Title

Speciation completion rates have limited impact on macroevolutionary diversification

Overview

This repository contains the scripts associated with the publication Speciation completion rates have limited impact on macroevolutionary diversification, in Philosophical Transactions of the Royal Society B (DOI : 10.1098/rstb.2023.0317). It has 4 main functions : 

1. Calculation of equivalent birth and death rates under the protracted birth death models.

2. Simulations and statistics of phylogenies under the protracted birth-death (PBD) and BD models following the works from 

Etienne, R. S., & Rosindell, J. (2012). Prolonging the Past Counteracts the Pull of the Present: Protracted Speciation Can Explain Observed Slowdowns in Diversification. Systematic Biology, 61, 204. DOI: 10.1093/sysbio/syr091

Etienne, R. S., Morlon, H., & Lambert, A. (2014). Estimating the duration of speciation from phylogenies. Evolution, 68, 2430–2440. DOI: 10.1111/evo.12433

3. Test of the analog expressions of birth and death rates from the PBD model. 

4. Fit a BD model to a truncated phylogeny based on trees simulated with he PBD model.

Project architecture

• 1-rates_analysis: calculate equivalent birth and death rates of the PBD model and analyse these rates.
• 2-simulate_trees: simulate trees under
  • the PBD model
  • the BD model with constant rates with equivalent constant rates to the PBD models
  • the BD model with time-dependent rates with equivalent rates to the PBD model
• 3-compare_PBD_BD_varBD : compare the trees obtained with the 3 models.
• 4-fit_BD_truncated_PBD_trees : fits a BD model to truncated phylogenies based on trees simulated with the PBD model.
• fig : directory to save the figures generated by the scripts
• modules: global functions used in the pipeline
• simulations_output : raw simulations.

Developers

• Pierre Veron
• Jérémy Andréoletti