A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny

(2017) Kasey K. Pham et al.   GENOME

Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America

(2017) John D. McVay et al.   GENOME

Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus)

(2017) Sorel Fitz-Gibbon et al.   GENOME

Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity

(2017) Andrew L. Hipp et al.   NEW PHYTOLOGIST

A genetic legacy of introgression confounds phylogeny and biogeography in oaks

(2017) John D. McVay et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A novel set of single-copy nuclear gene markers in white oak and implications for species delimitation

(2017) Jun Chen et al.   Tree Genetics & Genomes

Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks (Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes

(2017) Jia Yang et al.   Frontiers in Plant Science

Hybridization and divergence in multi-species oak (Quercus) communities

(2016) Alexis R. Sullivan et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Megaphylogenetic Specimen-level Approaches to the Carex (Cyperaceae) Phylogeny Using ITS, ETS, and matK Sequences: Implications for Classification

(2016) et al.   SYSTEMATIC BOTANY

Genetic characterization of hybridization between native and invasive bittersweet vines (Celastrus spp.)

(2015) David N. Zaya et al.   BIOLOGICAL INVASIONS

Historical introgression among the American live oaks and the comparative nature of tests for introgression

(2015) Deren A. R. Eaton et al.   EVOLUTION

Variation in morphological traits in a recent hybrid zone between closely related Quercus liaotungensis and Q. mongolica (Fagaceae)

(2015) L. Wei et al.   Journal of Plant Ecology

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

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

Taxonomic Relationships and Gene Flow in Four North American Quercus Species (Quercus section Lobatae)

(2015) Sandra A. Owusu et al.   SYSTEMATIC BOTANY

DNA barcodes for ecology, evolution, and conservation

(2015) W. John Kress et al.   TRENDS IN ECOLOGY & EVOLUTION

Variation in morphological traits in a recent hybrid zone between closely related Quercus liaotungensis and Q. mongolica (Fagaceae)

(2015) L. Wei et al.   Journal of Plant Ecology

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Resolving whether botanic gardens are on the road to conservation or a pathway for plant invasions

(2014) Philip E. Hulme   CONSERVATION BIOLOGY

Leaf morphological evidence of natural hybridization between two oak species (Quercus austrocochinchinensis and Q. kerrii) and its implications for conservation management

(2014) Yigang Song et al.   EUROPEAN JOURNAL OF FOREST RESEARCH

HOW COMMON IS HOMOPLOID HYBRID SPECIATION?

(2014) Molly Schumer et al.   EVOLUTION

Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species

(2014) Daniel J. Hasselman et al.   MOLECULAR ECOLOGY

Estimating exotic gene flow into native pine stands: zygotic vs. gametic components

(2014) G. M. Unger et al.   MOLECULAR ECOLOGY

Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?

(2014) Diana M. Percy et al.   MOLECULAR ECOLOGY

High Rates of Gene Flow by Pollen and Seed in Oak Populations across Europe

(2014) Sophie Gerber 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

Multiple nuclear genes stabilize the phylogenetic backbone of the genusQuercus

(2014) François Hubert et al.   SYSTEMATICS AND BIODIVERSITY

De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach

(2013) Venkatramana Pegadaraju et al.   BMC GENOMICS

Application of plastid and nuclear markers to DNA barcoding of Euro-Mediterranean oaks (Quercus, Fagaceae): problems, prospects and phylogenetic implications

(2013) Marco C. Simeone et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Imprints of Natural Selection Along Environmental Gradients in Phenology-Related Genes of Quercus petraea

(2013) F. J. Alberto et al.   GENETICS

Exploring tree species colonization potentials using a spatially explicit simulation model: implications for four oaks under climate change

(2013) Anantha M. Prasad et al.   GLOBAL CHANGE BIOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

(2013) Nicolas Heslot et al.   PLoS One

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

(2012) M. Kearse et al.   BIOINFORMATICS

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

(2012) Davide Scaglione et al.   BMC GENOMICS

Human-impacted landscapes facilitate hybridization between a native and an introduced tree

(2012) Sean M. Hoban et al.   Evolutionary Applications

Fine-scale environmental control of hybridization in oaks

(2012) Lélia Lagache et al.   MOLECULAR ECOLOGY

Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus

(2012) Mariangela Arca et al.   PLoS One

Genetic evidence for hybridization in red oaks (Quercus sect. Lobatae , Fagaceae)

(2011) Emily V. Moran et al.   AMERICAN JOURNAL OF BOTANY

Lengths and correlates of lag phases in upper-Midwest plant invasions

(2011) Daniel J. Larkin   BIOLOGICAL INVASIONS

Identification of SNP and SSR markers in eggplant using RAD tag sequencing

(2011) Lorenzo Barchi et al.   BMC GENOMICS

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

(2011) Emilie Chancerel et al.   BMC GENOMICS

RADSeq: next-generation population genetics

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

Next-generation hybridization and introgression

(2011) A D Twyford et al.   HEREDITY

Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (Quercus spp.)

(2011) E. GUICHOUX et al.   Molecular Ecology Resources

Choosing and Using a Plant DNA Barcode

(2011) Peter M. Hollingsworth et al.   PLoS One

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

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

Interspecific gene flow in a multispecies oak hybrid zone in the Sierra Tarahumara of Mexico

(2010) Juan Manuel Peñaloza-Ramírez et al.   ANNALS OF BOTANY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

(2010) Jérôme Durand et al.   BMC GENOMICS

Realized gene flow within mixed stands of Quercus robur L. and Q. petraea (Matt.) L. revealed at the stage of naturally established seedling

(2010) I. J. CHYBICKI et al.   MOLECULAR ECOLOGY

Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity

(2010) ROBERTA PIREDDA et al.   Molecular Ecology Resources

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex)

(2009) C Burgarella et al.   HEREDITY

High-throughput SNP genotyping with the GoldenGate assay in maize

(2009) Jianbing Yan et al.   MOLECULAR BREEDING

Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama

(2009) W. J. Kress et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

Estimation of Nucleotide Diversity, Disequilibrium Coefficients, and Mutation Rates from High-Coverage Genome-Sequencing Projects

(2008) M. Lynch   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH

Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio

(2008) M. J Hegarty et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Hybrid trait speciation and Heliconius butterflies

(2008) C. D Jiggins et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY

Taxonomy of Hill's Oak (Quercus ellipsoidalis: Fagaceae): Evidence from AFLP Data

(2008) Andrew L. Hipp et al.   SYSTEMATIC BOTANY

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

(2008) Chen Meng et al.   THEORETICAL POPULATION BIOLOGY

Speciation reversal and biodiversity dynamics with hybridization in changing environments

(2007) OLE SEEHAUSEN et al.   MOLECULAR ECOLOGY