Nearly complete 28S rRNA gene sequences confirm new hypotheses of sponge evolution

Integrative and Comparative Biology

Volumn 53, Issue 3, 2013, Pages 373-387

  Thacker, Robert W ^a   Hill, April L ^b   Hill, Malcolm S ^b   Redmond, Niamh E ^c   Collins, Allen G ^c   Morrow, Christine C ^d   Spicer, Lori ^b   Carmack, Cheryl A ^a   Zappe, Megan E ^a   Pohlmann, Deborah ^b   Hall, Chelsea ^b   Diaz, Maria C ^e   Bangalore, Purushotham V ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b UNIVERSITY OF RICHMOND   (United States)

^c DEPARTMENT OF PALEOBIOLOGY   (United States)

^d QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^e Museo Marino de Margarita   (Venezuela)

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER DNA; RNA 28S;

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

ANIMALS; BASE SEQUENCE; BAYES THEOREM; DNA PRIMERS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PANAMA; PHYLOGENY; PORIFERA; RNA, RIBOSOMAL, 28S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 84883031727     PISSN: 15407063     EISSN: 15577023     Source Type: Journal    
DOI: 10.1093/icb/ict071     Document Type: Conference Paper

References (29)

1. Bergquist PR, Cook SDC. 2002. Order Halisarcida Bergquist, 1996. In: Hooper JNA, Van Soest RWM, editors. Systema Porifera. New York, USA: Kluwer. p. 1077.
2. Borchiellini C, Chombard C, Lafay B, Boury-Esnault N. 2000. Molecular systematics of sponges (Porifera). Hydrobiology 420:15-27.
3. Boury-Esnault N, Rutzler K. 1997. Thesaurus of sponge morphology. Washington (DC): Smithsonian Institution Press.
4. Cárdenas P, Pérez T, Boury-Esnault N. 2012. Sponge systematics facing new challenges. Adv Mar Biol 61:79-209.
5. Diaz MC, Thacker RW, Redmond NE, Matterson KO, Collins AG. 2013. Phylogenetic novelties and geographic anomalies among tropical Verongida. Integr Comp Biol 53:482-94.
6. Gazave E, Carteron S, Chenuil A, Richelle-Maurer E, Boury-Esnault N, Borchiellini C. 2010. Polyphyly of the genus Axinella and of the family Axinellidae (Porifera: Demospongiaep). Mol Phyl Evol 57:35-47.
7. Hill MS, Hill AL, Lopez J, Peterson KJ, Pomponi S, Diaz MC, Thacker RW, Adamska M, Boury-Esnault N, Cárdenas P, et al. 2013. Reconstruction of family-level phylogenetic relationships within Demospongiae (Porifera) using nuclear encoded housekeeping genes. PLoS ONE 8:e50437.
8. Hooper JNA, Lévi C. 1994. Biogeography of Indo-west Pacific sponges: Microcionidae, Raspailiidae, Axinellidae. In: Van Soest RWM, van Kempen ThMG, Braekman JC, editors. Sponges in time and space. Rotterdam, Netherlands: Balkema. p. 191-212.
9. Hooper JNA, Van Soest RWM, editors. 2002. Systema Porifera. New York, USA: Kluwer.
10. Katoh K, Toh H. 2008. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics 9:212.
11. Kober KM, Nichols SA. 2007. On the phylogenetic relationships of hadromerid and poecilosclerid sponges. J Mar Biol Ass UK 87:1585-98.
12. Lartillot N, Lepage T, Blanquart S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25:2286-8.
13. Leal MC, Puga J, Serôdio J, Gomes NCM, Calado R. 2012. Trends in the discovery of new marine natural products from invertebrates over the last two decades-where and what are we bioprospecting? PLoS ONE 7:e30580.
14. Medina M, Collins AG, Silberman JD, Sogin ML. 2001. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc Natl Acad Sci USA 98:9707-12.
15. 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 Phyl Evol 62:174-90.
16. Morrow CC, Redmond NE, Picton BE, Thacker RW, Collins AG, Maggs CA, Sigwart JD, Allcock AL. 2013. Molecular phylogenies support homoplasy of multiple morphological characters used in the taxonomy of Heteroscleromorpha (Porifera: Demospongiae). Integr Comp Biol 53:428-46.
17. 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 Phyl Evol 34:81-96.
18. Olson PD, Cribb TH, Tkach VV, Bray RA, Littlewood DTJ. 2003. Phylogeny and classification of the Digenea (Platyhelminthes: Trematoda). Intl J Parasitol 33:733-55.
19. Redmond NE, McCormack GP. 2008. Large expansion segments in 18S rDNA support a new sponge clade (Class Demospongiae, Order Haplosclerida). Mol Phylogenet Evol 47:1090-9.
20. Redmond NE, Morrow C, Thacker RW, Diaz MC, Boury-Esnault N, Cárdenas P, Hajdu E, Lobo Hajdu G, Picton B, et al. 2013. Phylogeny and systematics of Demospongiae in light of new small subunit ribosomal DNA sequences. Integr Comp Biol 53:388-415.
21. Ridley CP, Faulkner DJ, Haygood MG. 2005. Investigation of Oscillatoria spongeliae-dominated bacterial communities in four dictyoceratid sponges. Appl Env Microbiol 72:7366-75.
22. Rützler K. 2012. The role of sponges in the Mesoamerican barrier-reef ecosystem, Belize. Adv Mar Biol 61:211-71.
23. Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57:758-71.
24. Tsagkogeorga G, Turon X, Hopcroft RR, Tilak MK, Feldstein T, Shenkar N, Loya Y, Huchon D, Douzery EJP, Delsuc F. 2009. BMC Evol Biol 9:187.
25. Van Soest RWM, Boury-Esnault N, Vacelet J, Dohrmann M, Erpenbeck D, et al. 2012. Global Diversity of Sponges (Porifera). PLoS ONE 7:e35105.
26. Voigt O, Collins AG, Pearse VB, Pearse JS, Ender A, Heike H, Schierwater B. 2004. Placozoa-no longer a phylum of one. Curr Biol 14:R944-5.
27. Voigt O, Wülfing E, Wörheide G. 2012. Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea). PLoS ONE 7:e33417.
28. Wörheide G, Dohrmann M, Erpenbeck D, Larroux C, Maldonado M, Voigt O, Borchiellini C, Lavrov DV. 2012. Deep phylogeny and evolution of sponges (Phylum Porifera). Adv Mar Biol 61:1-78.
29. Wulff J. 2012. Ecological interactions and the distribution, abundance, and diversity of sponges. Adv Mar Biol 61:273-344.