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...e assembled for two nuclear ribosomal genes (18S and 28S rRNA) and two mitochondrial ribosomal genes (12S and 16S rRNA). However, applying posterior probability analysis, as implemented in Phylobayes =-=[25]-=-, we found that the amount of homoplasy was significantly higher in the combined dataset than in the dataset of nuclear genes (Table D in S1 File). Consequently, mitochondrial ribosomal genes were exc...

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...e Table C in S1 File) we applied two approaches to minimize the problem. First we performed the phylogenetic reconstruction of the full data set using the non-stationary CAT-break point model (CATBP) =-=[30]-=-, as implemented in Nh-phylobayes [30]. This model, by implementing a multiple break point along the lineages, is able to account directly for compositional heterogeneity [30]. Among site variation wa...

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...can we start to have faith in the root position identified for asteroids. Testing support for competing hypotheses Support amongst competing hypotheses was assessed using a Bayes Factor (BF) approach =-=[39]-=-. The marginal likelihood for each constraint tree was estimated under GTR-Γ using the stepping-stone procedure, as implemented in MrBayes3.2 (with 10 million generations and sampling every 2500 gener...

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...ma categories. Convergence among chains was evaluated using compchain software, which is part of the Nh-phylobayes package. Additionally we performed site stripping as implemented in the program BMGE =-=[31]-=-. BMGE used a Stuart’s test of marginal homogeneity to remove compositionally heterogeneous sites. This removed 278 heterogeneous sites from our original data and generated a partition contain only co...

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...genetic signal is a common problem that can distort molecular phylogenies [20– 21]. Non-phylogenetic signal has multiple and disparate sources. The use of suboptimal models of evolution, missing data =-=[22]-=-, the presence of fast evolving taxa and compositional heterogeneity are all widely recognized as potential sources of false signal, with the latter two effects causing sequences to be erroneously gro...

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... Knott and Wray [17] using two mitochondrial genes found neither paxillosids nor forcipulatids as basal, instead placing a paraphyletic valvatids basal with velatids nested within this grade. Janies’ =-=[7]-=- combined morphological and molecular investigation of echinoderm class relationships included 16 asteroid genera. Although not specifically examining asteroid rooting this presented a fourth topology...

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...ssection Identifies the Root of Starfishes PLOS ONE | DOI:10.1371/journal.pone.0123331 May 8, 2015 3 / 14 Phylogenetic signal dissection and compositional heterogeneity Phylogenetic signal dissection =-=[27]-=- was performed to assess the effect of fast evolving sites on tree topology. Site-specific rates of evolution were estimated using the program TIGER [28], which assigns evolutionary rates to character...

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...r arms and a sucker for attachment) in velatids, valvatids and forcipulatids must be seen as a shared plesiomorphy. As the brachiolarian larva is preceded developmentally by a bipinnaria larval stage =-=[14, 44]-=-, and a bipinnaria stage is found in paxillosids, our tree implies that paxillosids must have truncated their development. Suckered tube feet are fully developed only in Spinulosida and Forcipulata so...

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...comp option (part of the Phylobayes package). Phylogenetic reconstruction was performed using maximum likelihood methods as implemented in PhyML under GTR-Γ. Node supports were evaluated using aBayes =-=[26]-=-. Phylogenetic Signal Dissection Identifies the Root of Starfishes PLOS ONE | DOI:10.1371/journal.pone.0123331 May 8, 2015 3 / 14 Phylogenetic signal dissection and compositional heterogeneity Phyloge...

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...he first data partition combines sites with extreme rate variation this partition poses an extreme problem for tree reconstructing methods and is expected to be misled more readily by systematic bias =-=[29]-=-. The presence of compositional heterogeneity was evaluated using posterior predictive analysis (PPA) as implemented in Phylobayes [25]. As composition heterogeneity was found to be an important issue...

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...l heterogeneity Phylogenetic signal dissection [27] was performed to assess the effect of fast evolving sites on tree topology. Site-specific rates of evolution were estimated using the program TIGER =-=[28]-=-, which assigns evolutionary rates to characters and places them in bins of approximately equal rate. This is tree independent, eliminating the need for a priori tree specification [28]. Two partition...

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...et comprises the best set of sites with a bona-fide phylogenetic signal. Since that performance of complex model such as CAT-GTR seems to be less efficient on small alignment (less then 1000 position—=-=[32]-=-) we decided to analyse all subpartitions under GTR-Γ using Phylobayes3.3e. However, CAT-GTR-Γ was used to confirm the topology obtained using the most reliable composition+rate homogeneous partition....

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...r arms and a sucker for attachment) in velatids, valvatids and forcipulatids must be seen as a shared plesiomorphy. As the brachiolarian larva is preceded developmentally by a bipinnaria larval stage =-=[14, 44]-=-, and a bipinnaria stage is found in paxillosids, our tree implies that paxillosids must have truncated their development. Suckered tube feet are fully developed only in Spinulosida and Forcipulata so...

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...ps included 16 asteroid genera. Although not specifically examining asteroid rooting this presented a fourth topology again with valvatids as paraphyletic but with velatids as basal. A later analysis =-=[8]-=-, again focusing on class relationships but including 35 asteroids and partial sequences from 7 genes, identified a clade comprising two velatids (Pteraster andHymenaster) and the highly divergent Xyl...

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...relationships amongst some of the five classes of echinoderms are also largely uncontroversial, with crinoids as sister group to the other four classes and holothurians and echinoids as sister groups =-=[29, 38]-=-. We used these relationships as an additional criterion: data and methods that do not recover these well-founded relationships cannot be relied upon to have identified the correct root position for a...

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...ety of possible taxa at the base of crown group asteroids (Fig 1). Initial analyses based on small data sets [14–15] identified Paxillosida as sister group to other asteroids. However, Knott and Wray =-=[17]-=- using two mitochondrial genes found neither paxillosids nor forcipulatids as basal, instead placing a paraphyletic valvatids basal with velatids nested within this grade. Janies’ [7] combined morphol...

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...oot of Starfishes PLOS ONE | DOI:10.1371/journal.pone.0123331 May 8, 2015 6 / 14 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 parti...

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...hology-based phylogenies of the Asteroidea were published that came to very different conclusions (Fig 1). Blake [4] identified the order Forcipulatida as sister group to other asteroids whereas Gale =-=[2]-=- followed traditional interpretations placing Paxillosida in that position. Since then Blake [5, PLOSONE | DOI:10.1371/journal.pone.0123331 May 8, 2015 1 / 14 OPEN ACCESS Citation: Feuda R, Smith AB (...

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...ampling every 2500 generations). The stepping-stone method has recently been developed and is known to outperform the traditional harmonic mean approach for estimating the marginal likelihood support =-=[40]-=-. We also compared the support for each of the topologies shown in Fig 1 (excluding [1], because of its incomplete coverage of asteroids orders) and Fig 2, in each data partition. Results The data par...

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...e most iconic of the five extant classes of echinoderm. This group includes around 1900 extant species classified into five major orders: Paxillosida, Spinulosida, Velatida, Valvatida and Forcipulata =-=[1]-=-. While there has never been any doubt about the monophyly of the crown group from a morphological [2–5] or molecular [6–9] perspective, relationships among the orders are far from settled. Disagreeme...

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... the paper and its Supporting Information files. Funding: The authors have no support or funding to report. Competing Interests: The authors have declared that no competing interests exist. 12], Gale =-=[3]-=- and others [13] have continued to debate the relative merits of each interpretation from a morphological perspective. Given this striking disagreement amongst morphologists, various attempts have bee...

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...entrotus) is unambiguously supported [33–34], as is the sister group relationship of Euryalida (Asteronyx, Gorgonocephalus) to Ophiurida (Ophioderma, Ophiopsammus, Ophiocoma, Ophiothrix, Ophiopholis) =-=[35]-=-. Similarly both morphological and molecular data place Elasipoda (Psychropotes) as sister group to the Aspidochirotida (Cucumaria, Holothuria) [36–37]. The relationships amongst some of the five clas...

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... debate between Mortensen and MacBride [10–11], and ignited again in 1987 when two morphology-based phylogenies of the Asteroidea were published that came to very different conclusions (Fig 1). Blake =-=[4]-=- identified the order Forcipulatida as sister group to other asteroids whereas Gale [2] followed traditional interpretations placing Paxillosida in that position. Since then Blake [5, PLOSONE | DOI:10...

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...its Supporting Information files. Funding: The authors have no support or funding to report. Competing Interests: The authors have declared that no competing interests exist. 12], Gale [3] and others =-=[13]-=- have continued to debate the relative merits of each interpretation from a morphological perspective. Given this striking disagreement amongst morphologists, various attempts have been made to resolv...