DOI: 10.5061/dryad.rxwdbrv64
title: Investigating sources of conflict in deep phylogenomics of vetigastropod snails

description: Phylogenetic analyses may suffer from multiple sources of error leading to
 conflict between genes and methods of inference. The evolutionary history
 of the mollusc clade Vetigastropoda makes them susceptible to these
 conflicts, their higher level phylogeny remaining largely unresolved.
 Originating over 350 million years ago, vetigastropods were the dominant
 marine snails in the Paleozoic. Multiple extinction events and new
 radiations have resulted in both very long and very short branches and a
 large extant diversity of over 4000 species. This is the perfect setting
 of a hard phylogenetic question in which sources of conflict can be
 explored. We present 41 new transcriptomes across the diversity of
 vetigastropods (62 terminals total), and provide the first genomic-scale
 phylogeny for the group. We find that deep divergences differ from
 previous studies in which long branch attraction was likely pervasive.
 Robust results leading to changes in taxonomy include the paraphyly of the
 order Lepetellida and the family Tegulidae. Tectinae subfam.
 nov. is designated for the clade
 comprising Tectus, Cittarium and Rochia. For two early divergences, topologies disagreed between concatenated analyses using site heterogeneous models vs. concatenated partitioned analyses and summary coalescent methods. We investigated rate and composition heterogeneity among genes, as well as missing data by locus and by taxon, none of which had an impact on the inferred topologies. We also found no evidence for ancient introgression throughout the phylogeny. We further tested whether uninformative genes and over-partitioning were responsible for this discordance by evaluating the phylogenetic signal of individual genes using likelihood mapping, and by analyzing the most informative genes with a full multispecies coalescent model. We find that most genes are not informative at the two conflicting nodes, but neither this nor gene-wise partitioning are the cause of discordant results. New method implementations that simultaneously integrate amino acid profile mixture models and the multispecies coalescent might be necessary to resolve these and other recalcitrant nodes in the Tree of Life.
description: README This dataset holds alignments, input
 files, tree files, supplementary figures, tables and R code. Below is a
 brief description of each item. See the Materials and Methods of the main
 paper for details. Supplementary_Table_S1.csv -
 Specimen information with vouchers and assembly statistics<br>
 Supplementary_Table_S2.csv - Assembly statistics from TransRate<br>
 Supplementary_Figures.pdf - Supplementary figures<br>
 Supplementary_Code_S1.html - R code to reproduce tree figures<br>
 Supplementary_Code_S2.html - R code to reproduce figures related to
 likelihood-mapping analyses<br> Supplementary_Code_S3.html - R code
 to reproduce figures related to concordance factors and partitioned
 coalescence support<br> Supplementary_Code_S4.html - R code related
 to the introgression analysis Assemblies:<br>
 assemblies_trinity_vetigastropoda.tar.gz - Trinity assemblies<br>
 assemblies_peptide_vetigastropoda.tar.gz - Peptide assemblies (input for
 orthology) Individual gene files:<br>
 alignments.tar.gz - Alignments of all 1027 genes<br>
 genetrees.tar.gz - Gene trees of all 1027 genes Trees -
 folder with tree files from all analyses, has its own README
 Input matrices for phylogenetic inference:<br>
 31taxa_concatenated.nex - Matrix 1<br> 44taxa_concatenated.nex -
 Matrix 2<br> EvoRates_concatenated.nex - Matrix 3<br>
 p4Homogeneous_concatenated.nex - Matrix 4<br> 70resolved.xml -
 Matrix 5<br> 75resolved.xml - Matrix 6 Gene
 content of each matrix (lists of named orthogroups):<br>
 Content_OGslice_31taxa - Matrix 1<br> Content_OGslice_44taxa -
 Matrix 2<br> Content_OGslice_EvoRates - Matrix 3<br>
 Content_OGslice_p4Homogeneous - Matrix 4<br>
 Content_OGslice_Resolved70 - Matrix 5<br> Content_OGslice_Resolved75
 - Matrix 6 Files related to the likelihood-mapping
 analyses (lmap):<br> (two independent tests, one for the
 recalcitrant node regarding the position of Haliotidae, another for the
 recalcitrant node regarding the position of Fissurellidae)<br>
 clusters-Haliotidae.nex - clusters of taxa, input for the test<br>
 clusters-Fissurellidae.nex - clusters of taxa, input for the
 test<br> Content_LMAP-Haliotidae - Set of genes included in
 test<br> Content_LMAP-Fissurellidae - Set of genes included in
 test<br> lmap_summary_Haliotidae - Summary of results over all
 genes<br> lmap_summary_Fissurellidae - Summary of results over all
 genes Output files from Concordance Factors and
 Partitioned Coalescence Support (pcs_cf):<br> (these are input for
 Supplementary Code S3)<br> iqtree-cat_31taxa_ConcFact.cf.stat -
 output based on topology 1 (IQTREE-cat, Matrix 1)<br>
 iqtree-part_31taxa_ConcFact.cf.stat - output based on topology 2
 (IQTREE-part, Matrix 1)<br> PCS_astral_31taxa - output based on the
 Astral tree of Matrix 1 Information of gene
 properties:<br> (used in Supplementary Code S2)<br>
 avg_trimal_scores - Evolutionary rates<br> occ.matrix.tsv -
 Occupancy of Matrix 1<br> p4_outcome_ordered.txt - Outcome of amino
 acid composition homogeneity test<br> size_alignments.csv -
 Alignment length Introgression:<br> (used in
 Supplementary Code S4)<br> (output files from Concordance Factors
 obtained after 2000 resamplings of gene trees)<br>
 iqtree-cat_31taxa/ConcFact_1-2000.cf.stat - outputs based on topology 1
 (IQTREE-cat, Matrix 1)<br>
 iqtree-part_31taxa/ConcFact_1-2000.cf.stat - outputs based on topology 2
 (IQTREE-part, Matrix 1)