Characterizing gene tree conflict in plastome-inferred phylogenies

Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes

(2019) Deise J.P. Gonçalves et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Testing adequacy for DNA substitution models

(2019) Wei Chen et al.   BMC BIOINFORMATICS

Plastid phylogenomic analysis of green plants: A billion years of evolutionary history

(2018) Matthew A. Gitzendanner et al.   AMERICAN JOURNAL OF BOTANY

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy

(2018) David A Duchêne et al.   Genome Biology and Evolution

Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea )

(2018) Charles S.P. Foster et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

(2018) Stephen A. Smith et al.   PLoS One

Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?

(2018) Emilie J. Richards et al.   SYSTEMATIC BIOLOGY

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty

(2018) Maria Chatzou et al.   SYSTEMATIC BIOLOGY

Analyzing Contentious Relationships and Outlier Genes in Phylogenomics

(2018) Joseph F Walker et al.   SYSTEMATIC BIOLOGY

Complete plastome sequences from Bertholletia excelsa and 23 related species yield informative markers for Lecythidaceae

(2018) Ashley M. Thomson et al.   Applications in Plant Sciences

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)

(2017) Alexis R. Sullivan et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes

(2017) Rubén Sancho et al.   NEW PHYTOLOGIST

Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium )

(2017) Oscar M. Vargas et al.   NEW PHYTOLOGIST

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

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

A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

(2016) Xing-Xing Shen et al.   Genome Biology and Evolution

Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses

(2016) Jeremy M. Brown et al.   SYSTEMATIC BIOLOGY

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Instability in progressive multiple sequence alignment algorithms

(2015) Kieran Boyce et al.   Algorithms for Molecular Biology

Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes

(2015) Joseph F. Walker et al.   AMERICAN JOURNAL OF BOTANY

Resolving basal lamiid phylogeny and the circumscription of Icacinaceae with a plastome-scale data set

(2015) Gregory W. Stull et al.   AMERICAN JOURNAL OF BOTANY

Molecular homology and multiple-sequence alignment: an analysis of concepts and practice

(2015) David A. Morrison et al.   AUSTRALIAN SYSTEMATIC BOTANY

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

A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the GenusCitrus

(2015) Jose Carbonell-Caballero et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effects of Partitioning on Phylogenetic Inference

(2015) David Kainer et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Susana Magallón et al.   NEW PHYTOLOGIST

ycf1, the most promising plastid DNA barcode of land plants

(2015) Wenpan Dong et al.   Scientific Reports

Phylogeny of Lamiidae

(2014) Nancy F. Refulio-Rodriguez et al.   AMERICAN JOURNAL OF BOTANY

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

Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: The tortoise and the hare IV

(2014) Joey Shaw et al.   AMERICAN JOURNAL OF BOTANY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

Erasing Errors due to Alignment Ambiguity When Estimating Positive Selection

(2014) Benjamin Redelings   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mitochondrion-to-plastid DNA transfer: it happens

(2014) David Roy Smith   NEW PHYTOLOGIST

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

Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

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

(2014) Liping Zeng et al.   Nature Communications

A Long PCR–Based Approach for DNA Enrichment Prior to Next-Generation Sequencing for Systematic Studies

(2014) Simon Uribe-Convers et al.   Applications in Plant Sciences

Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)

(2013) Shannon C.K. Straub et al.   Genome Biology and Evolution

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

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

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella

(2013) D. W. Rice et al.   SCIENCE

A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

(2013) Gregory W. Stull et al.   Applications in Plant Sciences

Targeted enrichment strategies for next-generation plant biology

(2012) Richard Cronn et al.   AMERICAN JOURNAL OF BOTANY

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complete cpDNA genome sequence of Smilax china and phylogenetic placement of Liliales – Influences of gene partitions and taxon sampling

(2012) Juan Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Primer development for the plastid region ycf1 in Annonaceae and other magnoliids

(2010) Kurt M. Neubig et al.   AMERICAN JOURNAL OF BOTANY

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

Discordant mtDNA and cpDNA phylogenies indicate geographic speciation and reticulation as driving factors for the diversification of the genus Picea

(2010) Marie Bouillé et al.   Tree Genetics & Genomes

Reconstructing the history of Campanulaceae with a Bayesian approach to molecular dating and dispersal–vicariance analyses

(2009) Cristina Roquet et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Why Would Phylogeneticists Ignore Computerized Sequence Alignment?

(2009) David A. Morrison   SYSTEMATIC BIOLOGY

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

Revealing the hidden complexities of mtDNA inheritance

(2008) DANIEL JAMES WHITE et al.   MOLECULAR ECOLOGY

Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns

(2008) Lara D. Shepherd et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH

Dealing with incongruence in phylogenomic analyses

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

Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

(2008) Kurt M. Neubig et al.   PLANT SYSTEMATICS AND EVOLUTION

Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene

(2008) Per Erixon et al.   PLoS One

Resolving an Ancient, Rapid Radiation in Saxifragales

(2008) Shuguang Jian et al.   SYSTEMATIC BIOLOGY