10.5061/DRYAD.51C59ZW5B
Zhang, Chi
0000-0001-6009-5273
Institute of Vertebrate Paleontology and Paleoanthropology
Selecting and averaging relaxed clock models in Bayesian tip dating of
Mesozoic birds
Dryad
dataset
2020
relaxed clock
model selection
model averaging
Mesozoic birds
2021-02-04T00:00:00Z
2021-02-04T00:00:00Z
en
129207 bytes
6
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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
birds 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.
Please see the Method section of the paper.
1. dataS1_simulations.zip: this zip archive contains (1) 100 birth-death
trees generated by TreeSim in R (bd.trees and sim.bd.r); (2) source code
of the simulator (src/ folder); (3) shell script of each simulation
setting in individual folders. 2. dataS2_birds.zip: this zip archive
contains MrBayes commands for (1) the morphological data matrix
(birds.nex); (2) stepping-stone sampling under the IGR clock model
(ss_igr) (3) stepping-stone sampling under the ILN clock model (ss_igr)
(4) stepping-stone sampling under the ALN(TK02) clock model (ss_aln) (5)
rjMCMC sampling for unpartitioned data (td_mix) (6) rjMCMC sampling for
partitioned data (td_p6_mix)