Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
???displayArticle.abstract???
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.
???displayArticle.pubmedLink???
25794146
???displayArticle.pmcLink???PMC4368666 ???displayArticle.link???PLoS One ???displayArticle.grants???[+]
Fig 1. Four competing hypotheses of the phylogenetic relationship of extant echinoderms.Most phylogenetic studies place Echinoidea and Holothuroidea as sister groups. The difficulty lies in the placement of Ophiuroidea; different methods favor different positions for brittle stars. A) The predominant hypotheses of how extant echinoderms are related are the Asterozoan and Cryptosyringid hypotheses. B) Two other alternate hypotheses based on mitochondrial gene alignments.
Fig 2. Phylogenetic relationship of extant echinoderms.Support values for the phylogenetic trees using RAxML and PhyloBayes on the dense and sparse supermatricies. Each node is scored with three support values; an asterisk denotes 100/100/100 support. The first support value is the dense supermatrix RAxML 1,000 bootstraps, the second value is the sparse supermatrix RAxML 100 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. for the tree topology predicted by the PhyloBayes analysis.
Burns,
Transcriptome pyrosequencing of the Antarctic brittle star Ophionotus victoriae.
2013, Pubmed,
Echinobase
Burns,
Transcriptome pyrosequencing of the Antarctic brittle star Ophionotus victoriae.
2013,
Pubmed
,
Echinobase
Candia Carnevali,
Microscopic overview of crinoid regeneration.
2001,
Pubmed
,
Echinobase
Cannon,
Phylogenomic resolution of the hemichordate and echinoderm clade.
2014,
Pubmed
,
Echinobase
Church,
Automation and Evaluation of the SOWH Test with SOWHAT.
2015,
Pubmed
Dunn,
Agalma: an automated phylogenomics workflow.
2013,
Pubmed
Dunn,
Broad phylogenomic sampling improves resolution of the animal tree of life.
2008,
Pubmed
Enright,
An efficient algorithm for large-scale detection of protein families.
2002,
Pubmed
Gahn,
Evolutionary history of regeneration in crinoids (Echinodermata).
2010,
Pubmed
,
Echinobase
Goldman,
Likelihood-based tests of topologies in phylogenetics.
2000,
Pubmed
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2011,
Pubmed
Haas,
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
2013,
Pubmed
Hart,
MOLECULAR PHYLOGENETIC ANALYSIS OF LIFE-HISTORY EVOLUTION IN ASTERINID STARFISH.
1997,
Pubmed
,
Echinobase
Hejnol,
Assessing the root of bilaterian animals with scalable phylogenomic methods.
2009,
Pubmed
Hinman,
Developmental gene regulatory network evolution: insights from comparative studies in echinoderms.
2014,
Pubmed
,
Echinobase
Janies,
Echinoderm phylogeny including Xyloplax, a progenetic asteroid.
2011,
Pubmed
,
Echinobase
Kanatani,
Isolation and indentification on meiosis inducing substance in starfish Asterias amurensis.
1969,
Pubmed
,
Echinobase
Kishino,
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea.
1989,
Pubmed
Lartillot,
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating.
2009,
Pubmed
Le,
Probabilistic error correction for RNA sequencing.
2013,
Pubmed
,
Echinobase
Matsubara,
The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences.
2005,
Pubmed
,
Echinobase
Perseke,
Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata.
2010,
Pubmed
,
Echinobase
Perseke,
The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny.
2013,
Pubmed
,
Echinobase
Pisani,
Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships.
2012,
Pubmed
,
Echinobase
Raff,
The active evolutionary lives of echinoderm larvae.
2006,
Pubmed
,
Echinobase
Reich,
Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa.
2015,
Pubmed
,
Echinobase
Smith,
The oldest echinoderm faunas from Gondwana show that echinoderm body plan diversification was rapid.
2013,
Pubmed
,
Echinobase
Smith,
Resolving the evolutionary relationships of molluscs with phylogenomic tools.
2011,
Pubmed
Sodergren,
The genome of the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Swanson,
The rapid evolution of reproductive proteins.
2002,
Pubmed
Telford,
Phylogenomic analysis of echinoderm class relationships supports Asterozoa.
2014,
Pubmed
,
Echinobase
Vaughn,
Sequencing and analysis of the gastrula transcriptome of the brittle star Ophiocoma wendtii.
2012,
Pubmed
,
Echinobase
Wada,
Mitochondrial rDNA phylogeny of the asteroidea suggests the primitiveness of the paxillosida.
1996,
Pubmed
,
Echinobase
Wessel,
Use of sea stars to study basic reproductive processes.
2010,
Pubmed
,
Echinobase
