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

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

Rounding up the usual suspects: a standard target-gene approach for resolving the interfamilial phylogenetic relationships of ecribellate orb-weaving spiders with a new family-rank classification (Araneae, Araneoidea)

(2016) Dimitar Dimitrov et al.   CLADISTICS

Population genomic evidence for multiple Pliocene refugia in a montane-restricted harvestman (Arachnida, Opiliones,Sclerobunus robustus) from the southwestern United States

(2016) Shahan Derkarabetian et al.   MOLECULAR ECOLOGY

Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province

(2016) Robert W. Bryson et al.   MOLECULAR ECOLOGY

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

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods

(2016) Kelly A. Meiklejohn et al.   SYSTEMATIC BIOLOGY

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics

(2016) Michael G. Harvey et al.   SYSTEMATIC BIOLOGY

Taxonomic revision of the tarantula genus Aphonopelma Pocock, 1901 (Araneae, Mygalomorphae, Theraphosidae) within the United States

(2016) Chris A. Hamilton et al.   ZooKeys

Spider phylogenomics: untangling the Spider Tree of Life

(2016) Nicole L. Garrison et al.   PeerJ

Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens

(2016) Bonnie B. Blaimer et al.   PLoS One

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

The art and science of species delimitation

(2015) Bruce Rannala   Current Zoology

Sequence capture of ultraconserved elements from bird museum specimens

(2015) John E. McCormack et al.   Molecular Ecology Resources

Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

(2015) Princess S. Gilbert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A phylogenomic analysis of turtles

(2015) Nicholas G. Crawford 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

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

(2015) Jeffrey W. Streicher et al.   SYSTEMATIC BIOLOGY

The art and science of species delimitation

(2015) Bruce Rannala   Current Zoology

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

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

Cross-bracing uncalibrated nodes in molecular dating improves congruence of fossil and molecular age estimates

(2014) Prashant P Sharma et al.   Frontiers in Zoology

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

(2014) Prashant P. Sharma 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

Species Delimitation using Genome-Wide SNP Data

(2014) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

A revised dated phylogeny of the arachnid order Opiliones

(2014) Prashant P. Sharma et al.   Frontiers in Genetics

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

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

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

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

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

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

(2013) Brant C. Faircloth 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

The diversity and evolution of chelicerate hemocyanins

(2012) Peter Rehm et al.   BMC EVOLUTIONARY BIOLOGY

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

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

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

(2012) Marshal Hedin et al.   PLoS One

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

(2010) Jerome C. Regier et al.   NATURE

Annotating non-coding regions of the genome

(2010) Roger P. Alexander et al.   NATURE REVIEWS GENETICS

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

REINTERPRETATION OF THE SILURIAN SCORPION PROSCORPIUS OSBORNI (WHITFIELD): INTEGRATING DATA FROM PALAEOZOIC AND RECENT SCORPIONS

(2008) JASON A. DUNLOP et al.   PALAEONTOLOGY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY