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

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

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

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

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

Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae)

(2016) Karolina Heyduk et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

(2016) Polina Yu Novikova et al.   NATURE GENETICS

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

Capturing protein-coding genes across highly divergent species

(2016) Chenhong Li et al.   BIOTECHNIQUES

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Polyploidy and genome evolution in plants

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

Irrational exuberance for resolved species trees

(2015) Matthew W. Hahn et al.   EVOLUTION

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

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

Genetic Enablers Underlying the Clustered Evolutionary Origins of C4 Photosynthesis in Angiosperms

(2015) Pascal-Antoine Christin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern AfricanOxalis(Oxalidaceae)

(2015) Roswitha Schmickl et al.   Molecular Ecology Resources

Life history lability underlies rapid climate niche evolution in the angiosperm clade Montiaceae

(2015) R. Matthew Ogburn et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

Ensembl Genomes 2016: more genomes, more complexity

(2015) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare

(2015) Dominik Brilhaus et al.   PLANT PHYSIOLOGY

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

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

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

(2015) James A. Nicholls et al.   Frontiers in Plant Science

MarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomes

(2015) Srikar Chamala et al.   Applications in Plant Sciences

Doubling down on genomes: Polyploidy and crop plants

(2014) Simon Renny-Byfield et al.   AMERICAN JOURNAL OF BOTANY

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

Shared origins of a key enzyme during the evolution of C4 and CAM metabolism

(2014) Pascal-Antoine Christin et al.   JOURNAL OF EXPERIMENTAL BOTANY

Multiple isoforms of phosphoenolpyruvate carboxylase in the Orchidaceae (subtribe Oncidiinae): implications for the evolution of crassulacean acid metabolism

(2014) Katia Silvera et al.   JOURNAL OF EXPERIMENTAL BOTANY

Phylogenetic Properties of 50 Nuclear Loci in Medicago (Leguminosae) Generated Using Multiplexed Sequence Capture and Next-Generation Sequencing

(2014) Filipe de Sousa et al.   PLoS One

Phylogenetic relationships in the Didiereaceae with special reference to subfamily Portulacarioideae

(2014) Peter V. Bruyns et al.   TAXON

Land plant origins and coalescence confusion

(2014) Mark S. Springer et al.   TRENDS IN PLANT SCIENCE

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

(2014) Naim Matasci et al.   GigaScience

MICROEVOLUTIONARY PROCESSES GENERATE PHYLOGENOMIC DISCORDANCE AT ANCIENT DIVERGENCES

(2013) Jeffrey C. Oliver   EVOLUTION

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

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

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

(2013) Juliane C. Dohm et al.   NATURE

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Greater efficiency of photosynthetic carbon fixation due to single amino-acid substitution

(2013) Judith Katharina Paulus et al.   Nature Communications

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees

(2012) Maureen Stolzer 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

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

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

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Angiosperm phylogeny: 17 genes, 640 taxa

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

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger 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 phylogenetics of suborder Cactineae (Caryophyllales), including insights into photosynthetic diversification and historical biogeography

(2010) Gilberto Ocampo et al.   AMERICAN JOURNAL OF BOTANY

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

(2010) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

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

Phylogenomics of C4 Photosynthesis in Sedges (Cyperaceae): Multiple Appearances and Genetic Convergence

(2009) G. Besnard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE