Simulated Phylogenies for: Inferring branch-specific rates of lineage diversification under the birth-death-shift process

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.
, , , # Simulated Phylogenies for: Inferring branch-specific rates of lineage diversification under the birth-death-shift process

Dataset DOI: [10.5061/dryad.95x69p8t2](https://doi.org/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](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...,