The limits of the constant-rate birth-death prior for phylogenetic tree topology inference

Birth-death models are stochastic processes describing speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under constant-rate birth-death (crBD) tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between crBD and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which crBD differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical..., Empirical trees used in the study are trees from the literature, collected by TimeTree (timetree.org).
Run ```Tree_Selection.R``` to select the empirical phylogenetic trees to be included from TimeTree. The output file ```final_timetrees.RData``` contains the final subset of empirical phylogenetic TimeTree trees used for analysis with anonymized tip labels.
2. Run ```Simulation_And_Analysis.R``` to fit birth and death parameters (assuming rho = 1) for each of the 1189 empirical trees, simulate 1000 trees per empirical tree, calculate tree index values for both empirical and simulated trees, and calculate z-scores comparing the simulated and empirical trees. Note that calculating the tree index values for the simulated trees is VERY time-consuming due to the number of trees. Run ```Supplementary_Fig_S1_Analysis.R``` to generate data for Supplementary Figure S1.
3. Run ```Meta_analysis.R``` to run the linear regression models to investigate the role of the prior/analysis type for the subs..., R version: 4.2.2
Other software: RevBayes (version 1.2.1) (Höhna et al. 2016) and IQ-TREE 2 (version 2.2.0) (Minh et al. 2020) were used for supplementary analyses., ## The limits of the constant-rate birth-death prior for phylogenetic tree topology inference

This repo contains code to reproduce the simulations, analyses, and figures for \"The limits of the constant-rate birth-death prior for phylogenetic tree topology inference\".

## Environment setup:

R version: 4.2.2

The following libraries are used:

```R
library(adegenet)
library(ape)
library(apTreeshape)
library(Claddis)
library(coda)
library(coefplot)
library(colorspace)
library(cowplot)
library(ctv)
library(devtools)
library(dispRity)
library(dotwhisker)
library(dplyr)
library(gamlss)
library(gamlss.dist)
library(gamlss.add)
library(githubinstall)
library(GGally)
library(ggbiplot)
library(ggExtra)
library(gghalves)
library(gginnards)
library(ggplot2)
library(ggplotify)
library(ggpmisc)
library(ggpp)
library(ggpubr)
library(gridExtra)
library(magrittr)
library(openxlsx)
library(parallel)
library(phangorn)
library(phylobase)
library(phyloTop)
library(phytools)
library(plyr)
library(seqinr)
l...