DOI: 10.5281/zenodo.15618052
title: Dinosaurs 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:

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.