v1.0.1

In this release, you will find the step-by-step tutorial with all the guidelines you need to follow to reproduce the results for the timetree inference analyses we carried out as part of our study: The nature of the Last Universal Common Ancestor and its impact on the early Earth system.

I have updated the following content if compared to the pre-release version that we made available while our manuscript was under review:

• Fixed all typos and broken links that I could find -- I apologise if I have missed some! If you find typos/broken links, please open an issue so that I can fix them, thank you!
• Updated the comments with instructions to run the various commands in the R scripts that users will need to run to reproduce our results. In essence, some comments were outdated and/or were part of an old PAML tutorial. Now, they have been updated following the comments and instructions I have in similar scripts in my latest MCMCtree tutorial.
• Included the data for the initial paralogues that were filtered prior to timetree inference (i.e., see raw_8pars_dat and the first paragraph in the corresponding README.md file for more details).
• Added some tsv files that were ignored.
• Added additional rows in the Calibnodes* files inside the calib_files directories (i.e., MCMCtree analyses) so that the plots with marginal densities VS calibration densities were also generated for cross-braced nodes. These new plots were generated for all the *MCMCtree directories inside directory 01_PAML and for those under 03_additional_analyses/00_indgenes_analyses as a safety check (i.e., they should be the same for all cross-braced nodes, and they are). Given that there were no issues identified and the safety check was passed, I decided to not add more files in this repository as it already takes a while to index all the files and commit changes. To this end, directories inside 01_lou_analyses and 02_blunc_analysis will have these plots for the first instance of nodes that are cross-braced (i.e., mirror nodes but not driver nodes) as they are essentially the same. Therefore, the Calibnodes* files have remained unchanged.
• Incorporated the link to the archive we stored at the University of Bristol data repository (~71Gb). Please note that this archive contains the same files that we have in the pre-release, and so the content may have been updated after I carried out the changes aforementioned.

If you use any of the resources in this GitHub repository for your own analyses, please cite the following:

• Álvarez-Carretero, S. (2024). sabifo4/LUCA-divtimes: v1.0.0 (LUCAdivtimes-prerelease). Zenodo. https://doi.org/10.5281/zenodo.11260523
• Moody, E.R.R., Álvarez-Carretero, S., Mahendrarajah, T.A. et al. The nature of the last universal common ancestor and its impact on the early Earth system. Nat Ecol Evol (2024). https://doi.org/10.1038/s41559-024-02461-1

v1.0.0

In this pre-release, you will find the current step-by-step tutorial with all the steps you need to follow to reproduce the results for the timetree inference analyses we carried out as part of our study: The nature of the Last Universal Common Ancestor and its impact on the early Earth system.

Please note that we may have to update some URLs in the current README.md file once the paper is published (perhaps some typos too!). We shall then create another release with the final changes :)