Spider‐specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae)

Phylogeny of the orb‐weaving spider family Araneidae (Araneae: Araneoidea)

(2019) Nikolaj Scharff et al.   CLADISTICS

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

(2019) Marshal Hedin et al.   PeerJ

Monophyly, Taxon Sampling, and the Nature of Ranks in the Classification of Orb-Weaving Spiders (Araneae: Araneoidea)

(2019) Robert J Kallal et al.   SYSTEMATIC BIOLOGY

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

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

(2018) Rosa Fernández et al.   CURRENT BIOLOGY

A phylotranscriptomic backbone of the orb-weaving spider family Araneidae (Arachnida, Araneae) supported by multiple methodological approaches

(2018) Robert J. Kallal et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny of a cosmopolitan family of morphologically conserved trapdoor spiders (Mygalomorphae, Ctenizidae) using Anchored Hybrid Enrichment, with a description of the family, Halonoproctidae Pocock 1901

(2018) Rebecca L. Godwin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Early Cretaceous greenhouse pumped higher taxa diversification in spiders

(2018) Lili Shao 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

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

From Gondwana to GAARlandia: Evolutionary history and biogeography of ogre-faced spiders (Deinopis )

(2018) Lisa Chamberland et al.   JOURNAL OF BIOGEOGRAPHY

Advancing mite phylogenomics: Designing ultraconserved elements for acari phylogeny

(2018) Matthew H. Van Dam et al.   Molecular Ecology Resources

Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources

(2018) Troy J. Kieran et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens

(2017) Sara Ruane et al.   Molecular Ecology Resources

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression

(2017) Paul L Babb et al.   NATURE GENETICS

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’

(2017) STEPHEN M. BACA et al.   SYSTEMATIC ENTOMOLOGY

A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment

(2017) Wayne P. Maddison et al.   ZooKeys

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

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

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) James Starrett et al.   Molecular Ecology Resources

Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga

(2016) Bonnie B. Blaimer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Spider phylogenomics: untangling the Spider Tree of Life

(2016) Nicole L. Garrison et al.   PeerJ

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

(2015) Brant C. Faircloth   BIOINFORMATICS

Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

(2015) Bonnie B. Blaimer et al.   BMC EVOLUTIONARY BIOLOGY

Sequence capture of ultraconserved elements from bird museum specimens

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

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

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

Function-based identification of mammalian enhancers using site-specific integration

(2014) Diane E Dickel et al.   NATURE METHODS

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

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

(2013)   JOURNAL OF HEREDITY

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Morphology to the rescue: molecular data and the signal of morphological characters in combined phylogenetic analyses-a case study from mysmenid spiders (Araneae, Mysmenidae), with comments on the evolution of web architecture

(2010) Lara Lopardo et al.   CLADISTICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Phylogenetic placement of the Tasmanian spider Acrobleps hygrophilus (Araneae, Anapidae) with comments on the evolution of the capture web in Araneoidea

(2007) Lara Lopardo et al.   CLADISTICS