in Centipede Phylogeny Using Transcriptomic Data Sets

(2014) Rosa Fernández et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic position of Myriapoda revealed by 454 transcriptome sequencing

(2014) Peter Rehm et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Hox gene duplications correlate with posterior heteronomy in scorpions

(2014) P. P. Sharma et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Distal-lessanddachshundpattern both plesiomorphic and apomorphic structures in chelicerates: RNA interference in the harvestmanPhalangium opilio(Opiliones)

(2013) Prashant P. Sharma et al.   EVOLUTION & DEVELOPMENT

The expression of limb gap genes in the miteArchegozetes longisetosusreveals differential patterning mechanisms in chelicerates

(2013) Austen A. Barnett et al.   EVOLUTION & DEVELOPMENT

SuperQ: Computing Supernetworks from Quartets

(2013) Stefan Grunewald et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

Deep metazoan phylogeny: When different genes tell different stories

(2013) Tetyana Nosenko et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Elongation factor-1α, a putative single-copy nuclear gene, has divergent sets of paralogs in an arachnid

(2013) Ronald M. Clouse et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

(2013) Adrian M. Altenhoff et al.   PLoS One

Ordinal-Level Phylogenomics of the Arthropod Class Diplopoda (Millipedes) Based on an Analysis of 221 Nuclear Protein-Coding Loci Generated Using Next-Generation Sequence Analyses

(2013) Michael S. Brewer et al.   PLoS One

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

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Conserved Genes, Sampling Error, and Phylogenomic Inference

(2013) Ricardo Betancur-R. et al.   SYSTEMATIC BIOLOGY

The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods

(2013) Zhijian Cao et al.   Nature Communications

Arthropod fossil data increase congruence of morphological and molecular phylogenies

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

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Evolution of the chelicera: adachshunddomain is retained in the deutocerebral appendage of Opiliones (Arthropoda, Chelicerata)

(2012) Prashant P. Sharma et al.   EVOLUTION & DEVELOPMENT

Hox gene expression in the harvestman Phalangium opilio reveals divergent patterning of the chelicerate opisthosoma

(2012) Prashant P. Sharma et al.   EVOLUTION & DEVELOPMENT

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

(2012) Ana Riesgo et al.   Frontiers in Zoology

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

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

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

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

Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

(2012) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomic Resolution of Paleozoic Divergences in Harvestmen (Arachnida, Opiliones) via Analysis of Next-Generation Transcriptome Data

(2012) Marshal Hedin et al.   PLoS One

Silurian horseshoe crab illuminates the evolution of arthropod limbs

(2012) D. E. G. Briggs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revised systematics of Palaeozoic ‘horseshoe crabs’ and the myth of monophyletic Xiphosura

(2012) James C. Lamsdell   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis

(2011) Victor Zeng et al.   BMC GENOMICS

The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus

(2011) Ben Ewen-Campen et al.   BMC GENOMICS

Random Addition Concatenation Analysis: A Novel Approach to the Exploration of Phylogenomic Signal Reveals Strong Agreement between Core and Shell Genomic Partitions in the Cyanobacteria

(2011) Apurva Narechania et al.   Genome Biology and Evolution

The evolutionary and biogeographic history of the armoured harvestmen - Laniatores phylogeny based on ten molecular markers, with the description of two new families of Opiliones (Arachnida)

(2011) Prashant P. Sharma et al.   INVERTEBRATE SYSTEMATICS

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

Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species

(2011) Matthias Obst et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genome of Tetranychus urticae reveals herbivorous pest adaptations

(2011) Miodrag Grbić et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Geological history and phylogeny of Chelicerata

(2010) Jason A. Dunlop   ARTHROPOD STRUCTURE & DEVELOPMENT

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

(2010) Almir R Pepato et al.   BMC EVOLUTIONARY BIOLOGY

The phylogenetic utility of the nuclear protein-coding gene EF-1α for resolving recent divergences in Opiliones, emphasizing intron evolution

(2010) Marshal Hedin et al.   JOURNAL OF ARACHNOLOGY

Untersuchungen zur Morphologie, Taxonomie und Phylogenie der Chelicerata1 I. Morphologische Untersuchungen

(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

Rare genomic changes and mitochondrial sequences provide independent support for congruent relationships among the sea spiders (Arthropoda, Pycnogonida)

(2010) Susan E. Masta et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2010) Jerome C. Regier et al.   NATURE

OMA 2011: orthology inference among 1000 complete genomes

(2010) A. M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

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

Arthropod phylogeny revisited, with a focus on crustacean relationships

(2009) Stefan Koenemann et al.   ARTHROPOD STRUCTURE & DEVELOPMENT

A multilocus approach to harvestman (Arachnida: Opiliones) phylogeny with emphasis on biogeography and the systematics of Laniatores

(2009) Gonzalo Giribet et al.   CLADISTICS

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

A 454 sequencing approach for large scale phylogenomic analysis of the common emperor scorpion (Pandinus imperator)

(2009) Falko Roeding et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis

(2009) Bernd Schierwater et al.   PLOS BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

(2008) S. A. Smith et al.   BIOINFORMATICS

Microanatomy of Early Devonian book lungs

(2008) C. Kamenz et al.   Biology Letters

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

Arachnid relationships based on mitochondrial genomes: Asymmetric nucleotide and amino acid bias affects phylogenetic analyses

(2008) Susan E. Masta et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

(2008) N. Lartillot et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY