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The scripts used to execute these analyses, as well as analysis reports, are available in a git repository [ 25 ]. These three phylogenetic analyses are the focus of the results presented here. Whole ovary was dissected from gravid females and placed in Trizol Invitrogen. The reads documented in S1 Table were processed and assembled using the agalma pipeline ver. The default settings were used within agalma to assemble all transcriptomes.

A total of three echinoderm public datasets were also de novo assembled and used in this analysis. One dataset consisting of combined 2 day SRR and 6 day SRR old larvae of Parastichopus parvimensis [ 29 ] was assembled as above. Two additional brittle star datasets were assembled using newbler DataAnalysis ver.

Key Points

Exemplar transcripts were then selected from the assembled datasets as previously described [ 31 ] and the script has been deposited in the github repository [ 25 ]. Seven RefSeq datasets were downloaded: Aplysia californica , Branchiostoma floridae , Gallus gallus , Homo sapiens , Nematostella vectensis , Saccoglossus kowalevskii , and Strongylocentrotus purpuratus. All except for the human dataset were from RefSeq release 62, dated Nov.

TransDecoder was used to translate sequences, and similar translated sequences were identified by a pair wise BLASTp followed by clustering using MCL [ 32 ] to identify orthologous genes. Both supermatrices and calculated phylograms can be downloaded from the Data Dryad Repository [ 33 ]. Baysian phylogenetic analyses were done with PhyloBayes 1. A total of 31, generations were run over three chains. All three chains converged within 2, generations S5 Fig. Three alternate hypothesis trees were constructed to test: A the cryptosyringid hypothesis, B Ophiuroidea sister to the rest of echinoderms, and C Asteroidea sister to Echinozoa S3 Fig.

All three analyses were stopped after at least 99 iterations because any additional sampling was very unlikely to change the results S3 Fig. Assembly statistics, agalma resource reports and scripts used in the analyses can be found in the git repository [ 25 ] and the supermatrix alignments and all trees including SOWH constraint trees can be downloaded from the Dryad Digital Repository [ 33 ]. All de novo transcriptomes can also be accessed on echinobase.

The assembly of the de novo Illumina transcriptomes yielded on average 24, high quality contigs with a match to SwissProt S1 Table. The number of transcripts with SwissProt hits in the de novo transcriptomes was comparable to the number of sequences in the RefSeq datasets we included for other taxa S1A Fig.

The number of SwissProt sequences did not appear to be artificially inflated by fragmented assemblies S1B Fig. The comparable number of SwissProt sequences and comparable size of the N50s of the de novo transcriptomes in relation to the RefSeq datasets both suggest that the assembled transcriptomes are of high quality; especially compared with the S.

All phylogenetic analyses with different sampling depth, aligned genes, models of molecular evolution, phylogenetic inference programs and matrix occupancy placed Ophiuroidea as the sister group to Asteroidea Figs. We find no support for alternative hypotheses of echinoderm phylogeny, such as the placement of Ophiuroidea as the sister group to all other echinoderms [ 19 ] or as the sister group to Echinozoa i. This is consistent with a recent transcriptome analysis based on a smaller number of genes and taxa [ 18 ]. In that study, Telford et al.

The first support value is the dense supermatrix RAxML 1, bootstraps, the second value is the sparse supermatrix RAxML bootstraps, and the third value is the dense supermatrix PhyloBayes posterior probabilities. The phylogram presented here is from the dense supermatrix RAxML analysis. See S2 Fig.

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In order to test further the placement of brittle stars as sister group to sea stars and not a member of Cryptosyringida Fig. In order to compare one a priori tree with the maximum likelihood RAxML tree generated from this dataset, the parametric SOWH can avoid any selection bias and is more appropriate [ 38 ]. We constructed a tree with all hypothesized members of Cryptosyringida Fig. These results strongly reject this alternate hypothesis.

The means, standard errors, variances, and standard deviations of the null distribution for all three analyses were all less than 3. Furthermore, the difference between the log-likelihood of the unconstrained RAxML tree and the log-likelihood of the constrained trees for the hypotheses Cryptosyringida, Asteroidea sister to Echinozoa, and Ophiuroidea sister to echinoderms was The SOWH test uses the constraint tree to simulate the evolution of the data assuming that the a priori tree is correct.

It then calculates the maximum likelihood of this tree and compares it with the maximum likelihood of the hypothesized tree; because the difference is so large for all three constraint trees, we can confidently reject the a priori trees in favor of the Asterozoa hypothesis. The strong support for the Asterozoa hypothesis of echinoderm phylogeny found here impacts our interpretation of the origin of multiple characters in these animals.

This includes, for example, the origin of a skeleton in larvae. A larval skeleton is present in both Ophiuroidea and Echinoidia, but not in the Holothuroidea. This would be a parsimonious explanation of the presence and absence of such a trait in this relationship, but is now also inconsistent with results obtained here.

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Recent experimental analyses of mesodermal gene regulation in a sea cucumber documents that only a rudimentary regulatory state appears to exist in an extant sea cucumber Parastichopus parvimensis , concluding that the common ancestor of the sea cucumber and the sea urchin, at best, had an undeveloped larval skeleton [ 39 ]. The premise of a plesiomorphic larval skeleton is also not compatible with the conclusion that transference of the adult skeleton gene regulatory network into the larval stage was a relatively simply reutilization of existing adult circuitry.

All classes of echinoderms have an adult skeleton, and since the larval skeleton does not appear to be a shared ancient character of a Cryptosyringid clade, we instead acknowledge and invoke the likely transference of the adult skeletal machinery into the larvae of the Ophiuroidea and Echinoidia, but not in Crinodea, Asteroidea, and Holothuroidea.

Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa.

We feel this is the most parsimonious explanation of the origin of larval skeletons, given the new support for echinoderm phylogenomics reported here. Asteroids are often used in the study of meiotic events. These animals harbor large oocytes, all stored fully grown in the ovary with their germinal vesicles intact. Upon spawning, the oocytes are induced to reinitiate meiotic divisions, and are often completed only after fertilization [ 7 ]. Since the trigger for meiotic resumption is well known to be 1-methyl-adenine [ 40 ], and the animal stores upwards of several million oocytes, investigators use this cell frequently for meiotic studies.

Echinoids, on the other hand, are the only deuterostome clade known to store their eggs already having completed meiosis.

28.5A: Phylum Echinodermata

This difference in oocyte maturation and fertilization greatly impacts the fertilization characteristics of course, but also likely the developmental strategy of the organism. The echinoids are also the only taxon with unequal cleavages early in development, that segregate their germ line within the first five cell divisions, and that have segregated all meiotic events from the rapid mitotic events of early development. Now gaining confidence in the evolutionary relationships of these organisms, we conclude that the major transitions in echinoids occurred following the split between Asterozoa and Echinozoa.

Since all the sequence analysis from this study was performed on tissue-matched samples of ovaries, which contain developing oocytes, we will not be focusing on Cryptosyringida as the last common ancestor for these transitions, and instead, will be honing comparisons within Holothuroidea. Additionally, the ovarian sequences presented here will be a rich source to test for speciation and reproductive isolation. Effective analysis of the sequences undergoing positive selection may reveal candidates for sperm interaction or support for different reproductive strategies [ 41 ].

All other deep nodes in the echinoderm phylogeny also had strong support across analyses, providing the most rigorous test yet of these relationships. Our analyses also provide insight into the relationships within some echinoderm subclades. A particularly interesting result is the internal phylogenetic relationships of the sea stars, which differ from a number of previous analyses [ 42 — 46 ]. We found evidence against Valvatacea as the three sampled species in this group Luidia clathrata , Patiria pectinifera , Patiria miniata are paraphyletic relative to Spinulosacea here represented by Henricia sp and Echinaster spinulosus.

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All our analyses support Pisaster as sister group to the clade comprised of Asterias and Leptasterias Fig. The largest difference between many of the previous studies of asteroidean phylogeny and the current results was the placement of Paxillosida represented in this study by Luidia clathrata. In the analyses reported here, Paxillosida was sister to Valvatida Patiria miniata and Spinulosida, which were in turn sister to each other Fig. This is in contrast to the previous placement of Paxillosida as a sister group to Forcipulatida [ 44 ], sister to all of Asteroidea [ 42 ], or branching much later in the evolution of Asteroidea [ 46 ].

The placement of Paxillosida presents several interesting hypotheses considering the lack of an anus and the suckers on tube feet in Paxillosida [ 47 , 48 ]. Either an anus and suckers were present in the most recent common ancestor of Asteroidea and then secondarily lost in Paxillosida, or these features arose independently in Forcipulatida and the clade comprised of Valvatida and Spinulosida. The size of data matricies and their occupancy has varied considerably over recent phylogenomic studies, which have differed substantially in the sequencing technologies used as well as methods for identification of orthologous genes and matrix construction.

The present study uses a similar matrix construction technique as previous analyses [ 31 ], but the occupancy of the matrix is much higher. This suggests that at least part of the reason for reduced occupancy in some previous analyses was due to data acquisition, and that future studies based entirely on the most recent sequencing technologies will have much improved gene sampling.

Overall, the present study provides the greatest depth and breadth of new sequence analysis for consideration of the phylogenetic relationships of echinoderms. Coupled with the recent study using genes for analysis from four newly sequenced echinoderms [ 18 ], and of a broader analysis of ambulacraria using genes, including six newly sequenced echinoderms [ 24 ], mostly non-overlapping tissues and animals from the present work, we now have a rich analysis to present.

Since each these studies used different animals, different methodology of analysis, and different depths of data consideration, yet they each came to the same conclusions in regards to the major echinoderm taxon relationships, we now have great confidence in the relationships of these animals and provide deep datasets for further analysis.


A The numbers of SwissProt transcripts is comparable between RefSeq datasets green and purple and de novo assembled transcriptomes orange. B Comparing the N50 of the SwissProt transcripts, the de novo transcriptomes are on average only slightly smaller than the RefSeq datasets. The S.

Echinoderm Animation Sea Star Body Plan

The number of transcriptomes is on the ordinate axis. The phylogram presented here is from the dense supermatrix PhyloBayes analysis. The SOWH tests were run for at least 99 iterations on the dense supermatrix and were stopped because any further iterations were unlikely to change. The three SOWH tests used the following tree topologies to test: A the crytosynirgid hypothesis, sea urchins, sea cucumbers, brittle stars , sea stars, feather star, outgroups ;, B Ophiuroidea sister to the rest of echinoderms, sea urchins, sea cucumbers, sea stars, feather star , brittle stars, outgroups ;, and C Asteroidea sister to Echinozoa sea urchins, sea cucumbers, sea stars , brittle stars, feather star, outgroups ;.

None of the three tests found support for any alternate hypothesis with p -values all equal to 0. Each horizontal row is a single taxa and each vertical column is a gene alignment; presence is marked in black and absence in white. The taxa are arranged from top to bottom from most genes present to least. All three independent chains converge with a maximum difference of 1.

Public datasets red background were obtained from RefSeq, the SRA and personal communication; new datasets from this study are in blue. Data from RefSeq green and purple background were compared with the de novo transcriptomes assembled in this study orange background. Members of Echinodermata are in purple or orange and organisms serving as phylogenetic outgroups are in green. The Sample Source denotes public data RefSeq , sequence data from Roche , and paired-end PE sequence data from Illumina of a given length 72bp, 80bp, or bp per read.