Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae)

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

Multi-locus plastid phylogenetic biogeography supports the Asian hypothesis of the temperate woody bamboos (Poaceae: Bambusoideae)

(2016) Xian-Zhi Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic estimation and morphological evolution of Arundinarieae (Bambusoideae: Poaceae) based on plastome phylogenomic analysis

(2016) Lakshmi Attigala et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2016) Santiago Herrera et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Taxonomic Revision of the Temperate Woody Bamboo Genus Kuruna (Poaceae: Bambusoideae: Arundinarieae)

(2016) Lakshmi Attigala et al.   SYSTEMATIC BOTANY

RAD-seq phylogenomics recovers a well-resolved phylogeny of a rapid radiation of mutualistic and antagonistic yucca moths

(2016) CLIVE T. DARWELL et al.   SYSTEMATIC ENTOMOLOGY

Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis

(2015) William P Wysocki et al.   BMC EVOLUTIONARY BIOLOGY

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

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

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

Biogeography and phylogenomics of New World Bambusoideae (Poaceae), revisited

(2014) Sean V. Burke et al.   AMERICAN JOURNAL OF BOTANY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

Restriction site-associated DNA sequencing, genotyping error estimation andde novoassembly optimization for population genetic inference

(2014) A. Mastretta-Yanes et al.   Molecular Ecology Resources

Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers

(2014) Jin Pan et al.   Molecular Ecology Resources

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

Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)

(2014) Peng-Fei Ma et al.   SYSTEMATIC BIOLOGY

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

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny 

(2014) Lakshmi Attigala et al.   Phytotaxa

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

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen 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

The monophyly of Chimonocalamus and conflicting gene trees in Arundinarieae (Poaceae: Bambusoideae) inferred from four plastid and two nuclear markers

(2013) Hong-Mei Yang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

(2013) Zhenhua Peng et al.   NATURE GENETICS

Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd

(2013) Pei Xu et al.   PLANT JOURNAL

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

Bergbambos and Oldeania, new genera of African bamboos (Poaceae, Bambusoideae)

(2013) Chris Stapleton   PhytoKeys

Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes

(2012) I. Keller et al.   MOLECULAR ECOLOGY

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle 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

Complex evolution in Arundinarieae (Poaceae: Bambusoideae): Incongruence between plastid and nuclear GBSSI gene phylogenies

(2012) Yu-Xiao Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring Phylogenies from RAD Sequence Data

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

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Quartet MaxCut: A fast algorithm for amalgamating quartet trees

(2011) Sagi Snir et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

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

(2010) G. Lunter et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Large multi-locus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals ten major lineages and low rate of molecular divergence

(2010) Chun-Xia Zeng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Phylogeny of the Temperate Bamboos (Poaceae: Bambusoideae: Bambuseae) with an Emphasis on Arundinaria and Allies

(2010) Jimmy K. Triplett et al.   SYSTEMATIC BOTANY

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s.

(2008) Sarawood Sungkaew et al.   JOURNAL OF PLANT RESEARCH

Large multi-gene phylogenetic trees of the grasses (Poaceae): Progress towards complete tribal and generic level sampling

(2008) Yanis Bouchenak-Khelladi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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