Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea)

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Voigt, Oliver ^a   Wülfing, Eilika ^a   Wörheide, Gert ^a,b  

^a UNIVERSITY OF MUNICH   (Germany)

^b BAYERISCHE STAATSSAMMLUNG FÜR PALÄONTOLOGIE UND GEOLOGIE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA;

ANIMAL TISSUE; ARTICLE; CALCAREA; CLADISTICS; DNA SEQUENCE; EVOLUTION; GENUS; MOLECULAR BIOLOGY; MORPHOLOGICAL TRAIT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES COMPOSITION; SPONGE (PORIFERA); TAXONOMY; ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; CHEMISTRY; CLASSIFICATION; GENETICS; HISTOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SPECIES DIFFERENCE;

AMPHORISCIDAE; CALCAREA; CALCARONEA; CALCINEA; CLATHRINIDA; GRANTIIDAE; HETEROPIIDAE; JENKINIDAE; LEUCALTIDAE; LEUCASCIDAE; LEUCETTA; LEUCETTIDA; LEUCETTIDAE; LEUCETTUSA; PORIFERA; SYCETTIDAE; SYCON; UTE;

ANIMALS; BAYES THEOREM; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PORIFERA; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 84858994985     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0033417     Document Type: Article

References (54)

1. Gavaze E, Lapébie P, Ereskovsky AV, Vacelet J, Renard E, et al. (2011) No longer Demospongiae: Homoscleromorpha formal nomination as a fourth class of Porifera. Hydrobiologia doi: 10.1007/s10750-011-0842-x.
2. Van Soest RWM, Boury-Esnault N, Hooper JNA, Rützler K, de Voogd NJ, et al. The World Porifera Database. Available: http://www.marinespecies.org/porifera. Accessed 2012 Feb 1.
3. Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, et al. (2009) Phylogenomics revives traditional views on deep animal relationships. Curr Biol 19: 706-712.
4. Pick KS, Philippe H, Schreiber F, Erpenbeck D, Jackson DJ, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27: 1983-1987.
5. Rapp HT, Janussen D, Tendal OS, (2011) Calcareous sponges from abyssal and bathyal depths in the Weddell Sea, Antarctica. Deep-Sea Res Pt Ii 58: 58-67.
6. Manuel M, Borchiellini C, Alivon E, Boury-Esnault N, (2004) Molecular phylogeny of calcareous sponges using 18S rRNA and 28S rRNA sequences. Boll Mus Ist Biol Univ Genova 68: 449-461.
7. Haeckel E, (1872) Die Kalkschwämme, Band 3: Atlas der Kalkschwämme (Calcispongien oder Grantien) Berlin Georg Reimer.
8. Haeckel E, (1872) Die Kalkschwämme, Band 1: Biologie der Kalkschwämme (Calcispongien oder Grantien). Georg Reimer.
9. Haeckel E, (1872) Die Kalkschwämme, Band 2: System der Kalkschwämme (Calcispongien oder Grantien) Berlin Georg Reimer.
10. Cavalcanti FF, Klautau M, (2011) Solenoid: a new aquiferous system to Porifera. Zoomorphology 130: 255-260.
11. Dohrmann M, Janussen D, Reitner J, Collins AG, Wörheide G, (2008) Phylogeny and evolution of glass sponges (Porifera, Hexactinellida). Syst Biol 57: 388-405.
12. Rossi AL, Farina M, Borojevic R, Klautau M, (2006) Occurrence of five-rayed spicules in a calcareous sponge: Sycon pentactinalis sp. nov. (Porifera: Calcarea). Cah Biol Mar 47: 261-270.
13. Manuel M, (2006) Phylogeny and evolution of calcareous sponges. Can J Zool 84: 225-241.
14. Bidder GP, (1898) The skeleton and classification of calcareous sponges. Proceedings of the Royal Society, London 6: 61-76.
15. Manuel M, Borojevic R, Boury-Esnault N, Vacelet J, (2002) Class Calcarea Bowerbank 1864. In: Hooper JNA, van Soest RWM, editors. Systema Porifera: A Guide to the Classification of Sponges New York Kluwer Academic/Plenum Publishers pp. 1103-1110.
16. Minchin EA, (1896) Suggestions for a Natural Classification of the Asconidae. Annals and Magazine of Natural History (6) 18: 349-362.
17. Hartman WD, (1958) A re-examination of Bidder's classification of the Calcarea. Syst Biol 7: 97-110.
18. Wörheide G, Hooper JNA, (1999) Calcarea from the Great Barrier Reef. 1: Cryptic Calcinea from Heron Island and Wistari Reef (Capricorn-Bunker Group). Mem Queensl Mus 43: 859-891.
19. Manuel M, Borchiellini C, Alivon E, Le Parco Y, Vacelet J, et al. (2003) Phylogeny and evolution of calcareous sponges: Monophyly of Calcinea and Calcaronea, high level of morphological homoplasy, and the primitive nature of axial symmetry. Syst Biol 52: 311-333.
20. Dohrmann M, Voigt O, Erpenbeck D, Wörheide G, (2006) Non-monophyly of most supraspecific taxa of calcareous sponges (Porifera, Calcarea) revealed by increased taxon sampling and partitioned Bayesian analysis of ribosomal DNA. Mol Phylogenet Evol 40: 830-843.
21. Vacelet J, (1961) The order Pharetronida in Hartman's classification of the Calcarea. Syst Zool 10: 45-47.
22. Vacelet J, (1981) Éponges hypercalcifées ('Pharétronides''Sclérosponges') des cavités des récifs coralliens de Nouvelle-Calédonie. Bull Mus Nat Hist Natur (Paris) 3: 313-351.
23. Borojevic R, Boury-Esnault N, Vacelet J, (1990) A revision of the supraspecific classification of the subclass Calcinea (Porifera, class Calcarea). Bull Mus Nat Hist Natur (Paris), Sec A 12: 243-276.
24. Borojevic R, Boury-Esnault N, Vacelet J, (2000) A revision of the supraspecific classification of the subclass Calcaronea (Porifera, class Calcarea). Zoosystema 22: 203-263.
25. Hooper JNA, van Soest RWM, (2002) Systema Porifera: a guide to the classification of sponges New York Kluwer Academic/Plenum Publishers.
26. Borojevic R, Boury-Esnault N, Manuel M, Vacelet J, (2002) Order Leucosolenida Hartman, 1958. In: Hooper JNA, Van Soest RWM, editors. Systema Porifera. A Guide to the Classification of Sponges New York Kluwer Academic/Plenum pp. 1157-1184.
27. Galtier N, Gouy M, Gautier C, (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12: 543-548.
28. Voigt O, Erpenbeck D, Wörheide G, (2008) Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera. BMC Evol Biol 8: 69.
29. Schnare MN, Damberger SH, Gray MW, Gutell RR, (1996) Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA. J Mol Biol 256: 701-719.
30. Jow H, Hudelot C, Rattray M, Higgs PG, (2002) Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol Biol Evol 19: 1591-1601.
31. Hudelot C, Gowri-Shankar V, Jow H, Rattray M, Higgs PG, (2003) RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences. Mol Phylogenet Evol 28: 241-252.
32. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
33. Wheeler WC, Honeycutt RL, (1988) Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. Mol Biol Evol 5: 90-96.
34. Hancock JM, Tautz D, Dover GA, (1988) Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster. Mol Biol Evol 5: 393-414.
35. Hillis DM, Dixon MT, (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol 66: 411-453.
36. Higgs PG, (2000) RNA secondary structure: physical and computational aspects. Q Rev Biophys 33: 199-253.
37. Savill NJ, Hoyle DC, Higgs PG, (2001) RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods. Genetics 157: 399-411.
38. Dixon MT, Hillis DM, (1993) Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Mol Biol Evol 10: 256-267.
39. Telford MJ, Wise MJ, Gowri-Shankar V, (2005) Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the Bilateria. Mol Biol Evol 22: 1129-1136.
40. Erpenbeck D, Nichols SA, Voigt O, Dohrmann M, Degnan BM, et al. (2007) Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches: Case studies with diploblast LSU. J Mol Evol 64: 543-557.
41. Schöniger M, von Haeseler A, (1994) A stochastic model for the evolution of autocorrelated DNA sequences. Mol Phylogenet Evol 3: 240-247.
42. Muse SV, (1995) Evolutionary analyses of DNA sequences subject to constraints on secondary structure. Genetics 139: 1429-1439.
43. Tillier ERM, Collins RA, (1995) Neighbor Joining and Maximum-Likelihood with RNA sequences- addressing the interdependence of sites. Biochem Syst Ecol 12: 7-15.
44. Tillier ERM, Collins RA, (1998) High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA. Genetics 148: 1993-2002.
45. Swofford DL, (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4 Sunderland, MA Sinauer Associates.
46. Maddison WP, Maddison DR, (2002) MacClade Sunderland, MA Sinauer Associates.
47. Shimodaira H, (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51: 492-508.
48. Shimodaira H, Hasegawa M, (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246-1247.
49. Rossi AL, De Moraes Russo CA, Solé-Cava AM, Rapp HT, Klautau M, (2011) Phylogenetic signal in the evolution of body colour and spicule skeleton in calcareous sponges. Zool J Linn Soc 163: 1026-1034.
50. Borojevic R, (1965) Éponges Calcaires des Côtes de France I. Amphiute paulini HANTISCH: les generes Amphiute HANITSCH et Paraheteropia n. gen. Arch Zool Exp Gen 106: 665-670.
51. Dendy A, (1893) Synopsis of the Australian Calcarea Heterocoela; with a proposed classification of the group and descriptions of some new genera and species. Proceedings of the Royal Society of Victoria 5: 69-116.
52. Borojevic R, Klautau M, (2000) Calcareous sponges from New Caledonia. Zoosystema 22: 187-201.
53. Klautau M, Valentine C, (2003) Revision of the genus Clathrina (Porifera, Calcarea). Zool J Linn Soc 139: 1-62.
54. Voigt O, Eichmann V, Wörheide G, (2011) First evaluation of mitochondrial DNA as a marker for phylogeographic studies of Calcarea: a case study from Leucetta chagosensis. Hydrobiologia doi: 10.1007/s10750-011-0800-7.