Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

Disparity, diversity, and duplications in the Caryophyllales

(2017) Stephen A. Smith et al.   NEW PHYTOLOGIST

Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention

(2017) Terezie Mandáková et al.   PLANT JOURNAL

An Efficient Field and Laboratory Workflow for Plant Phylotranscriptomic Projects

(2017) Ya Yang et al.   Applications in Plant Sciences

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

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

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

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

Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae

(2016) Michael S. Barker et al.   AMERICAN JOURNAL OF BOTANY

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

Has the connection between polyploidy and diversification actually been tested?

(2016) Elizabeth A Kellogg   CURRENT OPINION IN PLANT BIOLOGY

Of dups and dinos: evolution at the K/Pg boundary

(2016) Rolf Lohaus et al.   CURRENT OPINION IN PLANT BIOLOGY

Genomic legacies of the progenitors and the evolutionary consequences of allopolyploidy

(2016) Kim A Steige et al.   CURRENT OPINION IN PLANT BIOLOGY

Ancient WGD events as drivers of key innovations in angiosperms

(2016) Pamela S Soltis et al.   CURRENT OPINION IN PLANT BIOLOGY

Computing the Internode Certainty and Related Measures from Partial Gene Trees

(2016) Kassian Kobert et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Phylogeny and generic delimitation in Molluginaceae, new pigment data in Caryophyllales, and the new family Corbichoniaceae

(2016) Mats Thulin et al.   TAXON

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

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

Polyploidy and genome evolution in plants

(2015) Pamela S Soltis et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Untangling reticulate evolutionary relationships among New World and Hawaiian mints (Stachydeae, Lamiaceae)

(2015) Tilottama Roy et al.   MOLECULAR PHYLOGENETICS 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

Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales

(2015) Samuel F. Brockington et al.   NEW PHYTOLOGIST

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

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

(2015) Marina Marcet-Houben et al.   PLOS BIOLOGY

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

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

(2014) Alexandros Stamatakis   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

Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae)

(2014) L Fishman et al.   HEREDITY

Patterns of chromosomal variation in natural populations of the neoallotetraploid Tragopogon mirus (Asteraceae)

(2014) M Chester et al.   HEREDITY

Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

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

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

ChromEvol: Assessing the Pattern of Chromosome Number Evolution and the Inference of Polyploidy along a Phylogeny

(2014) Lior Glick et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution

(2014) Kevin Vanneste et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots

(2014) Yuannian Jiao et al.   PLANT CELL

Allopolyploidy, diversification, and the Miocene grassland expansion

(2014) Matt C. Estep et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus Viola (Violaceae)

(2014) Thomas Marcussen et al.   SYSTEMATIC BIOLOGY

Repeated Origin of Three-Dimensional Leaf Venation Releases Constraints on the Evolution of Succulence in Plants

(2013) R. Matthew Ogburn et al.   CURRENT BIOLOGY

Sequence Analysis of the Genome of Carnation (Dianthus caryophyllus L.)

(2013) M. Yagi et al.   DNA RESEARCH

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

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

Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives

(2013) Kathryn A. Hodgins et al.   Molecular Ecology Resources

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

(2013) Juliane C. Dohm et al.   NATURE

Age Estimates for the Buckwheat Family Polygonaceae Based on Sequence Data Calibrated by Fossils and with a Focus on the Amphi-Pacific Muehlenbeckia

(2013) Tanja M. Schuster et al.   PLoS One

Statistical Inference of Allopolyploid Species Networks in the Presence of Incomplete Lineage Sorting

(2013) Graham Jones et al.   SYSTEMATIC BIOLOGY

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

(2012) Limin Fu et al.   BIOINFORMATICS

Angiosperm Responses to a Low-CO2 World: CAM and C4 Photosynthesis as Parallel Evolutionary Trajectories

(2012) Erika J. Edwards et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Inference of Genome Duplications from Age Distributions Revisited

(2012) Kevin Vanneste et al.   MOLECULAR BIOLOGY AND EVOLUTION

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

Phylogenetics of the Chamaesyce clade (Euphorbia , Euphorbiaceae): Reticulate evolution and long-distance dispersal in a prominent C4 lineage

(2011) Ya Yang et al.   AMERICAN JOURNAL OF BOTANY

Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

(2011) Zhao Lai et al.   AMERICAN JOURNAL OF BOTANY

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

(2011) Torbjørn Rognes   BMC BIOINFORMATICS

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris)

(2011) Juliane C. Dohm et al.   PLANT JOURNAL

Contemporaneous and recent radiations of the world's major succulent plant lineages

(2011) M. Arakaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recently Formed Polyploid Plants Diversify at Lower Rates

(2011) I. Mayrose et al.   SCIENCE

Inferring Species Networks from Gene Trees in High-Polyploid North American and Hawaiian Violets (Viola, Violaceae)

(2011) Thomas Marcussen et al.   SYSTEMATIC BIOLOGY

The age and diversification of the angiosperms re-revisited

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

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

(2010) Ari Löytynoja et al.   BMC BIOINFORMATICS

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

Caryophyllalesphylogenetics: disentanglingPhytolaccaceaeandMolluginaceaeand description ofMicroteaceaeas a new isolated family

(2010) Bastian Schäferhoff et al.   Willdenowia

PADRE: a package for analyzing and displaying reticulate evolution

(2009) Martin Lott et al.   BIOINFORMATICS

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

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

COMPARATIVE GENOMIC AND POPULATION GENETIC ANALYSES INDICATE HIGHLY POROUS GENOMES AND HIGH LEVELS OF GENE FLOW BETWEEN DIVERGENTHELIANTHUSSPECIES

(2009) Nolan C. Kane et al.   EVOLUTION

Variations On A Theme: Repeated Evolution Of Succulent Life Forms In the Portulacineae (Caryophyllales)

(2009) Reto Nyffeler et al.   HASELTONIA

Phylogeny of the Caryophyllales Sensu Lato: Revisiting Hypotheses on Pollination Biology and Perianth Differentiation in the Core Caryophyllales

(2009) Samuel F. Brockington et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

The frequency of polyploid speciation in vascular plants

(2009) T. E. Wood 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

Probabilistic Models of Chromosome Number Evolution and the Inference of Polyploidy

(2009) Itay Mayrose et al.   SYSTEMATIC BIOLOGY

Evolution of Genome size in Hawaiian Endemic Genus Schiedea (Caryophyllaceae)

(2009) Maxim V. Kapralov et al.   Tropical Plant Biology

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

(2008) S. A. Smith et al.   BIOINFORMATICS

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION