DOI: 10.5281/zenodo.15618051
title: Bayesian analysis resolves dinosaur turnovers during the Jurassic–Cretaceous transition driven by climate shifts and biotic interactions

description: This folder contains all the original datasets, scripts, and results used in the study:

 

gcr: R code related to Grid-Cell Rarefaction, along with PyRate data and bash.

- DataS5_Raw_data.xlsx: Updated dinosaur dataset.

- gcr_function.r: Functions used for Grid-Cell Rarefaction.

- gcr_sample.r: Example of Grid-Cell Rarefaction (genus level). For the species-level run, filter the rows where the accepted_rank column equals species. Outputs reconstructed_coordinates1.csv, res, and results_sp/gn.

- gcr_species/ genus: Genus-/species-level data after Grid-Cell Rarefactio, as well as the PyRate input data, bash scripts for running PyRate, and PyRate outputs. The folder includes the following files/data:

- reconstructed_coordinates1.csv: Used to determine the paleogeographic location of occurrence points within each time bin during GCR resampling. Paleogeographic coordinates assigned to each occurrence point in each time bin (paleocoordinates are reconstructed based on max_age/min_age; during GCR, the paleocoordinate is taken as the mean of the two).

- epochs_sp/gn: Reassigned time-bin intervals (ensuring that differences in the numbers of species and occurrence points across time bins are not overly large).

- results_sp/gn: Comparison results across all input grid sizes and the corresponding maximum number of occurrence points within each grid size.

- res: For each region, the optimal grid size, the corresponding maximum number of occurrence points, and the resampling results.

- res_t: Results after merging occurrence points within each time bin across 10 batches (the same occurrence point with the same row_id across multiple time bins is merged into one), along with the converted PyRate input data and the final PyRate results.

- bash: Bash scripts for running PyRate analyses on the GCR-resampled data.

 

raw_data:

- raw_data_PBDB.csv: Raw occurrence data exported from the Paleobiology Database (PBDB), including all vertebrate fossil records from the Aalenian to Albian stages (174.7–100.5 Ma).

- dino.xlsx: Species-level dinosaur database after data cleaning and augmentation; red-highlighted fields indicate variables essential or relevant to the analyses.

- dino_singleton.xlsx: Species-level dinosaur database with all singleton taxa excluded; red-highlighted fields indicate variables essential or relevant to the analyses.

- dino1.xlsx: Genus-level dinosaur database after data cleaning and augmentation; red-highlighted fields indicate variables essential or relevant to the analyses.

- dino1_singleton.xlsx: Genus-level dinosaur database with all singleton taxa excluded; red-highlighted fields indicate variables essential or relevant to the analyses.

 

b_data  

- epochs_q.txt: Defines rate shift intervals in the PyRate analysis using a Time-Variable Poisson Process model, aligned with geological stages.  

- time_windows_a5.txt: Specifies time bins (0.5 Myr resolution) used in the PyRateBDNN analysis.  

- dino_con_e_165_125.txt: Time-continuous variables applied in PyRateBDNN modeling.  

- Backscale_e_165_125(_l).txt: Z-transformed means and standard deviations of time-continuous variables used for back-scaling model outputs to original data scales.

 

gen_dino1 (Genus-level dinosaur diversification analysis)  

- gen_dino1.py: Input dataset for PyRate analysis.  

- gen_dino1_trait.txt: Trait data for each taxon in the PyRateBDNN model.  

- RTT_groups_dino_gn_cl.csv: Species grouped by clade for RTT analysis in PyRateBDNN.  

- RTT_groups_dino_gn_le.csv: Species grouped by body size for RTT analysis in PyRateBDNN.  

- bash: Scripts for running PyRate and PyRateBDNN analyses.  

- result: Output from PyRate runs.  

- bdnn1_tw: Results from PyRateBDNN runs.

 

gen_dino1_singleton (Genus-level analysis excluding singleton taxa)  

- Files follow the same structure and naming conventions as in gen_dino1, adapted for analyses excluding singletons.

 

sp_dino (Species-level dinosaur diversification analysis)  

- sp_dino.py: Input dataset for PyRate analysis.  

- sp_dino_trait_tw.txt: Trait data for PyRateBDNN modeling.  

- RTT_groups_dino_sp_cl.csv: Species grouped by clade.  

- RTT_groups_dino_sp_le.csv: Species grouped by body size.  

- RTT_groups_dino_sp_ar.csv: Species grouped by palaeogeographic region.  

- bash: Scripts for running PyRate and PyRateBDNN analyses.  

- result: Output from PyRate runs.  

- bdnn1_tw: Results from PyRateBDNN runs.

 

sp_dino_singleton (Species-level analysis excluding singleton taxa)  

- Files follow the same structure as sp_dino, adapted for analyses excluding singleton occurrences.

 

J_K_result: Contains all results from the PyRate and PyRateBDNN analyses. The contents of each folder correspond to those described above. Files prefixed with RTT_group represent the RTT results from PyRateBDNN for each taxonomic group, body size category, or palaeogeographic region.