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The Prevalence and Impact of Model Violations in Phylogenetics Analysis
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Statistical tests of models of DNA substitution
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Estimating the pattern of nucleotide substitution
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
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Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
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Compositional Bias May Affect Both DNA-Based and Protein-Based Phylogenetic Reconstructions
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Evidence for the most basal split in land plants dividing bryophyte and tracheophyte lineages
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Lights out: the evolution of bacterial bioluminescence in Loliginidae
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A call for mtDNA data quality control in forensic science
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The mean value of the squared path-difference distance for rooted phylogenetic trees
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Improving the Analysis of Dinoflagellate Phylogeny based on rDNA
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Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA
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Testing the phylogenetic affinities of Southeast Asia’s rarest geckos: Flap-legged geckos (Luperosaurus), Flying geckos (Ptychozoon) and their relationship to the pan-Asian genus Gekko
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Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): Reconciling more than 100 years of taxonomic confusion
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Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea
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An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures
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Genome sequence of the human malaria parasite Plasmodium falciparum
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Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida
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Acoelomorph flatworms are deuterostomes related to Xenoturbella
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A synchronized global sweep of the internal genes of modern avian influenza virus
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Xenacoelomorpha is the sister group to Nephrozoa
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Tectonic collision and uplift of Wallacea triggered the global songbird radiation
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ModelFinder: fast model selection for accurate phylogenetic estimates
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Deep mitochondrial origin outside the sampled alphaproteobacteria
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An Approximately Unbiased Test of Phylogenetic Tree Selection
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Modeling Compositional Heterogeneity
inferredcites →https://doi.org/10.1080/10635150490468648openalex-snapshot
The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated
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Tracing the Decay of the Historical Signal in Biological Sequence Data
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Efficient Likelihood Computations with Nonreversible Models of Evolution
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inferredcites →https://doi.org/10.1093/bioinformatics/btl283openalex-snapshot
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inferredcites →https://doi.org/10.1093/bioinformatics/btn651openalex-snapshot
PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu157openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msg073openalex-snapshot
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Statistics and Truth in Phylogenomics
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inferredcites →https://doi.org/10.1093/molbev/msx281openalex-snapshot
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inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026201openalex-snapshot
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040182openalex-snapshot
Tests of applicability of several substitution models for DNA sequence data.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040220openalex-snapshot
On the use of nucleic acid sequences to infer early branchings in the tree of life.
inferredcites →https://doi.org/10.1093/sysbio/42.2.126openalex-snapshot
Distributions of Tree Comparison Metrics--Some New Results
inferredcites →https://doi.org/10.1093/sysbio/syp037openalex-snapshot
Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1093/sysbio/syr116openalex-snapshot
Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil-Rich Group: The Case of Nothofagus (Fagales)
inferredcites →https://doi.org/10.1093/sysbio/sys029openalex-snapshot
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
inferredcites →https://doi.org/10.1093/sysbio/sys046openalex-snapshot
Fitting Nonstationary General-Time-Reversible Models to Obtain Edge-Lengths and Frequencies for the Barry–Hartigan Model
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The Evolution of Pharyngognathy: A Phylogenetic and Functional Appraisal of the Pharyngeal Jaw Key Innovation in Labroid Fishes and Beyond
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Continental Diversification of an African Catfish Radiation (Mochokidae: Synodontis)
inferredcites →https://doi.org/10.1093/sysbio/syt016openalex-snapshot
A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences
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Bayesian Tests of Topology Hypotheses with an Example from Diving Beetles
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Addressing Gene Tree Discordance and Non-Stationarity to Resolve a Multi-Locus Phylogeny of the Flatfishes (Teleostei: Pleuronectiformes)
inferredcites →https://doi.org/10.1093/sysbio/syu002openalex-snapshot
Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit
inferredcites →https://doi.org/10.1093/sysbio/syu031openalex-snapshot
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inferredcites →https://doi.org/10.1093/sysbio/syv021openalex-snapshot
A New Hierarchy of Phylogenetic Models Consistent with Heterogeneous Substitution Rates
inferredcites →https://doi.org/10.1093/sysbio/syw021openalex-snapshot
RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
inferredcites →https://doi.org/10.1093/sysbio/syw037openalex-snapshot
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
inferredcites →https://doi.org/10.1093/sysbio/syw101openalex-snapshot
Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses
inferredcites →https://doi.org/10.1098/rspb.2002.1961openalex-snapshot
Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds
inferredcites →https://doi.org/10.1098/rspb.2013.0184openalex-snapshot
Large-scale phylogeny of chameleons suggests African origins and Eocene diversification
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Ancient host shifts followed by host conservatism in a group of ant parasitoids
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Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis
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Phylogenetic Relationships within Cation Transporter Families of Arabidopsis
inferredcites →https://doi.org/10.1111/evo.12534openalex-snapshot
Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway
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inferredcites →https://doi.org/10.1146/annurev.ecolsys.35.112202.130205openalex-snapshot
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inferredcites →https://doi.org/10.1146/annurev.ecolsys.36.102003.152633openalex-snapshot
Model Selection in Phylogenetics
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What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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The phylogenomic revolution and its conceptual innovations: a text mining approach
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Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models for Mammals
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The Influence of Model Violation on Phylogenetic Inference: A Simulation Study
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Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies
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