DOI: 10.5061/dryad.mgqnk995b
title: Pesto: Phylogenetic estimation of branch-specific shifts in the tempo of origination

description: Studying rates of species diversification is one of the key themes in
 macroevolution. In particular, we are interested in if some clades in a
 phylogeny diversify more rapidly/slowly than others due to branch-specific
 diversification rates. A common approach in neontological studies is to
 use a phylogenetic birth-death process to model species diversification.
 Specifically, the birth-death-shift process is used to model
 branch-specific shifts in the tempo of diversification. Here, we present
 Pesto, a new method and software that estimates branch-specific
 diversification rates using an empirical Bayes approach. Pesto does not
 rely on Markov chain Monte Carlo simulations and instead deterministically
 computes the posterior mean branch-specific diversification rates using
 only two traversals of the tree. This method is blazingly fast: the
 birth-death-shift model can be fitted to large phylogenies (&gt;20k
 taxa) in minutes on a personal computer while also providing
 branch-specific inference of diversification rate shift events. Thus, we
 can robustly infer branch-specific diversification rates and the number of
 diversification rate shift events for large-scale phylogenies, as well as
 explore the characteristics of the birth-death-shift model through complex
 and large-scale simulations. Here, we first describe the method and the
 software implementation \pesto and explore its behavior using trees
 simulated under the birth-death-shift model. Then, we explore the behavior
 of inferring significant branch-specific diversification rate shifts using
 both Bayes factors and effect sizes. We find few to no false positive
 inferences of diversification rate shift events, but many false negatives
 (reduced power). The most difficult parameter to estimate is the rate at
 which diversification rate shifts occur. Despite this, branch-specific
 diversification rate estimates are precise and nearly unbiased.
description: This dataset includes reconstructed phylogenetic trees that have
 been simulated under the birth-death-shift process. The trees are
 reconstructed, meaning that the extinct lineages are pruned or removed
 from the phylogeny, leaving only the lineages that survived until the
 present.
description: # Pesto: Phylogenetic estimation of branch-specific shifts in the tempo of
 origination
 [https://doi.org/10.5061/dryad.mgqnk995b](https://doi.org/10.5061/dryad.mgqnk995b) This repository contains the datasets (i.e., reconstructed phylogenetic trees) simulated under the birth-death-shift process, as used in the "Pesto" manuscript. It also includes the results of the analyses from the main text of the manuscript. ## Description of the data and file structure The `archive3.zip` is a file, which, when decompressed, contains several directories: * data: includes the primates' phylogeny * output: includes the benchmark times (JLD2 format), branch-specific estimation errors for the simulation-inference study (comma-separated values), and the log file from the RevBayes birth-death-shift inference with fixed parameters. * simulated trees: contains all 2000 simulated trees. The constant-rate birth-death parameter estimates are found in "cbdp_estimates.jld2", and the results of the "Pesto" inference are in the subdirectory "results", replicated, with three inference settings: "true_all", "true_div", and "unknown_rates". The .zip file can be decompressed as-is, placed into the directory of the GitHub repository [https://github.com/kopperud/pesto_ms_analyses](https://github.com/kopperud/pesto_ms_analyses) -- after which the scripts can be run. See the GitHub repository for how the scripts can be run.