标题
Characterizing gene tree conflict in plastome-inferred phylogenies
作者
关键词
-
出版物
PeerJ
Volume 7, Issue -, Pages e7747
出版商
PeerJ
发表日期
2019-09-24
DOI
10.7717/peerj.7747
参考文献
相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。- 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
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