Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere

Phylogenomic conflict coincides with rapid morphological innovation

(2021) Caroline Parins-Fukuchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient introgression between distantly related white oaks (Quercus sect Quercus) shows evidence of climate-associated asymmetric gene exchange

(2021) Scott T O’Donnell et al.   JOURNAL OF HEREDITY

The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans

(2021) Xinjun Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture

(2021) Ying-Ying Yang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle closely associated with the Cretaceous-Paleogene (K-Pg) Mass Extinction Event

(2020) Erik J M Koenen et al.   SYSTEMATIC BIOLOGY

Freezing and water availability structure the evolutionary diversity of trees across the Americas

(2020) Ricardo A. Segovia et al.   Science Advances

Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal

(2020) Jeffrey P Rose et al.   SYSTEMATIC BIOLOGY

Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files

(2020) Milan Malinsky et al.   Molecular Ecology Resources

Fagaceae in the Eocene Palynoflora of the South of Primorskii Region: New Data on Taxonomy and Morphology

(2020) N. N. Naryshkina et al.   PALEONTOLOGICAL JOURNAL

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

(2020) Shingo Miyauchi et al.   Nature Communications

Staminate inflorescences with in situ pollen from Eocene Baltic amber reveal high diversity in Fagaceae (oak family)

(2020) Eva-Maria Sadowski et al.   Willdenowia

Megaphylogeny resolves global patterns of mushroom evolution

(2019) Torda Varga et al.   Nature Ecology & Evolution

Uncovering the genomic signature of ancient introgression between white oak lineages ( Quercus )

(2019) Andrew A. Crowl et al.   NEW PHYTOLOGIST

Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

(2019) Bo-Wen Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Eocene Fagaceae from Patagonia and Gondwanan legacy in Asian rainforests

(2019) Peter Wilf et al.   SCIENCE

The oak syngameon: more than the sum of its parts

(2019) Charles H. Cannon et al.   NEW PHYTOLOGIST

Environment‐dependent introgression from Quercus dentata to a coastal ecotype of Quercus mongolica var. crispula in northern Japan

(2019) Teruyoshi Nagamitsu et al.   NEW PHYTOLOGIST

Adaptive introgression as a driver of local adaptation to climate in European white oaks

(2019) Thibault Leroy et al.   NEW PHYTOLOGIST

Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)

(2019) Yu Xing et al.   GigaScience

Genomic landscape of the global oak phylogeny

(2019) Andrew L. Hipp et al.   NEW PHYTOLOGIST

Global imprint of mycorrhizal fungi on whole-plant nutrient economics

(2019) Colin Averill et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oaks: an evolutionary success story

(2019) Antoine Kremer et al.   NEW PHYTOLOGIST

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

(2019) Nathan S. Upham et al.   PLOS BIOLOGY

A late Cretaceous fagalean inflorescence preserved in amber from New Jersey

(2018) Maria A. Gandolfo et al.   AMERICAN JOURNAL OF BOTANY

Adaptive introgression: a plant perspective

(2018) Adriana Suarez-Gonzalez et al.   Biology Letters

DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution

(2018) Xuhua Xia   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny and biogeography of East Asian evergreen oaks ( Quercus section Cyclobalanopsis ; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia

(2018) Min Deng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

(2018) Stephen A. Smith et al.   PLoS One

The role of land bridges, ancient environments, and migrations in the assembly of the North American flora

(2018) Alan Graham   Journal of Systematics and Evolution

A reference genome of the European beech (Fagus sylvatica L.)

(2018) Bagdevi Mishra et al.   GigaScience

Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary

(2018) Michael E. Alfaro et al.   Nature Ecology & Evolution

Incorporating fossils into the Pinaceae tree of life

(2018) David S. Gernandt et al.   AMERICAN JOURNAL OF BOTANY

Origin and macroevolution of micro-moths on sunken Hawaiian Islands

(2018) Chris A. Johns et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Diversification, adaptation, and community assembly of the American oaks (Quercus ), a model clade for integrating ecology and evolution

(2018) Jeannine Cavender-Bares   NEW PHYTOLOGIST

Contemporaneous radiations of fungi and plants linked to symbiosis

(2018) François Lutzoni et al.   Nature Communications

Oldest skeleton of a fossil flying squirrel casts new light on the phylogeny of the group

(2018) Isaac Casanovas-Vilar et al.   eLife

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

PhyloNetworks: A Package for Phylogenetic Networks

(2017) Claudia Solís-Lemus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

(2017) Jarkko Salojärvi et al.   NATURE GENETICS

Fine-scale species distribution changes in a mixed oak stand over two successive generations

(2017) Laura Truffaut et al.   NEW PHYTOLOGIST

Plant size: a key determinant of diversification?

(2017) Florian C. Boucher et al.   NEW PHYTOLOGIST

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

Contentious relationships in phylogenomic studies can be driven by a handful of genes

(2017) Xing-Xing Shen et al.   Nature Ecology & Evolution

A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation

(2016) Hussein A. Hejase et al.   BMC BIOINFORMATICS

Multispecies genetic structure and hybridization in theBetulagenus across Eurasia

(2016) Yoshiaki Tsuda et al.   MOLECULAR ECOLOGY

A genomic perspective on hybridization and speciation

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

Genomics of hybridization and its evolutionary consequences

(2016) Richard J. Abbott et al.   MOLECULAR ECOLOGY

A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides)

(2016) Knud Andreas Jønsson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Unearthing the roots of ectomycorrhizal symbioses

(2016) Francis Martin et al.   NATURE REVIEWS MICROBIOLOGY

The BIG Data Center: from deposition to integration to translation

(2016)   NUCLEIC ACIDS RESEARCH

Hybridization in Plants: Old Ideas, New Techniques

(2016) Benjamin E. Goulet et al.   PLANT PHYSIOLOGY

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

Plastome data reveal multiple geographic origins ofQuercusGroup Ilex

(2016) Marco Cosimo Simeone et al.   PeerJ

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

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

(2015) Richard O. Prum et al.   NATURE

Phylogenetic investigation of the complex evolutionary history of dispersal mode and diversification rates across living and fossil Fagales

(2015) Kathryn Larson-Johnson   NEW PHYTOLOGIST

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

Evolutionary trends and ecological differentiation in early Cenozoic Fagaceae of western North America

(2014) J. Bouchal et al.   AMERICAN JOURNAL OF BOTANY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos 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

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

(2014) Emilia Huerta-Sánchez et al.   NATURE

Large-scale phylogenetic analyses reveal fagalean diversification promoted by the interplay of diaspores and environments in the Paleogene

(2014) Xiao-Guo Xiang et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Genome size variation in the Fagaceae and its implications for trees

(2014) Si-Chong Chen et al.   Tree Genetics & Genomes

BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

(2014) Daniel L. Rabosky et al.   Methods in Ecology and Evolution

Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data

(2013) B. L. Browning et al.   GENETICS

Conservation and Functional Element Discovery in 20 Angiosperm Plant Genomes

(2013) D. Hupalo et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

Time Scales of Critical Events Around the Cretaceous-Paleogene Boundary

(2013) P. R. Renne et al.   SCIENCE

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

(2012) M. Kearse et al.   BIOINFORMATICS

Comparative mapping in the Fagaceae and beyond with EST-SSRs

(2012) Catherine Bodénès et al.   BMC PLANT BIOLOGY

Menispermaceae and the diversification of tropical rainforests near the Cretaceous-Paleogene boundary

(2012) Wei Wang et al.   NEW PHYTOLOGIST

Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

(2012) Dongmei Chen et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Genomics of Fagaceae

(2012) Antoine Kremer et al.   Tree Genetics & Genomes

Phylogeography and climatic niche evolution in live oaks (Quercus series Virentes) from the tropics to the temperate zone

(2011) Jeannine Cavender-Bares et al.   JOURNAL OF BIOGEOGRAPHY

Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

(2011) M. d. Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Testing for Ancient Admixture between Closely Related Populations

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

Phylogeographically concordant chloroplast DNA divergence in sympatric Nothofagus s.s. How deep can it be?

(2011) Andrea C. Premoli et al.   NEW PHYTOLOGIST

Fagaceae from the early Oligocene of Central Europe: Persisting new world and emerging old world biogeographic links

(2011) Thomas Denk et al.   REVIEW OF PALAEOBOTANY AND PALYNOLOGY

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

How plants manipulate the scatter-hoarding behaviour of seed-dispersing animals

(2010) S. B. Vander Wall   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis

(2010) Paola Bonfante et al.   Nature Communications

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

EXTREME HOST PLANT CONSERVATISM DURING AT LEAST 20 MILLION YEARS OF HOST PLANT PURSUIT BY OAK GALLWASPS

(2009) Graham N. Stone et al.   EVOLUTION

Significance of Pollen Characteristics for Infrageneric Classification and Phylogeny in Quercus (Fagaceae)

(2009) Thomas Denk et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Gene flow and species delimitation

(2009) Rémy J. Petit et al.   TRENDS IN ECOLOGY & EVOLUTION

Species Tree Inference by Minimizing Deep Coalescences

(2009) Cuong Than et al.   PLoS Computational Biology

Nucleotide variation in Quercus crispula Blume

(2008) N D Quang et al.   HEREDITY

Seed dispersal patterns in a temperate forest during a mast event: performance of alternative dispersal kernels

(2008) Isabel Martínez et al.   OECOLOGIA

A phylogenetic perspective on the distribution of plant diversity

(2008) M. J. Donoghue   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

(2008) S. A. Smith et al.   SCIENCE