Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies

Identifying along which lineages shifts in diversification rates occur is a central goal of comparative phylogenetics; these shifts may coincide with key evolutionary events such as the development of novel morphological characters, the acquisition of adaptive traits, polyploidization or other structural genomic changes, or dispersal to a new habitat and subsequent increase in environmental niche space. However, while multiple methods now exist to estimate diversification rates and identify shifts using phylogenetic topologies, the appropriate use and accuracy of these methods is hotly debated. Here we test whether five Bayesian methods—Bayesian Analysis of Macroevolutionary Mixtures (BAMM), two implementations of the Lineage-Specific Birth-Death-Shift model (LSBDS and PESTO), the approximate Multi-Type Birth-Death model (MTBD; implemented in BEAST2), and the cladogenetic diversification rate shift model (CLaDS2)—produce comparable results. We apply each of these methods to a set of 65 ..., , , # Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies

## Overview

This directory contains the code and analysis used in the paper Martínez-Gómez, Song and Tribble et al. 2023. In short, this study tests whether different Bayesian evolutionary models which, aim to estimate branch specific shifts in diversification rates on a phylogeny, infer similar or different shifts using a set of empirically derived phylogenies. In this study we test five different methods, BAMM, PESTO, MTBD, LSBDS, and ClaDS2. Please see the corresponding publication in [Evolution Letter](https://doi.org/10.1093/evlett/qrad044) for more details.

This repository contains two main files: **Output.tar.gz** and **CompDiv.tar.gz**. The **Output.tar.gz** file contains the outputs from running each of the five methods investigated in the study. The **CompDiv.tar.gz** file contains files associated with the analysis of the outputs o...