DOI: 10.5061/dryad.dr7sqvb2h
title: Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling

description: Abstract The clade Pancrustacea, comprising crustaceans and hexapods, is
 the most diverse group of animals on earth, containing over 80% of animal
 species and half of animal biomass. It has been the subject of several
 recent phylogenomic analyses, yet relationships within Pancrustacea show a
 notable lack of stability. Here, the phylogeny is estimated with expanded
 taxon sampling, particularly of malacostracans. We show small changes in
 taxon sampling have large impacts on phylogenetic estimation. By analyzing
 identical orthologs between two slightly different taxon sets, we show
 that the differences in the resulting topologies are due primarily to the
 effects of taxon sampling on the phylogenetic reconstruction method. We
 compare trees resulting from our phylogenomic analyses with those from the
 literature to explore the large tree space of pancrustacean phylogenetic
 hypotheses and find that statistical topology tests reject the previously
 published trees in favor of the maximum likelihood trees produced here.
 Our results reject several clades including Caridoida, Eucarida,
 Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda
 nested within Allotriocarida with high support and recover a novel
 relationship between decapods, euphausiids, and syncarids that we refer to
 as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister
 to this latter clade, which we collectively name Stomatocarida, dividing
 Malacostraca into three clades: Leptostraca, Peracarida, and
 Stomatocarida. A new Bayesian divergence time estimation is conducted
 using 13 vetted fossils. We review our results in the context of other
 pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample
 in future studies.
description: Phylogenetic trees and alignments from analyses in this
 study.
description: # Title of Dataset: Data from Major revisions in pancrustacean phylogeny
 and evidence of sensitivity to taxon sampling *** Matricies, treefiles,
 and alignments from: Major revisions in pancrustacean phylogeny and
 evidence of sensitivity to taxon sampling ## Description of the data and
 file structure zip files for: * divergence\_time\_files # chronograms from
 divergence time analyses * matrices # super matrices (full alignments)
 used in this study * orthologs # individual ortholog alignments and gene
 trees * treefiles # newick tree files (filenames refer to the figure
 numbers in the manuscript) * Dataset2\_homologs # unaligned fastas before
 ortholog filters Detailed Table of Contents *** * divergence\_time\_files
 * dating\_MCMCTree\_c1.chronogram # chronogram from chain 1 of MCMCTree
 divergence time analsis * dating\_MCMCTree\_c3.chronogram # chronogram
 from chain 2 of MCMCTree divergence time analsis *
 dating\_MCMCTree\_c2.chronogram # chronogram from chain 3 of MCMCTree
 divergence time analsis * dating\_MCMCTree\_prior.chronogram # chronogram
 under the prior of MCMCTree divergence time analsis *
 Phylobayes\_LN.chronogram # chronogram of 3 chains using the LN model in
 Phylobayes * Phylobayes\_LN\_prior.chronogram # chronogram of 3 chains
 under the prior of the LN model in Phylobayes * Phylobayes\_CIR.chronogram
 # chronogram of 3 chains using the CIR model in Phylobayes *
 Phylobayes\_CIR\_prior.chronogram # chronogram of 3 chains under the prior
 of the CIR model in Phylobayes * Phylobayes\_UGAM.chronogram # chronogram
 of 3 chains using the UGAM model in Phylobayes *
 Phylobayes\_UGAM\_prior.chronogram # chronogram of 3 chains using the UGAM
 model in Phylobayes * matrices * Dataset1\_matrix.phy # Dataset 1 is an
 earlier version of this study containing 98 taxa and 559 orthologs
 (details in manuscript text) *
 Dataset1\_shared\_orthologs\_only\_alignment.fasta # Matrix of the 98 taxa
 in Dataset 1 with only the 267 orthologs shared with Dataset 2 *
 Dataset2\_matrix.phy # Final matrix consisting of 105 taxa (details in
 manuscript text) * Dataset2\_50gene\_subset\_Phylobayes\_divergence.phy #
 Matrix of top 50 genes from Dataset 2 with highest Robinson-Foulds
 similarity to species tree from ML analysis of Dataset2\_matrix.phy *
 Dataset2\_matrix\_dayhoff\_recoded.phy # Dataset 2 matrix under Dayhoff6
 recoding * Dataset2\_minus\_fastestgenes\_matrix.phy # Dataset 2 with the
 10% (i.e., 57) fastest evolving genes removed *
 Dataset2\_shared\_orthologs\_only\_alignment.fasta # Matrix of the 105
 taxa in Dataset 2 with only the 267 orthologs shared with Dataset 1 *
 Dataset2\_matrix\_trimmed\_of\_added\_taxa.fasta # Taxon sampling
 experiment. Dataset 2 matrix after removing the additional taxa that were
 added relative to Dataset 1 (details in manuscript text) * orthologs *
 Dataset1\_ortholog\_alignments\_gblocks.zip # individual alignments for
 the 559 orthologs in Dataset 1 * Dataset1\_ortholog\_alignments.tar.gz #
 individual alignments for the 559 orthologs in Dataset 1 prior to trimming
 with gblocks * Dataset1\_ortholog\_trees.zip # individual gene trees for
 the 559 orthologs in Dataset 1 *
 Dataset2\_ortholog\_alignments\_gblocks.zip # individual alignments for
 the 576 orthologs in Dataset 2 * Dataset2\_ortholog\_alignments.tar.gz #
 individual alignments for the 576 orthologs in Dataset 2 prior to trimming
 with gblocks * Dataset2\_ortholog\_trees.zip # individual gene trees for
 the 576 orthologs in Dataset 2 *
 Datatset3\_vs\_Dataset1\_shared\_orthologs.txt # list of orthologs shared
 between Datasets 2 and 3 * treefiles * Fig2A\_Dataset2\_C60LG.tre # Tree
 resulting from LG+C60+F+G analysis of Dataset 2 AA matrix *
 FigS1A\_Dataset2\_raxml.tre # Tree resulting from RAxML analysis of
 Dataset 2 AA matrix * FigS1B\_Dataset2\_Dayhoff6\_raxml.tre # Tree
 resulting from RAxML analysis of Dataset 2 Dayhoff6 matrix *
 FigS1C\_Dataset2\_C60LG\_minusfastgenes.tre # Tree resulting from IQ-TREE
 LG+C60+F+G analysis of Dataset 2 AA matrix with 10% fastest evolving genes
 removed * FigS2A\_Dataset2\_CATGTR\_consensus.tre # Tree resulting from
 Phylobayes CAT-GTR analysis of Dataset 2 AA matrix - consensus of 3 chains
 * FigS2B\_Dataset2\_CATGTR\_c1.tre # Tree resulting from Phylobayes
 CAT-GTR analysis of Dataset 2 AA matrix - chain 1 *
 FigS2C\_Dataset2\_CATGTR\_c2.tre # Tree resulting from Phylobayes CAT-GTR
 analysis of Dataset 2 AA matrix - chain 2 *
 FigS2D\_Dataset2\_CATGTR\_c3.tre # Tree resulting from Phylobayes CAT-GTR
 analysis of Dataset 2 AA matrix - chain 3 *
 FigS3\_Dataset2\_Dayhoff6\_CATGTR\_consensus.tre # Tree resulting from
 Phylobayes CAT-GTR analysis of Dataset 2 Dayhoff6 matrix - consensus of 2
 chains * FigS4A\_Dataset2\_ATRAL.tre # Tree resulting from ASTRAL analysis
 of Dataset 2 orthologs * FigS4B\_Dataset2\_ASTRAL\_BS10.tre # Tree
 resulting from ASTRAL analysis of Dataset 2 orthologs, with nodes in gene
 trees with &lt;10% BS support collapsed *
 FigS4C\_Dataset2\_ASTRAL\_BS20.tre # Tree resulting from ASTRAL analysis
 of Dataset 2 orthologs, with nodes in gene trees with &lt;20% BS
 support collapsed * FigS4D\_Dataset2\_ASTRAL\_BS30.tre # Tree resulting
 from ASTRAL analysis of Dataset 2 orthologs, with nodes in gene trees with
 &lt;30% BS support collapsed *
 FigS5\_Dataset1\_C60LG\_speciestree.treefile # Tree resulting from
 LG+C60+F+G analysis of Dataset 1 AA matrix *
 FigS6\_Dataset1\_Dayhoff6\_raxml.tre # Tree resulting from RAxML analysis
 of Dataset 1 Dayhoff6 matrix * FigS7\_Dataset1\_CATGTR\_consensus.tre #
 Tree resulting from Phylobayes CAT-GTR analysis of Dataset 1 AA matrix -
 consensus of 4 chains * FigS8A\_Dataset1\_Dayhoff6\_CATGTR\_consensus.tre
 # Tree resulting from Phylobayes CAT-GTR analysis of Dataset 1 Dayhoff6
 matrix - consensus of 2 chains *
 FigS8B\_Dataset1\_Dayhoff6\_CATGTR\_c1.tre # Tree resulting from
 Phylobayes CAT-GTR analysis of Dataset 1 Dayhoff6 matrix - chain 1 *
 FigS8C\_Dataset1\_Dayhoff6\_CATGTR\_c2.tre # Tree resulting from
 Phylobayes CAT-GTR analysis of Dataset 1 Dayhoff6 matrix - chain 2 *
 FigS9A\_Dataset1\_ASTRAL.tre # Tree resulting from ASTRAL analysis of
 Dataset 1 orthologs * FigS9B\_Dataset1\_ASTRAL\_BS10.tre # Tree resulting
 from ASTRAL analysis of Dataset 1 orthologs, with nodes in gene trees with
 &lt;10% BS support collapsed * FigS9C\_Dataset1\_ASTRAL\_BS30.tre #
 Tree resulting from ASTRAL analysis of Dataset 1 orthologs, with nodes in
 gene trees with &lt;30% BS support collapsed *
 FigS10A\_Dataset1\_shared\_orthologs\_C60LG.tre # Trees results from
 IQ-TREE LG+C60+F+G analysis using only shared orthologs - Dataset 1 taxa *
 FigS10B\_Dataset2\_shared\_orthologs\_C60LG.tre # Trees results from
 IQ-TREE LG+C60+F+G analysis using only shared orthologs - Dataset 2 taxa *
 FigS11\_Dataset2\_C60LG\_trimmed\_taxa.tre # Trees resulting from
 LG+C60+F+G analysis of the Dataset 2 orthologs trimmed of additional taxa
 relative to Dataset 1 * Dataset2\_homologs.tar.gz # unaligned fastas
 before ortholog filters. Results from all vs all BLAST and MCL, clusters
 with &gt;40 taxa