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...nly representative of its clade, which could introduce a systematic bias. We then performed additional GTR analyses under the ML framework on the reduced, 103 taxa alignment. We run jModelTest v2.0.2 =-=[97]-=- on all codon alignments to look for the models that best fit our data. We analyzed all the nucleotide alignments under both the BI framework using PhyloBayes v3.3 and MrBayes v3.2.1 (MB) [98] and ML ...

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...tic relationships according to our data. To do so, we compared whether our data significantly rejected the best trees conforming to each of the a priori hypotheses (Table 2) using the CONSEL software =-=[99]-=-. For Bayesian inferences, a cross-validation was performed to find the model with the best fit to the data. Each alignment is randomly split in two unequal parts: a “learning dataset” with nine-tenth...

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...model, i.e. homogeneity of the substitution pattern across sites, is violated by most molecular data, rendering the correct capture of the phylogenetic signal present in our alignments more difficult =-=[50]-=-. The resulting topologies from CATGTR analyses differed significantly from the current consensus view of cnidarian phylogeny [1,2]. Using the best estimate as a working hypothesis for Kayal et al. BM...

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... v2.0.2 [97] on all codon alignments to look for the models that best fit our data. We analyzed all the nucleotide alignments under both the BI framework using PhyloBayes v3.3 and MrBayes v3.2.1 (MB) =-=[98]-=- and ML framework using RAxML v7.2.6 as described above. For PB analyses we use the Q-Matrix Mixture model (QMM) instead of GTR and CAT+GTR + Γ. The MB analyses used the GTR+ Γ + I model of sequence e...

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...including 10 octocorals and 20 hexacorals, to build several codon alignments. First, we create a codon alignment for each gene based on the concatenated amino acid alignment using the program PAL2NAL =-=[89]-=-, before concatenating all genes into a single alignment (CodAliM75tx, 9921 parsimony-informative characters). We then created several additional codon alignments by removing the third codon position ...

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...oa + Staurozoa] and [Hydrozoa + Scyphozoa] [12,13]. Furthermore, the early branching position of Staurozoa, as sister group to the remaining medusozoans only received moderate support in rRNA studies =-=[14]-=-. Even within the major cnidarian taxa, phylogenetic hypotheses remain to be assessed with independent datasets. Some studies have nested the monophyletic rhizostome jellyfish within a paraphyletic Se...

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...3:5 Page 9 of 18 http://www.biomedcentral.com/1471-2148/13/5occurrences of deviation from a bilateral Bauplan in several animal groups, such as siphonophores [59], myxozoans [60] and some bilaterians =-=[61,62]-=-. Bilaterality has evolved very early in animal evolution near the root of the metazoan tree [63], and our data support the view that such a step was taken before the divergence of Cnidaria. Future st...

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...l Bauplan in several animal groups, such as siphonophores [59], myxozoans [60] and some bilaterians [61,62]. Bilaterality has evolved very early in animal evolution near the root of the metazoan tree =-=[63]-=-, and our data support the view that such a step was taken before the divergence of Cnidaria. Future studies that resolve the position of cnidarians within the metazoan tree of life will shed light on...

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...phylogenetic results based on them. Indeed, it is known that inadequate taxon sampling and systematic errors can override genuine phylogenetic signal, resulting in flawed phylogenetic reconstructions =-=[40,41]-=-. We assembled a more taxonomically balanced mitogenomic dataset to investigate the evolutionary history of cnidarians. Our dataset contains newly published mitochondrial sequences from 24 representat...

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...list of author information is available at the end of the articlevided into two diverse subclasses Hexacorallia (hard corals and sea anemones) and Octocorallia (soft corals, sea pens, and gorgonians) =-=[1,2]-=-. The remaining four classes – Staurozoa (Marques and Collins 2004) were originally included in the class Scyphozoa (Götte 1887), but each has been promoted to the status of class, leaving three order...

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...ree after the 25% burn-in. Table 3 Species list Phylum Subphylum Class Subclass Order Species Accession number Reference Cnidaria Anthozoa Hexacorallia Actiniaria Metridium senile [GenBank:NC_000933] =-=[68]-=- Nematostella sp [GenBank:NC_008164] [22] Antipatharia Chrysopathes formosa [GenBank:NC_008411] [39] Cirripathes lutkeni [GenBank:NC_018377] this study Leiopathes glaberrima [GenBank:FJ597643] & [GenB...

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...haracters); and a combination of all three (CodAliM75tx-argleuser3, 4785 parsimonyinformative characters). All the alignments are available upon request. We used the program Net from the MUST package =-=[90]-=- to estimate the amino-acid composition per species in each of the alignments by assembling a 20 X 106 matrix containing the frequency of each amino acid. This matrix was then displayed as a two-dimen...

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...700944] [27] Lucernaria janetae [GenBank:JN700946] [27] Placozoa BZ10101 [GenBank:NC_008832] [82] BZ243 [GenBank:NC_008834] [82] BZ49 [GenBank:NC_008833] [82] Trichoplax adhaerens [GenBank:NC_008151] =-=[83]-=- Porifera Homoscleromorpha Corticium candelabrum [GenBank:NC_014872] [38] Oscarella carmela [GenBank:NC_009090] [84] Plakina monolopha [GenBank:NC_014884] [38] Plakinastrella cf. onkodes [GenBank:NC_0...

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...ecided to exclude sequences from bilaterian animals because they form long branches in mitochondrial phylogenomic trees that attract other long branches, resulting in Long Branch Attraction artifacts =-=[42,43]-=-. In the future, the inclusion of bilaterians in mtDNA-based phylogenies can be tested given better models of sequence evolution are available. We found maximum support for the monophyly of Medusozoa,...

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...questions about the relationships among and within the major cnidarian taxa remain. For instance, monophyly of Anthozoa is supported by numerous analyses of rRNA data [3-6], although only one of them =-=[7]-=- included a dense sampling of both anthozoan and medusozoan taxa. However, studies based on mitochondrial DNA data suggest that Anthozoa is paraphyletic, with octocorals forming a sister group relatio...

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...olutionary Biology 2013, 13:5 Page 9 of 18 http://www.biomedcentral.com/1471-2148/13/5occurrences of deviation from a bilateral Bauplan in several animal groups, such as siphonophores [59], myxozoans =-=[60]-=- and some bilaterians [61,62]. Bilaterality has evolved very early in animal evolution near the root of the metazoan tree [63], and our data support the view that such a step was taken before the dive...

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...:FJ597644] [69] Corallimorpharia Discosoma sp [GenBank:NC_008071] [22] Rhodactis sp [GenBank:NC_008158] [22] Ricordea florida [GenBank:NC_008159] [22] Scleractinia Acropora tenuis [GenBank:NC_003522] =-=[70]-=- Agaricia humilis [GenBank:NC_008160] [22] Anacropora matthai [GenBank:NC_006898] Unpublished Astrangia sp [GenBank:NC_008161] [22] Colpophyllia natans [GenBank:NC_008162] [22] Lophelia pertusa [GenBa...

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... with earlier studies that originated the name "stalked jellyfish" for staurozoans, and concluded that these species represented "degenerated" jellyfish descended from ancestors with a pelagic medusa =-=[14,16,64,65]-=-. Simplification or losses of the medusa form has also been documented in several Hydrozoa clades [18]. The acquisition of a pelagic form is significant given that a free-swimming medusa allows a high...

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... with earlier studies that originated the name "stalked jellyfish" for staurozoans, and concluded that these species represented "degenerated" jellyfish descended from ancestors with a pelagic medusa =-=[14,16,64,65]-=-. Simplification or losses of the medusa form has also been documented in several Hydrozoa clades [18]. The acquisition of a pelagic form is significant given that a free-swimming medusa allows a high...

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...divergence between Cnidaria and Bilateria. In fact in Cnidaria, increasing evidence supports the presence of bilateral symmetry in corals and sea anemones, where it is represented by the siphonoglyph =-=[56,57]-=-, while most medusozoans do not exhibit any bilateral symmetry [28,58], with siphonophores being an exception [59]. The tree topologies provided here strengthen the view that the ancestral cnidarian d...

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...y history within and between most metazoan groups. In non-bilaterian animals, recent increase in the number of completely sequenced mtDNAs has helped to resolve deep phylogenetic nodes within sponges =-=[9,38]-=- and Hexacorallia within Cnidaria [22,39]. Yet, the very poor sample size of medusozoan taxa in previous studies raises some question about the validity of phylogenetic results based on them. Indeed, ...

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...ecided to exclude sequences from bilaterian animals because they form long branches in mitochondrial phylogenomic trees that attract other long branches, resulting in Long Branch Attraction artifacts =-=[42,43]-=-. In the future, the inclusion of bilaterians in mtDNA-based phylogenies can be tested given better models of sequence evolution are available. We found maximum support for the monophyly of Medusozoa,...

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...phylogenetic results based on them. Indeed, it is known that inadequate taxon sampling and systematic errors can override genuine phylogenetic signal, resulting in flawed phylogenetic reconstructions =-=[40,41]-=-. We assembled a more taxonomically balanced mitogenomic dataset to investigate the evolutionary history of cnidarians. Our dataset contains newly published mitochondrial sequences from 24 representat...

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...p [GenBank:NC_008161] [22] Colpophyllia natans [GenBank:NC_008162] [22] Lophelia pertusa [GenBank:NC_015143] [71] Madracis mirabilis [GenBank:NC_011160] [72] Montastraea annularis [GenBank:NC_007224] =-=[73]-=- Montastraea faveolata [GenBank:NC_007226] [73] Montastraea franksi [GenBank:NC_007225] [73] Montipora cactus [GenBank:NC_006902] Unpublished Mussa angulosa [GenBank:NC_008163] [22] Pavona clavus [Gen...

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...p relationships between Trachylina and Hydroidolina within Hydrozoa [14], paraphyletic “Filifera” (Kühn 1913) within Hydroidolina [18,19]; monophyletic stony corals (Scleractinia) within Hexacorallia =-=[20,21]-=- in opposition to earlier studies [22]; and, two robust clades Carybdeida and Chirodropida composing box jellyfish (Cubozoa) [23]. In addition, rDNA-based studies have also exposed some disparities be...

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...ss-validation log-likelihood scores of the test datasets, averaged over the ten replicates. Finally, we sampled ten important morphological characters from previously published morphological matrices =-=[18,28,58,100]-=- and mapped them on the CATGTR based tree. To do so we used PAUP 4.0b10 for Unix [101] using DELTRAN and ACCRAN character-state optimization models. The scoring of each character is detailed in additi...

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...f cnidarian relationships obtained using mitochondrial prot1856; in accordance with rRNA-based analyses), some studies have suggested the groupings of [Cubozoa + Staurozoa] and [Hydrozoa + Scyphozoa] =-=[12,13]-=-. Furthermore, the early branching position of Staurozoa, as sister group to the remaining medusozoans only received moderate support in rRNA studies [14]. Even within the major cnidarian taxa, phylog...

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...droidolina within Hydrozoa [14], paraphyletic “Filifera” (Kühn 1913) within Hydroidolina [18,19]; monophyletic stony corals (Scleractinia) within Hexacorallia [20,21] in opposition to earlier studies =-=[22]-=-; and, two robust clades Carybdeida and Chirodropida composing box jellyfish (Cubozoa) [23]. In addition, rDNA-based studies have also exposed some disparities between classical taxonomy and molecular...

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...the asserted orthology of all genes [35] and the small genome structure being relatively conserved, which provides additional characters such as gene order (considered as Rare Genetic Changes or RGC) =-=[36,37]-=-. Despite some limitations, mtDNA-based phylogenetic trees are considered valid proxies of the evolutionary history within and between most metazoan groups. In non-bilaterian animals, recent increase ...

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...alignments from a subset of 75 species using the GTR and the QMM models under BI and the GTR model under the ML frameworks. It has been shown that codon usage bias can result in phylogenetic artifact =-=[44]-=-. In order to minimize the impact of codon usage bias on phylogenetic trees, we reanalyzed the codon dataset after removing the third codon position, as well as codons for arginine (AGR and CGN), leuc...

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...Craterolophus convolvulus [GenBank:JN700975] & [GenBank:JN700976] [27] Haliclystus sanjuanensis [GenBank:JN700944] [27] Lucernaria janetae [GenBank:JN700946] [27] Placozoa BZ10101 [GenBank:NC_008832] =-=[82]-=- BZ243 [GenBank:NC_008834] [82] BZ49 [GenBank:NC_008833] [82] Trichoplax adhaerens [GenBank:NC_008151] [83] Porifera Homoscleromorpha Corticium candelabrum [GenBank:NC_014872] [38] Oscarella carmela [...

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...c tree (Figure 2) with large nuclear DNA datasets.Within Medusozoa, Staurozoa is considered the first diverging clade, and the sister taxon to [Acraspeda (Cubozoa + Scyphozoa) +Hydrozoa] (reviewed in =-=[2]-=-). While the position of Linuche unguiculata is still ambiguous in our trees, we found no support for either the inclusion of coronates in Scyphozoa (PPs = 0; BV = 0), or for Acraspeda [Cubozoa + Scyp...

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...g rRNA sequences [17]. Other relevant findings include the sister group relationships between Trachylina and Hydroidolina within Hydrozoa [14], paraphyletic “Filifera” (Kühn 1913) within Hydroidolina =-=[18,19]-=-; monophyletic stony corals (Scleractinia) within Hexacorallia [20,21] in opposition to earlier studies [22]; and, two robust clades Carybdeida and Chirodropida composing box jellyfish (Cubozoa) [23]....

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...f cnidarian relationships obtained using mitochondrial prot1856; in accordance with rRNA-based analyses), some studies have suggested the groupings of [Cubozoa + Staurozoa] and [Hydrozoa + Scyphozoa] =-=[12,13]-=-. Furthermore, the early branching position of Staurozoa, as sister group to the remaining medusozoans only received moderate support in rRNA studies [14]. Even within the major cnidarian taxa, phylog...

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...the asserted orthology of all genes [35] and the small genome structure being relatively conserved, which provides additional characters such as gene order (considered as Rare Genetic Changes or RGC) =-=[36,37]-=-. Despite some limitations, mtDNA-based phylogenetic trees are considered valid proxies of the evolutionary history within and between most metazoan groups. In non-bilaterian animals, recent increase ...

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...an groups. In non-bilaterian animals, recent increase in the number of completely sequenced mtDNAs has helped to resolve deep phylogenetic nodes within sponges [9,38] and Hexacorallia within Cnidaria =-=[22,39]-=-. Yet, the very poor sample size of medusozoan taxa in previous studies raises some question about the validity of phylogenetic results based on them. Indeed, it is known that inadequate taxon samplin...

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...ratively higher rate of sequence evolution than other genes [54]. While future molecular studies of the evolutionary history of octocorals may focus their investigation to only a portion of the mtDNA =-=[55]-=-, complete mitogenomes provide additional genomic features such as gene order and the composition of intergenic regions (IGRs) that could be valuable to systematic studies [10]. Furthermore, the combi...

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...ksi [GenBank:NC_007225] [73] Montipora cactus [GenBank:NC_006902] Unpublished Mussa angulosa [GenBank:NC_008163] [22] Pavona clavus [GenBank:NC_008165] [22] Pocillopora damicornis [GenBank:NC_009797] =-=[74]-=- Pocillopora eydouxi [GenBank:NC_009798] [74] Porites porites [GenBank:NC_008166] [22] Seriatopora caliendrum [GenBank:NC_010245] [72] Seriatopora hystrix [GenBank:NC_010244] [72] Siderastrea radians ...

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...sidinae sp [GenBank:NC_010764] [78] Paracorallium japonicum [GenBank:NC_015405] [77] Pseudopterogorgia bipinnata [GenBank:NC_008157] [22] Sarcophyton glaucum [GenBank: AF064823] & [GenBank: AF063191] =-=[79,80]-=- Scleronephthya gracillimum [GenBank: GU047879] [10] Sinularia peculiaris [GenBank:NC_018379] this study Helioporacea Heliopora coerulea [GenBank:JX023267-JX023272] this study Pennatulacea Renilla mul...

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...drozoa Trachylina Limnomedusae Cubaia Aphrodite [GenBank:JN700942] [27] Hydroidolina Aplanulata Ectopleura larynx [GenBank:JN700938] [27] Hydra magnipapillata [GenBank:NC_011220] & [GenBank:NC_01122] =-=[81]-=- Hydra oligactis [GenBank:NC_010214] [8] Hydra vulgaris [GenBank:BN001179] & [GenBank:BN001180] [81] Capitata Millepora platyphylla [GenBank:JN700943] [27] Pennaria tiarella [GenBank:JN700950] [27] Fi...

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...008834] [82] BZ49 [GenBank:NC_008833] [82] Trichoplax adhaerens [GenBank:NC_008151] [83] Porifera Homoscleromorpha Corticium candelabrum [GenBank:NC_014872] [38] Oscarella carmela [GenBank:NC_009090] =-=[84]-=- Plakina monolopha [GenBank:NC_014884] [38] Plakinastrella cf. onkodes [GenBank:NC_010217] [84] Demospongiae G1 = Keratosa Igernella notabilis [GenBank:NC_010216] [84] Ircinia strobilina [GenBank:NC_0...

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...ure 3 Morphological character reconstruction in Cnidaria. Recon phylogenetic hypothesis based on mitogenomic data. (1) symmetry: b = medusoid stage (many hydrozoans have secondarily lost the medusoid =-=(5)-=- gastric filaments; (6) ephyrae; (7) radial canal (scored uncertain in Cub (10) gastrodermal muscles: e = in bunches of ectodermal origin, g = in b Morphological characters are taken from Marques and ...

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...relationships for the phylum Cnidaria is a prerequisite for the reconstruction of the evolutionary history of key morphological novelties in this group, e.g. life history and morphological characters =-=[14,18,25]-=-, medusan morphospace and swimming ability [26], the evolution of toxicity in cubozoans [23], the origin and evolution of reef-building corals [20,21], and mitochondrial genome structures [27]. One cr...

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...t scyphozoans contain both polyp and medusa stages. Hydrozoans display the widest range of diversity in their life cycle, with the absence of a sessile polyp in Trachymedusae (which may be diphyletic =-=[29]-=-) and many species of Narcomedusae, and a highly reduced or absent medusa in other lineages (e.g. some clades within Leptothecata and Aplanulata, including the freshwater hydras (Hydridae)) [1,7,18,30...

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...y history within and between most metazoan groups. In non-bilaterian animals, recent increase in the number of completely sequenced mtDNAs has helped to resolve deep phylogenetic nodes within sponges =-=[9,38]-=- and Hexacorallia within Cnidaria [22,39]. Yet, the very poor sample size of medusozoan taxa in previous studies raises some question about the validity of phylogenetic results based on them. Indeed, ...

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...itochondrial genome data, the monophyly of stony corals (Scleractinia) has recently been put into question [22], but more thorough studies employing alternative datasets have rejected this hypothesis =-=[21,52]-=-. Our analyses support the monophyly of Scleractinia under the preferred CATGTR model (PP = 0.51; AU = 0.25; KH = 0.17; SH = 0.53). Our phylogenetic analyses did not resolve relationships within octoc...

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...l symmetry in corals and sea anemones, where it is represented by the siphonoglyph [56,57], while most medusozoans do not exhibit any bilateral symmetry [28,58], with siphonophores being an exception =-=[59]-=-. The tree topologies provided here strengthen the view that the ancestral cnidarian displayed a bilateral symmetry from which the radial tetrameral symmetry (body divided into four identical parts) o...

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...sp [GenBank:NC_008164] [22] Antipatharia Chrysopathes formosa [GenBank:NC_008411] [39] Cirripathes lutkeni [GenBank:NC_018377] this study Leiopathes glaberrima [GenBank:FJ597643] & [GenBank:FJ597644] =-=[69]-=- Corallimorpharia Discosoma sp [GenBank:NC_008071] [22] Rhodactis sp [GenBank:NC_008158] [22] Ricordea florida [GenBank:NC_008159] [22] Scleractinia Acropora tenuis [GenBank:NC_003522] [70] Agaricia h...

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...nk: DQ640650] [22] Savalia savaglia [GenBank:NC_008827] [75] Ceriantharia Ceriantheopsis americanus [GenBank:JX023261-JX023265] this study Octocorallia Alcyonacea Acanella eburnea [GenBank:NC_011016] =-=[76]-=- Briareum asbestinum [GenBank:NC_008073] [22] Kayalet al.BM C Evolutionary Biology 2013,13:5 Page 11 of 18 http://w w w .biom edcentral.com /1471-2148/13/5 Table 3 Species list (Continued) Corallium k...

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...nk:NC_008073] [22] Kayalet al.BM C Evolutionary Biology 2013,13:5 Page 11 of 18 http://w w w .biom edcentral.com /1471-2148/13/5 Table 3 Species list (Continued) Corallium konojoi [GenBank:NC_015406] =-=[77]-=- Dendronephthya castanea [GenBank: GU047877] [10] Dendronephthya gigantean [GenBank:NC_013573] Unpublished Dendronephthya mollis [GenBank: HQ694725] [10] Dendronephthya putteri [GenBank: HQ694726] [10...

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...sidinae sp [GenBank:NC_010764] [78] Paracorallium japonicum [GenBank:NC_015405] [77] Pseudopterogorgia bipinnata [GenBank:NC_008157] [22] Sarcophyton glaucum [GenBank: AF064823] & [GenBank: AF063191] =-=[79,80]-=- Scleronephthya gracillimum [GenBank: GU047879] [10] Sinularia peculiaris [GenBank:NC_018379] this study Helioporacea Heliopora coerulea [GenBank:JX023267-JX023272] this study Pennatulacea Renilla mul...

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...p relationships between Trachylina and Hydroidolina within Hydrozoa [14], paraphyletic “Filifera” (Kühn 1913) within Hydroidolina [18,19]; monophyletic stony corals (Scleractinia) within Hexacorallia =-=[20,21]-=- in opposition to earlier studies [22]; and, two robust clades Carybdeida and Chirodropida composing box jellyfish (Cubozoa) [23]. In addition, rDNA-based studies have also exposed some disparities be...

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...lis [GenBank:NC_008160] [22] Anacropora matthai [GenBank:NC_006898] Unpublished Astrangia sp [GenBank:NC_008161] [22] Colpophyllia natans [GenBank:NC_008162] [22] Lophelia pertusa [GenBank:NC_015143] =-=[71]-=- Madracis mirabilis [GenBank:NC_011160] [72] Montastraea annularis [GenBank:NC_007224] [73] Montastraea faveolata [GenBank:NC_007226] [73] Montastraea franksi [GenBank:NC_007225] [73] Montipora cactus...

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...hai [GenBank:NC_006898] Unpublished Astrangia sp [GenBank:NC_008161] [22] Colpophyllia natans [GenBank:NC_008162] [22] Lophelia pertusa [GenBank:NC_015143] [71] Madracis mirabilis [GenBank:NC_011160] =-=[72]-=- Montastraea annularis [GenBank:NC_007224] [73] Montastraea faveolata [GenBank:NC_007226] [73] Montastraea franksi [GenBank:NC_007225] [73] Montipora cactus [GenBank:NC_006902] Unpublished Mussa angul...

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...a monolopha [GenBank:NC_014884] [38] Plakinastrella cf. onkodes [GenBank:NC_010217] [84] Demospongiae G1 = Keratosa Igernella notabilis [GenBank:NC_010216] [84] Ircinia strobilina [GenBank:NC_013662] =-=[85]-=- G2 = Myxospongiae Aplysina fulva [GenBank:NC_010203] [84] Chondrilla aff. nucula [GenBank:NC_010208] [84] Halisarca dujardini [GenBank:NC_010212] [84] G3 =marine Haplosclerida Amphimedon compressa [G...

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...len.ata thecata ulata eostomeae stomeae Discomedusae uction of key morphological characters in Cnidaria based on the laterial, r = radial or biradial; (2) gain (+) and loss (−) of free-swimming ase); =-=(3)-=- velum (lost in some leptothecate hydrozoans); (4) strobilation; oa); (8) circular canal; (9) square symmetry of horizontal cross section; ches of gastrodermal origin, n = not organized in bunches. ar...

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...racter reconstruction in Cnidaria. Recon phylogenetic hypothesis based on mitogenomic data. (1) symmetry: b = medusoid stage (many hydrozoans have secondarily lost the medusoid (5) gastric filaments; =-=(6)-=- ephyrae; (7) radial canal (scored uncertain in Cub (10) gastrodermal muscles: e = in bunches of ectodermal origin, g = in b Morphological characters are taken from Marques and Collins (2004) and C Ma...

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...rodite [GenBank:JN700942] [27] Hydroidolina Aplanulata Ectopleura larynx [GenBank:JN700938] [27] Hydra magnipapillata [GenBank:NC_011220] & [GenBank:NC_01122] [81] Hydra oligactis [GenBank:NC_010214] =-=[8]-=- Hydra vulgaris [GenBank:BN001179] & [GenBank:BN001180] [81] Capitata Millepora platyphylla [GenBank:JN700943] [27] Pennaria tiarella [GenBank:JN700950] [27] Filifera III Clava multicornis [GenBank:JN...

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...ent datasets. Some studies have nested the monophyletic rhizostome jellyfish within a paraphyletic Semaeostomeae [7,14-16], a view supported by the most recent phylogenetic study using rRNA sequences =-=[17]-=-. Other relevant findings include the sister group relationships between Trachylina and Hydroidolina within Hydrozoa [14], paraphyletic “Filifera” (Kühn 1913) within Hydroidolina [18,19]; monophyletic...

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...s [14,18,25], medusan morphospace and swimming ability [26], the evolution of toxicity in cubozoans [23], the origin and evolution of reef-building corals [20,21], and mitochondrial genome structures =-=[27]-=-. One critical character in cnidarian evolution is the ancestral state of the adult life stage, polyp or medusa, which has been a matter of controAnthozoa Medusozoa O c o t c o r a ll ia H e x a c o r...

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...letic [29]) and many species of Narcomedusae, and a highly reduced or absent medusa in other lineages (e.g. some clades within Leptothecata and Aplanulata, including the freshwater hydras (Hydridae)) =-=[1,7,18,30,31]-=-. While some earlier studies have proposed the medusa form has been lost in Anthozoa, the current view holds the medusa is an apomorphy (derived character) for Medusozoa [1,14]). Consequently, it is g...

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...t our alignments did not encompass sequences from the mtMutS gene, absent in all other cnidarian and animal taxa, and which displays a comparatively higher rate of sequence evolution than other genes =-=[54]-=-. While future molecular studies of the evolutionary history of octocorals may focus their investigation to only a portion of the mtDNA [55], complete mitogenomes provide additional genomic features s...

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...3:5 Page 9 of 18 http://www.biomedcentral.com/1471-2148/13/5occurrences of deviation from a bilateral Bauplan in several animal groups, such as siphonophores [59], myxozoans [60] and some bilaterians =-=[61,62]-=-. Bilaterality has evolved very early in animal evolution near the root of the metazoan tree [63], and our data support the view that such a step was taken before the divergence of Cnidaria. Future st...

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... with earlier studies that originated the name "stalked jellyfish" for staurozoans, and concluded that these species represented "degenerated" jellyfish descended from ancestors with a pelagic medusa =-=[14,16,64,65]-=-. Simplification or losses of the medusa form has also been documented in several Hydrozoa clades [18]. The acquisition of a pelagic form is significant given that a free-swimming medusa allows a high...

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...ted in several Hydrozoa clades [18]. The acquisition of a pelagic form is significant given that a free-swimming medusa allows a higher degree of offspring dispersion than by gametes and larvae alone =-=[66]-=-. Earlier studies have suggested several synapomorphies for the extended Acraspeda clade (Cubozoa + Scyphozoa + Staurozoa), namely radial tetrameral symmetry, medusa formation located at the apical en...

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...w .biom edcentral.com /1471-2148/13/5 Table 3 Species list (Continued) Geodia neptuni [GenBank:NC_006990] [37] Lubomirskia baicalensis [GenBank:NC_013760] [86] Suberites domuncula [GenBank:NC_010496] =-=[87]-=- Tethya actinia [GenBank:NC_006991] [37] Topsentia ophiraphidites [GenBank:NC_010204] [84] List of species, with their accession number and reference, used for this studies. Bold species are from this...

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...ae uction of key morphological characters in Cnidaria based on the laterial, r = radial or biradial; (2) gain (+) and loss (−) of free-swimming ase); (3) velum (lost in some leptothecate hydrozoans); =-=(4)-=- strobilation; oa); (8) circular canal; (9) square symmetry of horizontal cross section; ches of gastrodermal origin, n = not organized in bunches. artwright and Nawrocki (2010) studies. Drawings were...

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...bdeida and Chirodropida composing box jellyfish (Cubozoa) [23]. In addition, rDNA-based studies have also exposed some disparities between classical taxonomy and molecular phylogenies for some groups =-=[24]-=-and were unable to resolve phylogenetic relationships within others, e.g. Hydroidolina [14,19] and alcyonacean octocorals [24]. Thus, additional markers are necessary to achieve a better understanding...

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...te for the reconstruction of the evolutionary history of key morphological novelties in this group, e.g. life history and morphological characters [14,18,25], medusan morphospace and swimming ability =-=[26]-=-, the evolution of toxicity in cubozoans [23], the origin and evolution of reef-building corals [20,21], and mitochondrial genome structures [27]. One critical character in cnidarian evolution is the ...

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...ss-validation log-likelihood scores of the test datasets, averaged over the ten replicates. Finally, we sampled ten important morphological characters from previously published morphological matrices =-=[18,28,58,100]-=- and mapped them on the CATGTR based tree. To do so we used PAUP 4.0b10 for Unix [101] using DELTRAN and ACCRAN character-state optimization models. The scoring of each character is detailed in additi...

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...letic [29]) and many species of Narcomedusae, and a highly reduced or absent medusa in other lineages (e.g. some clades within Leptothecata and Aplanulata, including the freshwater hydras (Hydridae)) =-=[1,7,18,30,31]-=-. While some earlier studies have proposed the medusa form has been lost in Anthozoa, the current view holds the medusa is an apomorphy (derived character) for Medusozoa [1,14]). Consequently, it is g...

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... earlier [14,18]. On the other hand, we found a consistent grouping of capitate and aplanulate hydrozoans in all our trees (PPs = 1; BV = 88), which is in contradiction with earlier rDNAbased studies =-=[7,18,19,29,30,49,51]-=-. The high support values here suggest that higher resolution of the clade Hydroidolina may be achieved with an increase in the number of complete mtDNAs for representative taxa within this difficult ...

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...enetic relationships presented here. Recent molecular studies have refined our understanding of hydrozoan relationships, particularly the sister group relationship between Hydroidolina and Trachylina =-=[7,14,18,19,30,51]-=-. However, relationships within Hydroidolina have been very difficult to resolve based on either nuclear or mitochondrial rDNA genes. Here we have been able to sample five important hydroidolinan clad...

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...0.25; KH = 0.17; SH = 0.53). Our phylogenetic analyses did not resolve relationships within octocorals. This was predictable given the low-level of variation of mitochondrial genes in octocorals (see =-=[53]-=-), a pattern attributed to the activity of the mtMutS gene they encode. It is noteworthy mentioning that our alignments did not encompass sequences from the mtMutS gene, absent in all other cnidarian ...

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...sing evidence supports the presence of bilateral symmetry in corals and sea anemones, where it is represented by the siphonoglyph [56,57], while most medusozoans do not exhibit any bilateral symmetry =-=[28,58]-=-, with siphonophores being an exception [59]. The tree topologies provided here strengthen the view that the ancestral cnidarian displayed a bilateral symmetry from which the radial tetrameral symmetr...

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...ally symmetrical and vagile medusa evolved in the branch leading to Medusozoa. Our analyses support the view that the ancestor of cnidarians and bilaterians (UrEumetazoa) possessed bilateral symmetry =-=[67]-=-. According to our working hypothesis, synapomorphies traditionally associated with Acraspeda such as the presence of gastric filaments in the medusae and gastrodermal musculature organized in bunches...

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...enBank:NC_010244] [72] Siderastrea radians [GenBank:NC_008167] [22] Stylophora pistillata [GenBank:NC_011162] [72] Zoantharia Palythoa sp [GenBank: DQ640650] [22] Savalia savaglia [GenBank:NC_008827] =-=[75]-=- Ceriantharia Ceriantheopsis americanus [GenBank:JX023261-JX023265] this study Octocorallia Alcyonacea Acanella eburnea [GenBank:NC_011016] [76] Briareum asbestinum [GenBank:NC_008073] [22] Kayalet al...

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...ally, we sampled ten important morphological characters from previously published morphological matrices [18,28,58,100] and mapped them on the CATGTR based tree. To do so we used PAUP 4.0b10 for Unix =-=[101]-=- using DELTRAN and ACCRAN character-state optimization models. The scoring of each character is detailed in additional materials (Additional file 7). Additional files Additional file 1: Figure S1. Cni...