Pesto: Phylogenetic estimation of branch-specific shifts in the tempo of origination

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 (>20k taxa) in minutes on a personal computer while also providing branch-specific inference..., 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., , # 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\" inf...,