DOI: 10.5061/dryad.cfxpnvxdn
title: Data from: Chronospaces: an R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity

description: 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 reveal large differences in the impact of many
 common methodological decisions, with the choice of clock (uncorrelated
 vs. autocorrelated) and loci having strong effects on inferred ages. Other
 decisions have comparatively minor consequences, including the use of the
 computationally intensive site-heterogeneous model CAT-GTR. Notably, these
 conclusions are as valid for Cenozoic divergences as they are for the
 deepest eukaryote nodes. The package chronospace implements a
 range of graphical and analytical tools that assist in the exploration of
 sensitivity and the prioritization of computational resources in the
 inference of divergence times.
description: 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.
description: # 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. These were inferred using ParGenes v.1.0.1 and can be
 imported to R using function from package *ape*, or otherwise visualized
 using FigTree. 2. 'calibrations.txt': A text file including node
 calibrations in the format expected by PhyloBayes. This includes
 information of two terminal species bracketing the constrained nodes, as
 well as minimum and maximum age bounds of said node. 3.
 'outgroups.txt': A text file listing the terminal names of taxa
 considered outgroups to the clade of interest, one per line. 4.
 'partitions.txt': An RAxML-style partition file, specifying the
 type of data (in this case, amino acids), the partition name (numeric),
 and the interval of columns of the alignment that each loci cover. 5.
 'supermatrix.fa': A FASTA file phylogenomic matrix, which can be
 read into R using functions from package *phangorn*, as well as provided
 to various software for phylogenetic inference. 6.
 'topology.tre': A tree file in Newick format containing a single
 tree considered by the authors of each study as the best estimate of the
 phylogeny of the species studied, and used for divergence time estimation
 under a constrained topology in PhyloBayes. A second folder named
 'Results', includes the same three subfolders (one for each
 clade), in which the following files can be found: 1. 40 '.tre'
 files, each including 500 time-scaled phylogenies (chronograms) for the
 clade of interest, obtained using PhyloBayes under different parametric
 conditions (varying the type of clock, the model of molecular evolution,
 the subset of genes used, and the shape of the prior on constrained
 nodes). Each of these is the result of combining the posterior trees of
 two replicated chains and subsampling randomly only 500 trees. The
 conditions leading to the inference of each file is specified in the name
 of the file (e.g., file names that include 'ln' where inferred
 using a log-normal autocorrelated clock, while those that include
 'ugam' while inferred using an uncorrelated gamma-distributed
 clock). 2. A single R data object, stored as a '.Rda' file,
 containing the node ages of all 40 '.tre' files ready to be
 imported into R using function *load()*. These files were generated using
 function *extract_ages()* from package *chronospace*, and are provided
 here simply to ease the replication of results. Beyond these two folders,
 two R scripts are also provided. These are explained below ##
 Sharing/Access information Software used to generate these files include:
 * Lartillot, N., Rodrigue, N., Stubbs, D. & Richer, J. (2013)
 PhyloBayes MPI. Phylogenetic reconstruction with infinite mixtures of
 profiles in a parallel environment. *Systematic Biology,* **62,** 611-615.
 * Mongiardino Koch, N. (2021) Phylogenomic subsampling and the search for
 phylogenetically reliable loci. *Molecular Biology and Evolution,* **38**,
 4025-4038. * Morel, B., Kozlov, A.M. & Stamatakis, A. (2018) ParGenes:
 a tool for massively parallel model selection and phylogenetic tree
 inference on thousands of genes. *Bioinformatics,* **35,** 1771-1773.
 Genome-scale alignments, species trees, partition files, and fossil
 calibrations were obtained from: * Shin, S., Clarke, D.J., Lemmon, A.R.,
 Moriarty Lemmon, E., Aitken, A.L., Haddad, S., Farrell, B.D., Marvaldi,
 A.E., Oberprieler, R.G. & McKenna, D.D. (2018) Phylogenomic data yield
 new and robust insights into the phylogeny and evolution of weevils.
 *Molecular Biology and Evolution,* **35,** 823-836. * Strassert, J.F.,
 Irisarri, I., Williams, T.A. & Burki, F. (2021) A molecular timescale
 for eukaryote evolution with implications for the origin of red
 algal-derived plastids. *Nature Communications,* **12,** 1879. * Wolfe,
 J.M., Breinholt, J.W., Crandall, K.A., Lemmon, A.R., Lemmon, E.M., Timm,
 L.E., Siddall, M.E. & Bracken-Grissom, H.D. (2019) A phylogenomic
 framework, evolutionary timeline and genomic resources for comparative
 studies of decapod crustaceans. *Proceedings of the Royal Society B,*
 **286,** 20190079. ## Code/Software Script
 'prepare_and_analyze_datasets.R' includes code that takes the
 files present within each 'Dataset' subfolder, subsamples the
 phylogenomic matrices using various approaches, and produces the files
 needed to run time calibrated inference in PhyloBayes (including slurm
 batch files). The code also takes the results present in the
 'Results' folder and replicates the images included in the
 manuscript. Script 'genesortR_for_chronospaces.R' is a modified
 script of the *genesortR* pipeline (Mongiardino Koch 2021) that has been
 slightly modified to generate small subsampled molecular datasets for
 divergence time estimation. This second script is automatically run from
 within the first one.