Spider phylogenomics: untangling the Spider Tree of Life

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards

(2015) Matthew C Brandley et al.   BMC EVOLUTIONARY BIOLOGY

Total evidence analysis of the phylogenetic relationships of Lycosoidea spiders (Araneae, Entelegynae)

(2015) Daniele Polotow et al.   INVERTEBRATE SYSTEMATICS

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

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

Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence

(2015) Frédéric Legendre et al.   PLoS One

The Phylogeny and Evolution of Ants

(2014) Philip S. Ward   Annual Review of Ecology Evolution and Systematics

Evolutionary morphology of the male reproductive system, spermatozoa and seminal fluid of spiders (Araneae, Arachnida) – Current knowledge and future directions

(2014) Peter Michalik et al.   ARTHROPOD STRUCTURE & DEVELOPMENT

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 Morphology And Phylogeny Of Dionychan Spiders (Araneae: Araneomorphae)

(2014) Martín J. Ramírez   BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY

Phylogenomic Analysis of Spiders Reveals Nonmonophyly of Orb Weavers

(2014) Rosa Fernández et al.   CURRENT BIOLOGY

Phylogenomics Resolves a Spider Backbone Phylogeny and Rejects a Prevailing Paradigm for Orb Web Evolution

(2014) Jason E. Bond et al.   CURRENT BIOLOGY

Processing of recombinant spider silk proteins into tailor-made materials for biomaterials applications

(2014) Kristin Schacht et al.   CURRENT OPINION IN BIOTECHNOLOGY

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Analysis and Visualization of Complex Macroevolutionary Dynamics: An Example from Australian Scincid Lizards

(2014) Daniel L. Rabosky et al.   SYSTEMATIC BIOLOGY

Higher level molecular phylogeny of darkling beetles (Coleoptera: Tenebrionidae)

(2014) GAEL J. KERGOAT et al.   SYSTEMATIC ENTOMOLOGY

Spider genomes provide insight into composition and evolution of venom and silk

(2014) Kristian W. Sanggaard et al.   Nature Communications

High-Throughput Genomic Data in Systematics and Phylogenetics

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

Systematics, Phylogeny, and Evolution of Orb-Weaving Spiders

(2013) Gustavo Hormiga et al.   Annual Review of Entomology

PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics

(2013) Kevin M. Kocot et al.   Evolutionary Bioinformatics

Phylogenetic relationships of the spider family Psechridae inferred from molecular data, with comments on the Lycosoidea (Arachnida : Araneae)

(2013) Steffen Bayer et al.   INVERTEBRATE SYSTEMATICS

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

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

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

A giant spider from the Jurassic of China reveals greater diversity of the orbicularian stem group

(2013) Paul A. Selden et al.   NATURWISSENSCHAFTEN

Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

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

Timing and Patterns in the Taxonomic Diversification of Lepidoptera (Butterflies and Moths)

(2013) Niklas Wahlberg et al.   PLoS One

Identifying Hidden Rate Changes in the Evolution of a Binary Morphological Character: The Evolution of Plant Habit in Campanulid Angiosperms

(2013) Jeremy M. Beaulieu et al.   SYSTEMATIC BIOLOGY

Early Cretaceous angiosperms and beetle evolution

(2013) Bo Wang et al.   Frontiers in Plant Science

Spider-Venom Peptides: Structure, Pharmacology, and Potential for Control of Insect Pests

(2012) Glenn F. King et al.   Annual Review of Entomology

Phylogenetic placement of pelican spiders (Archaeidae, Araneae), with insight into evolution of the “neck” and predatory behaviours of the superfamily Palpimanoidea

(2012) Hannah Marie Wood et al.   CLADISTICS

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Reconsideration of the Classification of the Spider Infraorder Mygalomorphae (Arachnida: Araneae) Based on Three Nuclear Genes and Morphology

(2012) Jason E. Bond et al.   PLoS One

Early Events in the Evolution of Spider Silk Genes

(2012) James Starrett et al.   PLoS One

Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders

(2012) Hannah Marie Wood et al.   SYSTEMATIC BIOLOGY

Ants and the Fossil Record

(2011) John S. LaPolla et al.   Annual Review of Entomology

Patterns of habitat affinity and Austral/Holarctic parallelism in dictynoid spiders (Araneae�:�Entelegynae)

(2011) Joseph C. Spagna et al.   INVERTEBRATE SYSTEMATICS

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Tangled in a sparse spider web: single origin of orb weavers and their spinning work unravelled by denser taxonomic sampling

(2011) D. Dimitrov et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Phylogeny of entelegyne spiders: Affinities of the family Penestomidae (NEW RANK), generic phylogeny of Eresidae, and asymmetric rates of change in spinning organ evolution (Araneae, Araneoidea, Entelegynae)

(2010) Jeremy A. Miller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

FASconCAT: Convenient handling of data matrices

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

(2010) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Spider-Venom Peptides as Therapeutics

(2010) Natalie J. Saez et al.   Toxins

Fossil spiders

(2009) Paul A. Selden et al.   BIOLOGICAL REVIEWS

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Temporal lags and overlap in the diversification of weevils and flowering plants

(2009) D. D. McKenna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstructing web evolution and spider diversification in the molecular era

(2009) T. A. Blackledge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Structural Disorder in Silk Proteins Reveals the Emergence of Elastomericity

(2007) Cedric Dicko et al.   BIOMACROMOLECULES

More data, fewer shifts: Molecular insights into the evolution of the spinning apparatus in non-orb-weaving spiders

(2007) Joseph C. Spagna et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION