Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV

(2016)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics

(2016) Chien-Hsun Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale

(2016) Charles S. P. Foster et al.   SYSTEMATIC BIOLOGY

Evolution and protein interactions of AP2 proteins in Brassicaceae: Evidence linking development and environmental responses

(2015) Liping Zeng et al.   Journal of Integrative Plant Biology

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

(2015) Chien-Hsun Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Measuring the tempo of plant death and birth

(2015) Karl J. Niklas   NEW PHYTOLOGIST

Confluence, synnovation, and depauperons in plant diversification

(2015) Michael J. Donoghue et al.   NEW PHYTOLOGIST

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

(2015) David C. Tank et al.   NEW PHYTOLOGIST

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity

(2015) Susana Magallón et al.   NEW PHYTOLOGIST

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

Multiple shifts to different pollinators fuelled rapid diversification in sexually deceptiveOphrysorchids

(2014) Hendrik Breitkopf et al.   NEW PHYTOLOGIST

Tectonic-driven climate change and the diversification of angiosperms

(2014) Anne-Claire Chaboureau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

(2014) Liping Zeng et al.   Nature Communications

Data access for the 1,000 Plants (1KP) project

(2014) Naim Matasci et al.   GigaScience

Multicarpellate gynoecia in angiosperms: occurrence, development, organization and architectural constraints

(2013) Peter K. Endress   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

First Evidence for a Massive Extinction Event Affecting Bees Close to the K-T Boundary

(2013) Sandra M. Rehan et al.   PLoS One

Mammal disparity decreases during the Cretaceous angiosperm radiation

(2013) D. M. Grossnickle et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model

(2012) M Eric Schranz et al.   CURRENT OPINION IN PLANT BIOLOGY

New thoughts about the Cretaceous climate and oceans

(2012) William W. Hay et al.   EARTH-SCIENCE REVIEWS

Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification

(2012) Dries Vekemans et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

(2012) Ning Zhang et al.   NEW PHYTOLOGIST

Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

(2012) Marc T. J. Johnson 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

Phylogenetics of early branching eudicots: Comparing phylogenetic signal across plastid introns, spacers, and genes

(2012) Anna-Magdalena BARNISKE et al.   Journal of Systematics and Evolution

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

Angiosperm phylogeny: 17 genes, 640 taxa

(2011) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Phylogenetic Analysis of the Plastid Inverted Repeat for 244 Species: Insights into Deeper-Level Angiosperm Relationships from a Long, Slowly Evolving Sequence Region

(2011) Michael J. Moore et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A Functional Phylogenomic View of the Seed Plants

(2011) Ernest K. Lee et al.   PLoS Genetics

The age and diversification of the angiosperms re-revisited

(2010) Charles D. Bell et al.   AMERICAN JOURNAL OF BOTANY

Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants

(2010) Cédric Finet et al.   CURRENT BIOLOGY

An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants

(2010) S. A. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

(2010) M. J. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Angiosperm phylogeny inferred from sequences of four mitochondrial genes

(2010) Yin-Long QIU et al.   Journal of Systematics and Evolution

Reconstructing the ancestral angiosperm flower and its initial specializations

(2009) Peter K. Endress et al.   AMERICAN JOURNAL OF BOTANY

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogenetics of Dilleniaceae Using Sequence Data from Four Plastid Loci (rbcL, infA, rps4, rpl16 Intron)

(2009) James W. Horn   INTERNATIONAL JOURNAL OF PLANT SCIENCES

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Temporal lags and overlap in the diversification of weevils and flowering plants

(2009) D. D. McKenna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

(2009) M. E. Alfaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rosid radiation and the rapid rise of angiosperm-dominated forests

(2009) H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Saturation and base composition bias explain phylogenomic conflict in Plasmodium

(2008) Liliana M. Dávalos et al.   GENOMICS

Resolving an Ancient, Rapid Radiation in Saxifragales

(2008) Shuguang Jian et al.   SYSTEMATIC BIOLOGY