Open Access Highly Accessed Research article

Cnidarian phylogenetic relationships as revealed by mitogenomics

Ehsan Kayal12*, Béatrice Roure3, Hervé Philippe3, Allen G Collins4 and Dennis V Lavrov1

Author Affiliations

1 Dept. Ecology, Evolution, and Organismal Biology, Iowa State University, 50011, Ames, Iowa, USA

2 Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 20013-7012, Washington, DC, USA

3 Dept. Biochimie, Fac. Médecine, Université de Montral, Pavillon Roger-Gaudry, C.P. 6128, Succ. Centre-Ville, H3C 3J7, Montral, QC, Canada

4 National Systematics Laboratory of NOAA’s Fisheries Service, National Museum of Natural History, MRC-153, Smithsonian Institution, PO Box 37012, 20013-7012, Washington, DC, USA

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BMC Evolutionary Biology 2013, 13:5  doi:10.1186/1471-2148-13-5

Published: 9 January 2013

Additional files

Additional file 1:

Figure S1. Cnidarian phylogeny of mitochondrial protein genes using the reduced alignment AliMGred with 103 species. Phylogenetic analyses of cnidarian protein coding genes under the GTR model and CAT approximation with RAxML for the reduced AliMG alignment (AliMGred), where the coronate Linuche unguiculata, the tube anemone Ceriantheopsis americanus and the blue octocoral Heliopora coerulea were removed. Node supports correspond to the bootstraps values. Stars denote maximum support values. 1: Zoantharia; 2: Actiniaria; 3: Antipatharia; 4: Corallimorpharia; 5: Scleractinia; 6: Alcyonacea; 7: Pennatulacea; 8: Stauromedusae; 9: Carybdeida; 10: Chirodropida; 11: Limnomedusae; 12: Filifera III; 13: Filifera IV; 14: Leptothecata; 15: Capitata; 16: Aplanulata; 17: Semaeostomeae; 18: Rhizostomeae.

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Additional file 2:

Figure S2. Cnidarian phylogeny of mitochondrial protein genes using the codon alignment CodAliM75tx-argleuser3. Phylogenetic analyses of cnidarian protein coding genes under the QMM + Γ model with PhyloBayes for the CodAliM75tx-argleuser3 alignments (4785 parsimony-informative characters). Support values correspond to the posterior probabilities for the QMM, the GTR(BI) and bootstraps for GTR(ML) analyses, respectively. Stars denote support values of PP > 0.98 and BV > 95. A dash denotes discrepancy between the results obtained by different methods. 1: Zoantharia; 2: Actiniaria; 3: Antipatharia; 4: Corallimorpharia; 5: Scleractinia; 6: Alcyonacea; 7: Pennatulacea; 8: Stauromedusae; 9: Carybdeida; 10: Chirodropida; 11: Limnomedusae; 12: Filifera III; 13: Filifera IV; 14: Leptothecata; 15: Capitata; 16: Aplanulata; 17: Semaeostomeae; 18: Rhizostomeae; 19: Ceriantharia; 20: Helioporacea.

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Additional file 3:

Figure S3. Cnidarian phylogeny of mitochondrial protein genes using the codon alignment CodAliM75tx-ser3. Phylogenetic analyses of cnidarian protein coding genes under the QMM + Γ model with PhyloBayes for the CodAliM75tx-ser3 alignments (5318 parsimony-informative characters). Support values correspond to the posterior probabilities for QMM and GTR(BI) and bootstraps for GTR(ML) analyses, respectively. A star denotes support values of PP > 0.98 and BV > 95. A dash denotes discrepancy between the results obtained by different methods. 1: Zoantharia; 2: Actiniaria; 3: Antipatharia; 4: Corallimorpharia; 5: Scleractinia; 6: Alcyonacea; 7: Pennatulacea; 8: Stauromedusae; 9: Carybdeida; 10: Chirodropida; 11: Limnomedusae; 12: Filifera III; 13: Filifera IV; 14: Leptothecata; 15: Capitata; 16: Aplanulata; 17: Semaeostomeae; 18: Rhizostomeae; 19: Ceriantharia; 20: Helioporacea.

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Additional file 4:

Figure S4. The use of several statistical tests verifying the validity of some groups in cnidarians for the reduced alignment AliMGred. Probability values for the AU, KH and SH tests and BI values for several clades traditionally recognized in Cnidaria for the reduced alignment AliMGred containing 103 species, where the coronate Linuche unguiculata, the tube anemone Ceriantheopsis americanus and the blue octocoral Heliopora coerulea were removed.

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Additional file 5:

Figure S5. Composition of the amino acid alignment used in this study. Principal component analysis of the amino acid composition per species for the amino acid alignment AliMG used in this study. Species have been color-coded per group corresponding to each of the main cnidarian clades (Coronatae, Cubozoa, Discomedusa, Hexacorallia, Hydrozoa, Octocorallia, and Staurozoa), Porifera and Placozoa. The axes explain 33 and 22 per cent of the data.

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Additional file 6:

Figure S6. Alignment AliMG. Alignments AliMG (3485 positions, 106 taxa) created using the combination MUSCLE + Gblocks.

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Additional file 7:

Figure S7. Table of morphological characters mapped on the best tree. Mapping of morphological characters under DELTRAN and ACCTRAN models differed only for characters (5) and (7). (1) symmetry: medusozoan taxa have been scored radial, but Marques and Collins (2004) subdivided it into radial, biradial, or radial tetramerous; Octocorallia, Zoantharia and Ceriantharia are scored bilateral (Won et al. 2001), while the remnant of Hexacorallia was scored radial (Marques and Collins 2004); bilaterial symmetry is inferred the ancestral state for Cnidaira. (2) free-swimming medusoid stage: Hexa-, Octocorallia and Staurozoa all lack a free-living adult form (Marques and Collins 2004); the medusoid stage is also lacking in some Hydrozoa species but Collins (2002) and Cartwright and Nawrocki (2010) have inferred that the ancestral Hydrozoa had a medusoid stage. (3) velum: only present in Hydrozoa (Marques and Collins 2004). (4) strobilation: only described in Coronatae and Discomedusae (Marques and Collins 2004). (5) gastric filaments: we scored them as present in Cubozoa (Brigde et al. 1995), Staurozoa, Coronatae and Discomedusae (Marques and Collins 2004), and absent in Hydrozoa (Brigde et al. 1995), although suggested to be present in some Aplanulata (Bouillon et al. 2004); we decided to opt for the most parsimonious scenario. (6) ephyrae: only described in Coronatae and Discomedusae (Marques and Collins 2004). (7) radial canals: described in Coronatae, Discomedusae, and some Hydrozoa, absent in Staurozoa and unresolved in Cubozoa (Marques and Collins 2004); we choose two independent gains in Coronatae and Discomedusae as the most parsimonious scenario. (8) circular canals: present in Discomedusae and Hydrozoa, absent in the rest of Medusozoa. Marques and Collins (2004) have further distinguished the level of development of these structures that are partial in Discomedusae and full in Hydrozoa. (9) quadrate symmetry of horizontal cross section: present only in Cubozoa and Staurozoa (Marques and Collins 2004). (10) organization of the gastrodermal muscles of the polyp: organized in bunches of gastrodermic origin in all Hexacorallia but Ceriantharia, and inferred as the ancestral state for Cnidaria; organized in bunches of epidermic origin in all Medusozoa but Hydrozoa. In Hydrozoa and Ceriantharia, gastrodermal muscle are not organized in bunches (Marques and Collins 2004).

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