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)

Zoological Studies

Volumn 45, Issue 3, 2006, Pages 404-418

  Wei, Nu Wei Vivian ^a,b   Wallace, Carden C ^c   Dai, Chang Feng ^b   Pillay, Kamla Ruby Moothien ^d   Chen, Chaolun Allen ^a,b  

^a BIODIVERSITY RESEARCH CENTER   (Taiwan)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^c MUSEUM OF TROPICAL QUEENSLAND   (Australia)

^d France Centre   (Mauritius)

Author keywords

Acropora; Ancient divergence; Concerted evolution; Hybridization; Ribosomal DNA

Indexed keywords

ACROPORA; ACROPORIDAE; ANTHOZOA; ISOPORA; SCLERACTINIA;

EID: 33749653470     PISSN: 10215506     EISSN: 1810522X     Source Type: Journal    
DOI: None     Document Type: Article

References (51)

1. Alverez I, JF Wendel. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 29: 417-434.
2. Avise JC. 2004. Molecular markers, natural history, and evolution, 2nd ed. Sunderland, MA: Sinauer Associates.
3. Baldwin BG. 1992. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae. Mol. Phylogenet. Evol. 1: 3-16.
4. Buckler ES IV, TP Holtford. 1996. Zea systematics: ribosomal ITS evidence. Mol. Biol. Evol. 13: 612-622.
5. Budd AF, TA Stemann, KG Johnson. 1994. Stratigraphic distributions of neogene to recent Caribbean reef corals: a new compilation. J. Paleontol. 68: 951-959.
6. Chen CA, CC Chang, NV Wei, 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.
7. Chen CA, CC Wallace, J Wolstenholme. 2002. Analysis of mitochondrial 12S RNA gene supports a two-clade hypothesis of the evolutionary history of scleractinian corals. Mol. Phylogenet. Evol. 23: 137-149.
8. Chen CA, JK Yu, NW Wei. 2000. Strategies for amplification by polymerase chain reaction of the complete sequence of nuclear large subunit ribosomal RNA-encoding gene in corals. Mar. Biotechnol. 6: 558-570.
9. Diekmann OE, RPM Bak, WT Stam, JL Olsen. 2001. Molecular genetic evidence for probable reticulate speciation in the coral genus Madracis from a Caribbean fringing reef slope. Mar. Biol. 139: 221-223.
10. Dover GA. 1982. Molecular drive, a cohesive model of species evolution. Nature 299: 111-117.
11. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376.
12. Forsman ZH. 2003. Phylogeny and phylogeography of Porites and Siderastrea (Scleractinia: Cnidaria) species in the Caribbean and eastern Pacific; based on the nuclear ribosomal ITS region. PhD dissertation. Univ. of Houston, Houston, TX.
13. Forsman ZH, HM Guzman, CA Chen, GE Fox, GM Wellington. 2005. An ITS region phylogeny of Siderastrea (Cnidaria: Anthozoa): Is S. glynni endangered or introduced? Coral Reefs 24: 343-347.
14. Forsman ZH, CL Hunter, GE Fox, GM Wellington. Is the ITS region the solution to the "species problem" in corals? Intragenomic variation and alignment permutation in Porites, Siderastrea and outgroup taxa. Proceedings of the 10th International Coral Reef Symposium. Okinawa, Japan. (in press)
15. Fukami H, AF Budd, G Paulay, A Sole-Cava, CA Chen, K Iwao, N Knowlton. 2004. Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals. Nature 427: 832-835.
16. Fukami H, M Omori, M Hatta. 2000. Phylogenetic relationships in the coral family Acroporidae, reassessed by inference from mitochondrial genes. Zool. Sci. 17: 689-696.
17. Gilbert DC. 1994. SeqApp 1.9. A biological sequence editor and analysis program for Macintosh computers. Available via an anonymous ftp at ftp://bio.indiana.edu.
18. Hillis DM, MT Dixon. 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. Q. Rev. Biol. 66: 411-453.
19. Hillis DM, C Moritz, CA Porter, RJ Baker. 1991. Evidence for biased gene conversion in concerted evolution of ribosomal DNA. Science 251: 308-310.
20. Hunter CL, CW Morden, CM Smith. 1997. The utility of ITS sequences in assessing relationships among zooxanthellae and corals. Proc. 8th Int. Coral Reef Sym. 2: 1599-1602.
21. Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
22. Lam K, B Morton. 2003. Morphological and ITS1, 5.8S, and partial ITS2 ribosomal DNA sequence distinctions between two species Playtygyra (Cnidaria; Scleractinia) from Hong Kong. Mar. Biotechnol. 5: 555-567.
23. Li P, J Bousquet. 1992. Relative-rate test for nucleotide substitutions between two lineages. Mol. Biol. Evol. 9: 1185-1189.
24. Li WH. 1997. Molecular evolution. Sunderland, MA: Sinauer Associates.
25. Lopez J, N Knowlton. 1997. Discrimination of species in the Montastraea annularis complex using multiple genetic loci. Proc. 8th Int. Coral Reef Sym. 2: 1613-1618.
26. Mai JC, AW Coleman. 1997. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. J. Mol. Evol. 44: 258-271.
27. Marquez LM, 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.
28. Medina M, E Weil, AM Szmant. 1999. Examination of the Montastraea annularis species complex (Cnidaria: Scleractinia) using ITS and COI sequences. Mar. Biotechnol. 1: 89-97.
29. Moothien Pillay KRM, T Asahida, CA Chen, H Terashima, H Ida. 2005. ITS ribosomal DNA distinctions and genetic structure of populations in two sympatric species of Pavona (Cnidaria: Scleractinia) from Mauritius. Zool. Stud. 45: 132-144.
30. Miller DJ, MJH van Oppen. 2003. A "fair go" for coral hybridization. Mol. Ecol. 12: 805-807.
31. Muir G, CC Fleming, C Schlotterer. 2001. Three divergent rDNA clusters predate the species divergence in Quercus petraea (Matt.) Liebl. and Quercus robur L. Mol. Biol. Evol. 18: 112-119.
32. Muse SV, BS Weir. 1992. Testing for equality of evolutionary rates. Genetics 132: 269-276.
33. Odorico DM, DJ Miller. 1997. Variation in the ribosomal internal transcribed spacers and 5.8S rDNA among five species of Acropora (Cnidaria; Scleractinia): patterns of variation consistent with reticulate evolution. Mol. Biol. Evol. 14: 465-473.
34. Oliverio M, M Cervelli, P Mariottini. 2002. ITS2 rRNA evolution and its congruence with the phylogeny of muricid neogastropods (Caenogastropoda, Muricoidea). Mol. Phylogenet. Evol. 25: 63-69.
35. Posada D, KA Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818.
36. Robinson M, M Gouy, C Gautier, D Mouchiroud. 1998. Sensitivity of the relative-rate test to taxonomic sampling. Mol. Biol. Evol. 15: 1091-1098.
37. Rodriguez-Lanetty M, O Hoegh-Guldberg. 2002. The phylogeography and connectivity of the latitudinally widespread scleractinian coral Plesiastrea versipora in the Western Pacific. Mol. Ecol. 11: 1177-1189.
38. Romano SL, SD Cairns. 2000. Molecular phylogenetic hypotheses for the evolution of scleractinian corals. Bull. Mar. Sci. 67: 1043-1068.
39. Schlötterer C, M Hauser, A von Haeseler, D Tautz. 1994. Comparative evolutionary analysis of rDNA ITS regions in Drosophila. Mol. Biol. Evol. 11: 513-522.
40. Schmidt HA, K Strimmer, M Vingron, A von Haeseler. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
41. Swofford DL. 2002. PAUP 4.0b10: Phylogenetic Analysis Using Parsimony (and other methods). Sunderland, MA: Sinauer Associates.
42. Thompson JD, DG Higgins, TJ Gibson. 1994. CLUSTAL X: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
43. van Oppen MJH, EM Koolmees, JEN Veron. 2004. Patterns of evolution in the scleractinian coral genus Montipora (Acroporidae). Mar. Biol. 144: 9-18.
44. van Oppen MJH, BJ McDonald, BL 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.
45. van Oppen MJH, BL Willis, T van Rheede, DJ Miller. 2002. Spawning times, reproductive compatibilities and genetic structuring in the Acropora aspera group: evidence for natural hybridization and semi-permeable species boundaries in corals. Mol. Ecol. 11: 1363-1376.
46. van Oppen MJH, B 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.
47. Vollmer SV, SR Palumbi. 2002. Hybridization and the evolution of reef coral diversity. Science 296: 2023-2025.
48. Vollmer SV, SR Palumbi. 2004. Testing the utility of internally transcribed spacer sequences in coral phylogenetics. Mol. Ecol. 13: 2763-2772.
49. Wallace CC. 1999. Staghorn corals of the world: a revision of the coral genus Acropora (Scleractinia; Astrocoeniina; Acroporidae) worldwide, with emphasis on morphology, phylogeny and biogeography. Collingwood, Australia: CSIRO Publishing.
50. Weekers PHH, FJ de Jonckheere, HJ Dumont. 2001. Phylogenetic relationships inferred from ribosomal ITS sequences and biogeographic patterns in representative of the genus Calopteryx (Insecta: Odonata) of the West Mediterranean and adjacent west European zone. Mol. Phylogenet. Evol. 20: 89-99.
51. Wu CI, WH Li. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82: 1741-1745.