CRABS: Congruent Rate Analyses in Birth-death Scenarios

Sebastian Höhna

Bjørn T. Kopperud

Andrew F. Magee

Jérémy Andréoletti

2023-10-23

1 Overview

This is a vignette, or long-form documentation, accompanying the R-package CRABS: Congruent Rate Analyses in Birth-death Scenarios.

The main purpose of CRABS is to explore congruence classes of macroevolutionary diversification rates. Specifically, this tutorial has two main aims/applications:

• For a given speciation and extinction rate, you can compute the alternative speciation and extinction rates via the pulled net-diversification rate
• For a given speciation and extinction rate, which might have been estimated from a phylogenetic tree or provided simply for exploration purposes, you can explore the entire congruence class given some rate assumptions (e.g., type of change or min and max rates).

The first use case corresponds to testing specific hypotheses while the second use case corresponds to exploring the congruence class for general patterns/trends. We will explain these in detail below with an empirical example.