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

Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life

(2018) Rosa Fernández et al.   CURRENT BIOLOGY

Cryptic elevational zonation in trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus janus complex) from the California southern Sierra Nevada

(2018) James Starrett et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Next-generation museum genomics: Phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea)

(2018) Hannah M. Wood et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae)

(2018) Marshal Hedin et al.   ZooKeys

A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements

(2018) Shahan Derkarabetian et al.   ZooKeys

On the universality of target-enrichment baits for phylogenomic research

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

Phylogenomic reclassification of the world’s most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution

(2018) Marshal Hedin et al.   Scientific Reports

Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization

(2018) Ruth B. McCole et al.   Cell Reports

Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae

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

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Conserved non-coding elements: developmental gene regulation meets genome organization

(2017) Dimitris Polychronopoulos et al.   NUCLEIC ACIDS RESEARCH

Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life

(2016) Chris A. Hamilton et al.   BMC EVOLUTIONARY BIOLOGY

The spider tree of life: phylogeny of Araneae based on target-gene analyses from an extensive taxon sampling

(2016) Ward C. Wheeler et al.   CLADISTICS

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

(2016) James Starrett et al.   Molecular Ecology Resources

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Spider phylogenomics: untangling the Spider Tree of Life

(2016) Nicole L. Garrison et al.   PeerJ

Edwa maryaegen. et sp. nov. in the Norian Blackstone Formation of the Ipswich Basin—the first Triassic spider (Mygalomorphae) from Australia

(2015) Robert J. Raven et al.   ALCHERINGA

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

(2015) Brant C. Faircloth   BIOINFORMATICS

Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution

(2015) Thomas H. Clarke et al.   Genome Biology and Evolution

Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

(2015) Julia Chifman et al.   JOURNAL OF THEORETICAL BIOLOGY

Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae)

(2015) Dean H. Leavitt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

(2015) P. P. Sharma et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen 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

Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

(2014) Mandy Man-Ying Tin et al.   PLoS One

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

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

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

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

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

Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae

(2013) James Starrett et al.   GENE

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

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

Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low-dispersal mygalomorph spiders (Antrodiaetidae,Antrodiaetus) from California

(2012) Marshal Hedin et al.   MOLECULAR ECOLOGY

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

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Inferring Species Trees from Gene Trees in a Radiation of California Trapdoor Spiders (Araneae, Antrodiaetidae, Aliatypus)

(2011) Jordan D. Satler et al.   PLoS One

A revision of the purse-web spider genus Calommata Lucas, 1837 (Araneae, Atypidae) in the Afrotropical Region

(2011) Charles Haddad et al.   ZooKeys

Closing the ring: historical biogeography of the salamander ring speciesEnsatina eschscholtzii

(2009) Shawn R. Kuchta et al.   JOURNAL OF BIOGEOGRAPHY

Evaluating the efficacy of continuous quantitative characters for reconstructing the phylogeny of a morphologically homogeneous spider taxon (Araneae, Mygalomorphae, Antrodiaetidae, Antrodiaetus)

(2009) Brent E. Hendrixson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Fossil evidence for the origin of spider spinnerets, and a proposed arachnid order

(2008) P. A. Selden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA