Molecular phylogenies support homoplasy of multiple morphological characters used in the taxonomy of heteroscleromorpha (Porifera: Demospongiae)

Integrative and Comparative Biology

Volumn 53, Issue 3, 2013, Pages 428-446

  Morrow, Christine C ^a   Redmond, Niamh E ^b   Picton, Bernard E ^c   Thacker, Robert W ^d   Collins, Allen G ^b   Maggs, Christine A ^a   Sigwart, Julia D ^a   Allcock, A Louise ^e  

^a QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^b DEPARTMENT OF PALEOBIOLOGY   (United States)

^c Department of Geology   (United Kingdom)

^d UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^e NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; PRIMER DNA; RNA 18S; RNA 28S;

ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; CONFERENCE PAPER; DNA SEQUENCE; GENETICS; HISTOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; SPONGE (PORIFERA); STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; DNA PRIMERS; ELECTRON TRANSPORT COMPLEX IV; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PORIFERA; RNA, RIBOSOMAL, 18S; RNA, RIBOSOMAL, 28S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 84882979436     PISSN: 15407063     EISSN: 15577023     Source Type: Journal    
DOI: 10.1093/icb/ict065     Document Type: Conference Paper

References (71)

1. Bergquist PR. 1967. Additions to the Sponge Fauna of the Hawaiian Islands. Micronesica 3:159-74.
2. Bergquist PR. 1970. The Marine Fauna of New Zealand: Porifera Demospongiae, Part 2 (Axinellida and Halichondrida). NZ Dept Sci Ind Res Bull [NZ Oceanogr Inst Mem 51] 197:1-85.
3. Bergquist PR. 1978. Sponges. London, UK: Hutchinson.
4. Borchiellini C, Chombard C, Manuel M, Alivon E, Vacelet J, Boury-Esnault N. 2004. Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution. Mol Phylogenet Evol 32:823-37.
5. Boury-Esnault N. 2006. Systematics and evolution of Demospongiae. Can J Zool 84:205-24.
6. Cárdenas P. 2010. Phylogeny, Taxonomy and Evolution of the Astrophorida (Porifera, Demospongiae). PhD Thesis, University of Bergen, Norway.
7. Cardenas P, Pérez T, Boury-Esnault N. 2012. Sponge systematics facing new challenges. Adv Mar Biol 61:79-209.
8. Cárdenas P, Xavier JR, Reveillaud J, Schander C, Rapp HT. 2011. Molecular Phylogeny of the Astrophorida (Porifera, Demospongiaep) Reveals an Unexpected High Level of Spicule Homoplasy. PLoS ONE 6(4):e18318. doi:10.1371/journal.pone.0018318.
9. Cedro VR, Hajdu E, Correia MD. Forthcoming. Three new intertidal sponges (Porifera Demospongiae) from Brazil's fringing urban reefs (Maceió Alagoas Brazil), and support for Rhabderemia's exclusion from Poecilosclerida. J Nat Hist.
10. Chombard C, Boury-Esnault N, Tillier S. 1998. Reassessment of homology of morphological characters in tetractinellid sponges based on molecular data. Syst Biol 47:351-66.
11. Chombard C, Boury-Esnault N, Tiller S, Vacelet J. 1997. Polyphyly of "sclerosponges" (Porifera Demospongiae) supported by 28S ribosomal sequences. Biol Bull 193:359-67.
12. Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models new heuristics and parallel computing. Nat Methods 9:772.
13. De Weerdt WH. 1989. Phylogeny and vicariance biogeography of North Atlantic Chalinidae (Haplosclerida Demospongiae). Beaufortia 39:55-90.
14. Drummond AJ, Ashton B, Cheung M, Heled J, Kearse M, Moir R, Stones-Havas S, Thierer T, Wilson A. 2009. Geneious Pro v47. (http://wwwgeneiouscom/).
15. Edgar RC. 2004a. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-7.
16. Edgar RC. 2004b. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.
17. Erpenbeck D, Hooper JNA, Wörheide G. 2006. CO1 phylogenies in diploblasts and the 'Barcoding of Life'-are we sequencing a suboptimal partition? Mol Ecol Notes 6:550-3.
18. Erpenbeck D, Cleary DFR, Voigt O, Nichols SA, Degnan BM, Hooper JNA, Wörheide G. 2007a. Analysis of evolutionary biogeographical and taxonomic patterns of nucleotide composition in demosponge rRNA. J Mar Biol Assoc UK 87:1607-14.
19. Erpenbeck D, Duran S, Rützler K, Paul V, Hooper JNA, Wörheide G. 2007b. 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 Assoc UK 87:1563-70.
20. Erpenbeck D, Hall K, Alvarez B, Büttner G, Sacher K, Schätzle S, Schuster A, Vargas S, Hooper JNA, Wörheide G. 2012. The phylogeny of halichondrid demosponges: past and present re-visited with DNA-barcoding data. Org Divers Evol 12:57-70.
21. Erpenbeck D, Hooper JNA, List-Armitage SE, Degnan BM, Wörheide G, van Soest RWM. 2007c. Affinities of the family Sollasellidae (Porifera Demospongiae): II Molecular evidence. Contrib Zool 76:95-102.
22. 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 32:388-95.
23. Fromont JP, Bergquist PR. 1990. Structural characters and their use in sponge taxonomy; when is a sigma not a sigma? In: Rützler K, editor. New perspectives in sponge biology. Washington (DC): Smithsonian Institution Press. p. 273-8.
24. Gazave E, Lapébie P, Renard E, Vacelet J, Rocher C, Ereskovsky A, Lavrov D, Borchiellini C. 2010a. Molecular Phylogeny restores the supra-generic subdivision of Homoscleromorph sponges (Porifera, Homoscleromorpha). PLoS One 5:e14290.
25. Gazave E, Carteron S, Chenuil A, Richelle-Maurer E, Boury-Esnault N, Borchiellini C. 2010b. Polyphyly of the genus Axinella and of the family Axinellidae (Porifera: Demospongiaep). Mol Phylogenet Evol 57:35-47.
26. Graybeal A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol 47:9-17.
27. Hajdu E, van Soest RWM. 2002. Family Desmacellidae Ridley & Dendy 1886. In: Hooper JNA, van Soest RWM, editors. Systema Porifera. A guide to the classification of sponges. New York: Kluwer Academic/Plenum Publishers.
28. Hallmann EF. 1917. A revision of the genera with microscleres included or provisionally included in the family Axinellidae; with descriptions of some Australian species Part III. Proc Linn Soc NSW 41:634-75.
29. Hartman WD. 1982. Porifera. In: Parker SP, editor. Synopsis and classification of living organisms. Vol. 1. New York: McGraw-Hill. p. 640-66.
30. Hentschel E. 1923. Erste Unterabteilung der Metazoa: Parazoa Porifera-Schwämme. In: Kükenthal W, Krumbach T, editors. Handbuch der Zoologie Eine Naturgeschichteder Stämme des Tierreiches Vol 1 Protozoa Porifera Coelenterata Mesozoa. Berlin and Leipzig: Walter de Gruyter und Co. p. 307-418.
31. Hill MS, Hill AL, Lopez J, Peterson KJ, Pomponi S, Diaz MC, Thacker RW, Adamska M, BouryEsnault N, Cárdenas P, et al. 2013. Reconstruction of family-level phylogenetic relationships within Demospongiae (Porifera) using nuclear encoded housekeeping genes. PLoS One 8:e50437.
32. Holmes B, Blanch H. 2007. Genus-specific associations of marine sponges with group I crenarchaeotes. Mar Biol 150:759-72.
33. Hooper JNA. 1984. Sigmaxinella soelae and Desmacella ithystela, two new desmacellid sponges (Porifera Axinellida Desmacellidae) from the Northwest Shelf of Western Australia with a revision of the family Desmacellidae. North Territ Mus Arts Sci Mon Ser 2:1-58.
34. Hooper JNA. 1990a. Character stability systematics and affinities between Microcionidae (Poecilosclerida) and Axinellida. In: Rützler K, editor. New perspectives in sponge biology. Washington (DC): Smithsonian Institution Press. p. 284-94.
35. Hooper JNA. 1990b. A new species of Rhabderemia Topsent (Porifera: Demospongiae) from the Great Barrier Reef. The Beagle, Records of the North Territ Mus Arts Sci 7, 1: 65-78.
36. Hooper JNA. 2002. Family Rhabderemiidae Topsent 1928. In: Hooper JNA, van Soest RWM, editors. Systema Porifera. A guide to the classification of sponges. New York: Kluwer Academic/Plenum Publishers.
37. Hooper JNA. 1991. Revision of the family Raspailiidae (Porifera: Demospongiae) with description of Australian species. Invertebr Taxon 5:1179-418.
38. Hooper JNA, van Soest RWM. 2002. Systema Porifera. A guide to the classification of sponges. New York: Kluwer Academic/Plenum Publishers.
39. Jenner RA. 2004. When molecules and morphology clash: reconciling conflicting phylogenies of the Metazoa by considering secondary character loss. Evol Dev 6:372-8.
40. Kott P. 2004. New and little-known species of Didemnidae (Ascidiacea, Tunicata) from Australia (part I). J Nat Hist 38:2455-526.
41. Lafay B, Boury-Esnault N, Vacelet J, Christen R. 1992. An analysis of partial 28S ribosomal RNA sequences suggests early radiation of sponges. BioSystems 28:139-51.
42. Lavrov DV, Wang X, Kelly M. 2008. Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data. Mol Phylogenet Evol 49:111-24.
43. Lévi C. 1953. Sur une nouvelle classification des Démosponges. Compt Rend Hebdom Séan Acad Sci Paris 236:853-5.
44. Lévi C. 1955. Les Clavaxinellides, Démosponges Tétractinomorphes. Arch Zool exp et gén 92 (Notes et Revue 2):78-87.
45. Lévi C. 1956. E ́ tude des Halisarca de Roscoff. Embryologie et systématiquedes démosponges. Arch Zool exp et gén 93:1-181.
46. Lévi C. 1957. Ontogeny and systematics in sponges. Syst Zool 6:174-83.
47. Lévi C. 1973. Systématique de la classe des Demospongiaria (Démosponges). In: Grassé P-P, editor. Traité de Zoologie Vol. 3 Spongiaires. Paris: Masson et Cie. p. 577-632.
48. Morrow CC, Picton BE, Erpenbeck D, Boury-Esnault N, Maggs CA, Allcock AL. 2012. Congruence between nuclear and mitochondrial genes in Demospongiae: a new hypothesis for relationships within the G4 clade (Porifera: Demospongiae). Mol Phylogenet Evol 62:174-90.
49. 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.
50. Redmond NE, Morrow CC, Thacker RW, Diaz MC, Boury-Esnault N, Cárdenas P, Hajdu E, Lôbo-Hajdu G, Picton BE, Collins AG. 2013. Phylogeny and systematics of Demospongiae in light of new small subunit ribosomal DNA sequences. Integr Comp Biol 53:388-415.
51. Ridley SO, Dendy A. 1887. Report on the Monaxonida collected by HMS 'Challenger' during the years 1873-1876 Report on the Scientific Results of the Voyage of HMS 'Challenger' 1873-6. Zoology 20:i-lxviii. 1-275 pls I-LI, 1 map.
52. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-4.
53. Sperling EA, Peterson KJ, Pisani D. 2009. Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Mol Biol Evol 26:2261-74.
54. Sperling EA, Robinson JM, Pisani D, Peterson KJ. 2010. Where's the Glass? Biomarkers molecular clocks and microRNAs suggest a 200 million year missing precambrian fossil record of siliceous sponge spicules. Geobiology 8:24-36.
55. Stamatakis A, Hoover P J, Rougemont A. 2008. Rapid Bootstrap Algorithm for the RAxML Web-Servers. Syst Biol 75:758-71.
56. Thacker RW, Hill A, Hill M, Redmond N, Collins AG, Morrow CC, Spicer L, Carmack CA, Zappe M, Bangalore P. 2013. Nearly complete 28S rRNA gene sequences confirm new hypotheses of sponge evolution. Integr Comp Biol. 53:373-87.
57. Topsent E. 1897. Sur le genre Halicnemia Bowerbank. Mém Soc Zool France 10:235-51.
58. Uriz MJ. 1988. Deep-water sponges from the continental shelf and slope off Namibia (Southwest Africa): Classses Hexactinellida and Demospongia. Monograf́as de Zooloǵa Marina 3:9-157.
59. van Soest RWM. 1984a. Deficient Merlia normani Kirkpatrick 1908 from the Curaçao reefs with a discussion on the phylogenetic interpretation of sclerosponges. Bijdr Dierkd 54:211-9.
60. van Soest RWM. 1984b. Marine sponges from Curaçao and other Caribbean localities. Part III. Poecilosclerida. In: Hummelinck PW, van der Steen LJ, editors. Uitgaven van de Natuurwetenschappelijke Studiekring voor Suriname en de Nederlandse Antillen. No. 112. Studies on the Fauna of Curaçao and other Caribbean Islands 62:1-173.
61. van Soest RWM. 1987. Phylogenetic exercises with monophyletic groups of sponges. p 227-41.
62. In: Vacelet J, Boury-Esnault N, editors. Taxonomy of Porifera from the NE Atlantic and Mediterranean Sea NATO ASI Series G13. Berlin Heidelberg: Springer Verlag p. 332.
63. van Soest RWM. 1990. Toward a phylogenetic classification of sponges. In: Rützler K, editor. New perspectives in sponge biology. Washington (DC): Smithsonian Institution. p. 344-8.
64. van Soest RWM. 1991. Demosponge higher taxa classification re-examined. In: Reitner J, Keupp H, editors. Fossil and recent sponges. Berlin, Heidelberg: Springer Verlag. p. 54-71.
65. van Soest RWM, Boury-Esnault N, Hooper JNA, Rützler K, de Voogd NJ, Alvarez de Glasby B, Hajdu E, Pisera AB, Manconi R, Schoenberg C, et al. 2013. World Porifera database. (http://www.marinespeciesorg/porifera) on January 20, 2013.
66. van Soest RWM, Diaz MC, Pomponi SA. 1990. Phylogenetic classification of the halichondrids (Porifera Demospongiae). Beaufortia 40:15-62.
67. van Soest RWM, Hooper JNA. 1993. Taxonomy phylogeny and biogeography of the marine sponge genus Rhabderemia Topsent, 1890 (Demospongiae Poecilosclerida). In: Uriz M-J, Rützler K, editors. Recent advances in ecology and systematics of sponges. Sci Mar 57:319-51.
68. Vosmaer GCJ. 1912. On the Distinction between the genera Axinella, Phakellia, Acanthella a.o. Zool Jahrb Jena Suppl 15:307-22. pls 15-16.
69. Wiens JJ. 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst Biol 47:625-40.
70. Wilson HV. 1921. The genus Raspailia and the independent variability of diagnostic features. J Elisha Mitchell Sci Soc 37:54-60.
71. Wörheide G, Erpenbeck D, Menke C. 2007. The Sponge Barcoding Project-aiding in the identification and description of poriferan taxa. In: Custó dio MR, Lôbo-Hajdu G, Hajdu E, Muricy G, editors. Porifera Research: Biodiversity, Innovation & Sustainability. Museu Nacional, Série livros 28, Rio de Janeiro. pp. 123-8.