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

Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop

(2017) Markus G. Stetter et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Disentangling geographical, biotic, and abiotic drivers of plant diversity in neotropical Ruellia (Acanthaceae)

(2017) Erin A. Tripp et al.   PLoS One

Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae

(2016) R. Massatti et al.   AMERICAN JOURNAL OF BOTANY

Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon

(2016) Carolyn A. Wessinger et al.   AMERICAN JOURNAL OF BOTANY

RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

(2016) Santiago Herrera 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

Phylogeny and biogeography of the American live oaks (QuercussubsectionVirentes): a genomic and population genetics approach

(2015) Jeannine Cavender-Bares et al.   MOLECULAR ECOLOGY

When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny

(2015) Shea M. Lambert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased

(2015) Zhenxiang Xi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

What's in an Outgroup? The Impact of Outgroup Choice on the Phylogenetic Position of Thalattosuchia (Crocodylomorpha) and the Origin of Crocodyliformes

(2015) Eric W. Wilberg   SYSTEMATIC BIOLOGY

Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

(2015) James A. Nicholls et al.   Frontiers in Plant Science

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

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Concatenated alignments and the case of the disappearing tree

(2014) Thorsten Thiergart et al.   BMC EVOLUTIONARY BIOLOGY

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

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

(2014) Frederic Bertels et al.   MOLECULAR BIOLOGY AND EVOLUTION

Should genes with missing data be excluded from phylogenetic analyses?

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

A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses

(2014) Mark P. Simmons   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

A Rich Fossil Record Yields Calibrated Phylogeny for Acanthaceae (Lamiales) and Evidence for Marked Biases in Timing and Directionality of Intercontinental Disjunctions

(2014) Erin A. Tripp et al.   SYSTEMATIC BIOLOGY

Missing Data and Influential Sites: Choice of Sites for Phylogenetic Analysis Can Be As Important As Taxon Sampling and Model Choice

(2013) Liat Shavit Grievink et al.   Genome Biology and Evolution

A New Method for Genome-wide Marker Development and Genotyping Holds Great Promise for Molecular Primatology

(2013) Christina M. Bergey et al.   INTERNATIONAL JOURNAL OF PRIMATOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

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

Páramo is the world's fastest evolving and coolest biodiversity hotspot

(2013) Santiago Madriñán et al.   Frontiers in Genetics

Low levels of climate niche conservatism may explain clade diversity patterns in the South African genus Pelargonium (Geraniaceae)

(2012) Hugo I. Martínez-Cabrera et al.   AMERICAN JOURNAL OF BOTANY

Phylogenetic Relationships within Ruellieae (Acanthaceae) and a Revised Classification

(2012) Erin A. Tripp et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide association genetics of an adaptive trait in lodgepole pine

(2012) THOMAS L. PARCHMAN 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Inferring Phylogenies from RAD Sequence Data

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

Distribution Models and a Dated Phylogeny for Chilean Oxalis Species Reveal Occupation of New Habitats by Different Lineages, not Rapid Adaptive Radiation

(2012) Christoph Heibl et al.   SYSTEMATIC BIOLOGY

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

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

(2010) G. Lunter et al.   GENOME RESEARCH

Global Conservation Significance of Ecuador's Yasuní National Park

(2010) Margot S. Bass et al.   PLoS One

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

Unparalleled rates of species diversification in Europe

(2010) L. M. Valente et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Taxonomic Revision of Ruellia Section Chiropterophila (Acanthaceae): a Lineage of Rare and Endemic Species from Mexico

(2010) Erin A. Tripp   SYSTEMATIC BOTANY

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

Evolution, origin and age of lineages in the Californian and Mediterranean floras

(2009) David D. Ackerly   JOURNAL OF BIOGEOGRAPHY

Stochastic properties of generalised Yule models, with biodiversity applications

(2008) Tanja Gernhard et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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