Simulated Phylogenies for: Inferring branch-specific rates of lineage diversification under the birth-death-shift process
Data files
Jan 16, 2026 version files 6.41 MB
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README.md
2.33 KB
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simulated_data.zip
6.41 MB
Abstract
Inferring how rates of speciation and extinction vary across lineages has proven to be a difficult statistical problem. Here we describe a stochastic-diversification model—called the birth-death-shift (BDS) process—in which diversification rates may vary across both extant and extinct (and/or unsampled) lineages. We estimate the parameters of this model in a Bayesian framework from phylogenies of exclusively extant species. We perform simulation studies to validate the implementation of our method and to characterize its statistical behavior. We also perform analyses of an empirical (primates) dataset, which reveals that estimates of branch-specific diversification rates are robust to the assumed prior distribution on the number of diversification-rate shifts. Our implementation of the BDS model in RevBayes provides biologists with a flexible approach for estimating branch-specific diversification rates under a mathematically coherent model.
Dataset DOI: 10.5061/dryad.95x69p8t2
Description of the data and file structure
We simulated 100 trees under the birth-death-shift process forward in time with parameters chosen so that there are relatively few, relatively large diversification-rate shifts. Both the speciation and extinction rates were allowed to vary. The specific code for the simulations can be found at https://github.com/hoehna/birth-death-shift-analyses. In total, we have 1000 simulation replicates.
Files and variables
File: simulated_data.zip
Description: For each simulation replicate, we have the following files:
params_xxx.csv, which provides the rate categories, and shift rate
priors_xxx.csv, which provides the prior mean, prior sd, and prior rate
sim_xxx.tree simulate phylogeny in newick format
true_div_rates_xxx.csv: true branch-specific net-diversification rates. The indices match as in the tree file.
true_ext_rates_xxx.csv: true branch-specific extinction rates. The indices match as in the tree file.
true_n_events_xxx.csv: true branch-specific number of events. The indices match as in the tree file.
true_spec_rates_xxx.csv: true branch-specific speciation rates. The indices match as in the tree file.
supplementary_material.pdf: This supplementary file explains the birth–death–shift (BDS) model, a Bayesian framework for estimating how speciation and extinction rates vary across branches of a phylogenetic tree. It details the mathematical formulation, model parameterizations, and MCMC algorithms (including data augmentation and reversible-jump MCMC) used to infer where and how diversification rates shift. The document also validates the method through simulations and special cases, and applies it to empirical data (primates) to study lineage-specific diversification patterns.
Code/Software
The scripts for simulating the data can be found at https://github.com/hoehna/birth-death-shift-analyses. The software used for the simulations was https://revbayes.github.io.