DOI: 10.5061/dryad.22sf3
title: Data from: Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa

description: Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea
 cucumbers) are a group of diverse organisms, second in number within
 deuterostome species to only the chordates. Echinoderms serve as excellent
 model systems for developmental biology due to their diverse developmental
 mechanisms, tractable laboratory use, and close phylogenetic distance to
 chordates. In addition, echinoderms are very well represented in the
 fossil record, including some larval features, making echinoderms a
 valuable system for studying evolutionary development. The internal
 relationships of Echinodermata have not been consistently supported across
 phylogenetic analyses, however, and this has hindered the study of other
 aspects of their biology. In order to test echinoderm phylogenetic
 relationships, we sequenced 23 de novo transcriptomes from all five clades
 of echinoderms. Using multiple phylogenetic methods at a variety of
 sampling depths we have constructed a well-supported phylogenetic tree of
 Echinodermata, including support for the sister groups of Asterozoa (sea
 stars and brittle stars) and Echinozoa (sea urchins and sea cucumbers).
 These results will help inform developmental and evolutionary studies
 specifically in echinoderms and deuterostomes in general.
description: Dense
 supermatrixThis phylip format
 supermatrix alignment was generated using agalma 0.3.5 and orthologous
 genes were identified by pair wise BLASTp followed by clustering using
 MCL. The dense supermatrix has all 30 taxa and 70% matrix occupancy, with
 1,125 peptide sequences and 101,652 amino acid sites.supermatrix.dense.phylipSparse supermatrixThis phylip format supermatrix alignment was generated using agalma 0.3.5 and orthologous genes were identified by pair wise BLASTp followed by clustering using MCL. The sparse supermatrix has all 30 taxa and 34% matrix occupancy, with 4,645 peptide sequences and 630,945 amino acid sites.supermatrix.sparse.phylipSpecies tree from PhyloBayes analysis on dense supermatrixBaysian phylogenetic analyses were done with PhyloBayes 1.3b-mpi on the dense supermatrix using the CAT-GTR model with the following command: “pb_mpi -S -d supermatrix.dense.phylip -cat -gtr outputFile”. A total of 31,623 generations were run over three chains.PhyloBayes.Results.Dense.treSpecies tree from RAxML analysis on dense supermatrixMaximum likelihood phylogenetic analyses were done with RAxML 7.7.6 on the dense supermatrix using the GAMMAWAG model with 1,000 boot strap iterations.RAxML.Results.Dense.treSpecies tree from RAxML analysis on sparse supermatrixMaximum likelihood phylogenetic analyses were done with RAxML 7.7.6 on the sparse supermatrix using the GAMMAWAG model with 100 boot strap iterations.RAxML.Results.Sparse.treSOWHAT constraint tree - Asteroidea and EchinozoaThe SOWH test was implemented using the sowhat software package, with the following command: “perl sowhat --constraint=Alternate.hypo.tre --aln=supermatrix.dense.phylip --model=PROTGAMMAWAG --dir=outDir --name=outFile --rax='raxmlHPC-PTHREADS-SSE3 -T 16' --seqgen=seq-gen --reps=500 --stop &gt;output.txt”. This constraint tree was constructed to test if Asteroidea was a sister group to Echinozoa.SOWHATconstraintTree-AsterSister2Echinozoa.treSOWHAT constraint tree - Crytosynirgid hypothesisThe SOWH test was implemented using the sowhat software package, with the following command: “perl sowhat --constraint=Alternate.hypo.tre --aln=supermatrix.dense.phylip --model=PROTGAMMAWAG --dir=outDir --name=outFile --rax='raxmlHPC-PTHREADS-SSE3 -T 16' --seqgen=seq-gen --reps=500 --stop &gt;output.txt”. This constraint tree was constructed to test the Cryptosynirgid hypothesis.SOWHATconstraintTree-Crytosynirgid.treSOWHAT constraint tree - Ophiuroidea and echinodermsThe SOWH test was implemented using the sowhat software package, with the following command: “perl sowhat --constraint=Alternate.hypo.tre --aln=supermatrix.dense.phylip --model=PROTGAMMAWAG --dir=outDir --name=outFile --rax='raxmlHPC-PTHREADS-SSE3 -T 16' --seqgen=seq-gen --reps=500 --stop &gt;output.txt”. This constraint tree was constructed to test if Ophiuroidea was a sister group to the rest of echinoderms.SOWHATconstraintTree-OphioSister2Echinoderms.tre