Supplement to Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction

This repository contains the supplementary files for:

Allen BJ, Volkova Oliveria MV, Stadler T, Vaughan TG, Warnock RCM. 2024. Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction. Cambridge Prisms: Extinction.

Description of files

This repository contains the cleaned tree files, tables of age constraints, XML files for running the analyses in BEAST2, and R code to process the datasets.

Benson1clean.tree, Benson2clean.tree, Lloyd1clean.tree, Lloyd2clean.tree - the cleaned tree files containing the phylogenies inputted into BEAST2, with tip names matched to age data from the Paleobiology Database

Tree modifications log.xlsx - a description of the modifications made to each input phylogeny compared to their state in the data supplement of their original papers

dinosaur_ages.csv - the raw dinosaur age data downloaded from the Paleobiology Database

tip_constraints.csv - the dinosaur age data converted into a format to input into BEAST2, to provide age constraints for tips

change_times.txt - a text file describing the change times for the piecewise constant trajectories in the two phylodynamic analyses

BDSKY.xml, PiecewiseCoalescent.xml - XML files describing the BEAST2 configuration for each of the two phylodynamic models

BDSKY_logs.zip, BDSKY_trees.zip, Coalescent_logs.zip, Coalescent_trees.zip - compressed folders containing the output log files and inferred phylogenies for each of the 16 analysed phylogenies

Supplementary_tables.zip - Tables containing summary statistics for each of the parameters inferred in each of the models

Description of R code

The R code is subdivided into the following files:

Wrangle_trees.R - code for checking, cleaning, and splitting the phylogenies used in the analyses

PBDB_tip_constraints.R - code for converting the raw age data from the Paleobiology Database into a format ready for input into BEAST2 as tip constraints

BDSKY_post_processing.R, Coalescent_post_processing.R - code for cleaning and plotting data from the BEAST2 log files, for each of the two phylodynamic models