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PLoS One
2015 May 08;105:e0123331. doi: 10.1371/journal.pone.0123331.
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Phylogenetic signal dissection identifies the root of starfishes.
Feuda R
,
Smith AB
.
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Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors--Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution--have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented.
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25955729
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Fig 1. Current competing hypotheses of relationships derived from morphological or molecular data for the major starfish clades considered in this paper.
Fig 2. Cladograms summarizing inferred asteroid relationships obtained from the different partitions and under different substitution models.Numbers at nodes indicate Bayesian posterior probability support under CAT-GTR- Γ (bold), Bayesian posterior probability under GTR- Γ (italic bold) and maximum likelihood abayes bootstrap under GTR- Γ (italic). For all the trees except 2a, the branch lengths are estimated under Bayesian GTR- Γ.
Fig 3. Bayes Factor support for the alterative topologies in the different partitions.Supports are coded according to [45]. Rates hom. = homogeneous rates partition; comp. hom. = compositionally homogeneous partition; rates+comp. hom. = homogeneous rates and composition partition; rates heter. = heterogeneous rates partition. In this table the red color implies that competing tree is rejected and the darker the red the stronger the evidence for rejection.
Fig 4. Resultant tree from analysis of the homogenous rates and compositional data set under CAT-GTR-Γ.Support at the nodes indicates posterior probability under CAT-GTR- Γ (bold), posterior probability GTR- Γ (italic bold) and maximum likelihood abayes bootstrap under GTR- Γ (italic).
Anisimova,
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes.
2011, Pubmed
Anisimova,
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes.
2011,
Pubmed
Bergsten,
Bayesian tests of topology hypotheses with an example from diving beetles.
2013,
Pubmed
Blake,
Comments on "the phylogeny of post-Palaeozoic Asteroidea (Neoasteroidea, Echinodermata)" by A.S. Gale and perspectives on the systematics of the Asteroidea.
2014,
Pubmed
,
Echinobase
Blanquart,
A site- and time-heterogeneous model of amino acid replacement.
2008,
Pubmed
Criscuolo,
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments.
2010,
Pubmed
Cummins,
A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases.
2011,
Pubmed
Foster,
Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions.
1999,
Pubmed
Janies,
Echinoderm phylogeny including Xyloplax, a progenetic asteroid.
2011,
Pubmed
,
Echinobase
Lartillot,
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating.
2009,
Pubmed
Mah,
Global diversity and phylogeny of the Asteroidea (Echinodermata).
2012,
Pubmed
,
Echinobase
Matsubara,
The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences.
2005,
Pubmed
,
Echinobase
McEdward,
Life Cycle Evolution in Asteroids: What is a Larva?
1993,
Pubmed
,
Echinobase
Okanishi,
Molecular phylogeny of the order Euryalida (Echinodermata: Ophiuroidea), based on mitochondrial and nuclear ribosomal genes.
2011,
Pubmed
,
Echinobase
Perseke,
Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata.
2010,
Pubmed
,
Echinobase
Philippe,
Resolving difficult phylogenetic questions: why more sequences are not enough.
2011,
Pubmed
Pisani,
Identifying and removing fast-evolving sites using compatibility analysis: an example from the Arthropoda.
2004,
Pubmed
Pisani,
Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships.
2012,
Pubmed
,
Echinobase
Quang,
Empirical profile mixture models for phylogenetic reconstruction.
2008,
Pubmed
Rota-Stabelli,
Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study.
2013,
Pubmed
Rota-Stabelli,
A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata.
2011,
Pubmed
Roure,
Impact of missing data on phylogenies inferred from empirical phylogenomic data sets.
2013,
Pubmed
Smith,
Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata).
2006,
Pubmed
,
Echinobase
Sperling,
Molecular paleobiological insights into the origin of the Brachiopoda.
2011,
Pubmed
Sperling,
Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa.
2009,
Pubmed
Telford,
Phylogenomic analysis of echinoderm class relationships supports Asterozoa.
2014,
Pubmed
,
Echinobase
Wada,
Mitochondrial rDNA phylogeny of the asteroidea suggests the primitiveness of the paxillosida.
1996,
Pubmed
,
Echinobase
Xie,
Improving marginal likelihood estimation for Bayesian phylogenetic model selection.
2011,
Pubmed
