DOI: 10.5061/dryad.k6tq2
title: Data from: Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

description: Background: Understanding the phylogenetic relationships among major
 lineages of multicellular animals (the Metazoa) is a prerequisite for
 studying the evolution of complex traits such as nervous systems, muscle
 tissue, or sensory organs. Transcriptome-based phylogenies have
 dramatically improved our understanding of metazoan relationships in
 recent years, although several important questions remain. The branching
 order near the base of the tree, in particular the placement of the
 poriferan (sponges, phylum Porifera) and ctenophore (comb jellies, phylum
 Ctenophora) lineages is one outstanding issue. Recent analyses have
 suggested that the comb jellies are sister to all remaining metazoan phyla
 including sponges. This finding is surprising because it suggests that
 neurons and other complex traits, present in ctenophores and eumetazoans
 but absent in sponges or placozoans, either evolved twice in Metazoa or
 were independently, secondarily lost in the lineages leading to sponges
 and placozoans. Results: To address the question of basal metazoan
 relationships we assembled a novel dataset comprised of 1080 orthologous
 loci derived from 36 publicly available genomes representing major
 lineages of animals. From this large dataset we procured an optimized set
 of partitions with high phylogenetic signal for resolving metazoan
 relationships. This optimized data set is amenable to the most appropriate
 and computationally intensive analyses using site-heterogeneous models of
 sequence evolution. We also employed several strategies to examine the
 potential for long-branch attraction to bias our inferences. Our analyses
 strongly support the Ctenophora as the sister lineage to other Metazoa. We
 find no support for the traditional view uniting the ctenophores and
 Cnidaria. Our findings are supported by Bayesian comparisons of
 topological hypotheses and we find no evidence that they are biased by
 long-branch attraction. Conclusions: Our study further clarifies
 relationships among early branching metazoan lineages. Our phylogeny
 supports the still-controversial position of ctenophores as sister group
 to all other metazoans. This study also provides a workflow and
 computational tools for minimizing systematic bias in genome-based
 phylogenetic analyses. Future studies of metazoan phylogeny will benefit
 from ongoing efforts to sequence the genomes of additional invertebrate
 taxa that will continue to inform our view of the relationships among the
 major lineages of animals.
description: Binned
 AnalysesResults of ML analyses
 of matrices binned according to rate of locus evolution. Separate analyses
 were carried out for 60-, 108-, and 216-locus bins. The text files contain
 support for the topologies of interest.Binned_analyses.zipCodeScripts used in analyses and plotting selected figures. See also https://github.com/marekborowiec/metazoan_phylogenomics/blob/master/gene_stats.RPartition StatisticsSpreadsheet containing data for all of the partition-specific statistics used to construct the various matrices described in the paper.gene_stats.xlsxJackknifeResults of 108-locus and 20-locus jackknife analyses. See Figure 3.Data MatricesAll concatenated matrices in PHYLIP and NEXUS formats. The names of the concatenated matrices correspond to Table 1.Matrices.zipOrthologous GroupsTrimmed alignments for each of 1,161 orthologous groups recovered from OrhtologID analyses of gene models from the 36 metazoan and outgroup genomes.OGs.zipOrthologID OutputData partitions from OrthologID aligned and in NEXUS format. "full" dataset includes all orthologs recovered and "m27" includes only partitions present in at least 27 taxa.OrthologID.zipPartitionFinder ResultsControl files, data and results for all PartitionFinder analyses on concatenated matrices conducted in the study.PartitionFinder.zipPhyloBayes ResultsResults of all PhyloBayes analyses conducted in the study including Bayesien posterior densities and traces of selected parameters as well as consensus trees.PhyloBayes.zipProgressive Concatenation Data and ResultsMatrices and RAxML result files from progressive concatenation analyses presented in order of slow- to fast-evolving loci.Progressive_concatenation.zipRAxML ConcatenatedData matrices and results from all RAxML analyses of concatenated datasets described in the studyRAxML_concatenated.zipRAxML_single_genesResults for each of 1,080 single gene RAxML analysesSingle Gene AlignmentsTrimmed alignments for all 1080 loci in FASTA format.single_gene_alignments.zipTaxonomic DescriptionsThis spreadsheet contains taxonomic information on the species used in the present study.taxa.xlsxTopology_testsResults of Bayesian tests of topology carried out in MrBayes. Subfolder names correspond to alternative topologies tested. See Table 2 and manuscript text for explanations.