Table of contents

• Title
• Overview
• Project architecture
• Figures
• Contact

Title

A theoretical framework linking the birth-death and protracted birth-death models, with implications for the phylogenetic analysis of diversification.

Preprint: Veron, P., Andréoletti, J., Giraud, T. & Morlon, H. (2024). BioRxiv. DOI: 10.1101/2024.07.01.601000

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 ([email protected])
• Jérémy Andréoletti