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Bayesian priors for tree calibration: Evaluating two new approaches based on fossil intervals

https://doi.org/10.1101/014340
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What this work says

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

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Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates
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Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges
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Sampling-through-time in birth–death trees
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Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea)
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Molecular phylogenetics and microsatellite analysis reveal cryptic species of speckled dace (Cyprinidae: Rhinichthys osculus) in Oregon’s Great Basin
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The impact of calibration and clock-model choice on molecular estimates of divergence times
inferredcites →https://doi.org/10.1017/s0094837300009672openalex-snapshot
Confidence intervals on stratigraphic ranges
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Confidence intervals on stratigraphic ranges: partial relaxation of the assumption of randomly distributed fossil horizons
inferredcites →https://doi.org/10.1017/s0094837300016146openalex-snapshot
On the probability of ancestors in the fossil record
inferredcites →https://doi.org/10.1017/s0094837300016766openalex-snapshot
Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons
inferredcites →https://doi.org/10.1017/s0094837300026890openalex-snapshot
Origination and extinction components of taxonomic diversity: General problems
inferredcites →https://doi.org/10.1073/pnas.1319091111openalex-snapshot
The fossilized birth–death process for coherent calibration of divergence-time estimates
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Age and rate of diversification of the Hawaiian silversword alliance (Compositae)
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The Well-Calibrated Bayesian
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Dating Lineages: Molecular and Paleontological Approaches to the Temporal Framework of Clades
inferredcites →https://doi.org/10.1086/427734openalex-snapshot
Assessing Concordance of Fossil Calibration Points in Molecular Clock Studies: An Example Using Turtles
inferredcites →https://doi.org/10.1086/587523openalex-snapshot
A Simple Method for Bracketing Absolute Divergence Times on Molecular Phylogenies Using Multiple Fossil Calibration Points
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Calibrating the Tree of Life: fossils, molecules and evolutionary timescales
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Estimation of a Truncation Point
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A Note on Estimation of Bounds of Random Variables
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Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds
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Paleontological Evidence to Date the Tree of Life
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
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Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0
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When Did Decapods Invade Hydrothermal Vents? Clues from the Western Pacific and Indian Oceans
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025731openalex-snapshot
A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025892openalex-snapshot
Estimating the rate of evolution of the rate of molecular evolution
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040214openalex-snapshot
Molecular phylogeny and divergence times of drosophilid species.
inferredcites →https://doi.org/10.1093/sysbio/23.3.305openalex-snapshot
Stochastic Simulation and Evolution of Morphology-Towards a Nomothetic Paleontology
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Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times
inferredcites →https://doi.org/10.1093/sysbio/syp078openalex-snapshot
The Impact of the Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times
inferredcites →https://doi.org/10.1093/sysbio/syq054openalex-snapshot
Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data
inferredcites →https://doi.org/10.1093/sysbio/syr019openalex-snapshot
Integrating Fossil Preservation Biases in the Selection of Calibrations for Molecular Divergence Time Estimation
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/syr075openalex-snapshot
Evaluating Fossil Calibrations for Dating Phylogenies in Light of Rates of Molecular Evolution: A Comparison of Three Approaches
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/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/10.1098/rsbl.2011.0710openalex-snapshot
Exploring uncertainty in the calibration of the molecular clock
inferredcites →https://doi.org/10.1111/2041-210x.12088openalex-snapshot
Modelling distributions of fossil sampling rates over time, space and taxa: assessment and implications for macroevolutionary studies
inferredcites →https://doi.org/10.1111/2041-210x.12091openalex-snapshot
Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution
inferredcites →https://doi.org/10.1111/evo.12322openalex-snapshot
THE COMPLEX EVOLUTIONARY HISTORY OF SEEING RED: MOLECULAR PHYLOGENY AND THE EVOLUTION OF AN ADAPTIVE VISUAL SYSTEM IN DEEP-SEA DRAGONFISHES (STOMIIFORMES: STOMIIDAE)
inferredcites →https://doi.org/10.1111/j.0014-3820.2005.tb01825.xopenalex-snapshot
FOSSIL CALIBRATIONS AND MOLECULAR DIVERGENCE TIME ESTIMATES IN CENTRARCHID FISHES (TELEOSTEI: CENTRARCHIDAE)
inferredcites →https://doi.org/10.1111/j.0908-8857.2007.04168.xopenalex-snapshot
Calibrating molecular estimates of substitution rates and divergence times in birds
inferredcites →https://doi.org/10.1111/j.1420-9101.2009.01789.xopenalex-snapshot
Eusociality and the success of the termites: insights from a supertree of dictyopteran families
inferredcites →https://doi.org/10.1111/j.1558-5646.1991.tb04408.xopenalex-snapshot
COMPARISONS OF OBSERVED PHYLOGENETIC TOPOLOGIES WITH NULL EXPECTATIONS AMONG THREE MONOPHYLETIC LINEAGES
inferredcites →https://doi.org/10.1126/science.158.3805.1200openalex-snapshot
Immunological Time Scale for Hominid Evolution
inferredcites →https://doi.org/10.1186/1471-2148-7-214openalex-snapshot
BEAST: Bayesian evolutionary analysis by sampling trees
inferredcites →https://doi.org/10.1186/s12862-014-0169-0openalex-snapshot
Phylogenetic informativeness reconciles ray-finned fish molecular divergence times
inferredcites →https://doi.org/10.1371/journal.pone.0066245openalex-snapshot
A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses
inferredcites →https://doi.org/10.1371/journal.pone.0073535openalex-snapshot
Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families
inferredcites →https://doi.org/10.1371/journal.pone.0110308openalex-snapshot
Evolutionary Diversification of New Caledonian Araucaria
inferredcites →https://doi.org/10.1644/1545-1542(2003)084<0444:etfppi>2.0.co;2openalex-snapshot
EXTRACTING TIME FROM PHYLOGENIES: POSITIVE INTERPLAY BETWEEN FOSSIL AND GENETIC DATA
inferredcites →https://doi.org/10.1666/0022-3360(2004)078<0001:wcacce>2.0.co;2openalex-snapshot
When clocks (and communities) collide: Estimating divergence time from molecules and the fossil record
inferredcites →https://doi.org/10.1666/0094-8373(2003)029<0181:eosrwf>2.0.co;2openalex-snapshot
Estimation of stratigraphic ranges when fossil finds are not randomly distributed
inferredcites →https://doi.org/10.1666/0094-8373-36.1.51openalex-snapshot
The completeness of the continental fossil record and its impact on patterns of diversification
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing

What points at this work

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

inferred← citeshttps://doi.org/10.1002/ajb2.1056openalex-snapshot
Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)
inferred← citeshttps://doi.org/10.1111/2041-210x.13977openalex-snapshot
CladeDate : Calibration information generator for divergence time estimation
inferred← citeshttps://doi.org/10.1111/nph.13676openalex-snapshot
Puzzling rocks and complicated clocks: how to optimize molecular dating approaches in historical phytogeography
inferred← citeshttps://doi.org/10.1111/nph.15137openalex-snapshot
Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta)
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