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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).
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