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A Simulation-Based Evaluation of Total-Evidence Dating Under the Fossilized Birth-Death Process

https://doi.org/10.1101/436303
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Outgoing claims: the papers this work cites, builds on, or argues with.

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On incomplete sampling under birth–death models and connections to the sampling-based coalescent
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An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)
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Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees
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Putting scales into evolutionary time: the divergence of major scale insect lineages (Hemiptera) predates the radiation of modern angiosperm hosts
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The fossilized birth–death process for coherent calibration of divergence-time estimates
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APE: Analyses of Phylogenetics and Evolution in R language
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ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R
inferredcites →https://doi.org/10.1093/molbev/msm115openalex-snapshot
The Impact of Fossils and Taxon Sampling on Ancient Molecular Dating Analyses
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Phylogenetic Estimation of Timescales Using Ancient DNA: The Effects of Temporal Sampling Scheme and Uncertainty in Sample Ages
inferredcites →https://doi.org/10.1093/sysbio/34.1.75openalex-snapshot
The Use of Tree Comparison Metrics
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Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales
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Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times
inferredcites →https://doi.org/10.1093/sysbio/syr029openalex-snapshot
Simulating Trees with a Fixed Number of Extant Species
inferredcites →https://doi.org/10.1093/sysbio/syr047openalex-snapshot
Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia
inferredcites →https://doi.org/10.1093/sysbio/syr087openalex-snapshot
Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation
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/syv080openalex-snapshot
Total-Evidence Dating under the Fossilized Birth–Death Process
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/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/syw076openalex-snapshot
Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes
inferredcites →https://doi.org/10.1093/sysbio/syw107openalex-snapshot
Bayesian Morphological Clock Methods Resurrect Placoderm Monophyly and Reveal Rapid Early Evolution in Jawed Vertebrates
inferredcites →https://doi.org/10.1093/sysbio/syx086openalex-snapshot
The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data
inferredcites →https://doi.org/10.1093/sysbio/syy032openalex-snapshot
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
inferredcites →https://doi.org/10.1093/sysbio/syy035openalex-snapshot
Inferring Diversification Rate Variation From Phylogenies With Fossils
inferredcites →https://doi.org/10.1093/zoolinnean/zlw014openalex-snapshot
Systematics and evolution of the whirligig beetle tribe Dineutini (Coleoptera: Gyrinidae: Gyrininae)
inferredcites →https://doi.org/10.1098/rsbl.2015.0194openalex-snapshot
Biogeographic calibrations for the molecular clock
inferredcites →https://doi.org/10.1098/rsbl.2016.0237openalex-snapshot
Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)
inferredcites →https://doi.org/10.1098/rsbl.2016.0328openalex-snapshot
Inferring node dates from tip dates in fossil Canidae: the importance of tree priors
inferredcites →https://doi.org/10.1098/rspb.2000.1278openalex-snapshot
Testing macro–evolutionary models using incomplete molecular phylogenies
inferredcites →https://doi.org/10.1098/rspb.2016.2290openalex-snapshot
Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data
inferredcites →https://doi.org/10.1098/rspb.2017.0227openalex-snapshot
Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution
inferredcites →https://doi.org/10.1098/rspb.2017.1771openalex-snapshot
Mass extinction in tetraodontiform fishes linked to the Palaeocene–Eocene thermal maximum
inferredcites →https://doi.org/10.1098/rspb.2018.1071openalex-snapshot
Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record
inferredcites →https://doi.org/10.1098/rstb.2015.0129openalex-snapshot
Bayesian phylogenetic estimation of fossil ages
inferredcites →https://doi.org/10.1098/rstb.2015.0130openalex-snapshot
The non-uniformity of fossil preservation
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/10.1098/rstb.2016.0020openalex-snapshot
The evolution of methods for establishing evolutionary timescales
inferredcites →https://doi.org/10.1098/rstb.2016.0098openalex-snapshot
Tectonic blocks and molecular clocks
inferredcites →https://doi.org/10.1101/242875openalex-snapshot
Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales
inferredcites →https://doi.org/10.1111/1755-0998.12320openalex-snapshot
Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
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/10.1111/2041-210x.12084openalex-snapshot
Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the C retaceous‐ P alaeogene boundary
inferredcites →https://doi.org/10.1111/brv.12390openalex-snapshot
Bayesian molecular dating: opening up the black box
inferredcites →https://doi.org/10.1111/j.1558-5646.1985.tb00398.xopenalex-snapshot
FACTORS DETERMINING THE ACCURACY OF CLADOGRAM ESTIMATION: EVALUATION USING COMPUTER SIMULATION
inferredcites →https://doi.org/10.1111/nph.13570openalex-snapshot
Phylogenetic investigation of the complex evolutionary history of dispersal mode and diversification rates across living and fossil Fagales
inferredcites →https://doi.org/10.1111/pala.12361openalex-snapshot
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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/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
inferredcites →https://doi.org/10.1371/journal.pcbi.1003919openalex-snapshot
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
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Phylogenetics: The Theory and Practice of Phylogenetic Systematics.
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Phylogenetics: The Theory and Practice of Phylogenetic Systematics.
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R: A Language and Environment for Statistical Computing
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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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The Molecular Clock as a Tool for Understanding Host-Parasite Evolution
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Phylogeny, ancestors, and anagenesis in the hominin fossil record
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Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity
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Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth–death process
inferred← citeshttps://doi.org/10.1101/679084openalex-snapshot
Mismatch of the morphology model is mostly unproblematic in total-evidence dating: insights from an extensive simulation study
inferred← citeshttps://doi.org/10.1101/772558openalex-snapshot
Incorporating uncertainty is essential to macroecological inferences: Grass, grit, and the evolution of kangaroos
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Molecular and morphological clocks for estimating evolutionary divergence times
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Molecular and morphological clocks for estimating evolutionary divergence times
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Molecular and morphological clocks for estimating evolutionary divergence times
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Molecular and morphological clocks for estimating evolutionary divergence times
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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