Code and data: Exploring congruent diversification histories with flexibility and parsimony

This repository contains the code and data for the article "Exploring congruent diversification histories with flexibility and parsimony" (abstract bellow).

Data :

• 4705sp_mammal-time.tree: Species-level calibrated mammalian phylogeny from Alvarez-Carretero et al. (https://doi.org/10.6084/m9.figshare.14885691)
• mammals_samplingfraction.csv : Clade-specific sampling fractions from Quintero et al.(https://www.biorxiv.org/content/10.1101/2022.08.09.503355v1.full).

Code :

• CRABS-v1.1.0.9004.zip: Archived version of the CRABS package with our extension.
• Mammalian_rates_EBD_HSMRF.rev: Rev script for the mammalian diversification analysis in RevBayes with regularized priors on diversification rates.
• Mammalian_rates_EBD_independent.rev: Rev script for the mammalian diversification analysis in RevBayes with independent diversification rates at each interval.
• Mammals_proccess_RevBayes_outputs.Rmd: R notebook for processing the outputs from the RevBayes mammalian diversification analysis, plotting the rates through time, and saving the median trajectories used for further analyses.
• Exploring_congruent_diversification_histories_with_flexibility_and_parsimony.Rmd: R notebook for comparing the initial CRABS features and our new extensions. It enables replicating the figures in the article.

Outputs :

• output_inferredIntervals_fixedRhp_HSMRF.zip & output_inferredIntervals_fixedRhp_independent.zip: The raw traces from the RevBayes analysis, and the resulting median rate trajectories that are used to construct the congruence class illustrated in the article.

Abstract

1. Using phylogenies of present-day species to estimate diversification rate trajectories -- speciation and extinction rates over time -- is a challenging task due to non-identifiability issues. Given a phylogeny, there exists an infinite set of trajectories that result in the same likelihood; this set has been coined a congruence class. Previous work has developed approaches for sampling trajectories within a given congruence class, with the aim to assess the extent to which congruent scenarios can vary from one another. Based on this sampling approach, it has been suggested that rapid changes in speciation or extinction rates are conserved across the class. Reaching such conclusions requires to sample the broadest possible set of distinct trajectories.
2. We introduce a new method for exploring congruence classes, that we implement in the R package CRABS. Whereas existing methods constrain either the speciation rate or the extinction rate trajectory, ours provides more flexibility by sampling congruent speciation and extinction rate trajectories simultaneously. This allows covering a more representative set of distinct diversification rate trajectories. We also implement a filtering step that allows selecting the most parsimonious trajectories within a class.
3. We demonstrate the utility of our new sampling strategy using a simulated scenario. Next, we apply our approach to the study of mammalian diversification history. We show that rapid changes in speciation and extinction rates need not be conserved across a congruence class, but that selecting the most parsimonious trajectories shrinks the class to concordant scenarios.
4. Our approach opens new avenues both to truly explore the myriad of potential diversification histories consistent with a given phylogeny, embracing the uncertainty inherent to phylogenetic diversification models, and to select among these different histories. This should help refining our inference of diversification trajectories from extant data.