Phylogenetic relationships of the marine Haplosclerida (Phylum Porifera) employing ribosomal (28s rRNA) and mitochondrial (cox1, nad1) gene sequence data

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Redmond, Niamh E ^a,b   Raleigh, Jean ^b   van Soest, Rob W M ^c   Kelly, Michelle ^d   Travers, Simon A A ^e   Bradshaw, Brian ^b   Vartia, Salla ^b   Stephens, Kelly M ^b   McCormack, Grace P ^b  

^a DEPARTMENT OF PALEOBIOLOGY   (United States)

^b NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

^d NATIONAL INSTITUTE OF WATER AND ATMOSPHERIC RESEARCH   (New Zealand)

^e UNIVERSITY OF THE WESTERN CAPE   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA 28S; CYTOCHROME C OXIDASE;

AMPHIMEDON QUEENSLANDICA; ARTICLE; BAYES THEOREM; CALLYSPONGIA; COX1 GENE; DNA SEQUENCE; GENE SEQUENCE; HALICLONA; HAPLOSCLERIDA; HAPLOSCLERIDA SIMULANS; HAPLOSCLERIDA VANSOESTI; MAXIMUM LIKELIHOOD METHOD; MITOCHONDRIAL GENE; NAD1 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPONGE (PORIFERA); TABULOCALYX; ANIMAL; AQUATIC SPECIES; CLASSIFICATION; ENZYMOLOGY; GENETICS; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; STATISTICAL MODEL;

AKA (SPONGE); AMPHIMEDON; CALLYSPONGIA; CHALINIDAE; DEMOSPONGIAE; HALICLONA; HALICLONA SIMULANS; HALICLONA VANSOESTI; HAPLOSCLERIDA; NIPHATIDAE; PETROSIIDAE; PHLOEODICTYIDAE; PORIFERA;

ANIMALS; AQUATIC ORGANISMS; BASE SEQUENCE; DATABASES, NUCLEIC ACID; ELECTRON TRANSPORT COMPLEX IV; GENES, MITOCHONDRIAL; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PORIFERA; RNA, RIBOSOMAL, 28S; SEQUENCE ANALYSIS, DNA;

EID: 80052737210     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024344     Document Type: Article

References (61)

1. de Weerdt WH, (1985) A systematic revision of the North Eastern Atlantic shallow-water Haplosclerida (Porifera, Demospongiae), Part I: Introduction, Oceanapiidae and Petrosiidae. Beaufortia 35: 61-91.
2. van Soest RWM, Hooper JNA, (2002a) Order Haplosclerida Topsent 1928. In: Hooper JNA, van Soest RWM, editors. Systema Porifera: A Guide to the Classification of Sponges New York Kluwer Academic/Plenum Publishers pp. 831-832.
3. Liu H F, Mishima Y, Fujiwara T, Nagai H, Kitazawa A, et al. (2004) Isolation of araguspongine M, a new stereoisomer of an araguspongine/xestospongin alkaloid, and dopamine from the marine sponge Neopetrosia exigua collected in Palau. Mar Drugs 2: 154-163.
4. Erickson KL, Beutler JA, Cardellina IJ, Boyd MR, (1997) Salicylihalamides A and B, Novel Cytotoxic Macrolides from the Marine Sponge Haliclona sp. J Org Chem 62: 8188-8192.
5. Borchiellini C, Chombard C, Manuel M, Alivon E, Vacelet J, et al. (2004) Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution. Mol Phylogenet Evol 32: 823-837.
6. Topsent, E, (1928) Spongiaires de l′Atlantique et de la Méditerranée proveenant des croisiéres de Prince Albert ler de Monaco. Rés Camp Sci Prince Albert ler Monaco 74: 1-376.
7. Boury-Esnault N, van Beveren M, (1982) Les Démosponges du plateau continental de Kerguelen-Heard. Comité National Francais des Recherches Antarctiques 52: 1-75.
8. Manconi R, Pronzato R, (2002) Suborder Spongillina subord. Nov.: Freshwater Sponges. In: Hooper JNA, van Soest RWM, editors. Systema Porifera: A Guide to the Classification of Sponges New York Kluwer Academic/Plenum Publishers pp. 921-927.
9. Nichols SA, (2005) An evaluation of support for order level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I. Mol Phylogenet Evol 34: 81-96.
10. Redmond NE, van Soest RWM, Kelly M, Raleigh J, Travers SAA, McCormack GP, (2007) Reassessment of the classification of the Order Haplosclerida (Class Demospongiae, Phylum Porifera) using 18S rRNA gene sequence data. Mol Phylogenet Evol 43: 344-352.
11. Itskovich VB, Belikov SI, Efremova SM, Masuda Y, Perez T, et al. (2007) Phylogenetic relationships between freshwater and marine Haplosclerida (Porifera, Demospongiae) based on full length 18S rRNA and partial COXI gene sequences. In: Custódio MR, Lôbo-Hadju G, Hajdu Muricy G, editors. Porifera Research: Biodiversity, Innovation and Sustainability Série Livros. Museu Nacional, Rio de Janeiro pp. 1-9.
12. Lavrov DV, Wang X, Kelly M, (2008) Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data. Mol Phylogenet Evol 49: 111-124.
13. 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.
14. Sperling E, Petersen K, Pisani D, (2009) Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa. Mol Biol Evol 26: 2261-2274.
15. Lévi C, (1956) Etude des Halisarca de Roscoff. Embryologie et systématique des démosponges. Arch Zool Exp Gen 93: 1-184.
16. Griessinger JM, (1971) Etude des Renierides de Mediterranee (demosponges, haplsocerides). Bull Museum National d'Histoire Naturelle, Paris (Zoologie) 3: 97-182.
17. Weidenmayer F (1977) A monograph of the shallow-water sponges of the western Bahamas. Basel and Stuttgart Birkhauser Verlag pp. 78-126.
18. Bergquist P, Warne K, (1980) The marine fauna of New Zealand. Porifera, Demospongiae part 3 (Haplosclerida and Nephilospongida). New Zealand Oceanographical Institute Memoirs 87: 1-78.
19. van Soest RWM, (1980) Marine sponges from Curacao and other Caribbean localities. Part II Haplosclerida. Studies on the fauna of Curacao and other Caribbean islands 62: 1-173.
20. de Weerdt WH, (1989) Phylogeny and vicariance biogeography of North Atlantic Chalinidae (Haplosclerida: Demospongiae). Beaufortia 39: 55-88.
21. van Soest RWM, Hooper JNA, (2002b) Suborder Haplosclerina Topsent 1928. In: Hooper JNA, van Soest RWM, editors. Systema Porifera: A Guide to the Classification of Sponges New York Kluwer Academic/Plenum Publishers pp. 833-834.
22. van Soest RWM, Hooper JNA, (2002c) Suborder Petrosina Boury-Esnault and van Beveren, 1982. In: Hooper JNA, van Soest RWM, editors. Systema Porifera: A Guide to the Classification of Sponges New York Kluwer Academic/Plenum Publishers pp. 891-892.
23. van Soest RWM, Braekman JC, (1999) Chemosystematics of Porifera: a review. Mem Queensl Mus 44: 569-589.
24. Raleigh J, Redmond NE, Delehan E, Torpey S, van Soest RWM, et al. (2007) Mitochondrial cytochrome oxidase 1 phylogeny supports alternative taxonomic scheme for marine Haplosclerida. J Mar Biol Ass UK 87: 1577-1584.
25. de Laubenfels MW, (1936) A discussion of the sponge fauna of the dry Tortugas in particular and the West Indies in general, with material for a revision of the families and orders of the Porifera. 30 Carnegie Institute of Washington (Tortugas Laboratory paper No.467): 1-225.
26. Desqueyroux-Faúndez, R, Valentine C, (2002) Family Phloeodictyidae Carter, 1882. In: Hooper JNA, van Soest RWM, editors. Systema Porifera: A Guide to the Classification of Sponges New York Kluwer Academic/Plenum Publishers pp. 893-905.
27. Gray, E J, (1867) Notes on the arrangement of sponges, with the description of some new genera. Proc Zoo Soc Lond pp. 492-558.
28. von Lendenfeld R, (1887) Die Chalineen des australischen Gebietes. Zoologische Jahrbucher 2: 723-828.
29. de Weerdt WH, (1986) A Systematic Revision of the North-Eastern Atlantic Shallow-Water Haploslcerida (Porifera, Demospongiae), Part II: Chalinidae. Beaufortia 36: 81-165.
30. de Weerdt WH, (2002) Family Chalinidae Gray, 1867. In: Hooper JNA, van Soest RWM, editors. Systema Porifera: A Guide to the Classification of Sponges New York Kluwer Academic/Plenum Publishers pp. 852-873.
31. Erpenbeck D, Breeuwer JAJ, Parra-Velandia FJ, van Soest RWM, (2006) Speciation with spiculation?-Three independent gene fragments and biochemical characters versus morphology in Demosponge higher classification. Mol Phylogenet Evol 38: 293-305.
32. Redmond NE, McCormack, (2009) Ribosomal internal transcribed spacer regions are not suitable for intra- and inter-specific reconstruction in haplosclerid sponges. J Mar Biol Ass UK 89 (6): 1251-1256.
33. Erpenbeck D, McCormack GP, Breeuwer JAJ, van Soest RWM, (2004) Order level differences in the structure of partial LSU across demosponges (Porifera): new insights into an old taxon. Mol Phylogenet Evol 32: 388-395.
34. Redmond NE, McCormack GP, (2008) Large expansion segments in 18S rDNA support a new sponge clade (Class Demospongiae, Order Haplosclerida). Mol Phylogenet Evol 47: 1090-1099.
35. Erpenbeck D, Wörheide G, (2007) On the molecular phylogeny of sponges (Porifera). Zootaxa 1668: 107-126.
36. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R, (1994) DNA primers for amplification of mitochondrial cytochrome C oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotech 3: 294-299.
37. Wang X, Lavrov D, (2008) Seventeen New Complete mtDNA Sequences Reveal Extensive Mitochondrial Genome Evolution within the Demospongiae. PLoS One 3 (7): e2723.
38. Fredslund J, Schauser L, Madsen LH, Sandal N, Stougaard J, (2005) PriFi: using multiple alignment of related sequences to find primers for amplification of homologs. Nucl Acids Res 33 (suppl 2): W516-520.
39. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Evol 215: 403-410.
40. Maddison WP, Maddison DR, (1998) MacClade, Version 4.03. Sinauer Associates.
41. Stamatakis A, (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
42. Posada D, (2008) jModelTest: Phylogenetic Model Averaging. Mol Biol Evol 25: 1253-1256.
43. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
44. Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17: 754-755.
45. Ronquist F, Huelsenbeck JP, (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
46. Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F, (2004) Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407-415.
47. Erpenbeck D, Duran S, Rützler, K, Paul V, Hooper JNA, et al. (2007a) Towards a DNA taxonomy of Caribbean demosponges: a gene tree reconstructed from partial mitochondrial CO1 gene sequences supports previous rDNA phylogenies and provides a new perspective on the systematics of Demospongiae. J Mar Biol Ass UK 87: 1563-1570.
48. López-Legentil S, Erwin PM, Henkel TP, Loh TL, Pawlik JR, (2010) Phenotypic plasticity in the Caribbean sponge Callyspongia vaginalis (Porifera: Haplosclerida). Scientia Marina 74 (3): 445-453.
49. Harcet M, Bilandzija H, Bruvo-Madaric B, Cetkovic H, (2010) Taxonomic position of Eunapius subterraneus (Porifera, Spongillidae) inferred from molecular data- A revised classification needed? Mol Phylogenet Evol 54 (3): 1021-1027.
50. Rot C, Goldfarb I, Ilan M, Huchon D, (2006) Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria. BMC Evolutionary Biology 6: 71.
51. DeBiasse MB, Richards VP, Shivji MS, (2010) Genetic assessment of connectivity in the common reef sponge, Callyspongia vaginalis (Demospongiae: Haplosclerida) reveals high population structure along the Florida reef tract. Coral Reefs 29: 47-55.
52. Becking LE, Nakao Y, de Voogd NJ, van Soest RWM, Fusetani N, et al. (2007) Perplexing distribution of 3-alkylpyridines in haplosclerid sponges. In: Custódio MR, Lôbo-Hadju G, Hajdu Muricy G, editors. Porifera Research: Biodiversity, Innovation and Sustainability Rio de Janeiro Série Livros. Museu Nacional pp. 173-178.
53. Erpenbeck D, van Soest RWM, (2007c) Status and perspective of sponge chemosystematics. Mar Biotech 9 (1): 2-19.
54. Urban S, Hickford SJH, Blunt JW, Munro MHG, (2000) Distribution of the pyrroloquinolines (M Kelly), Bioactive Marine Alkaloids. Curr Org Chem 4: 793-795.
55. Hu, JF, Hamann, MT, Hill R, Kelly M, (2003) The manzamine alkaloids. The Alkaloids: Chemistry and Biology 60: 207-285.
56. Fromont J, Kerr S, Kerr R, Riddle M, Murphy P, (1994) Chemotaxonomic relationships within, and comparisons between, the Orders Haplosclerida and Petrosida (Porifera: Demospongiae) using sterol complements. Biochem Syst Ecol 22: 735-752.
57. van Soest RWM, Fusetani N, Andersen RJ, (1998) Straight-chain acetylenes as chemosystematic markers of marine Haplosclerida. In: Watanabe Y, Fuseani, editors. Sponge Sciences- Multidisciplinary Perspectives Tokyo Springer pp. 3-30.
58. Bergquist PR, Sinclair ME, Green CR, Silyn-Roberts H, (1979) Comparative morphology and behaviour of larvae of Demospongiae. Colloques int Cent Nant Rech Scient 191: 103-111.
59. McCormack GP, Erpenbeck D, van Soest RWM, (2002) Major discrepancy between phylogenetic hypotheses based on molecular and morphological criteria within the Order Haplosclerida (Phylum Porifera: Class Demospongiae). J Zool Syst Evol Res 40: 237-240.
60. Erpenbeck D, Voigt O, Adamski M, Adamska M, Hooper JNA, et al. (2007b) Mitochondrial diversity of early-branching metazoa is revealed by the complete mt genome of a haplosclerid demosponge. Mol Biol Evol 24: 19-22.
61. Telford MJ, (2004) Animal Phylogeny: Back to the Coelomata. Curr Biol 14 (7): R274-R276.