Causes and analytical impacts of missing data in RADseq phylogenetics: Insights from an African frog (Afrixalus )

Vanishing refuge? Testing the forest refuge hypothesis in coastal East Africa using genome-wide sequence data for seven amphibians

(2018) Christopher D. Barratt et al.   MOLECULAR ECOLOGY

RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia

(2017) Erin A. Tripp et al.   Ecology and Evolution

Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering

(2017) Richard G. J. Hodel et al.   Scientific Reports

Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes

(2016) Jeffrey W. Streicher et al.   EVOLUTION

RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data

(2016) Sandra L. Hoffberg et al.   Molecular Ecology Resources

RAD-seq data point to a northern origin of the arctic–alpine genus Cassiope (Ericaceae)

(2016) Yan Hou et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Tempo and mode of speciation in Holacanthus angelfishes based on RADseq markers

(2016) Juliette Tariel et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ddRAD-seq phylogenetics based on nucleotide, indel, and presence–absence polymorphisms: Analyses of two avian genera with contrasting histories

(2016) Jeffrey M. DaCosta et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Harnessing the power of RADseq for ecological and evolutionary genomics

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

Comments on detecting rogue taxa using RogueNaRok

(2016) Mark Wilkinson et al.   SYSTEMATICS AND BIODIVERSITY

Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrusspp, Serranidae)

(2016) Sophie Picq et al.   Ecology and Evolution

Multiple glacial refugia lead to genetic structuring and the potential for reproductive isolation in a herbaceous plant

(2015) Karen B. Barnard-Kubow et al.   AMERICAN JOURNAL OF BOTANY

Deeply divergent sympatric mitochondrial lineages of the earthworm Lumbricus rubellus are not reproductively isolated

(2015) Iwona Giska et al.   BMC EVOLUTIONARY BIOLOGY

Reed frog diversification in the Gulf of Guinea: Overseas dispersal, the progression rule, and in situ speciation

(2015) Rayna C. Bell et al.   EVOLUTION

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris)

(2015) Hayley C. Lanier et al.   MOLECULAR ECOLOGY

Evolutionary and biogeographical patterns of barnacles from deep-sea hydrothermal vents

(2015) Santiago Herrera et al.   MOLECULAR ECOLOGY

A RAD-based phylogenetics for Orestias fishes from Lake Titicaca

(2015) Tetsumi Takahashi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The evolutionary history of the embiotocid surfperch radiation based on genome-wide RAD sequence data

(2015) Gary Longo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Processes Driving the Adaptive Radiation of a Tropical Tree (Diospyros, Ebenaceae) in New Caledonia, a Biodiversity Hotspot

(2015) Ovidiu Paun et al.   SYSTEMATIC BIOLOGY

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

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

Phylogenomics of polyploidFothergilla(Hamamelidaceae) by RAD-tag based GBS-insights into species origin and effects of software pipelines

(2015) Zhe-Chen Qi et al.   Journal of Systematics and Evolution

Assessing the phylogeographic history of the montane caddisflyThremma gallicumusing mitochondrial and restriction-site-associated DNA (RAD) markers

(2015) Jan-Niklas Macher et al.   Ecology and Evolution

Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae)

(2015) Yan Hou et al.   PLoS One

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

Use of RAD sequencing for delimiting species

(2014) E Pante et al.   HEREDITY

Phylogeny of Zebrafish, a “Model Species,” within Danio, a “Model Genus”

(2014) Braedan M. McCluskey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Empirical Assessment of RAD Sequencing for Interspecific Phylogeny

(2014) Astrid Cruaud 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

Genomic atolls of differentiation in coral reef fishes (Hypoplectrusspp.,Serranidae)

(2014) O. Puebla et al.   MOLECULAR ECOLOGY

Phylogenomic analyses reveal latitudinal population structure and polymorphisms in heat stress genes in the North Atlantic snailNucella lapillus

(2014) Nathaniel D. Chu et al.   MOLECULAR ECOLOGY

Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock

(2014) Tetsumi Takahashi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Should genes with missing data be excluded from phylogenetic analyses?

(2014) Wei Jiang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

(2014) Andrew L. Hipp et al.   PLoS One

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

High-Throughput Genomic Data in Systematics and Phylogenetics

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

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

Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics

(2013) A. M. Reitzel et al.   MOLECULAR ECOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing

(2013) X. Q. Wang et al.   Molecular Ecology Resources

Replicate Phylogenies and Post-Glacial Range Expansion of the Pitcher-Plant Mosquito, Wyeomyia smithii, in North America

(2013) Clayton Merz et al.   PLoS One

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

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

(2013) Marie Cariou et al.   Ecology and Evolution

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

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner 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

A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases

(2011) Carla A. Cummins et al.   SYSTEMATIC BIOLOGY

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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