Comparative performance of double-digest RAD sequencing across divergent arachnid lineages

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

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

Applications of next-generation sequencing to the study of biological invasions

(2015) Marc Rius et al.   Current Zoology

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

Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

(2015) Adam D. Leaché et al.   Genome Biology and Evolution

Next-Generation Sequencing Panels for the Diagnosis of Colorectal Cancer and Polyposis Syndromes: A Cost-Effectiveness Analysis

(2015) Carlos J. Gallego et al.   JOURNAL OF CLINICAL ONCOLOGY

Sun skink landscape genomics: assessing the roles of micro-evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape

(2015) Anthony J. Barley et al.   MOLECULAR ECOLOGY

Combined next-generation sequencing and morphology reveal fine-scale speciation in Crocodile Skinks (Squamata: Scincidae:Tribolonotus)

(2015) Eric N. Rittmeyer et al.   MOLECULAR ECOLOGY

Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird

(2015) Nicholas A. Mason et al.   MOLECULAR ECOLOGY

Assessing the utility of whole genome amplified DNA for next-generation molecular ecology

(2015) Christopher Blair et al.   Molecular Ecology Resources

Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms

(2015) Hans Recknagel et al.   Molecular Ecology Resources

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

Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake (Crotalus atrox)

(2015) Drew R. Schield et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

(2015) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

EpiRADseq: scalable analysis of genomewide patterns of methylation using next-generation sequencing

(2015) Drew R. Schield et al.   Methods in Ecology and Evolution

Applications of next-generation sequencing to the study of biological invasions

(2015) Marc Rius et al.   Current Zoology

Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species

(2015) Michael G. Harvey et al.   PeerJ

Unnoticed in the tropics: phylogenomic resolution of the poorly known arachnid order Ricinulei (Arachnida)

(2015) Rosa Fernández et al.   Royal Society Open Science

Limitations of Climatic Data for Inferring Species Boundaries: Insights from Speckled Rattlesnakes

(2015) Jesse M. Meik et al.   PLoS One

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Multi-tissue transcriptomics of the black widow spider reveals expansions, co-options, and functional processes of the silk gland gene toolkit

(2014) Thomas H Clarke et al.   BMC GENOMICS

Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq)

(2014) Xiaojing Zhou et al.   BMC GENOMICS

Dramatic expansion of the black widow toxin arsenal uncovered by multi-tissue transcriptomics and venom proteomics

(2014) Robert A Haney et al.   BMC GENOMICS

Development of novel microsatellite markers for the spider genusLoxosceles(Sicariidae) using next-generation sequencing

(2014) Enric Planas et al.   JOURNAL OF ARACHNOLOGY

New sequencing technologies, the development of genomics tools, and their applications in evolutionary arachnology

(2014) Michael S. Brewer et al.   JOURNAL OF ARACHNOLOGY

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

(2014) Prashant P. Sharma et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

(2014) Jeffrey W. Streicher et al.   MOLECULAR ECOLOGY

Genetic consequences of postglacial range expansion in two codistributed rodents (genusDipodomys) depend on ecology and genetic locus

(2014) Tereza Jezkova et al.   MOLECULAR ECOLOGY

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches

(2014) Olivier Lepais et al.   Molecular Ecology Resources

Use of genotyping by sequencing data to develop a high-throughput and multifunctional SNP panel for conservation applications in Pacific lamprey

(2014) Jon E. Hess et al.   Molecular Ecology Resources

The promise and challenge of high-throughput sequencing of the antibody repertoire

(2014) George Georgiou et al.   NATURE BIOTECHNOLOGY

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

(2014) G Albert Wu et al.   NATURE BIOTECHNOLOGY

The common marmoset genome provides insight into primate biology and evolution

(2014) Kim C Worley et al.   NATURE GENETICS

Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol

(2014) Jeffrey M. DaCosta et al.   PLoS One

High-throughput sequencing reveals inbreeding depression in a natural population

(2014) J. I. Hoffman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species Delimitation using Genome-Wide SNP Data

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

Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

(2014) Carlos W Nossa et al.   GigaScience

De novo Ixodes ricinus salivary gland transcriptome analysis using two next-generation sequencing methodologies

(2013) Alexandra Schwarz et al.   FASEB JOURNAL

The evolutionary history ofXiphophorusfish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing

(2013) Julia C. Jones et al.   MOLECULAR ECOLOGY

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

(2013) Juliane C. Dohm et al.   NATURE

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Three new species in the harvestmen genus Acuclavella (Opiliones, Dyspnoi, Ischyropsalidoidea), including description of male Acuclavella quattuor Shear, 1986

(2013) Casey Richart et al.   ZooKeys

The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods

(2013) Zhijian Cao et al.   Nature Communications

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

(2013) Marie Cariou et al.   Ecology and Evolution

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Orthologous genes identified by transcriptome sequencing in the spider genus Stegodyphus

(2012) Tiina M Mattila et al.   BMC GENOMICS

Extreme mitochondrial population subdivision in southern Appalachian paleoendemic spiders (Araneae: Hypochilidae: Hypochilus), with implications for species delimitation

(2012) Robin Keith et al.   JOURNAL OF ARACHNOLOGY

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

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

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

(2012) Marshal Hedin et al.   PLoS One

The correlation of genome size and DNA methylation rate in metazoans

(2012) Marcus Lechner et al.   THEORY IN BIOSCIENCES

The Many Landscapes of Recombination in Drosophila melanogaster

(2012) Josep M. Comeron et al.   PLoS Genetics

Landscape of Next-Generation Sequencing Technologies

(2011) Thomas P. Niedringhaus et al.   ANALYTICAL CHEMISTRY

Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome

(2011) M. V. EVERETT et al.   Molecular Ecology Resources

Genetic diversification without obvious genitalic morphological divergence in harvestmen (Opiliones, Laniatores, Sclerobunus robustus) from montane sky islands of western North America

(2011) Shahan Derkarabetian et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular systematics of sclerosomatid harvestmen (Opiliones, Phalangioidea, Sclerosomatidae): Geography is better than taxonomy in predicting phylogeny

(2011) Marshal Hedin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genome of Tetranychus urticae reveals herbivorous pest adaptations

(2011) Miodrag Grbić et al.   NATURE

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Insects as innovative models for functional studies of DNA methylation

(2011) Frank Lyko et al.   TRENDS IN GENETICS

Repeated and Time-Correlated Morphological Convergence in Cave-Dwelling Harvestmen (Opiliones, Laniatores) from Montane Western North America

(2010) Shahan Derkarabetian et al.   PLoS One

An evaluation of R2 as an inadequate measure for nonlinear models in pharmacological and biochemical research: a Monte Carlo approach

(2010) Andrej-Nikolai Spiess et al.   BMC Pharmacology & Toxicology

Molecular systematics of eastern North American Phalangodidae (Arachnida: Opiliones: Laniatores), demonstrating convergent morphological evolution in caves

(2009) Marshal Hedin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation

(2008) Kristi Kerkel et al.   NATURE GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One