Data and code from: Evaluating the impact and detectability of mass extinctions on total-evidence dating

Fossils are crucial for accurately dating phylogenetic trees because their ages provide vital constraints on the timing of macroevolutionary events, and their morphological characters offer key information on evolutionary rates and phylogenetic positions. The fossilized birth-death (FBD) process is a diversification model that incorporates both extant and extinct species, serving as a tree prior that seamlessly integrates fossils into phylogenetic inference. While the FBD model can account for mass extinctions, which caused rapid, widespread organismal loss, few studies have utilized FBD models incorporating these events in phylogenetic inference. This is likely because the detectability of mass extinctions and their impact on phylogenetic inference remain unclear. Through simulations, we assessed the influence of mass extinctions on divergence time and topology inference and evaluated the detectability of mass extinction signals in total-evidence dating. We examined three FBD tree..., , , # Data and code from: Evaluating the impact and detectability of mass extinctions on total-evidence dating

## Scripts

### simulation

Scripts for simulating phylogenetic trees and morphological and molecular characters.

* Simu_ME.R: Simulates phylogenetic trees along with morphological and molecular characters.
* sample_morph.R: Randomly samples 25 morphological characters from an initial set of 250.
* SimuRelaxedClock.R: Simulates relaxed clock and complex substitution model.
* Substitution.R: Summarize the expected number of substitutions per site and the number of invariant characters in the simulation

#### compare-ME-WME-Tree

Scripts for simulating trees with and without mass extinction, and comparing summary statistics.

* Compare-ME-WME-Tree.py: Calculates and compares summary statistics of the simulated trees.
* xml: Simulated XML files.

### inference/

Scripts for performing inference using RevBayes, BEAST2, and MrBayes under FBD models.

#### Rev/simulation

* KnownTime: ..., ,