Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity

# Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity This README is for: "Fossil-calibrated molecular clock enables reconstruction of steps leading to differentiated multicellularity in the Volvocine algae" by CR Lindsey, AH Knoll, MD Herron, and F Rosenzweig. DOI = [https://doi.org/10.1186/s12915-024-01878-1](https://doi.org/10.1186/s12915-024-01878-1) The contents of this file include the following: 1. **phytools_r_scripts.zip:** R scripts used to run simmap analyses in Phytools Specifically, these are the R scripts used to generate simmap analyses for Kirk's 12 developmental traits, certain sexual traits, and misc. traits in the Volvocine algae. 2. **MBASR_run_script_template:** MBASR template script used to run all the ancestral state reconstructions in MBASR 3. **gene_alns_263.zip)**: All 263 alignment files used in our maximum likelihood and Mr. Bayes phylogenetic analyses . 4. **phylobayes_<8/16>gene_input_files.zip:** 8-gene and 16-gene alignment files used in our Phylobayes molecular clock analyses. Fossil calibration include the specific node calibrations for our molecular clock analyses. Each zip file contains the following: **archaeplastida_fossil_calibrations_mins_and_ranges.txt**: fossil calibration files **ds<1/5>*gshop_trimalv7v3_042723*<8/16>genes_**: a gene alignment file **nwk_trimalv7v3_042723.tre**: newick tree formatted file **outgroup.txt**: outgroup taxa file 5. **IQtree_files.zip:** Concatenated 263-gene alignment files used in our IQtree and Mr. Bayes phylogenetic analyses. Contains the concatenated gene alignment **IQtree_aln_file.fa** and character partition files **IQtree_charpartition.nex**. MrBayes input is **mrbayes_file_263genes.nex** 6. **astral_263genetrees_file.tre:** ASTRAL 263-gene tree file . This is file has all of our single-gene phylogenies concatenated into one file. All single-gene trees (263 total) have been individually uploaded in the following ZIP file: **single_gene_trees_trimalv7v3_042723.zip**. #### Usage Notes A) .tre files may be viewed but not limited to the following software: Figtree or TreeGraph2. B) alns = alignments C) FASTA (.fa) and NEXUS (.nex) files may be viewed using any text editor such as Sublime Text. D) MBASR template script is a text file used with the program MBASR ([https://www.biorxiv.org/content/10.1101/2021.01.10.426107v1.full.pdf)](https://www.biorxiv.org/content/10.1101/2021.01.10.426107v1.full.pdf\)) E) "CB" and "ML" acronyms are used in filenames to specify which phylogenetic analysis the tree branching order belongs. "CB" and "ML" correspond to coalescent-based and maximum-likelihood, respectively. Additional files uploaded to Zenodo: 7\. **phylobayes_fossil_calibrations_and_chronograms.zip:** Phylobayes outputs of the following items for each clock model from 16-gene analyses: chronograms, dates, and labels 8\. **command_line_arguments.pdf:** Command line PDF with software repo links.