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Evaluating the Impact of Anatomical Partitioning on Summary Topologies Obtained with Bayesian Phylogenetic Analyses of Morphological Data

https://doi.org/10.1093/sysbio/syac076
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Corroboration among Data Sets in Simultaneous Analysis: Hidden Support for Phylogenetic Relationships among Higher Level Artiodactyl Taxa
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The Dorsal Integument of the Southern Long-Nosed Armadillo Dasypus hybridus (Cingulata, Xenarthra), and a Possible Neural Crest Origin of the Osteoderms. Discussing Evolutive Consequences for Amniota
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Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: An avian case study
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Combining genomic, phenotypic and Sanger sequencing data to elucidate the phylogeny of the two-clawed spiders (Dionycha)
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Seven rules for simulations in paleobiology
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Mammalian skull heterochrony reveals modular evolution and a link between cranial development and brain size
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Endochondral bone in an Early Devonian ‘placoderm’ from Mongolia
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Sustained high rates of morphological evolution during the rise of tetrapods
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A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data
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Bayesian Phylogenetic Analysis of Combined Data
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The Importance of Proper Model Assumption in Bayesian Phylogenetics
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The Role of Morphological Data in Phylogeny Reconstruction
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Partitioned Bayesian Analyses, Partition Choice, and the Phylogenetic Relationships of Scincid Lizards
inferredcites →https://doi.org/10.1080/10635150601087641openalex-snapshot
Accurate Branch Length Estimation in Partitioned Bayesian Analyses Requires Accommodation of Among-Partition Rate Variation and Attention to Branch Length Priors
inferredcites →https://doi.org/10.1080/10635150701546249openalex-snapshot
The Importance of Data Partitioning and the Utility of Bayes Factors in Bayesian Phylogenetics
inferredcites →https://doi.org/10.1080/10635150802022231openalex-snapshot
Mosaicism, Modules, and the Evolution of Birds: Results from a Bayesian Approach to the Study of Morphological Evolution Using Discrete Character Data
inferredcites →https://doi.org/10.1093/bioinformatics/btaa614openalex-snapshot
Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees
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Mesoamerica is a cradle and the Atlantic Forest is a museum of Neotropical butterfly diversity: insights from the evolution and biogeography of Brassolini (Lepidoptera: Nymphalidae)
inferredcites →https://doi.org/10.1093/isd/ixz006openalex-snapshot
A Systematist’s Guide to Estimating Bayesian Phylogenies From Morphological Data
inferredcites →https://doi.org/10.1093/jhered/esq092openalex-snapshot
Recent Trends in Molecular Phylogenetic Analysis: Where to Next?
inferredcites →https://doi.org/10.1093/molbev/mss020openalex-snapshot
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
inferredcites →https://doi.org/10.1093/molbev/msv026openalex-snapshot
The Effects of Partitioning on Phylogenetic Inference
inferredcites →https://doi.org/10.1093/molbev/msw260openalex-snapshot
PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses
inferredcites →https://doi.org/10.1093/molbev/msw279openalex-snapshot
RWTY (R We There Yet): An R package for examining convergence of Bayesian phylogenetic analyses
inferredcites →https://doi.org/10.1093/molbev/msz291openalex-snapshot
Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference
inferredcites →https://doi.org/10.1093/sysbio/44.1.3openalex-snapshot
Approaches for Assessing Phylogenetic Accuracy
inferredcites →https://doi.org/10.1093/sysbio/syaa012openalex-snapshot
Morphological Phylogenetics Evaluated Using Novel Evolutionary Simulations
inferredcites →https://doi.org/10.1093/sysbio/syaa059openalex-snapshot
Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees
inferredcites →https://doi.org/10.1093/sysbio/syab020openalex-snapshot
Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity
inferredcites →https://doi.org/10.1093/sysbio/syab100openalex-snapshot
Robust Analysis of Phylogenetic Tree Space
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Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection
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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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Among-Character Rate Variation Distributions in Phylogenetic Analysis of Discrete Morphological Characters
inferredcites →https://doi.org/10.1093/sysbio/syv052openalex-snapshot
A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology
inferredcites →https://doi.org/10.1093/sysbio/syv122openalex-snapshot
Modeling Character Change Heterogeneity in Phylogenetic Analyses of Morphology through the Use of Priors
inferredcites →https://doi.org/10.1093/sysbio/syw068openalex-snapshot
Novel Approaches for Phylogenetic Inference from Morphological Data and Total-Evidence Dating in Squamate Reptiles (Lizards, Snakes, and Amphisbaenians)
inferredcites →https://doi.org/10.1093/sysbio/syy058openalex-snapshot
Phylogeny, Macroevolutionary Trends and Historical Biogeography of Sloths: Insights From a Bayesian Morphological Clock Analysis
inferredcites →https://doi.org/10.1093/sysbio/syy071openalex-snapshot
Serial Homology and Correlated Characters in Morphological Phylogenetics: Modeling the Evolution of Dental Crests in Placentals
inferredcites →https://doi.org/10.1093/sysbio/syy077openalex-snapshot
Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model
inferredcites →https://doi.org/10.1093/sysbio/syz001openalex-snapshot
Homoplasy-Based Partitioning Outperforms Alternatives in Bayesian Analysis of Discrete Morphological Data
inferredcites →https://doi.org/10.1093/sysbio/syz005openalex-snapshot
Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits
inferredcites →https://doi.org/10.1093/sysbio/syz050openalex-snapshot
The Invariant Nature of a Morphological Character and Character State: Insights from Gene Regulatory Networks
inferredcites →https://doi.org/10.1093/sysbio/syz077openalex-snapshot
Craniodental and Postcranial Characters of Non-Avian Dinosauria Often Imply Different Trees
inferredcites →https://doi.org/10.1093/zoolinnean/zlab010openalex-snapshot
Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
inferredcites →https://doi.org/10.1093/zoolinnean/zlac041openalex-snapshot
Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models
inferredcites →https://doi.org/10.1098/rsbl.2016.0033openalex-snapshot
Multiple morphological clocks and total-evidence tip-dating in mammals
inferredcites →https://doi.org/10.1098/rsbl.2016.0081openalex-snapshot
Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data
inferredcites →https://doi.org/10.1098/rsbl.2018.0632openalex-snapshot
Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets
inferredcites →https://doi.org/10.1098/rsos.182062openalex-snapshot
Bayesian tip dating reveals heterogeneous morphological clocks in Mesozoic birds
inferredcites →https://doi.org/10.1098/rspb.2017.1636openalex-snapshot
Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al.
inferredcites →https://doi.org/10.1098/rspb.2017.2150openalex-snapshot
Differences between hard and soft phylogenetic data
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dispRity: A modular R package for measuring disparity
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Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology
inferredcites →https://doi.org/10.1111/cla.12380openalex-snapshot
Likelihood approximations of implied weights parsimony can be selected over the Mk model by the Akaike information criterion
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What does modularity mean?
inferredcites →https://doi.org/10.1111/evo.12884openalex-snapshot
Sampling diverse characters improves phylogenies: Craniodental and postcranial characters of vertebrates often imply different trees
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The impact of missing data on real morphological phylogenies: influence of the number and distribution of missing entries
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Relations and interactions between cranial mesoderm and neural crest populations
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Comparative evaluation of maximum parsimony and Bayesian phylogenetic reconstruction using empirical morphological data
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Evolution of the mammalian middle ear: a historical review
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Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data
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Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model
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Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample
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Modularity: Genes, Development, and Evolution
inferredcites →https://doi.org/10.1186/2041-9139-2-21openalex-snapshot
Heterochrony and developmental modularity of cranial osteogenesis in lipotyphlan mammals
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Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates
inferredcites →https://doi.org/10.1371/journal.pone.0109210openalex-snapshot
Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data
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Innovative Bayesian and Parsimony Phylogeny of Dung Beetles (Coleoptera, Scarabaeidae, Scarabaeinae) Enhanced by Ontology-Based Partitioning of Morphological Characters
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A Concern for Evidence and a Phylogenetic Hypothesis of Relationships Among Epicrates (Boidae, Serpentes)
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Individual Comparisons by Ranking Methods
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Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures
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First phylogenetic analysis of the Miocene armadillo Vetelia reveals novel affinities with Tolypeutinae

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC)
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Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations
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Practical Guide and Review of Fossil Tip-Dating in Phylogenetics
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A Covarion Model for Phylogenetic Estimation Using Discrete Morphological Data Sets
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State Space Misspecification in Morphological Phylogenetics: A Pitfall for Models and Parsimony Alike
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rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits
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Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data
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Evaluating Bayesian Morphological Clocks for Estimating a Dated Phylogeny in a Relict and Fossil‐Rich Family of Wasps (Hymenoptera, Chrysidoidea)
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Comparative Morphology of the Stingless Bees (Apidae, Meliponini) and Its Phylogenetic Relevance
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Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC)
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Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC)
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