Selecting and averaging relaxed clock models in Bayesian tip dating of Mesozoic birds

Relaxed clock models are fundamental in Bayesian clock dating, but a single distribution characterizing the clock variation is typically selected. Hence, I developed a new reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm for drawing posterior samples between the independent lognormal (ILN...

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Bibliographic Details
Published inPaleobiology Vol. 48; no. 2; pp. 340 - 352
Main Author Zhang, Chi
Format Journal Article
LanguageEnglish
Published New York, USA The Paleontological Society 01.05.2022
Cambridge University Press
Paleontological Society
Subjects
Algorithms
Aves
Bayesian analysis
Bayesian theory
biologic evolution
Birds
Chordata
Clocks
computer programs
data processing
Dating
Divergence
Efficiency
Markov chain analysis
Markov chains
Mathematical models
Mesozoic
methods
Monte Carlo analysis
morphological clocks
Morphology
Paleontology
phylogeny
Probability
Probability theory
Random variables
rates
Software
statistical analysis
Statistical methods
Tetrapoda
Vertebrata
vertebrate
White noise
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Summary:Relaxed clock models are fundamental in Bayesian clock dating, but a single distribution characterizing the clock variation is typically selected. Hence, I developed a new reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm for drawing posterior samples between the independent lognormal (ILN) and independent gamma rates (IGR) clock models. The ability of the rjMCMC algorithm to infer the true model was verified through simulations. I then applied the algorithm to the Mesozoic bird data previously analyzed under the white noise (WN) clock model. In comparison, averaging over the ILN and IGR models provided more reliable estimates of the divergence times and evolutionary rates. The ILN model showed slightly better fit than the IGR model and much better fit than the autocorrelated lognormal (ALN) clock model. When the data were partitioned, different partitions showed heterogeneous model fit for ILN and IGR clocks. The implementation provides a general framework for selecting and averaging relaxed clock models in Bayesian dating analyses.
ISSN:0094-8373
1938-5331
DOI:10.1017/pab.2021.42