GitHunt
PI

pierre-veron/PBD_analog

Analogy between the protracted birth death model and the classical birth death model

macroevolutionmicroevolutionphylogenyspeciation

Zenodo available at https://doi.org/10.5281/zenodo.14001155

Open access publication

Table of contents

Title

Speciation completion rates have limited impact on macroevolutionary diversification

Veron, P., Andréoletti, J., Giraud, T. & Morlon, H. (2025). Phil. Trans. R. Soc. B 380, 20230317. DOI: 10.1098/rstb.2023.0317

Overview

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

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

Test of the analog expressions of birth and death rates from the 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 : figures generated by the scripts
  • illustrations : hand-made figures for the publication
  • modules: global functions used in the pipeline
  • simulations_output : raw of the simulations.

Figures

The file customstyle.mplstyle defines a global style for the Matplotlib figures.

# Python
import matplotlib.pyplot as plt
plt.style.use("customstyle.mplstyle")

This repository contains the scripts used to generate all the figures in the manuscript.

Figure File name Script to generate
1 illustrations/schema_horizon.pdf illustrations/schema_horizon.svg
2 illustrations/schema_probas.pdf illustrations/schema_probas.svg
3 fig/PBD_time_dep_rates.pdf 1-rates_analysis/1-calculate_probas_rates.ipynb
4 fig/simp_influence_parameters.pdf 1-rates_analysis/4-influence_params_simplifiedPBD.ipynb
5 fig/statistics_tree.pdf 3-compare_PBD_BD_varBD/1-compare_stats.ipynb
S1 fig/SM_probabilities_vs_simulations.pdf 1-rates_analysis/1-calculate_probas_rates.ipynb
S2 fig/SM_time_dep_rates_initiation.pdf 1-rates_analysis/1-calculate_probas_rates.ipynb
S3 fig/SM_time_dep_rates_extinction.pdf 1-rates_analysis/1-calculate_probas_rates.ipynb
S4 fig/SM_time_dep_rates_comparison_simplified_PBD.pdf 2-simulate_trees/3-varBD/1-predict_variable_BD_rates.ipynb
S5 fig/SM_relative_influence_el2.pdf and fig/SM_relative_influence_bl2.pdf 1-rates_analysis/4-influence_params_simplifiedPBD.ipynb
S6 fig/SM_relative_influence_l1l2.pdf, fig/SM_relative_influence_m2l2.pdf and fig/influence_parameters.pdf 1-rates_analysis/3-influence_params.ipynb
S7 fig/SM_truncation_lambda.pdf and fig/SM_truncation_mu.pdf 4-fit_BD_truncated_PBD_trees\3-plot_comparison.R

Contact

  • Pierre Veron (pierre.veron.2017@polytechnique.org)
  • Jérémy Andréoletti

Languages

Jupyter Notebook53.4%HTML45.9%R0.3%Python0.3%Shell0.0%

Contributors

PIJE
Created February 26, 2024
Updated March 3, 2025
pierre-veron/PBD_analog | GitHunt