Climate‐influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone

Phylogenetic relationships, hybridization events, and drivers of diversification of East Asian wild grapes as revealed by phylogenomic analyses

(2022) Zhi‐Yao Ma et al.   Journal of Systematics and Evolution

Untangling the Evolution of American Wild Grapes: Admixed Species and How to Find Them

(2020) Giovanni Zecca et al.   Frontiers in Plant Science

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

Recent accelerated diversification in rosids occurred outside the tropics

(2020) Miao Sun et al.   Nature Communications

Phylogenomic relationships and character evolution of the grape family (Vitaceae)

(2020) Zhi-Yao Ma et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Combinatorial View on Speciation and Adaptive Radiation

(2019) David A. Marques et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

(2019) Emily J Roycroft et al.   SYSTEMATIC BIOLOGY

Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times

(2019) Qiqing Tao et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic landscape of the global oak phylogeny

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

PHYLOGENETIC CONFLICTS, COMBINABILITY, AND DEEP PHYLOGENOMICS IN PLANTS

(2019) Stephen A Smith et al.   SYSTEMATIC BIOLOGY

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

(2018) Laura L. Klein et al.   AMERICAN JOURNAL OF BOTANY

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

(2018) James B. Pease et al.   AMERICAN JOURNAL OF BOTANY

Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus

(2018) Heather Rose Kates et al.   AMERICAN JOURNAL OF BOTANY

Adaptive introgression: a plant perspective

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

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Reconstructing deep-time palaeoclimate legacies in the clusioid Malpighiales unveils their role in the evolution and extinction of the boreotropical flora

(2018) Andrea S. Meseguer et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

(2018) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Anchored Hybrid Enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex

(2018) Diego Bogarín et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

(2018) Diego F. Morales-Briones et al.   NEW PHYTOLOGIST

Testing reticulate evolution of four Vitis species from East Asia using restriction-site associated DNA sequencing

(2018) Zhi-Yao Ma et al.   Journal of Systematics and Evolution

Chloroplast phylogenomics of the New World grape species (Vitis , Vitaceae)

(2018) Jun Wen et al.   Journal of Systematics and Evolution

An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus )

(2018) Julie A. Lee-Yaw et al.   NEW PHYTOLOGIST

Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae)

(2018) Daniel J MacGuigan et al.   SYSTEMATIC BIOLOGY

PhyloNetworks: A Package for Phylogenetic Networks

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

Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium )

(2017) Oscar M. Vargas et al.   NEW PHYTOLOGIST

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families

(2017) David A Duchêne et al.   SYSTEMATIC BIOLOGY

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

(2017) Dahiana Arcila et al.   Nature Ecology & Evolution

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

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

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

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

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

Multilocus species tree analyses resolve the ancient radiation of the subtribe Zizaniinae (Poaceae)

(2015) Liang Tang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Deep phylogenetic incongruence in the angiosperm clade Rosidae

(2015) Miao Sun et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Temperate radiations and dying embers of a tropical past: the diversification ofViburnum

(2015) Elizabeth L. Spriggs et al.   NEW PHYTOLOGIST

Genetic Analysis of East Asian Grape Cultivars Suggests Hybridization with Wild Vitis

(2015) Nami Goto-Yamamoto et al.   PLoS One

Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming

(2015) Ning Zhang et al.   PLoS One

A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution

(2014) Wendy L. Clement 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

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

FOSSILS AND A LARGE MOLECULAR PHYLOGENY SHOW THAT THE EVOLUTION OF SPECIES RICHNESS, GENERIC DIVERSITY, AND TURNOVER RATES ARE DISCONNECTED

(2014) Yaowu Xing et al.   EVOLUTION

Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

(2014) Rezwana Reaz et al.   PLoS One

Integrating Fossils, Phylogenies, and Niche Models into Biogeography to Reveal Ancient Evolutionary History: The Case of Hypericum (Hypericaceae)

(2014) Andrea S. Meseguer et al.   SYSTEMATIC BIOLOGY

Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades

(2014) Nicholas J. Matzke   SYSTEMATIC BIOLOGY

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

Oldest fruits of the grape family (Vitaceae) from the Late Cretaceous Deccan Cherts of India

(2013) Steven R. Manchester et al.   AMERICAN JOURNAL OF BOTANY

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

Transcriptome Sequences Resolve Deep Relationships of the Grape Family

(2013) Jun Wen et al.   PLoS One

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

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

Bayesian Analysis of Biogeography when the Number of Areas is Large

(2013) Michael J. Landis et al.   SYSTEMATIC BIOLOGY

treePL: divergence time estimation using penalized likelihood for large phylogenies

(2012) Stephen A. Smith et al.   BIOINFORMATICS

Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae)

(2012) Ze-Long Nie et al.   BMC EVOLUTIONARY BIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Molecular phylogeny of Cissus L. of Vitaceae (the grape family) and evolution of its pantropical intercontinental disjunctions

(2012) Xiu-Qun Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genetic diversity, structure, and patterns of differentiation in the genus Vitis

(2012) M. Aradhya et al.   PLANT SYSTEMATICS AND EVOLUTION

Estimating divergence times in large molecular phylogenies

(2012) K. Tamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Grasses and Grassland Ecosystems

(2011) Caroline A.E. Strömberg   Annual Review of Earth and Planetary Sciences

Long-Term Ecological Records and Their Relevance to Climate Change Predictions for a Warmer World

(2011) K.J. Willis et al.   Annual Review of Ecology Evolution and Systematics

Origin and global diversification patterns of tropical rain forests: inferences from a complete genus-level phylogeny of palms

(2011) Thomas LP Couvreur et al.   BMC BIOLOGY

Seed Morphology of Vitaceae

(2011) Iju Chen et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

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

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

Mass Extinction, Gradual Cooling, or Rapid Radiation? Reconstructing the Spatiotemporal Evolution of the Ancient Angiosperm Genus Hedyosmum (Chloranthaceae) Using Empirical and Simulated Approaches

(2011) Alexandre Antonelli et al.   SYSTEMATIC BIOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Molecular phylogeny and biogeographic diversification of Parthenocissus (Vitaceae) disjunct between Asia and North America

(2010) Ze-Long Nie et al.   AMERICAN JOURNAL OF BOTANY

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

Vitis seeds (Vitaceae) from the late Neogene Gray Fossil Site, northeastern Tennessee, U.S.A.

(2010) Fade Gong et al.   REVIEW OF PALAEOBOTANY AND PALYNOLOGY

The Role of Hybridization in Plant Speciation

(2009) Pamela S. Soltis et al.   Annual Review of Plant Biology

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Increased seasonality through the Eocene to Oligocene transition in northern high latitudes

(2009) James S. Eldrett et al.   NATURE

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Speciation in fungi

(2008) Tatiana Giraud et al.   FUNGAL GENETICS AND BIOLOGY

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

(2008) G DROUIN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics

(2008) James C. Zachos et al.   NATURE

Introduction. Extent, processes and evolutionary impact of interspecific hybridization in animals

(2008) K. Schwenk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis

(2008) Richard H. Ree et al.   SYSTEMATIC BIOLOGY