Combining genomic, phenotypic and Sanger sequencing data to elucidate the phylogeny of the two-clawed spiders (Dionycha)

Phylogenetic analysis of the subfamily Prodidominae (Arachnida: Araneae: Gnaphosidae)

(2020) Bruno V B Rodrigues et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Sequence Capture Phylogenomics of True Spiders Reveals Convergent Evolution of Respiratory Systems

(2020) Martín J Ramírez et al.   SYSTEMATIC BIOLOGY

Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research

(2020) Nuria Macías-Hernández et al.   Diversity-Basel

Combined-evidence analyses of ultraconserved elements and morphological data: an empirical example in iguanian lizards

(2020) Simon G. Scarpetta   Biology Letters

Interrogating genomic-scale data to resolve recalcitrant nodes in the Spider Tree of Life

(2020) Siddharth Kulkarni et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultraconserved yet informative for species delimitation: Ultraconserved elements resolve long‐standing systematic enigma in Central European bees

(2020) Morgan Gueuning et al.   MOLECULAR ECOLOGY

Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

(2020) Matthew H Van Dam et al.   SYSTEMATIC BIOLOGY

Homoplasy-based partitioning outperforms alternatives in Bayesian analysis of discrete morphological data

(2019) Brunno B Rosa et al.   SYSTEMATIC BIOLOGY

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

(2019) Marshal Hedin et al.   PeerJ

Myrmecicultoridae, a New Family of Myrmecophilic Spiders from the Chihuahuan Desert (Araneae: Entelegynae)

(2019) Martín J. Ramírez et al.   AMERICAN MUSEUM NOVITATES

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

(2019) Siddharth Kulkarni et al.   Molecular Ecology Resources

A demonstration of unsupervised machine learning in species delimitation

(2019) Shahan Derkarabetian et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reassessing the role of morphology in bryophyte phylogenetics: Combined data improves phylogenetic inference despite character conflict

(2019) Jorge R. Flores et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data

(2019) Vera Opatova et al.   SYSTEMATIC BIOLOGY

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

(2018) Uyen Mai et al.   BMC GENOMICS

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

(2018) Rosa Fernández et al.   CURRENT BIOLOGY

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

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

(2018) Marshal Hedin et al.   Scientific Reports

Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae

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

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

(2017) Erin K Molloy et al.   SYSTEMATIC 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

Hidden histories of gene flow in highland birds revealed with genomic markers

(2016) Eugenia Zarza et al.   MOLECULAR ECOLOGY

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

(2016) James Starrett et al.   Molecular Ecology Resources

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

Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

(2015) Sara Ruane et al.   BMC EVOLUTIONARY BIOLOGY

Morphological Phylogenetics in the Genomic Age

(2015) Michael S.Y. Lee et al.   CURRENT BIOLOGY

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

(2015) Daniele Polotow et al.   INVERTEBRATE SYSTEMATICS

A phylogenetic classification of jumping spiders (Araneae: Salticidae)

(2015) Wayne P. Maddison   JOURNAL OF ARACHNOLOGY

Morphology should not be forgotten in the era of genomics–a phylogenetic perspective

(2015) Gonzalo Giribet   ZOOLOGISCHER ANZEIGER

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Morphology And Phylogeny Of Dionychan Spiders (Araneae: Araneomorphae)

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

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

Molecular phylogeny of the spider family Sparassidae with focus on the genus Eusparassus and notes on the RTA-clade and ‘Laterigradae’

(2014) Majid Moradmand et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The deep phylogeny of jumping spiders (Araneae, Salticidae)

(2014) Wayne Maddison et al.   ZooKeys

High-Throughput Genomic Data in Systematics and Phylogenetics

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

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

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

The Great Silk Alternative: Multiple Co-Evolution of Web Loss and Sticky Hairs in Spiders

(2013) Jonas O. Wolff et al.   PLoS One

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Molecular systematics of Selenops spiders (Araneae: Selenopidae) from North and Central America: implications for Caribbean biogeography

(2010) SARAH C. CREWS et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

A new dimension in combining data? The use of morphology and phylogenomic data in metazoan systematics

(2009) Gonzalo Giribet   ACTA ZOOLOGICA

A comparison of populations of island and adjacent mainland species of Caribbean Selenops (Araneae: Selenopidae) spiders

(2009) Sarah C. Crews et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Weighting against homoplasy improves phylogenetic analysis of morphological data sets

(2008) Pablo A. Goloboff et al.   CLADISTICS

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

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