High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections

Exploiting Wild Relatives for Genomics-assisted Breeding of Perennial Crops

(2017) Zoë Migicovsky et al.   Frontiers in Plant Science

Patterns of genomic and phenomic diversity in wine and table grapes

(2017) Zoë Migicovsky et al.   Horticulture Research

Single nucleotide polymorphism discovery via genotyping by sequencing to assess population genetic structure and recurrent polyploidization in Andropogon gerardii

(2016) Christine A. McAllister et al.   AMERICAN JOURNAL OF BOTANY

Climatic Niche Characterization of 13 North American Vitis Species

(2016) S. T. Callen et al.   AMERICAN JOURNAL OF ENOLOGY AND VITICULTURE

Genomic ancestry estimation quantifies use of wild species in grape breeding

(2016) Zoë Migicovsky et al.   BMC GENOMICS

Phylogeny of the Ampelocissus–Vitis clade in Vitaceae supports the New World origin of the grape genus

(2016) Xiu-Qun Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes

(2016) Emily J. Warschefsky et al.   TRENDS IN PLANT SCIENCE

Climate change decouples drought from early wine grape harvests in France

(2016) Benjamin I. Cook et al.   Nature Climate Change

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)

(2016) Simon Uribe-Convers et al.   PLoS One

Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

(2015) Julia Chifman et al.   JOURNAL OF THEORETICAL BIOLOGY

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

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

Latent developmental and evolutionary shapes embedded within the grapevine leaf

(2015) Daniel H. Chitwood et al.   NEW PHYTOLOGIST

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

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

Expression patterns ofAP1,FUL,FTandLEAFYorthologs in Vitaceae support the homology of tendrils and inflorescences throughout the grape family

(2015) Ning Zhang et al.   Journal of Systematics and Evolution

Enhancing the Conservation of Crop Wild Relatives in England

(2015) Hannah Fielder et al.   PLoS One

Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine

(2015) Katie E. Hyma et al.   PLoS One

The Genetic Structure of Marijuana and Hemp

(2015) Jason Sawler et al.   PLoS One

Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [Prunus persica (L.) Batsch]

(2015) Douglas Gary Bielenberg 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

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

(2014) Jeffrey C. Glaubitz et al.   PLoS One

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

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

Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

(2014) Jiangfeng He et al.   Frontiers in Plant Science

A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change

(2013) Yizhen Wan et al.   BMC EVOLUTIONARY BIOLOGY

A Modern Ampelography: A Genetic Basis for Leaf Shape and Venation Patterning in Grape

(2013) D. H. Chitwood et al.   PLANT PHYSIOLOGY

Vitis Phylogenomics: Hybridization Intensities from a SNP Array Outperform Genotype Calls

(2013) Allison J. Miller et al.   PLoS One

Climate change, wine, and conservation

(2013) L. Hannah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) M. Kearse et al.   BIOINFORMATICS

Chestnut resistance to the blight disease: insights from transcriptome analysis

(2012) Abdelali Barakat et al.   BMC PLANT BIOLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genotyping-by-Sequencing for Plant Breeding and Genetics

(2012) Jesse A. Poland et al.   Plant Genome

From forest to field: Perennial fruit crop domestication

(2011) Allison J. Miller et al.   AMERICAN JOURNAL OF BOTANY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The timing and the mode of evolution of wild grapes (Vitis)

(2011) Giovanni Zecca et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

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

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

Genetic structure and domestication history of the grape

(2011) Sean Myles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular phylogeny of the genus Vitis (Vitaceae) based on plastid markers

(2010) Dorothee Tröndle et al.   AMERICAN JOURNAL OF BOTANY

Genetic variation and biogeography of the disjunct Vitis subg. Vitis (Vitaceae)

(2010) Jean-Pierre Péros et al.   JOURNAL OF BIOGEOGRAPHY

The evolutionary ecology of clonally propagated domesticated plants

(2010) Doyle McKey et al.   NEW PHYTOLOGIST

Variation Within and Among Vitis spp. for Foliar Resistance to the Powdery Mildew Pathogen Erysiphe necator

(2010) Lance Cadle-Davidson et al.   PLANT DISEASE

Evolution and history of grapevine (Vitis vinifera) under domestication: new morphometric perspectives to understand seed domestication syndrome and reveal origins of ancient European cultivars

(2009) Jean-Frédéric Terral et al.   ANNALS OF BOTANY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

(2008) S. A. Smith et al.   BIOINFORMATICS

Variation Within and Between Vitis spp. for Foliar Resistance to the Downy Mildew Pathogen Plasmopara viticola

(2008) Lance Cadle-Davidson   PLANT DISEASE