Files for phylogenetic analysis

Main_analyses.zip contains files necessary to replicate the results of Smith & Long et al. These are modelled on Workflows for phylogenetic analysis of morphological data.Conservative.zip contains a repeat of our phylogenetic analyses after re-coding as ambiguous any character in Youti yuanshi whose state at adulthood is not unequivocal.Each archive contains files within a common subdirectory structure:MrBayesFolder containing input and output files for analysis in MrBayes.mbank_X27231_2024-03-22-1117.nex: NEXUS format character matrix downloaded from MorphoBank (project 3927), with addition of MrBayes block specifying search parameters.Other files are output files in the standard MrBayes format; sampled trees are contained in files ending .t.Phylogenetics.zip also contains marginal likelihood estimates under topological constraints that impose Tactopoda (Euarthropoda + Tardigrada) and Arthropoda (Euarthropoda + Onychophora):Output of stepping stone analyses are contained within files ending .ss.marginal_likelihood.R is a simple R script that computes marginal likelihoods and Bayes Factors from stepping stone analysis; it can be executed in R or RStudio.TreeSearchScripts for phylogenetic analysis under parsimony, with an approximate correction for inapplicable data.analyse.R: R script used to perform analysis. Can be executed within R / RStudio, or run directly on Windows by modifying Analyse.lnk to point to a local R installation.common.R: R file included from other scripts; loads packages and defines utility functionsplot.R: R file included from other scripts; defines plotting parameters, including colour and format of tip labels.visualize.R: R script for visualizing search results generated by analyse.R, and the distribution of trees in tree space. Can be executed within R / RStudio, or run directly on Windows by modifying Visualize.lnk to point to a local R installation.mbank_X27231_2024-03-22-1117.nex: NEXUS format character matrix downloaded from MorphoBank (project 3927).XXX_mbank_X27231_2024-03-22-1117.nex.trees: NEXUS file containing results of parsimony search under the weighting system specified by XXX. ew = equal weights; iw# = implied weighting under concavity constant (k) = #.Character_report.Rmd: R Markdown file used to generate character report. Can be compiled into a standalone document using the "knit" command in RStudio.Character_report_template.docx: Word Document file providing style templates used when rendering the character report and the supplementary information (see folder SI).TNTScripts for phylogenetic analysis under parsimony, with no correction for inapplicable data.mbank_X27231_2024-03-22-1117.tnt: TNT format character matrix downloaded from MorphoBank (project 3927).tnt.run: TNT script used to perform analysis. Can be executed within TNT.XXX.tre: Most parsimonious trees in TNT format, as recovered under the weighting strategy denoted by XXX. ew = equal weights; iw# = implied weighting under concavity constant (k) = #.XXX.sym: Strict consensus trees under each weighting strategy, with symmetric resampling node support values, in TNT format.XXX.pdf: Visualization of strict consensus trees under each weighting strategy, after removal of rogue taxa using 'fast' heuristic of Smith (2022); tips coloured by stability.visualize.R: R script used to produce PDF visualizations.SIFiles used to render supplementary information documents.map_trees.Rmd: R Markdown document used to compile and summarise results of tree search under Bayesian and parsimony analyses. Can be compiled as a standalone document using the "knit" command in RStudio.SI.Rmd: Wrapper file used to collate components into a single output file. Using the "knit" command in RStudio will compile the supplementary information document._bookdown.yml: YAML-formatted configuration file to control output settings.