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.
Dense supermatrix
This 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.phylip
Sparse supermatrix
This 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.phylip
Species tree from PhyloBayes analysis on dense supermatrix
Baysian 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.tre
Species tree from RAxML analysis on dense supermatrix
Maximum 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.tre
Species tree from RAxML analysis on sparse supermatrix
Maximum 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.tre
SOWHAT constraint tree - Asteroidea and Echinozoa
The 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 >output.txt”. This constraint tree was constructed to test if Asteroidea was a sister group to Echinozoa.
SOWHATconstraintTree-AsterSister2Echinozoa.tre
SOWHAT constraint tree - Crytosynirgid hypothesis
The 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 >output.txt”. This constraint tree was constructed to test the Cryptosynirgid hypothesis.
SOWHATconstraintTree-Crytosynirgid.tre
SOWHAT constraint tree - Ophiuroidea and echinoderms
The 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 >output.txt”. This constraint tree was constructed to test if Ophiuroidea was a sister group to the rest of echinoderms.
SOWHATconstraintTree-OphioSister2Echinoderms.tre