DOI: 10.5061/dryad.s11f216
title: Data from: A phylogenomic resolution of the sea urchin tree of life

description: Background: Echinoidea is a clade of marine animals including sea urchins,
 heart urchins, sand dollars and sea biscuits. Found in benthic habitats
 across all latitudes, echinoids are key components of marine communities
 such as coral reefs and kelp forests. A little over 1,000 species inhabit
 the oceans today, a diversity that traces its roots back at least to the
 Permian. Although much effort has been devoted to elucidating the echinoid
 tree of life using a variety of morphological data, molecular attempts
 have relied on only a handful of genes. Both of these approaches have had
 limited success at resolving the deepest nodes of the tree, and their
 disagreement over the positions of a number of clades remains unresolved.
 Results: We performed de novo sequencing and assembly of 17 transcriptomes
 to complement available genomic resources of sea urchins and produce the
 first phylogenomic analysis of the clade. Multiple methods of
 probabilistic inference recovered identical topologies, with virtually all
 nodes showing maximum support. In contrast, the coalescent-based method
 ASTRAL-II resolved one node differently, a result apparently driven by
 gene tree error induced by evolutionary rate heterogeneity. Regardless of
 the method employed, our phylogenetic structure deviates from the
 currently accepted classification of echinoids, with neither
 Acroechinoidea (all euechinoids except echinothurioids), nor
 Clypeasteroida (sand dollars and sea biscuits) being monophyletic as
 currently defined. We show that phylogenetic signal for novel resolutions
 of these lineages is strong and distributed throughout the genome, and
 fail to recover systematic biases as drivers of our results. Conclusions:
 Our investigation substantially augments the molecular resources available
 for sea urchins, providing the first transcriptomes for many of its main
 lineages. Using this expanded genomic dataset, we resolve the position of
 several clades in agreement with early molecular analyses but in
 disagreement with morphological data. Our efforts settle multiple
 phylogenetic uncertainties, including the position of the enigmatic
 deep-sea echinothurioids and the identity of the sister clade to sand
 dollars. We offer a detailed assessment of evolutionary scenarios that
 could reconcile our findings with morphological evidence, opening up new
 lines of research into the development and evolutionary history of this
 ancient clade.
description: Echinoidea 70% occupancy
 matrixContains 331,188 aligned
 aminoacid positions for 32 taxa, in fasta format. Output by Agalma v.
 1.0.1.echinoids70.fa70% matrix without Arbacia punctulataContains 331,188 aligned aminoacid positions for 31 taxa, in fasta format. Same as 'echinoids70.fa' but without Arbacia punctulata. Most analyses in the manuscript were performed using this matrix.echinoids70_noarba.fa70% matrix with decontaminated ArbaciaAll loci in the transcriptome of Arbacia punculata that are identical to those of Eucidaris tribuloides have been deleted in this version of the matrix.echinoids70_nocont_arba.fa70% matrix without Arbacia output by TreeShrinkThis matrix was obtained with TreeShrink which eliminated 345 sequences that behaved as outliers with regards to branch length.echinoids70_noarba_treeshrink.faPartition fileContains the start and end of loci. Output by Agalma v. 1.0.1.echinoids70_partition.txtAll 1,040 gene treesObtained using RAxML v8.2.1 under the model that minimizes the BIC for each loci. Individual gene sequences come from file 'echinoids70_noarba.fa'. Trees are in newick format.all_gene_trees_no_arba.treML phylogeny inferred under mixture model LG4XContains the tree with bootstrap support values in Newick format. Obtained using RAxML-NG v. 0.5.1 using matrix 'echinoids70_noarba.fa'.noarba_unpartitioned_LG4X.raxml.supportML phylogeny inferred under best-fit partitioning schemeContains the tree with bootstrap support values in Newick format. Obtained using RAxML v8.2.1 using matrix 'echinoids70_noarba.fa'. Partitioning obtained using IQ-TREE v1.6.6 using the fast-relaxed clustering algorithm among the top 50% of schemes.RAxML_bipartitions.partitioned_MLML phylogeny inferred under mixture model PMSFContains the tree with bootstrap support values in Newick format. Obtained using IQ-TREE v1.6.6 using matrix 'echinoids70_noarba.fa'.iqtree_echinoids.treefileBayesian phylogeny inferred under best-fit modelContains the consensus tree with posterior probabilities in Newick format. Obtained using ExaBayes v. 1.5 using matrix 'echinoids70_noarba.fa'.ExaBayes.treBayesian phylogeny inferred under CAT-PoissonContains the consensus tree with posterior probabilities in Newick format. Obtained using PhyloBayes-MPI v. 1.8.1 using matrix 'echinoids70_noarba.fa'.echinoidscatpoisson.tre.con.treBayesian phylogeny inferred under CAT-GTRContains the consensus tree with posterior probabilities in Newick format. Obtained using PhyloBayes-MPI v. 1.8.1 using matrix 'echinoids70_noarba.fa'. WARNING: this analysis was run for only 3,000 cycles and did not converge.bpcomp.con.trePhylogeny inferred using coalescent methodContains tree with local posterior probabilities in Newick format. Obtained using ASTRAL-II using trees in file 'all_gene_trees_no_arba.tre'.all_trees_ASTRAL.tre345 gene trees selected for coalescent inferenceSubsampling of 345 gene trees from file 'all_gene_trees.tre' with the lowest branch-length heterogeneity and saturation levels. Individual gene sequences come from file 'echinoids70_noarba.fa'.354trees_for_ASTRAL.trePhylogeny inferred using coalescent method using 345 treesContains tree with local posterior probabilities in Newick format. Obtained using ASTRAL-II using trees in file '354trees_for_ASTRAL.tre'.354trees_ASTRAL.trePhylogenies inferred after pruning by TreeShrinkThe .rar file contains the topologies obtained using matrix 'echinoids70_noarba_treeshrink.fa' with IQ-TREE v1.6.6 (model PMSF), ExaBayes v. 1.5 (automatic model selection) and ASTRAL-II.trees_after_TreeShrink.rarSpecies trees inferred from randomly subsampled gene trees100 species trees obtained using ASTRAL-II, each one inferred from 345 randomly subsampled gene trees from file 'all_gene_trees.tre'.results_astral_randreplicates.treR code and necessary data filesR code to replicate all analyses, as well as data files needed for some of the calculations.Echinoids.rar