DOI: 10.5061/dryad.t76hdr89k
title: Is the deuterostome clade an artefact?

description: There is a long-standing consensus that the animal phyla closest to our
 own phylum of Chordata are the Echinodermata and Hemichordata. These three
 phyla constitute the major clade of Deuterostomia. Recent analyses have
 questioned the support for the monophyly of Deuterostomia, however,
 showing that the branch leading to deuterostomes is very short and may be
 influenced by systematic error. Here we use a site-by-site approach to
 explore possible sources of error. Under conditions that promote
 long-branch attraction (LBA) – especially branch-length heterogeneity and
 sites constrained in their amino acid composition – we find that
 deuterostome monophyly is strongly supported. When we make efforts to
 mitigate these sources of error, support for Deuterostomia markedly
 decreases or even disappears. Our results call into question one of the
 longest established major branches of the animal kingdom. A very short, or
 non-existent, deuterostome branch has implications for interpretating
 putative deuterostome fossils and for reconstructing the bilaterian
 ancestor.
description: # Is the deuterostome clade an artefact? ## Directory list:
 `dataProvenance.xlsx`: contains the accession numbers and sources for the
 proteomic and transcriptomic data used in this study `rawData.zip`:
 contains the pre-processed input data * OrthoFinder_input contains the raw
 genomes/proteomes/transcriptomes listed in dataProvenance.xlsx *
 orthoGroups_raw.zip contains the raw [OrthoFinder
 output](https://github.com/davidemms/OrthoFinder), excluding the
 WorkingDirectory and the empty Single_Copy_Orthologue_Sequences *
 orthoGroups_paraFilter contains the 183 paralogue filtered orthogroups,
 see main text for methodology `scripts.zip`: contains any additional
 script needed to run/modify analyses or their output that are not already
 available from GitHub repositories (cited in main text). The scripts are
 roughly organised by task: * dataProcessing * IQTreeOutputProcessing *
 IQTreeSearches * plotting * renamingScripts * simulations From here all
 subfolders follow these naming conventions: * Taxon sampling (see main
 paper): * setting6_fast or S6: includes fast-evolving taxa * setting7_slow
 or S7: does not include fast-evolving taxa * Topology (see Fig. 2 in main
 paper for tree topologies) * MonoDeut: monophyletic Deuterostomia topology
 * ProtAmbu: Orthozoa topology * ProtChord: Centroneuralia topology *
 ProtPara: paraphyletic Protostomia * Amino acid substitution model: LG,
 CAT, EDM; if '_G' in folder name the models were set up as LG+G,
 CAT+G or EDM+G (see main paper for methodology details) `alignments.zip`
 folder: contains the concatenated alignments used for all phylogenetic
 analyses (306-taxon and subsetted alignments) * concatenated_306taxa: list
 of taxa and the fasta (*.aln) and phylip (*.phy) formatted concatenated
 alignment * setting6_fast: subsetted alignments including long-branched
 taxa * fasta: folder with 100 fasta-formatted randomly subsetted
 alignments * phylip: folder with 100 phylip-formatted randomly subsetted
 alignments * setting7_slow: subsetted alignments excluding long-branched
 taxa * fasta: folder with 100 fasta-formatted randomly subsetted
 alignments * phylip: folder with 100 phylip-formatted randomly subsetted
 alignments `crossVals.zip`: contains the output of leave-one-out
 cross-validation (loocv) analyses. PhyloBayes run files can be provided on
 request, omitted from repository to limit size. * aln68_S7 and aln69_S6:
 contain the phylip alignments, guide trees and EDM category file used as
 input to [PhyloBayes](https://github.com/bayesiancook/pbmpi) * Each output
 folder contains the *.cpo and *.sitelogl files needed to summarise the
 lcoov analyses with the PhyloBayes-provided scripts (details pages 16-17
 of the
 [manual](https://github.com/bayesiancook/pbmpi/blob/master/pb_mpiManual1.9.pdf)) `EDCfiles.zip`: contains the [IQTREE](https://github.com/iqtree/iqtree2)-compatible EDM category file generated with the [EDCluster](https://github.com/dschrempf/EDCluster) package `inputTrees.zip`: contains the guide trees used for the IQTREE topology-scoring analyses * setting6_fast: contains the pruned trees for 100 subsetted alignments * setting7_slow: contains the pruned trees for 100 subsetted alignments * treesToPrune: original 306-taxa unpruned trees for MonoDeut, ProtAmbu and ProtChord hypotheses `IQTreeOutputFiles.zip`: contains the output files from IQTREE's topology-scoring runs, organised by subsetting strategy and substitution model used (e.g. setting6_fast/EDM_G/). Within each of these subfolders analyses are organised into: * aln#_MonoDeut * aln#_ProtAmbu * aln#_ProtChord * This EXACT folder structure is needed to run the IQTreeOutput_manipulation.R script. Each subfolder contains the standard IQTREE output files, plus a file with the per site log-likelihood score (*.sitelh) and a file with the per site rate category (*.rate), which are the input files for the IQTreeOutput_manipulation.R script. `results.zip`: contains edited files with site likelihoods, rate categories and supported topologies * pseudoRateCat_noGamma: contains the files needed to generate the supplementary plots S1 and S3 * for each setting*/model/ * sitelhRatesTables: output of the IQTreeOutput_manipulation.R script, file extensions explained in script. * siteSupportedTopology: output of the likelihood_transform.py script. Output of interest compiled in the allReps_labelled.stats file. * siteProfiles: files needed to generate figure 5 in the main text `topoSims.zip`: contains the alignments and the IQTree output for the simulation analyses * Deut: data simulated under the Deuterostomia topology * setting6_fast: * deutSup_aln14: data simulated from the long-branched subsetted alignment 14 * alignments: simulated alignments * IQTreeRuns: follow IQTreeOutputFiles.zip structure and naming convention but all analyses ran with the gamma parameter * siteProfileSims.zip: PhyloBayes site-profiles and EDCluster EDM category files for simulated alignments 40, 80, 120, 160 and 200 * paraSup_aln91: data simulated from the long-branched subsetted alignment 91 * same subfolders as deutSup_aln14 * setting7_slow: * deutSup_aln47: data simulated from the short-branched subsetted alignment 47 * same subfolders as setting6_fast/deutSup_aln14 * paraSup_aln62: data simulated from the short-branched subsetted alignment 62 * same subfolders as setting6_fast/deutSup_aln14 * Orth: data simulated under Orthozoa topology * subfolders identical to Deut folder `RELLbootstraps.zip`: contains the R script and workspace image to generate the supplementary plots S6-7 ## Change Log **20 Jun 2025**: Minor updates to README.