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PLOS ONE  2012 

Molecular Phylogenetic Evaluation of Classification and Scenarios of Character Evolution in Calcareous Sponges (Porifera, Class Calcarea)

DOI: 10.1371/journal.pone.0033417

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Abstract:

Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a thorough revision, which cannot be achieved by considering morphology alone or relying on a taxon sampling based on the current classification below the subclass level.

References

[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 Kalkschw?mme, Band 3: Atlas der Kalkschw?mme (Calcispongien oder Grantien). Berlin: Georg Reimer.
[8]  Haeckel E (1872) Die Kalkschw?mme, Band 1: Biologie der Kalkschw?mme (Calcispongien oder Grantien). 484 p. Georg Reimer.
[9]  Haeckel E (1872) Die Kalkschw?mme, Band 2: System der Kalkschw?mme (Calcispongien oder Grantien). Berlin: Georg Reimer. 416 p.
[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, W?rheide 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]  W?rheide 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, W?rheide 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. 1810 p.
[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, W?rheide 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]  Sch?niger 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 C?tes 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, W?rheide 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.

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