1. Shearer TL, van Oppen MJH, Romano SL, Wo¨rheide G (2002) Slow
mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol
11: 2475–2487.
2. Romano SL, Palumbi SR (1996) Evolution of scleractinian corals inferred from
molecular systematics. Science 271: 640–642.
3. Romano SL, Palumbi SR (1997) Molecular evolution of a portion of the
mitochondrial 16S ribosomal gene region in scleractinian corals. J Mol Evol 45:
397–411.
4. Romano SL, Cairns SD (2000) Molecular phylogenetic hypotheses for the
evolution of scleractinian corals. Bull Mar Sci 67: 1043–1068.
5. Chen CA, Wallace CC, Wolstenholme J (2002) Analysis of mitochondrial 12S
RNA gene supports a two-clade hypothesis of the evolutionary history of
scleractinian corals. Mol Phyl Evol 23: 137–149.
6. Fukami H, Budd AF, Paulay G, Sole-Cava A, Chen CA, et al. (2004)
Conventional taxonomy obscures deep divergence between Pacific and Atlantic
corals. Nature 427: 832–835.
7. Kerr AM (2005) Molecular and morphological supertree of stony corals
(Anthozoa: Scleractinia) using matrix representation parsimony. Biol Rev 80:
543–558.
8. Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL (2006) Naked corals:
Skeleton loss in Scleractinia. Proc Natl Acad Sci U S A 103: 9096–9100.
9. Brugler MR, France SC (2007) The complete mitochondrial genome of the
black coral Chrysopathes formosa (Cnidaria:Anthozoa:Antipatharia) supports
classification of antipatharians within the subclass Hexacorallia. Mol Phyl Evol
42: 776–788.
10. Veron JEN, Odorico DM, Chen CA, Miller DJ (1996) Reassessing evolutionary
relationships of scleractinian corals. Coral Reefs 15: 1–9.
11. Daly M, Fautin DG, Cappola VA (2003) Systematics of the Hexacorallia
(Cnidaria: Anthozoa). Zool J Linn Soc 139: 419–437.
12. Le Goff-Vitry MC, Rogers AD, Baglow D (2004) A deep-sea slant on the
molecular phylogeny of the Scleractinia. Mol Phyl Evol 30: 167–177.
13. Cuif JP, Lecointre G, Perrin C, Tillier A, Tillier S (2003) Patterns of septal
biomineralization in Scleractinia compared with their 28S rRNA phylogeny: a
dual approach for a new taxonomic framework. Zool Scri 32: 459–473.
14. den Hartog JC (1980) Caribbean shallow water Corallimorpharia. Zool
Verhand Leiden 176: 1–82.
15. Wei WV, Wallace CC, Dai CF, Moothien Pillay RK, Chen CA (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.
16. Chace MW, Fay MF, Savolainen V (2000) Higher-level classification in the
angiosperms: new insights from the perspective of DNA sequence data. Taxon
49: 685–704.
17. Boury-Esnault N (2006) Systematics and evolution of Demospongiae. Can J Zool
84: 205–224.
18. Willis BL, van Oppen MJH, Miller DJ, Vollmer SV, Ayre DJ (2006) The role of
hybridization in the evolution of reef corals. Ann Rev Ecol Evol Syst 37:
489–517.
19. Vaughan TW, Wells JW (1943) Revision of the suborders, families and genera of
the Scleratinia. Geol Soc Am Spec Pap 44: 1–363, pl.1–51.
20. Alloiteau J (1957) Contribution a la syste´matique des madre´poraires fossiles.
CNRS, Paris. pp 1–462, 286 figs, 20 pls.
21. Benzoni F, Stefani F, Stolarski J, Pichon M, Mitta G, et al. (2007) Debating
phylogenetic relationships of the scleractinian Psammocora: molecular and
morphological evidences. Contr Zool 76: 35–54.
22. Budd AF, Stolarksi J (2008) Searching for new morphological characters in the
systematics of scleractinian reef corals: comparison of septal teeth and granules
between Atlantic and Pacific Mussidae. Acta Zool 89: (in press).
23. Bellwood DR, Hughes TP (2001) Regional-scale assembly rules and biodiversity
of coral reefs. Science 292: 1532–1534.
24. Carpenter KE, Abrar M, Aeby G, Aronson RB, Banks S, et al. (2008) One third
of reef-building corals face elevated extinction risk from climate change and local
impacts. Science 321: 560–563.
25. Mace GM, Gittleman JL, Purvis A (2003) Preserving the tree of life. Science 300:
1707–1709.
26. Chen CA, Chang CC, Wei NV, Chen CH, Lein IT, et al. (2004) Secondary
structure and phylogenetic utility of the ribosomal internal transcribed spacer 2
in the scleractinian corals. Zool Stud 43: 759–771.
27. Posada D, Crandall KA (1998) Modeltest: Testing the model of DNA
substitution. Bioinformatics 14: 817–818.
28. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of
large biological sequence datasets under the maximum likelihood criterion, ver.
0.95. Ph.D. (www.bio.utexas.edu/faculty/antisense/garli/Garli.html).
29. Goloboff P, Farris S, Nixon K (2000) TNT:Tree analysis using New Technology
(BETA), ver. 1.0. Argentina: Tucuma´n.
30. Ronquist R, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference
under mixed models. Bioinformatics 19: 1572–1574.
31. Beagley CT, Okimoto R, Wolstenholme DR (1998) The mitochondrial genome
of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes,
and a near-standard genetic code. Genetics 148: 1091–1108.
32. Shimodaira H, Hasegawa M (2001) CONSEL: For assessing the confidence of
phylogenetic tree selection. Bioinformatics 17: 1246–1247.
33. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree
selection. Syst Biol 51: 492–508.
34. Kishino H, Hasegawa M (1989) Evaluation of the maximum-likelihood estimate
of the evolutionary tree topologies from DNA sequence data, and the branching
order in Hominoidea. J Mol Evol 29: 170–179.
35. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with
applications to phylogenetic inference. Mol Biol Evol 16: 1114–1116.
36. Swofford DL (2002) PAUP*:Phylogenetic Analysis Using Parsimony (and Other
Methods), version 4.0b10. Sunderland, MA: Sinauer.
37. Buckley TR (2002) Model misspecification and probabilistic tests of topology:
Evidence from empirical data sets. Syst Biol 51: 509–523.