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Mismatch of the morphology model is mostly unproblematic in total-evidence dating: insights from an extensive simulation study

https://doi.org/10.1101/679084
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Phylogenetic Model Evaluation
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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
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Among-site rate variation and its impact on phylogenetic analyses
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Sampling-through-time in birth–death trees
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Rocks and clocks: calibrating the Tree of Life using fossils and molecules
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Phylogenetic relationships and timing of diversification in gonorynchiform fishes inferred using nuclear gene DNA sequences (Teleostei: Ostariophysi)
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An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)
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Phylogenetic analysis of molecular and morphological data highlights uncertainty in the relationships of fossil and living species of Elopomorpha (Actinopterygii: Teleostei)
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Evolutionary Rate at the Molecular Level
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The fossilized birth–death process for coherent calibration of divergence-time estimates
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A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data
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Ontogeny Discombobulates Phylogeny: Paedomorphosis and Higher-Level Salamander Relationships
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Wagner and Dollo: A Stochastic Duet by Composing Two Parsimonious Solos
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APE: Analyses of Phylogenetics and Evolution in R language
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phangorn: phylogenetic analysis in R
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A Generation Time Effect on the Rate of Molecular Evolution in Invertebrates
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Reducing Model Complexity of the General Markov Model of Evolution
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The Impact of the Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times
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Simulating Trees with a Fixed Number of Extant Species
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/sys058openalex-snapshot
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
inferredcites →https://doi.org/10.1093/sysbio/sys092openalex-snapshot
Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders
inferredcites →https://doi.org/10.1093/sysbio/syt110openalex-snapshot
Morphological Clocks in Paleontology, and a Mid-Cretaceous Origin of Crown Aves
inferredcites →https://doi.org/10.1093/sysbio/syu098openalex-snapshot
Among-Character Rate Variation Distributions in Phylogenetic Analysis of Discrete Morphological Characters
inferredcites →https://doi.org/10.1093/sysbio/syv027openalex-snapshot
Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms
inferredcites →https://doi.org/10.1093/sysbio/syv052openalex-snapshot
A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology
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Modeling Character Change Heterogeneity in Phylogenetic Analyses of Morphology through the Use of Priors
inferredcites →https://doi.org/10.1093/sysbio/syw035openalex-snapshot
Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree
inferredcites →https://doi.org/10.1093/sysbio/syw060openalex-snapshot
Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins
inferredcites →https://doi.org/10.1093/sysbio/syx051openalex-snapshot
More on the Best Evolutionary Rate for Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/sysbio/syx074openalex-snapshot
The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates
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/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/syz037openalex-snapshot
The Effect of Fossil Sampling on the Estimation of Divergence Times with the Fossilized Birth–Death Process
inferredcites →https://doi.org/10.1098/rsbl.2011.0523openalex-snapshot
Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates
inferredcites →https://doi.org/10.1098/rsbl.2011.0710openalex-snapshot
Exploring uncertainty in the calibration of the molecular clock
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/rspb.2014.1278openalex-snapshot
Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals
inferredcites →https://doi.org/10.1098/rspb.2018.2418openalex-snapshot
Rapid morphological evolution in placental mammals post-dates the origin of the crown group
inferredcites →https://doi.org/10.1098/rstb.2015.0136openalex-snapshot
Closing the gap between rocks and clocks using total-evidence dating
inferredcites →https://doi.org/10.1101/219048openalex-snapshot
What drives results in Bayesian morphological clock analyses?
inferredcites →https://doi.org/10.1101/436303openalex-snapshot
A Simulation-Based Evaluation of Total-Evidence Dating Under the Fossilized Birth-Death Process
inferredcites →https://doi.org/10.1111/1755-0998.12352openalex-snapshot
Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences
inferredcites →https://doi.org/10.1111/j.0014-3820.2002.tb00118.xopenalex-snapshot
TESTING THE RELATIONSHIP BETWEEN MORPHOLOGICAL AND MOLECULAR RATES OF CHANGE ALONG PHYLOGENIES
inferredcites →https://doi.org/10.1111/j.0014-3820.2006.tb01129.xopenalex-snapshot
NEUTRAL THEORY, PHYLOGENIES, AND THE RELATIONSHIP BETWEEN PHENOTYPIC CHANGE AND EVOLUTIONARY RATES
inferredcites →https://doi.org/10.1111/j.1420-9101.2010.02128.xopenalex-snapshot
Gene flow and species cohesion following the spread of Schiedea globosa (Caryophyllaceae) across the Hawaiian Islands
inferredcites →https://doi.org/10.1111/j.1439-0469.2007.00425.xopenalex-snapshot
The role of character loss in phylogenetic reconstruction as exemplified for the Annelida
inferredcites →https://doi.org/10.1111/j.1558-5646.1997.tb01461.xopenalex-snapshot
CORRELATED RATES OF MOLECULAR AND MORPHOLOGICAL EVOLUTION
inferredcites →https://doi.org/10.1111/nph.15708openalex-snapshot
How deep is the conflict between molecular and fossil evidence on the age of angiosperms?
inferredcites →https://doi.org/10.1111/pala.12245openalex-snapshot
Mosaicism in a new E ocene pufferfish highlights rapid morphological innovation near the origin of crown tetraodontiforms
inferredcites →https://doi.org/10.1111/pala.12353openalex-snapshot
Parsimony and model‐based phylogenetic methods for morphological data: comments on O'Reilly et al.
inferredcites →https://doi.org/10.1111/pala.12361openalex-snapshot
Empirical realism of simulated data is more important than the model used to generate it: a reply to Goloboff et al.
inferredcites →https://doi.org/10.1126/science.1257570openalex-snapshot
Phylogenomics resolves the timing and pattern of insect evolution
inferredcites →https://doi.org/10.1126/science.aaa5460openalex-snapshot
Comment on “Phylogenomics resolves the timing and pattern of insect evolution”
inferredcites →https://doi.org/10.1186/s12862-017-1090-0openalex-snapshot
Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia)
inferredcites →https://doi.org/10.1186/s12862-018-1192-3openalex-snapshot
A comparison of methods for estimating substitution rates from ancient DNA sequence data
inferredcites →https://doi.org/10.1186/s12862-018-1218-xopenalex-snapshot
The soft explosive model of placental mammal evolution
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pone.0212942openalex-snapshot
Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix
inferredcites →https://doi.org/10.1600/036364410792495809openalex-snapshot
Effects of Substitution Models on Divergence Time Estimates: Simulations and an Empirical Study of Model Uncertainty Using Cornales
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.4159/harvard.9780674063396openalex-snapshot
Full House: The Spread of Excellence from Plato to Darwin
inferredcites →https://doi.org/10.7717/peerj.4553openalex-snapshot
Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data

What points at this work

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

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Toward Phylomics in Entomology: Current Systematic and Evolutionary Morphology
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Phylogeny, evolution, and classification of the ant genus Lasius , the tribe Lasiini and the subfamily Formicinae (Hymenoptera: Formicidae)
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Profile of a flower: How rates of morphological evolution drive floral diversification in Ericales and angiosperms
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The Molecular Clock as a Tool for Understanding Host-Parasite Evolution
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Phylogenetic Trees and Absolute Time
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Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches
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Understanding the Tripartite Approach to Bayesian Divergence Time Estimation
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Bayesian inference of phylogenetic trees is not misled by correlated discrete morphological characters
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Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity
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Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution
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The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics
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But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating
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Incorporating Continuous Characters in Joint Estimation of Dicynodont Phylogeny
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Impacts of Taxon-Sampling Schemes on Bayesian Molecular Dating under the Unresolved Fossilized Birth-Death Process
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Evolution and systematics of the Aculeata and kin (Hymenoptera), with emphasis on the ants (Formicoidea: †@@@idae fam. nov., Formicidae)
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Inaccurate fossil placement does not compromise tip-dated divergence times
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Profile of a flower: How rates of morphological evolution drive floral diversification in Ericales
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But the clock, tick-tock: the preeminence of relaxed clock models in total-evidence dated phylogenetics
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The age of insects and the revival of the minimum age tree
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Inaccurate fossil placement does not compromise tip‐dated divergence times
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INACCURATE FOSSIL PLACEMENT DOES NOT COMPROMISE TIP-DATED DIVERGENCE TIMES
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Integrating Fossil Observations Into Phylogenetics Using the Fossilized Birth–Death Model
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Molecular and morphological clocks for estimating evolutionary divergence times
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Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates
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Craniodental Morphology and Phylogeny of Marsupials
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Twenty-five well-justified fossil calibrations for primate divergences
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Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference
inferred← citeshttps://doi.org/10.6084/m9.figshare.14583455openalex-snapshot
Additional file 1 of Molecular and morphological clocks for estimating evolutionary divergence times
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