Secondary structure of the rRNA ITS2 region reveals key evolutionary patterns in acroporid corals

Journal of Molecular Evolution

Volumn 67, Issue 4, 2008, Pages 389-396

  Coleman, Annette W ^a   Van Oppen, Madeleine J H ^b  

^a BROWN UNIVERSITY   (United States)

^b AUSTRALIAN INSTITUTE OF MARINE SCIENCE   (Australia)

Author keywords

Acropora; Corals; Hybridization; ITS2 transcript secondary structure; Ribosomal RNA; Scleractinia

Indexed keywords

INTERNAL TRANSCRIBED SPACER 2; RIBOSOME RNA;

ARTICLE; CORAL; GENE SEQUENCE; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; POLYPLOIDY; PROTEIN SECONDARY STRUCTURE; RNA TRANSCRIPTION;

ANIMALS; ANTHOZOA; BASE SEQUENCE; CARIBBEAN REGION; CONSERVED SEQUENCE; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; POLYPLOIDY; RNA, MESSENGER; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 5.8S;

ACROPORA; ACROPORA CERVICORNIS; ACROPORA PALMATA; ACROPORIDAE; ANTHOZOA; EUKARYOTA; ISOPORA; SCLERACTINIA;

EID: 54349124515     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-008-9160-y     Document Type: Article

References (32)

1. CA Chen CC Wallace J Wolstenholme 2002 Analysis of the mitochondrial 12S rRNA gene supports a two-clade hypothesis of the evolutionary history of scleractinian corals Mol Phylogenet Evol 23 137 149
2. CA Chen VWN Chang CC CH Chen YT Lein HE Lin CF Dai CC Wallace 2004 Secondary structure and phylogenetic utility of the ribosomal internal transcribed spacer 2 (ITS2) in scleractinian corals Zool Stud 43 759 771
3. AW Coleman 2007 Pan-eukaryote ITS2 homologies revealed by RNA secondary structure Nucleic Acids Res 35 3322 3329
4. GT Concepcion M Medina RJ Toonen 2006 Noncoding mitochondrial loci for corals Mol Ecol Notes 6 1208 1211
5. CA Cote CL Greer BA Peculis 2002 Dynamic conformational model for the role of ITS2 in pre-RNA processing in yeast RNA 8 786 797
6. JP Cuif G Lecointre C Perrin A Tillier S Tillier 2003 Patterns of septal biomineralization in Scleractinia compared with their 28S rRNA phylogeny: a dual approach for a new taxonomic framework Zool Scripta 32 459 473
7. H Fukami N Knowlton 2005 Analysis of complete mitochondrial DNA sequences of three members of the Montastraea annularis coral species complex (Cnidaria, Anthozoa, Scleractinia) Coral Reefs 24 410 417
8. H Fukami M Omori M Hatta 2000 Phylogenetic relationships in the coral family Acroporidae, reassessed by inference from mitochondrial genes Zool Sci 17 689 696
9. H Fukami AF Budd G Paulay A Sola-Cava CA Chen K Iwao N Knowlton 2004 Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals Nature 427 832 835
10. M Hatta H Fukami WQ Wang M Omori K Shimoike T Hayashibara Y Ina T Sugiyama 1999 Reproductive and genetic evidence for a reticulate evolutionary history of mass-spawning corals Mol Biol Evol 16 1607 1613
11. ME Hellberg 2006 No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation BMC Evol Biol 6 24
12. JC Kenyon 1997 Models of reticulate evolution in the coral genus Acropora based on chromosome numbers: parallels with plants Evolution 51 756 767
13. MC Le Goff-Vitry AD Rogers D Baglow 2004 A deep-sea slant on the molecular phylogeny of Scleractinia Mol Phylogenet Evol 30 167 177
14. LM Márquez DJ Miller JB MacKenzie MJH van Oppen 2003 Pseudogenes contribute to the extreme diversity of nuclear ribosomal DNA in the hard coral Acropora Mol Biol Evol 20 1077 1086
15. M Medina AG Collins TL Takaoka JV Kuehl JL Boore 2006 Naked corals: skeleton loss in Scleractinia Proc Natl Acad Sci USA 103 9096 9100
16. T Proschold EH Harris AW Coleman 2005 Portrait of a species: Chlamydomas reinhardtii Genetics 170 1601 1610
17. SL Romano SD Cairns 2000 Molecular phylogenetic hypotheses for the evolution of scleractinian corals Bull Mar Sci 67 1043 1068
18. SL Romano SR Palumbi 1996 Evolution of scleractinian corals inferred from molecular systematics Science 271 640 642
19. SL Romano SR Palumbi 1997 Molecular evolution of a portion of the mitochondrial 16S ribosomal gene region in scleractinian corals J Mol Evol 45 397 411
20. TL Shearer MJH van Oppen SL Romano G Woerheide 2002 Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria) Mol Ecol 11 2475 2487
21. GDJ Stanley DG Fautin 2001 The origins of modern corals Science 291 1913 1914
22. MJH van Oppen BL Willis DJ Miller 1999 Atypically low rate of cytochrome b evolution in the scleractinian coral genus Acropora Proc Roy Soc Lond B Biol Sci 266 179 183
23. MJH van Oppen BL Willis HWJA van Vugt DJ Miller 2000 Examination of species boundaries in the Acropora cervicornis group (Scleractinia, Cnidaria) using nuclear DNA sequence analyses Mol Ecol 9 1363 1373
24. MJH van Oppen BJ McDonald B Willis DJ Miller 2001 The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence? Mol Biol Evol 18 1315 1329
25. MJH van Oppen G Woerheide M Takabayashi 2002 Nuclear markers in evolutionary and population genetic studies of scleractinian corals and sponges Proc 9th Int Coral Reef Symp Bali 1 131 138
26. MJH van Oppen BL Willis T van Rheede DJ Miller 2002 Differences in spawning time and genetic structuring among reproductively compatible corals: an example from the Acropora aspera species group Mol Ecol 11 1363 1376
27. Veron JEN (1995) Corals in space and time. UNSW Press, Sydney
28. SV Vollmer SR Palumbi 2002 Hybridization and the evolution of reef coral diversity Science 296 2023 2025
29. SV Vollmer SR Palumbi 2004 Testing the utility of internally transcribed spacer sequences in coral phylogenetics Mol Ecol 13 2763 2772
30. CC Wallace CA Chen H Fukami PR Muir 2007 Recognition of separate genera within Acropora based on new morphological, reproductive and genetic evidence from Acropora togianensis, and elevation of the subgenus Isopora Studer, 1878 to genus (Scleractinia: Astrocoeniidae; Acroporidae) Coral Reefs 26 231 239
31. NV Wei CC Wallace C-F Dai KR Moothien Pillay CA Chen 2006 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 45 404 418
32. BL Willis MJH van Oppen DJ Miller SV Vollmer DJ Ayre 2006 The role of hybridization in the evolution of reef corals Annu Rev Ecol Syst 37 489 517