Chronospaces: an R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity

Much of our understanding of the history of life hinges upon time calibration, the process of assigning absolute times to cladogenetic events. Bayesian approaches to time scaling phylogenetic trees have dramatically grown in complexity, and depend today upon numerous methodological choices. Arriving at objective justifications for all of these is difficult and time consuming. Thus, divergence times are routinely inferred under only one or a handful of parametric conditions, often times chosen arbitrarily. Progress towards building robust biological timescales necessitate the development of better methods to visualize and quantify the sensitivity of results to these decisions.
Here, we present an R package that assists in this endeavor through the use of chronospaces, i.e., graphical representations summarizing variation in the node ages contained in time-calibrated trees. We further test this approach using three empirical datasets spanning widely differing timeframes.
Our results revea..., Data included in this repository include the publicly-available, genome-scale datasets originally gathered by Shin et al. 2018 (Curculionoidea), Wolfe et al. 2019 (Decapoda), and Strassert et al. (2021) Eukaryota. These were subsampled into various subsets of genes using R code that is provided, and used to generate alternative reconstructions of the diversification of these clades, using PhyloBayes v.4.1 (Lartillot et al. 2013). Posterior distributions of topologies for each of these files are provided, along with R code to process the data and generate the results that are presented in the manuscript., , # Data from: Chronospaces: an R package for the statistical exploration of divergence times reveals extreme dependence on molecular clocks and gene choice

The data contained in this repository supports the results presented in Mongiardino Koch & Milla Carmona (2024), introducing the R package *chronospace*, and exploring its use to understand sources of uncertainty in divergence time estimation.

## Description of the data and file structure

The repository contains two folders, which have been zipped for convenience.

The first of these, 'Datasets', includes in turn three subfolders, containing the data obtained from three publications dealing with the diersification of three clades, and whose names denote the focal clade (i.e., 'Curculionoidea', 'Decapoda', and 'Eukaryota'). Each of these folders contain the same set of files:

1. 'all_gene_trees.tre': A tree file containing all gene trees, ordered as in the phylogenomic dataset (see below), and formatted in Newick style. Thes...