DOI: 10.5061/dryad.95x69p8t2
title: Simulated Phylogenies for: Inferring branch-specific rates of lineage diversification under the birth-death-shift process

description: 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.
description: # 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 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](https://github.com/hoehna/birth-death-shift-analyses). The software used for the simulations was [https://revbayes.github.io.](https://revbayes.github.io)