Phylogenetic hypotheses of gorgoniid octocorals according to ITS2 and their predicted RNA secondary structures

Molecular Phylogenetics and Evolution

Volumn 43, Issue 3, 2007, Pages 774-786

  Aguilar, Catalina ^a   Sánchez, Juan Armando ^a  

^a UNIVERSIDAD DE LOS ANDES   (Colombia)

Author keywords

Gorgonians; Gorgoniidae; ITS2; Molecular morphometrics; Molecular systematics; Octocorals; Phylogeny; RNA secondary structure

Indexed keywords

RIBOSOMAL SPACER DNA; RIBOSOME RNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; CLASSIFICATION; COELENTERATE; CONFORMATION; DNA SEQUENCE; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ANIMALS; CNIDARIA; DNA, RIBOSOMAL SPACER; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, RIBOSOMAL; SEQUENCE ANALYSIS, DNA;

ALCYONARIA; CNIDARIA; COELENTERATA; EUKARYOTA; GORGONACEA; GORGONIA; GORGONIIDAE; LEPTOGORGIA; MURICEOPSIS; PACIFIGORGIA; PLEXAURELLA; PLEXAURELLA NUTANS; PLEXAURIDAE; PSEUDOPTEROGORGIA; PTEROGORGIA; PTEROGORGIA CITRINA;

EID: 34248540337     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.11.005     Document Type: Article

References (40)

1. Aguilar, C., Sánchez, J.A. (2007). Molecular morphometrics: contribution of ITS2 sequences and predicted RNA secondary structures to octocoral systematics. Bull. Mar. Sci., in press.
2. Bayer F.M. The shallow water Octocorallia of the West Indian region. Stud. Fauna Curaçao 12 (1961) 1-373
3. Berntson E.A., Bayer F.M., McArthur A.G., and France S.G. Phylogenetic relationships within the Octocorallia (Cnidaria : Anthozoa) based on nuclear 18S rRNA sequences. Mar. Biol. 138 (2001) 235-246
4. Billoud B., Guerrucci M.A., Masselot M., and Deutsch J.S. Cirripede phylogeny using a novel approach: molecular morphometrics. Mol. Biol. Evol. 17 (2000) 1435-1445
5. Caetano-Anollés G. Tracing the evolution of RNA structure in ribosomes. Nucleic Acids Res. 30 (2002) 2575-2587
6. Chen C.A., Chang C.C., Wei N.V., Chen C.H., Lein Y.T., Lin H.E., Dai C.F., and Wallace C.C. Secondary structure and phylogenetic utility of the ribosomal internal transcribed spacer 2 (ITS2) in Scleractinian Corals. Zool. Stud. 43 (2004) 759-771
7. Coleman A.W. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends Gen. 19 (2003) 370-375
8. Cote C.A., Greer C.L., and Peculis B.A. Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast. RNA 8 (2002) 786-797
9. Fabry S., Kohler A., and Coleman A.W. Intraspecies analysis: comparison of ITS sequence data and gene intron sequence data with breeding data for a worldwide collection of Gonium pectorale. J. Mol. Evol. 48 (1999) 94-101
10. Gottschling M., and Plötner J. Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoagellates. Nucl. Acids Res. 32 (2004) 307-315
11. Grasshoff M., and Alderslade P. Gorgoniidae of Indo-Pacific reefs with descriptions of two new genera (Coelenterata: Octocorallia). Senckenbergiana biologica 77 (1997) 23-25
12. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 41 (1999) 95-98
13. Harris D.J., and Crandall K.A. Intragenomic variation within ITS1 and ITS2 of freshwater crayfishes (Decapoda: Cambaridae): Implications for phylogenetic and microsatellite studies. Mol. Biol. Evol. 17 (2000) 284-291
14. Hillis D.M., and Huelsenbeck J.P. Signal, noise, and reliability in molecular phylogenetic analysis. J. Hered. 83 (1992) 189-195
15. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
16. Joseph N., Krauskopf E., Vera M.I., and Michot B. Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acids Res. 27 (1999) 4533-4540
17. Knowlton N. Molecular genetic analyses of species boundaries in the sea. Hydrobiologia 420 (2000) 73-90
18. LaJeunesse T.C. Investigating the biodiversity, ecology, and phylogeny of endosymbiotic dinoflagellates in the genus Symbiodinium using the its region: in search of a "species" level marker. J. Phycol. 37 (2001) 866-880
19. LePard, A., 2003. Analysis of variation in the mitochondrial encoded MSH1 in the genus Leptogorgia (Cnidaria: Octocorallia) and implications for population and systematics studies. M.S. thesis. University/College Charleston, Charleston, USA.
20. McFadden C.S., Donahue R., Hadland B.K., and Weston R. A molecular phylogenetic analysis of reproductive trait evolution in the soft coral genus Alcyonium. Evolution 55 (2001) 54-67
21. McFadden C.S., and Hutchinson M.B. Molecular evidence for the hybrid origin of species in the soft coral genus Alcyonium (Cnidaria: Anthozoa: Octocorallia). Mol. Ecol. 13 (2004) 1495-1505
22. Mallet J., and Willmott K. Taxonomy: renaissance or tower of babel?. Trends Ecol. Evol. 18 (2003) 57-59
23. Marquez L., Miller D., MacKenzie J., and Van Oppen M.J.H. Pseudogenes contribute to the extreme diversity of nuclear ribosomal DNA in the hard coral Acropora. Mol. Biol. Evol. 207 (2003) 1077-1086
24. Posada D., and Buckley T.R. Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53 (2004) 793-808
25. Schultz J., Maisel S., Gerlach D., Müller T., and Wolf M. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 11 (2005) 361-364
26. Sánchez J.A. Systematics of the Southwestern Caribbean Muriceopsis Aurivillius (Cnidaria: Octocorallia) with description of a new species. Bull. Biol. Soc. Wash. 10 (2001) 160-180
27. Sánchez J.A. Evolution and dynamics of branching colonial form in marine modular Cnidarians: Gorgonian Octocorals. Hydrobiologia 530 (2004) 283-290
28. Sánchez, J.A., in press. A new genus of Atlantic octocorals (Octocorallia: Gorgoniidae): systematics of gorgoniids with asymmetric sclerites. J. Nat. Hist.
29. Sánchez J.A., and Cairns S.D. An unusual new gorgonian coral from the Aleutian Islands, North Pacific, Alaska. Zool. Med. 78 (2004) 265-274
30. Sánchez J.A., and Lasker H.R. Patterns of morphologic integration in branching colonies of marine modular organisms: supra-module organization in Gorgonian Corals. Proc. R. Soc. Lond. B 270 (2003) 2039-2044 10.1098/rspb.2003.2471
31. Sánchez J.A., Lasker H.R., and Taylor D.J. Phylogenetic analyses among octocorals (Cnidaria) according to mitochondrial and nuclear DNA sequences (lsu-rRNA 16S, and ssu-rRNA 18S) support two convergent clades of branching gorgonians. Mol. Phylogenet. Evol. 29 (2003) 31-42 10.1016/S1055-7903(03)00090-3
32. Sánchez J.A., Mcfadden C.S., France S.C., and Lasker H.R. Molecular phylogenetic analyses of shallow-water Caribbean octocorals. Mar. Biol. 142 (2003) 975-987 10.1007/s00227-003-1018-7
33. Shearer T.L., van Oppen M.J.H., Romano S.L., and Wörheide G. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol. Ecol. 11 12 (2002) 2475-2487
34. Swain T.D., and Taylor D.J. Structural rRNA characters support monophyly of raptorial limbs and paraphyly of limb specialization in water fleas. Proc. R. Soc. Lond. B 270 (2003) 887-896
35. Swofford, D.L., 2002. PAUP*, phylogenetic analysis using parsimony (* and other methods). Version 4.0b10. Sunderland: Sinauer Associates.
36. Vollmer S.V., and Palumbi S.R. Testing the utility of internally transcribed spacer sequences in coral phylogenetics. Mol. Ecol. 13 (2004) 2763-2772
37. Wei N.W.V., Wallace C.C., Dai C.F., Pillay K.R.M., and Chen C.A. Analyses of the ribosomal internal transcribed spacers (ITS) and the 5.8S gene indicate that extremely high rDNA heterogeneity is a unique feature in the Scleractinian Coral Genus Acropora (Scleractinia; Acroporidae). Zool. Stud. 45 (2006) 404-418
38. Williams G.C., and Lindo K.G. A review of the Octocorallian genus Leptogorgia (Anthozoa: Gorgonidae) in the Indian Ocean and subantarctic, with description of a new species and comparisons with related taxa. Proc. Calif. Acad. Sci. 49 (1997) 499-521
39. Wirshing H.H., Messing C.G., Douady C.J., Reed J., Stanhope M.J., and Shivji M.S. Molecular evidence for multiple lineages in the gorgonian family Plexauridae (Anthozoa: Octocorallia). Mar. Biol. 147 (2005) 497-508
40. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415