From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Constructing a broadly inclusive seed plant phylogeny

(2018) Stephen A. Smith 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

10KP: A phylodiverse genome sequencing plan

(2018) Shifeng Cheng et al.   GigaScience

Living under temporarily arid conditions - succulence as an adaptive strategy

(2018) Urs Eggli et al.   Bradleya

A portrait of the C4photosynthetic family on the 50th anniversary of its discovery: species number, evolutionary lineages, and Hall of Fame

(2017) Rowan F. Sage   JOURNAL OF EXPERIMENTAL BOTANY

Disparity, diversity, and duplications in the Caryophyllales

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

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

(2017) Ya Yang et al.   NEW PHYTOLOGIST

Relaxation of tyrosine pathway regulation underlies the evolution of betalain pigmentation in Caryophyllales

(2017) Samuel Lopez-Nieves et al.   NEW PHYTOLOGIST

Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales)

(2017) Abigail J Moore et al.   SYSTEMATIC BIOLOGY

Resolving Recent Plant Radiations: Power and Robustness of Genotyping-by-Sequencing

(2017) Mario Fernández-Mazuecos et al.   SYSTEMATIC BIOLOGY

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

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses

(2017) Jacob D. Washburn et al.   Scientific Reports

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

Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny

(2016) Stephen A. Smith et al.   BRIEFINGS IN BIOINFORMATICS

Computing the Internode Certainty and Related Measures from Partial Gene Trees

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

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary origins of abnormally large shoot sodium accumulation in nonsaline environments within the Caryophyllales

(2016) Philip J. White et al.   NEW PHYTOLOGIST

Ecophysiological traits of Antarctic vascular plants: their importance in the responses to climate change

(2016) Lohengrin A. Cavieres et al.   PLANT ECOLOGY

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

(2016) Mats Thulin et al.   TAXON

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

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

The Phylogenetic Association Between Salt Tolerance and Heavy Metal Hyperaccumulation in Angiosperms

(2015) Camile Moray et al.   Evolutionary Biology

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

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

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

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

Model-based approach to test hard polytomies in theEulaemusclade of the most diverse South American lizard genusLiolaemus(Liolaemini, Squamata)

(2015) Melisa Olave et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

A taxonomic backbone for the global synthesis of species diversity in the angiosperm orderCaryophyllales

(2015) Patricia Hernández-Ledesma et al.   Willdenowia

Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae)

(2014) Joseph F. Walker et al.   AMERICAN JOURNAL OF BOTANY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

New evidence on the origin of carnivorous plants

(2014) Thomas J. Givnish   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

On the disintegration of Molluginaceae: a new genus and family (Kewa, Kewaceae) segregated from Hypertelis, and placement of Macarthuria in Macarthuriaceae

(2014) Maarten J.M. Christenhusz et al.   Phytotaxa

Agalma: an automated phylogenomics workflow

(2013) Casey W Dunn et al.   BMC BIOINFORMATICS

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

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

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

(2012) Limin Fu et al.   BIOINFORMATICS

A broader model for C4 photosynthesis evolution in plants inferred from the goosefoot family (Chenopodiaceae s.s.)

(2012) G. Kadereit et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The C4 plant lineages of planet Earth

(2011) R. F. Sage et al.   JOURNAL OF EXPERIMENTAL BOTANY

Resolving the evolutionary relationships of molluscs with phylogenomic tools

(2011) Stephen A. Smith et al.   NATURE

Complex pigment evolution in the Caryophyllales

(2011) Samuel F. Brockington et al.   NEW PHYTOLOGIST

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

COMPLEX EVOLUTIONARY TRANSITIONS AND THE SIGNIFICANCE OF C3-C4 INTERMEDIATE FORMS OF PHOTOSYNTHESIS IN MOLLUGINACEAE

(2010) Pascal-Antoine Christin et al.   EVOLUTION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Caryophyllalesphylogenetics: disentanglingPhytolaccaceaeandMolluginaceaeand description ofMicroteaceaeas a new isolated family

(2010) Bastian Schäferhoff et al.   Willdenowia

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

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

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

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Salinity tolerance in halophytes*

(2008) Timothy J. Flowers et al.   NEW PHYTOLOGIST

Dealing with incongruence in phylogenomic analyses

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

Testing Congruence in Phylogenomic Analysis

(2008) Jessica W. Leigh et al.   SYSTEMATIC BIOLOGY

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY