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

Extensive recent secondary contacts between four European white oak species

(2017) Thibault Leroy et al.   NEW PHYTOLOGIST

A genomic perspective on hybridization and speciation

(2016) Bret A. Payseur et al.   MOLECULAR ECOLOGY

A maximum pseudo-likelihood approach for phylogenetic networks

(2015) Yun Yu et al.   BMC GENOMICS

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

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

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

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

(2015) James B. Pease et al.   SYSTEMATIC BIOLOGY

Genetic structure of a natural oak community in central Italy: Evidence of gene flow between three sympatric white oak species (Quercus, Fagaceae)

(2015) Gaby Antonecchia et al.   Annals of Forest Research

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Two are better than one: combining landscape genomics and common gardens for detecting local adaptation in forest trees

(2014) Olivier Lepais et al.   MOLECULAR ECOLOGY

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

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

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interspecific gene flow and maintenance of species integrity in oaks

(2014) Oliver Gailing et al.   Annals of Forest Research

Fast algorithms and heuristics for phylogenomics under ILS and hybridization

(2013) Yun Yu et al.   BMC BIOINFORMATICS

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

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

Genetic structure of Quercus rubra L. and Quercus ellipsoidalis E. J. Hill populations at gene-based EST-SSR and nuclear SSR markers

(2013) Jennifer F. Lind et al.   Tree Genetics & Genomes

Computational approaches to species phylogeny inference and gene tree reconciliation

(2013) Luay Nakhleh   TRENDS IN ECOLOGY & EVOLUTION

Networks: expanding evolutionary thinking

(2013) Eric Bapteste et al.   TRENDS IN GENETICS

Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae

(2012) Mathieu Piednoël et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

(2012) Eric M. O'Neill et al.   MOLECULAR ECOLOGY

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exploring Species Limits in Two Closely Related Chinese Oaks

(2010) Yan-Fei Zeng et al.   PLoS One

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Phylogenetic and trait similarity to a native species predict herbivory on non-native oaks

(2009) I. S. Pearse 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

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

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