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

Polyploidy: Pitfalls and paths to a paradigm

(2016) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Has the connection between polyploidy and diversification actually been tested?

(2016) Elizabeth A Kellogg   CURRENT OPINION IN PLANT BIOLOGY

Macroevolutionary dynamics in the early diversification of Asteraceae

(2016) Jose L. Panero et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

(2015) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Phylogenetic uncertainty and fossil calibration of Asteraceae chronograms

(2015) Jose L. Panero   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reply to Panero: Robust phylogenetic placement of fossil pollen grains: The case of Asteraceae

(2015) Viviana D. Barreda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early evolution of the angiosperm clade Asteraceae in the Cretaceous of Antarctica

(2015) Viviana D. Barreda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The butterfly plant arms-race escalated by gene and genome duplications

(2015) Patrick P. Edger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

(2015) Jun Inoue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using phylogenomics to resolve mega-families: An example from Compositae

(2015) Jennifer R. Mandel et al.   Journal of Systematics and Evolution

Early genome duplications in conifers and other seed plants

(2015) Z. Li et al.   Science Advances

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Phylogenetic approaches for studying diversification

(2014) Hélène Morlon   ECOLOGY LETTERS

TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

(2014) Torsten H. Struck   Evolutionary 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 Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

(2014) Steven B. Cannon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae

(2014) Jose L. Panero et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Polyploid Evolution of the Brassicaceae during the Cenozoic Era

(2014) Sateesh Kagale et al.   PLANT CELL

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

Reconstructing the evolution and biogeographic history of tribe Cardueae (Compositae)

(2013) L. Barres et al.   AMERICAN JOURNAL OF BOTANY

A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana

(2013) Jeremy M Beaulieu et al.   BMC EVOLUTIONARY BIOLOGY

Disruption of the petal identity gene APETALA3-3 is highly correlated with loss of petals within the buttercup family (Ranunculaceae)

(2013) R. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polyploids Exhibit Higher Potassium Uptake and Salinity Tolerance in Arabidopsis

(2013) D.-Y. Chao et al.   SCIENCE

Range expansion of a selfing polyploid plant despite widespread genetic uniformity

(2012) Nicole Voss et al.   ANNALS OF BOTANY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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

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

Rarely successful polyploids and their legacy in plant genomes

(2012) Nils Arrigo et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2012) Ning Zhang et al.   NEW PHYTOLOGIST

Genetic Analysis of Floral Symmetry in Van Gogh's Sunflowers Reveals Independent Recruitment of CYCLOIDEA Genes in the Asteraceae

(2012) Mark A. Chapman et al.   PLoS Genetics

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications

(2011) Corey M. Hudson et al.   Genome Biology and Evolution

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Petal-specific subfunctionalization of an APETALA3 paralog in the Ranunculales and its implications for petal evolution

(2011) Bharti Sharma et al.   NEW PHYTOLOGIST

Two-Phase Resolution of Polyploidy in theArabidopsisMetabolic Network Gives Rise to Relative and Absolute Dosage Constraints

(2011) Michaël Bekaert et al.   PLANT CELL

Recently Formed Polyploid Plants Diversify at Lower Rates

(2011) I. Mayrose et al.   SCIENCE

Insights from the Comparison of Plant Genome Sequences

(2010) Andrew H. Paterson et al.   Annual Review of Plant Biology

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Piecemeal or big bangs: correlating the vertebrate evolution with proposed models of gene expansion events

(2010) Amir Ali Abbasi   NATURE REVIEWS GENETICS

2R or not 2R is not the question anymore

(2010) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

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

Diversity dynamics: molecular phylogenies need the fossil record

(2010) Tiago B. Quental et al.   TRENDS IN ECOLOGY & EVOLUTION

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Calibrating the Tree of Life: fossils, molecules and evolutionary timescales

(2009) Félix Forest   ANNALS OF BOTANY

Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

(2009) Michael Freeling   Annual Review of Plant Biology

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

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

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates

(2009) M. W. Hahn   JOURNAL OF HEREDITY

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

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

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

(2009) H. Tang 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

Surviving the K-T mass extinction: New perspectives of polyploidization in angiosperms

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

Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

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

Pollinator and nonpollinator selection on ray morphology in Leucanthemum vulgare (oxeye daisy, Asteraceae)

(2008) S. Andersson   AMERICAN JOURNAL OF BOTANY

Angiosperm diversification through time

(2008) Susana Magallón et al.   AMERICAN JOURNAL OF BOTANY

Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years

(2008) M. S. Barker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Positive Selection and Expression Divergence Following Gene Duplication in the Sunflower CYCLOIDEA Gene Family

(2008) M. A. Chapman et al.   MOLECULAR BIOLOGY AND EVOLUTION

The value of sampling anomalous taxa in phylogenetic studies: Major clades of the Asteraceae revealed

(2008) Jose L. Panero et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

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

(2008) James C. Zachos et al.   NATURE