Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): Finding the molecular and morphological gap in Caribbean gorgonian corals

BMC Evolutionary Biology

Volumn 7, Issue , 2007, Pages

  Grajales, Alejandro ^a   Aguilar, Catalina ^a   Sánchez, Juan A ^a  

^a UNIVERSIDAD DE LOS ANDES   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

INTERNAL TRANSCRIBED SPACER 2; RIBOSOME DNA; RIBOSOMAL SPACER DNA; RIBOSOME RNA;

ARTICLE; BAYES THEOREM; CHEMICAL STRUCTURE; EVOLUTION; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; PHYLOGENY; SCANNING ELECTRON MICROSCOPE; ANIMAL; ANTHOZOA; CLASSIFICATION; CONFORMATION; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; SPECIES DIFFERENTIATION;

ANTHOZOA; CANDELABRUM; EUKARYOTA; EUNICEA; EUNICEA FUSCA; EUNICEA LACINIATA; EUNICEA LAXISPICA; EUNICEA MAMMOSA; EUNICEA TOURNEFORTI; GORGONIA; PLEXAURA; PLEXAURA FLEXUOSA; PSEUDOPLEXAURA;

ANIMALS; ANTHOZOA; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; GENETIC SPECIATION; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, RIBOSOMAL; VARIATION (GENETICS);

EID: 34447306903     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-90     Document Type: Article

References (33)

1. Tracing the evolution of RNA structure in ribosomes. G Caetano-Anollés, Nucleic Acids Res 2002 30 2575 2587 12034847 10.1093/nar/30.11.2575
2. A molecular phylogenetic analysis of reproductive trait evolution in the soft coral genus Alcyonium. CS McFadden R Donahue BK Hadland R Weston, Evolution 2001 55 54 67 11263746
3. 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. JA Sánchez HR Lasker DJ Taylor, Mol Phylogenet Evol 2003 29 31 42 (DOI:10.1016/S1055-7903(03)00090-3) 10.1016/S1055-7903(03)00090-3 12967605
4. Molecular Phylogenetic analyses of shallow-water Caribbean octocorals. JA Sánchez CS Mcfadden SC France HR Lasker, Marine Biol 2003 142 975 987 (DOI10.1007/s00227-003-1018-7)
5. Contribution of ITS2 sequences and predicted RNA secondary structures to octocoral systematics. C Aguilar JA Sánchez, Bull Marine Sci
6. Secondary structure and phylogenetic utility of the ribosomal internal transcribed spacer 2 (ITS2) in Scleractinian Corals. CA Chen CC Chang NV Wei CH Chen YT Lein HE Lin CF Dai CC Wallace, Zool Stud 2004 43 759 771
7. Intraspecies analysis: Comparison of ITS sequence data and gene intron sequence data with breeding data for a worldwide collection of Gonium pectorale. S Fabry A Kohler AW Coleman, J Mol Evol 1999 48 94 101 10.1007/PL00006449 9873081
8. Intragenomic variation within ITS1 and ITS2 of freshwater crayfishes (Decapoda: Cambaridae): Implications for phylogenetic and microsatellite studies. DJ Harris KA Crandall, Mol Biol Evol 2000 17 284 291 10677851
9. Molecular genetic analyses of species boundaries in the sea. N Knowlton, Hydrobiología 2000 420 73 90 10.1023/A:1003933603879
10. Phylogenetic relationships within the Octocorallia (Cnidaria : Anthozoa) based on nuclear 18S rRNA sequences. EA Berntson FM Bayer AG McArthur SG France, Marine Biol 2001 138 235 246 10.1007/s002270000457
11. Investigating the biodiversity, ecology, and phylogeny of endosymbiotic dinoflagellates in the genus Symbiodinium using the ITS region: in search of a "species" level marker. TC LaJeunesse, J Phycol 2001 37 866 880 10.1046/j.1529-8817.2001.01031.x
12. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). TL Shearer MJH van Oppen SL Romano G Wörheide, Mol Ecol 2002 11 2475 2487 10.1046/j.1365-294X.2002.01652.x 12453233
13. An unusual new gorgonian coral from the Aleutian Islands, North Pacific, Alaska. JA Sánchez SD Cairns, Zool Med 2004 78 265 274
14. DNA sequences of the mitochondrial COI gene have low levels of divergence among deep-sea octocorals (Cnidaria: Anthozoa). SC France LL Hoover, Hydrobiologia 2002 471 149 155 10.1023/A:1016517724749
15. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. J Schultz S Maisel D Gerlach T Müller M Wolf, RNA 2005 11 361 364 15769870 10.1261/rna.7204505
16. Cirripede phylogeny using a novel approach: molecular morphometrics. B Billoud MA Guerrucci M Masselot JS Deutsch, Mol Biol Evol 2000 17 1435 1445 11018151
17. Structural rRNA characters support monophyly of raptorial limbs and paraphyly of limb specialization in water fleas. TD Swain DJ Taylor, Proc Roy Soc London B 2003 270 887 896 10.1098/rspb.2002.2297
18. A field key to the identification of zooxanthellate octocorals from the Caribbean and Western Atlantic. JA Sánchez H Wirshing, Caribbean J Sci 2005 41 508 522
19. The shallow water Octocorallia of the West Indian region. FM Bayer, Stud Fauna Curaçao 1961 12 1 373
20. JVF Lamouroux, Exposition méthodique des genres de l'ordre des Polypiers, avec description et celles des principales espèces, figurées dans 84 planches; les 63 premières appartenant a l'Histoire des Zoophytes d'Ellis et Solander Paris 1821
21. Role of the ITS2-proximal item and evidence for indirect recognition of processing sites in pre-rRNA processing in yeast. CA Cote BA Peculis, Nuc Acids Res 2001 29 2106 2116 10.1093/nar/29.10.2106
22. Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast. CA Cote CL Greer BA Peculis, RNA 2002 8 786 797 12088151 10.1017/S1355838202023063
23. Assessing an unknown evolutionary process: Effect of increasing site-specific knowledge through taxon addition. DD Pollock WJ Bruno, Mol Biol Evol 2000 17 1854 1858 11110901
24. A likelihood approach to estimating phylogeny from discrete morphological character data. PO Lewis, Syst Biol 2001 50 913 925 10.1080/106351501753462876 12116640
25. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. TA Hall, Nucl Acids Symp 1999 41 95 98
26. Phylogenetic hypotheses of gorgoniid octocorals according to ITS2 and their predicted RNA secondary structures. C Aguilar JA Sánchez, Mol Phylogenet Evol 2007 43 774 786 doi:10.1016/j.ympev.2006.11.005. 10.1016/j.ympev.2006.11.005 17254805
27. Mfold web server for nucleic acid folding and hybridization prediction. M Zuker, Nucl Acids Res 2003 31 3406 3415 12824337 10.1093/nar/gkg595
28. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucl Acids Res 1994 22 4673 4680 7984417 10.1093/nar/22.22.4673
29. PAUP*. DL Swofford, Phylogenetic Analysis Using Parsimony (and other methods). Version 4.0b10 Sunderland, MA: Sinauer Associates 2002
30. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. DM Hillis JJ Bull, Syst Biol 1993 42 182 192 10.2307/2992540
31. Modeltest: testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics 1998 14 817 818 10.1093/bioinformatics/14.9.817 9918953
32. Bayesian inference of phylogenetic trees. JP Huelsenbeck F Ronquist, Bioinformatics 2001 17 754 755 10.1093/bioinformatics/17.8.754 11524383
33. Bayesian phylogenetic analysis of combined data. JAA Nylander F Ronquist JP Huelsenbeck JL Nieves-Aldrey, Syst Biol 2004 53 47 67 10.1080/ 10635150490264699 14965900