DOI: 10.5061/dryad.8931zcrx5
title: Data from: phylogenomics of the Neogastropoda: the backbone hidden in the bush

description: The molluscan order Neogastropoda encompasses over 15,000 almost
 exclusively marine species playing important roles in benthic communities
 and in the economics of coastal countries. Neogastropoda underwent
 intensive cladogenesis in early stages of diversification, generating a
 ‘bush’ at the base of their evolutionary tree, that has been hard to
 resolve even with high throughput molecular data. In the present study we
 analyze a comprehensive exon capture dataset of 1,817 loci (79.6% data
 occupancy), comprising 112 taxa of 48 (out of 60) recent Neogastropoda
 families with a variety of phylogenetic inference methods to resolve their
 relationships. Our results show consistent topologies and high support in
 all analyses at (super)family level, supporting monophyly of Muricoidea,
 Mitroidea, Conoidea, and, with some reservations, Olivoidea and
 Buccinoidea. Volutoidea and Turbinelloidea as currently circumscribed are
 clearly paraphyletic. Despite our analyses consistently resolve most
 backbone nodes, three prove problematic. First, uncertain placement of
 Cancellariidae, as a sister group of either a Ficoidea-Tonnoidea clade, or
 of the rest of Neogastropoda, leaves monophyly of Neogastropoda
 unresolved. Second, relationships are contradictory at the base of the
 major grouping the ‘core Neogastropoda’. Third, coalescence-based analyses
 reject monophyly of the Buccinoidea in relation to Vasidae. We analysed
 loci phylogenetic signal in relation with potential biases, and propose
 most probable resolutions in the two latter recalcitrant nodes. The
 uncertain placement of Cancellariidae may be explained by orthology
 violations due to the differential paralog loss short after the whole
 genome duplication, and should be resolved with a curated set of longer
 loci.
description: # Phylogenomics of the Neogastropoda: the backbone hidden in the bush
 [https://doi.org/10.5061/dryad.8931zcrx5](https://doi.org/10.5061/dryad.8931zcrx5) The present repository contains The phylogenetic matrices, gene alignments and trees, as well as the original scripts and raw output files from software tools used for crucial steps of the data analysis ## Description of the data and file structure \# Data from: Phylogenomics of Neogastropoda: the backbone hidden in the bush Contact Corresponding Author Information Name: Alexander Fedosov Institution: Swedish Museum of Natural History Address: Frescativägen 40, 114 18 Stockholm, Sweden Email: [fedosovalexander@gmail.com](mailto:fedosovalexander@gmail.com) \####### Data files overview filename file type content SData1_Orthogroups.GeneCount.tsv tab separated text file Orthofinder2 output file, comprising counts of sequences per specimen per orthogroup. SData2_Orthogroup_alignments.zip zip archive 1817 Orthogroup alignments in fasta format. Header formatting as follows '&gt;sample ID|target exon ID|sample assembly contig ID' SData3_Orthogroup_trees.zip zip archive 1817 RAxML Orthogroup trees in newick format. Taxa names correspond to the fasta headers in the SData2. SData4_Concatenated aminoacid matrices.zip zip archive ├── NEO_NL70p_aa_123taxa.fasta Matrix NEO70 alignment ├── NEO_NL70p_aa_123taxa_partitions Matrix NEO70 unmerged partiton breakdown ├── NEO_NL95p_aa_123taxa.fasta Matrix NEO95 alignment ├── NEO_NL95p_aa_123taxa_partitions Matrix NEO95 unmerged partiton breakdown ├── NEO_NL95p_aa_GSR500_123taxa.fasta Matrix NEO95_500 alignment └── NEO_NL95p_aa_GSR500_123taxa_partitions Matrix NEO95_500 unmerged partiton breakdown SData5_GeneSortR_properties_sorted_dataset.csv comma separated text file GenesortR output file, comprising loci statistics inferred by GenesortR. SData6_PB_matrixNEO95.zip zip archive ├── CH23x5000bpcomp.bpdiff output of phylobayes bpcomp metrics of topological convergence between chains ├── CH23x5000bpcomp.bplist output of phylobayes bpcomp list of bipartitions ├── CH23x5000bpcomp.tre output of phylobayes bpcomp consensus tree ├── CH23x10000bpcomp.bpdiff output of phylobayes bpcomp metrics of topological convergence between chains ├── CH23x10000bpcomp.bplist output of phylobayes bpcomp list of bipartitions ├── CH23x10000bpcomp.tre output of phylobayes bpcomp consensus tree ├── NEO_NL95p_aa_123_catgtr.chain2.trace phylobayes trace file chain parameters └── NEO_NL95p_aa_123_catgtr.chain3.trace phylobayes trace file chain parameters SData7_PB_matrixNEO95_GSR500.zip zip archive ├── CH24x2500bpcomp.bpdiff output of phylobayes bpcomp metrics of topological convergence between chains ├── CH24x2500bpcomp.bplist output of phylobayes bpcomp list of bipartitions ├── CH24x2500bpcomp.tre output of phylobayes bpcomp consensus tree ├── CH24x6000bpcomp.bpdiff output of phylobayes bpcomp metrics of topological convergence between chains ├── CH24x6000bpcomp.bplist output of phylobayes bpcomp list of bipartitions ├── CH24x6000bpcomp.tre output of phylobayes bpcomp consensus tree ├── NEO_NL95p_GSR500_aa_123_catgtr.chain2.trace phylobayes trace file chain parameters └── NEO_NL95p_GSR500_aa_123_catgtr.chain4.trace phylobayes trace file chain parameters SData8_PCA.zip zip archive ├── 2BI_trees_PCA_matrix.txt Clades presence-absence matrix for PCA └── clades Taxa content of the 208 unique clades retrieved from the Trees 1-14. SData7_dGLS.zip zip archive ├── constrained_topologies (dir) IQTree output tree files (newick format) constrained for a desired topology for dGLS tests │ ├── constrained_A_NEO_NL95p_aa_123taxa_partitions.treefile NEO95 IQTree-part output tree file (newick format) constrained for sister relationship of Ficoider-Tonnoidea and Cancellariidae │ ├── constrained_A1_NEO_NL95p_aa_123taxa.fasta.treefile NEO95 IQTree-PMM output tree file (newick format) constrained for monophyletic Neogastropoda │ ├── constrained_C1_NEO_NL95p_aa_123taxa.fasta.treefile NEO95 IQTree-PMM output tree file (newick format) constrained for paraphyletic Buccinoidea │ ├── constrained_C1_NEO_NL95p_aa_123taxa_partitions.treefile NEO95 IQTree-part output tree file (newick format) constrained for paraphyletic Buccinoidea │ ├── constrained_ColumbariidaeFirst_NEO_NL95p_aa_123taxa.fasta.treefile NEO95 IQTree-PMM output tree file (newick format) constrained for Columbariidae being first offshoot of core Neogastropoda │ └── constrained_CoMuFirst_NEO_NL95p_aa_123taxa_partitions.treefile NEO95 IQTree-part output tree file (newick format) constrained for Columbariidae+Muricidae being first offshoot of core Neogastropoda │ ├── AU_output (dir) AU test on the significance of preference for one or another alternative topology │ ├── NEO95_AA1_GAMMALG4X_AU at the base of Neogastropoda under GAMMALG4X model for NEO95 matrix │ ├── NEO95_CC1_GAMMALG4X_AU at the base of Buccinoidea under GAMMALG4X model for NEO95 matrix │ ├── NEO95_part-A1A_AU at the base of Neogastropoda under best models for merged partitions for NEO95 matrix │ ├── NEO95_part-CC1_AU at the base of Buccinoidea under best models for merged partitions for NEO95 matrix │ ├── NEO95_PGLG4X_CM-Cfirst_AU at the base of core Neogastropoda under GAMMALG4X model for NEO95 matrix │ └── NEO95part_Cfirst-CM_AU at the base of core Neogastropoda under best models for merged partitions for NEO95 matrix │ ├── T-test (dir) results of T test of loci statistics (Saturation, missing data, Evolutionary rate, Compositional heterogeneity, Alignment length, Average bootstrap, RF distance to species tree) for three groups of loci: --10% dGLS (strong support for alternative topology), rest 80% (weak support for either of the two topologies), ++10% dGLS (strong support for the main topology) │ ├── AA1_GAMMALG4X_t-test_10-80-10_dGLS.txt For loci showing varying signal for alternative topologies at the base of Neogastropoda under GAMMALG4X model for NEO95 matrix │ ├── CC1_GAMMALG4X_t-test_10-80-10_dGLS.txt For loci showing varying signal for alternative topologies at the base of Buccinoidea under GAMMALG4X model for NEO95 matrix │ ├── CM-Cfirst_GAMMALG4X_t-test_10-80-10_dGLS.txt For loci showing varying signal for alternative topologies at the base of core Neogastropoda under GAMMALG4X model for NEO95 matrix │ ├── partA1A_t-test_10-80-10_dGLS.txt For loci showing varying signal for alternative topologies at the base of Neogastropoda under best models for merged partitions for NEO95 matrix │ ├── partCC1_t-test_10-80-10_dGLS.txt For loci showing varying signal for alternative topologies at the base of Neogastropoda under best models for merged partitions for NEO95 matrix │ └── partCfirst-CM__t-test_10-80-10_dGLS.txt For loci showing varying signal for alternative topologies at the base of core Neogastropoda under best models for merged partitions for NEO95 matrix │ ├── NEO95_AA1_GAMMALG4X.sitelh Site likelyhood score output of the RAxML for alternative topologies at the base of Neogastropoda under GAMMALG4X model for NEO95 matrix ├── NEO95_CC1_GAMMALG4X.sitelh Site likelyhood score output of the RAxML for alternative topologies at the base of Buccinoidea under GAMMALG4X model for NEO95 matrix ├── NEO95_CM-Cfirst_GAMMALG4X.sitelh Site likelyhood score output of the RAxML for alternative topologies at the base of core Neogastropoda under GAMMALG4X model for NEO95 matrix ├── NEO95_part-A1A.sitelh Site likelyhood score output of the RAxML for alternative topologies at the base of Neogastropoda under best models for merged partitions for NEO95 matrix ├── NEO95_part-CC1.sitelh Site likelyhood score output of the RAxML for alternative topologies at the base of Neogastropoda under best models for merged partitions for NEO95 matrix └── NEO95_part-Cfirst-CM.sitelh Site likelyhood score output of the RAxML for alternative topologies at the base of core Neogastropoda under best models for merged partitions for NEO95 matrix SData11_all_assemblies.tar.gz gz archive 154 original assemblies files (Trinity assemblies for transcriptomic data sets, and clustered by CD-Hit for exon capture data sets). SData12_unfiltered_orthogroup_sequences.tar.gz gz archive 3000 unfiltered, but codon-aligned fasta files with exon sequences per orthogroup as inferred by Orthofinder2. ## Sharing/Access information The original sequencing data (RAW reads) can be accessed in the GenBank under the Bioproject PRJNA885117 ## Code/Software SData10_Custom Python scripts.zip ###### Note all scripts contain paths to directories with data files, specific to our system, and need to be edited. ###### Note most codes are written in Python 2.7 and should be run in terminal by 'python2' ###### Functionality and usage information is provided in each script. SData10_Scripts Script_S10-1_separate_Loci.py Script_S10-2_slice-translate_ginsi_remove_identical_poolback_to_taxa_corr.py Script_S10-3_Remove_CC_run_PPP Script_S10-4_Remove_LB.py Script_S10-5_testPairwiseDistancesDistribution.py Script_S10-6_trees2PCAmatrix.py Script_S10-7_check_sort_summ_dSLS_boxplots.py Script_S10-8_FTonnoCancellariidaeNEO_brlens.py