Coral Reefs

, 30:1033 | Cite as

Comparison of morphological and genetic analyses reveals cryptic divergence and morphological plasticity in Stylophora (Cnidaria, Scleractinia)

  • Fabrizio StefaniEmail author
  • F. Benzoni
  • S.-Y. Yang
  • M. Pichon
  • P. Galli
  • C. A. Chen


A combined morphological and genetic study of the coral genus Stylophora investigated species boundaries in the Gulf of Aden, Yemen. Two mitochondrial regions, including the hypervariable IGS9 spacer and the control region, and a fragment of rDNA were used for phylogenetic analysis. Results were compared by multivariate analysis on the basis of branch morphology and corallite morphometry. Two species were clearly discriminated by both approaches. The first species was characterised by small corallites and a low morphological variability and was ascribed to a new geographical record of Stylophora madagascarensis on the basis of its phylogenetic distinction and its morphological similarity to the type material. The second species was characterised by larger corallite size and greater morphological variability and was ascribed to Stylophora pistillata. The analysis was extended to the intrageneric level for other S. pistillata populations from the Red Sea and the Pacific Ocean. Strong internal divergence was evident in the genus Stylophora. S. pistillata populations were split into two highly divergent Red Sea/Gulf of Aden and western Pacific lineages with significant morphological overlap, which suggests they represent two distinct cryptic species. The combined use of morphological and molecular approaches, so far proved to be a powerful tool for the re-delineation of species boundaries in corals, provided novel evidence of cryptic divergence in this group of marine metazoans.


Stylophora Gulf of Aden rDNA Control region IGS9 spacer Western Pacific 



The authors thank E. Dutrieux (CREOCEAN), C.H. Chaineu (Total SA), and R. Hirst (Yemen LNG) for allowing, organising, and financing fieldwork in Yemen. We are grateful to S. Basheen (Professional Divers Yemen) for impeccable fieldwork logistics. C. Riva, S. Montano, and A. Caragnano are acknowledged for their help during the fieldwork, and S. Montano and P. Gentile are acknowledged for help with SEM imaging. We thank Dr C. Wallace (MTQ, Townsville) for allowing analysis of the S. madagascarensis holotype and for fruitful discussions, and Dr R. Baron-Szabo for providing references on the Stylophora fossil record. We are grateful to E. Reynaud (Adéquation & Développement) for kindly donating the laboratory instruments for this study. Finally, we thank three anonymous referees for their helpful suggestions and corrections. S-Y. Yang and A.C. Chen were supported by grants from the National Science Council (NSC-96-2628-B-001-004-MY3) and Academia Sinica Thematic Grants (2008–2010). This is contribution no. 62 from the Coral Reef Evolutionary Ecology and Genetics Group, Biodiversity Research Centre, Academia Sinica.

Supplementary material

338_2011_797_MOESM1_ESM.doc (46 kb)
Supplementary material 1 (DOC 49 kb)


  1. Antunes A, Ramos MJ (2005) Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes. Genomics 86:708–717PubMedCrossRefGoogle Scholar
  2. Barber PH, Palumbi SR, Erdmann MV, Moosa MK (2000) A marine Wallace’s line? Nature 406:692–693PubMedCrossRefGoogle Scholar
  3. Baron-Szabo RC (2002) Scleractinian corals of the Cretaceous. A guide to Cretaceous forms with descriptions, illustrations, and remarks on their taxonomic position. Privately published, Knoxville, TennesseeGoogle Scholar
  4. Bensasson D, Zhang D, Hartl DL, Hewitt GM (2001) Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol Evol 16:314–321PubMedCrossRefGoogle Scholar
  5. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580PubMedCrossRefGoogle Scholar
  6. Benzie JAH, Ballment E, Forbes AT, Demetriades NT, Sugama K, Haryanti, Moria S (2002) Mitochondrial DNA variation in Indo-Pacific populations of the giant tiger prawn, Penaeus monodon. Mol Ecol 11:2553–2569PubMedCrossRefGoogle Scholar
  7. Benzoni F, Bianchi CN, Morri C (2003) Coral communities of the North-western Gulf of Aden (Yemen): variation in framework building related to environmental factors and biotic conditions. Coral Reefs 22:475–497CrossRefGoogle Scholar
  8. Benzoni F, Stefani F, Stolarski J, Pichon M, Galli P (2007) Debating phylogenetic relationships of the scleractinian Psammocora: molecular and morphological evidences. Contrib Zool 76:33–52Google Scholar
  9. Benzoni F, Stefani F, Pichon M, Galli P (2010) The name game: morpho-molecular species boundaries in the genus Psammocora (Cnidaria, Scleractinia). Zool J Linn Soc 160:421–456CrossRefGoogle Scholar
  10. Bickford D, Lohman DJ, Sohdi NS, Ng PKL, Meier R, Winker K, Ingram KK, Das I (2007) Cryptic species as a window on diversity and conservation. Trends Ecol Evol 22:148–155PubMedCrossRefGoogle Scholar
  11. Budd AF, Johnson KG, Potts DC (1994) Recognising morphospecies in colonial reef corals: I. Landmark-based methods. Paleobiology 20:484–505Google Scholar
  12. Budd AF, Romano SL, Smith ND, Barbeitos MS (2010) Rethinking the phylogeny of ccleractinian corals: A review of morphological and molecular data. Integr Comp Biol 50:411–427PubMedCrossRefGoogle Scholar
  13. Carpenter KE, Harrison PL, Hodgson G, Alsaffar AH, Alhazeem SH (1997) The corals and reef fishes of Kuwait. Kuwait Institute for Scientific Research, Environmental Public Authority, Kuwait CityGoogle Scholar
  14. Chen CC, Chang CC, Wei NV, Chen CH, Lein YT, Dai CF, Wallace C (2004) Secondary structure and phylogenetic utility of ribosomal internal spacer 2 (ITS2) in Scleractinian corals. Zool Stud 43:759–771Google Scholar
  15. Chen C, Chiou C-Y, Dai C-F, Chen CA (2008a) Unique mitogenomic features in the scleractinian family Pocilloporidae (Scleractinia: Astrocoeniina). Mar Biotechnol 10:538–553PubMedCrossRefGoogle Scholar
  16. Chen C, Dai C-F, Plathong S, Chiou C-Y, Chen CA (2008b) The complete mitochondrial genomes of needle corals, Seriatopora spp. (Scleractinian; Pocilloporidae): an idiosyncratic atp8, duplicated trnW gene, and hypervariable regions used to determine species phylogenies and recently diverged populations. Mol Phylogenet Evol 46:19–33PubMedCrossRefGoogle Scholar
  17. Claereboudt M (2006) Reef corals and coral reefs of the Gulf of Oman. Historical Association of Oman, RuwiGoogle Scholar
  18. Crandall ED, Frey MA, Grosberg RK, Barber PH (2008) Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropods. Mol Ecol 17:611–626PubMedCrossRefGoogle Scholar
  19. Diekmann OE, Bak RPM, Stam WT, Olsen JL (2001) Molecular genetic evidence for probable reticulate speciation in the coral genus Madracis from a Caribbean fringing reef slope. Mar Biol 139:221–233CrossRefGoogle Scholar
  20. Dong HK, Byung-Dong K (2006) The organization of mitochondrial atp6 gene region in male fertile and CMS lines of pepper (Capsicum annuum L.). Curr Genet 49:59–67CrossRefGoogle Scholar
  21. Duda TF, Bolin MB, Meyer CP, Kohn AJ (2008) Hidden diversity in a hyperdiverse gastropod genus: discovery of previously unidentified members of a Conus species complex. Mol Phyl Evol 49:867–876CrossRefGoogle Scholar
  22. Farris JS, Källersjö M, Kluge AG, Bult C (1995) Testing significance of incongruence. Cladistics 10:315–319CrossRefGoogle Scholar
  23. Flot JF, Tillier S (2007) The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: the putative D-loop and a novel ORF of unknown function. Gene 401:80–87PubMedCrossRefGoogle Scholar
  24. Flot JF, Magalon H, Cruaud C, Couloux A, Tillier S (2008a) Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology. Comptes Rendus Biol 331:239–247CrossRefGoogle Scholar
  25. Flot JF, Licuanan WY, Nakano Y, Payri C, Cruaud C, Tillier S (2008b) Mitochondrial sequences of Seriatopora corals show little agreement with morphology and reveal the duplication of a tRNA gene near the control region. Coral Reefs 27:789–794CrossRefGoogle Scholar
  26. Forsman ZH, Barshis DJ, Hunter CL, Toonen RJ (2009) Shape-shifting corals: Molecular markers show morphology is evolutionarily plastic in Porites BMC. Evol Biol 9:45CrossRefGoogle Scholar
  27. Frade PR, Bongaerts P, Winkelhagen AJS, Tonk L, Bak RPM (2008a) In situ photobiology of corals over large depth ranges: A multivariate analysis on the roles of environment, host, and algal symbiont. Limnol Oceanogr 53:2711–2723CrossRefGoogle Scholar
  28. Frade PR, Englebert N, Faria J, Visser PM, Bak RPM (2008b) Distribution and photobiology of Symbiodinium types in different light environments for three colour morphs of the coral Madracis pharensis: is there more to it than total irradiance. Coral Reefs 27:913–925CrossRefGoogle Scholar
  29. Frade PR, De Jongh F, Vermeulen F, Van Bleijswijk J, Bak RPM (2008c) Variation in symbiont distribution between closely related coral species over large depth ranges. Mol Ecol 17:691–703PubMedCrossRefGoogle Scholar
  30. Frade PR, Reyes-Nivia MC, Faria J, Kaandorp JA, Luttikhuizen PC, Bak RPM (2010) Semi-permeable species boundaries in the coral genus Madracis: Introgression in a brooding coral system. Mol Phylogenet Evol 57:1072–1090PubMedCrossRefGoogle Scholar
  31. Fukami H, Knowlton N (2005) Analysis of complete mitochondrial DNA sequences of three members of the Montastraea annularis coral species complex (Cnidaria, Anthozoa, Scleractinia). Coral Reefs 24:410–417CrossRefGoogle Scholar
  32. Fukami H, Budd AF, Levitan DR, Jara J, Kersanach R, Knowlton N (2004) Geographic differences in species boundaries among members of the Montastrea annularis complex based on molecular and morphological markers. Evolution 58:324–337PubMedGoogle Scholar
  33. Gattuso J-P, Pichon M, Jaubert J (1991) Physiology and taxonomy of scleractinian corals: a case study in the genus Stylophora. Coral Reefs 9:173–182CrossRefGoogle Scholar
  34. Gittenberger A, Hoeksema BW (2006) Phenotypic plasticity revealed by molecular studies on reef corals of Fungia (Cycloseris) spp. (Scleractinia: Fungiidae) near river outlets. Contrib Zool 75:195–201Google Scholar
  35. Gittenberger A, Reijnen BT, Hoeksema BW (2011) A molecularly based phylogeny reconstruction of mushroom corals (Scleractinia: Fungiidae) with taxonomic consequences and evolutionary implications for life history traits. Contrib Zool 80:107–132Google Scholar
  36. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp 41:95–98Google Scholar
  37. Hoeksema BW (1993) Phenotypic corallum variability in Recent mobile reef corals. Courier Forschungs-Institut Senckenberg 164:263–272Google Scholar
  38. Hoeksema BW (2007) Delineation of the Indo-Malayan centre of maximum marine biodiversity: the Coral Triangle. In: Renema W (ed) Biogeography, time and place: distributions, barriers and islands. Springer, Dordrecht, pp 117–178CrossRefGoogle Scholar
  39. Hoeksema BW, Moka W (1989) Species assemblages and ecomorph variation of mushroom corals (Scleractinia: Fungiidae) related to reef habitats in the Flores Sea. Neth J Sea Res 23:149–160CrossRefGoogle Scholar
  40. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:745–755CrossRefGoogle Scholar
  41. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310–2314PubMedCrossRefGoogle Scholar
  42. Kemp JM, Benzoni F (1999) Monospecific coral areas on the northern shore of the Gulf of Aden. Coral Reefs 18:280CrossRefGoogle Scholar
  43. Kemp JM, Benzoni F (2000) A preliminary study of the coral communities in the northern Gulf of Aden. Fauna Arabia 18:67–86Google Scholar
  44. Knowlton N (2000) Molecular genetic analyses of species boundaries in the sea. Hydrobiologia 420:73–90CrossRefGoogle Scholar
  45. Kon T, Nohara M, Nishida M, Sterrer W, Nishikawa T (2006) Hidden ancient diversification in the circumtropical lancelet Asymmetron lucayanum complex. Mar Biol 149:875–883CrossRefGoogle Scholar
  46. Lourie SA, Green D, Vincent ACJ (2005) Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Sygnathidae: Hippocampus). Mol Ecol 14:1073–1094PubMedCrossRefGoogle Scholar
  47. Marquez ML, Miller DJ, MacKenzie JB, Van Oppen MJH (2003) Pseudogenes contribute to the extreme diversity of nuclear ribosomal DNA in the hard coral Acropora. Mol Biol Evol 20:1077–1086PubMedCrossRefGoogle Scholar
  48. McMillan WO, Palumbi SR (1995) Concordant evolutionary patterns among Indo-West Pacific butterflyfishes. Proc Biol Sci 260:229–236PubMedCrossRefGoogle Scholar
  49. Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL (2006) Naked corals: skeleton loss in scleractinia. Proc Natl Acad Sci USA 103:9096–9100PubMedCrossRefGoogle Scholar
  50. Mourier T, Hansen AJ, Willerslev E, Arctander P (2001) The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus. Mol Biol Evol 18:1833–1837PubMedGoogle Scholar
  51. Nunes F, Fukami H, Vollmer SV, Norris RD, Knowlton N (2008) Re-evaluation of the systematics of the endemic corals of Brazil by molecular data. Coral Reefs 27:423–432CrossRefGoogle Scholar
  52. Nuryanto A, Kochzius M (2009) Highly restricted gene flow and deep evolutionary lineages in the giant clam Tridacna maxima. Coral Reefs 28:607–619CrossRefGoogle Scholar
  53. Oren M, Amar KO, Douek J, Rosenzweig T, Paz G, Rinkevich B (2010) Assembled catalog of immune-related genes from allogeneic challenged corals that unveils the participation of vWF-like transcript. Dev Comp Immunol 34:630–637PubMedCrossRefGoogle Scholar
  54. Ow YX, Todd PA (2010) Light-induced morphological plasticity in the scleractinian coral Goniastrea pectinata and its functional significance. Coral Reefs 29:797–808CrossRefGoogle Scholar
  55. Palumbi SR (1994) Genetic divergence, reproductive isolation, and marine speciation. Annu Rev Ecol Syst 25:547–572CrossRefGoogle Scholar
  56. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818PubMedCrossRefGoogle Scholar
  57. Rambaut A, Drummond AJ (2003) Tracer: MCMC trace analysis tool. University of Oxford, OxfordGoogle Scholar
  58. Read CI, Bellwood DR, van Herwerden L (2006) Ancient origins of Indo-Pacific coral reef fish biodiversity: a case study of the leopard wrasses (Labridae: Macropharyngodon). Mol Phyl Evol 38:808–819CrossRefGoogle Scholar
  59. Reid DG, Lal K, Mackenzie-Dodds J, Kaligis F, Littlewood DTJ, Williams ST (2006) Comparative phylogeography and species boundaries in Echinolittorina snails in the central Indo-West Pacific. J Biogeogr 33:990–1006CrossRefGoogle Scholar
  60. Richly E, Leister D (2004) NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 21:1081–1084PubMedCrossRefGoogle Scholar
  61. Scheer G, Pillai CSG (1983) Report on the stony corals from the Red Sea. Zoologica 133:1–198Google Scholar
  62. Sheppard CRC, Sheppard ALS (1991) Corals and coral communities of Arabia. Fauna of Saudi Arabia 12:3–170Google Scholar
  63. Sirna Terranova M, Lo Brutto S, Arculeo M, Mitton JB (2007) A mitochondrial phylogeography of Brachidontes variabilis (Bivalvia: Mytilidae) reveals three cryptic species. J Zool Systs Evol Res 45:289–298CrossRefGoogle Scholar
  64. Souter P (2010) Hidden genetic diversity in a key model species of coral. Mar Biol 157:875–885. doi: 10.1007/s00227-009-1370-3 CrossRefGoogle Scholar
  65. Stefani F, Benzoni F, Pichon M, Cancelliere C, Galli P (2008) A multidisciplinary approach to the definition of species boundaries in branching species of the coral genus Psammocora (Cnidaria, Scleractinia). Zool Scr 37:71–91Google Scholar
  66. Stobart B (2000) A taxonomic reappraisal of Montipora digitata based on genetic and morphometric evidence. Zool Stud 39:179–190Google Scholar
  67. Swofford DL (2001) PAUP* Version 4.0b10—Phylogenetic Analysis Using Parsimony. Sinauer Assoc, SunderlandGoogle Scholar
  68. Takabayashi M, Carter D, Loh W, Hoegh-Guldberg O (1998) A coral-specific primer for PCR amplification of the internal transcribed spacer region in ribosomal DNA. Mol Ecol 7:928–930Google Scholar
  69. Takabayashi M, Carter D, Lopez J, Hoegh-Guldberg O (2003) Genetic variation of the scleractinian coral Stylophora pistillata from western Pacific reefs. Coral Reefs 22:17–22Google Scholar
  70. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  71. Teske PR, Winker H, McQuaid CD, Barker NP (2009) A tropical/subtropical biogeographic disjunction in southeastern Africa separates two Evolutionarily Significant Units of an estuarine prawn. Mar Biol 156:1265–1275CrossRefGoogle Scholar
  72. Todd PA (2008) Morphological plasticity in scleractinian corals. Biol Rev 83:315–337PubMedCrossRefGoogle Scholar
  73. Todd PA, Sanderson PG, Chou LM (2001) Morphological variation in the polyps of the scleractinian coral Favia speciosa (Dana) around Singapore. Hydrobiologia 444:227–235CrossRefGoogle Scholar
  74. Todd PA, Sidle RC, Chou ML (2002a) Plastic corals from Singapore: 1. Coral Reefs 21:391–392Google Scholar
  75. Todd PA, Sidle RC, Chou ML (2002b) Plastic corals from Singapore: 2. Coral Reefs 21:407–408Google Scholar
  76. Todd PA, Ladle RJ, Lewin-Koh NJI, Chou LM (2004) Genotype x environment interactions in transplanted clones of the massive corals Favia speciosa and Diploastrea heliopora. Mar Ecol Prog Ser 271:167–182CrossRefGoogle Scholar
  77. Tseng C-C, Wallace CC, Chen CA (2005) Mitogenomic analysis of Montipora cactus and Anacropora matthai (Cnidaria; Scleractinia; Acroporidae) indicates an unequal rate of mitochondrial evolution among Acroporidae corals. Coral Reefs 2005:502–508CrossRefGoogle Scholar
  78. van Oppen MJ, Catmull J, McDonald BJ, Hislop NR, Hagerman PJ, Miller DJ (2002) The mitochondrial genome of Acropora tenuis (Cnidaria; Scleractinia) contains a large group I intron and a candidate control region. J Mol Evol 55:1–13PubMedCrossRefGoogle Scholar
  79. Veron JEN (2000) Corals of the world. Australian Institute of Marine Science, TownsvilleGoogle Scholar
  80. Veron JEN (2002) New species described in ‘Corals of the World’. Aust Inst Mar Sci Monogr Ser 11, Townsville, p 206Google Scholar
  81. Veron JEN, Pichon M (1976) Scleractinia of Eastern Australia. Vol 1: Part I. Families Thamnasteriidae, Astrocoeniidae, Pocilloporidae. Aust Inst Mar Sci Monogr Ser, TownsvilleGoogle Scholar
  82. Veron JEN, DeVantier LM, Turak E, Green AL, Kininmonth S, Stafford-Smith M, Peterson N (2009) Delineating the Coral Triangle. Galaxea 11:91–100CrossRefGoogle Scholar
  83. Wei NWV, Wallace CC, Dai CF, Pillay KR, CA Chen (2006) Analyses of the ribosomal internal transcribed spacers (ITS) and the 5.8S gene indicated that extremely high rDNA heterogeneity is a unique feature in the scleractinian coral genus Acropora (Scleractinia; Acroporidae). Zool Stud 45:404–418Google Scholar
  84. Wells JW (1964) Fossil corals from Eniwetok Atoll. US Geol Survey Prof Papers. 260:1101–1110Google Scholar
  85. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols. A guide to methods and application. Academic Press Inc, San Diego, pp 315–322Google Scholar
  86. White DJ, Wolff JN, Pierson M, Gemmell NJ (2008) Revealing the hidden complexities of mtDNA inheritance. Mol Ecol 17:4925–4942PubMedCrossRefGoogle Scholar
  87. Wiklund H, Glover AG, Johannessen PJ, Dahlgren TG (2009) Cryptic speciation at organic-rich marine habitats: a new bacteriovore annelid from whale-fall and fish farms in the North–East Atlantic. Zool J Lin Soc 4:774–785CrossRefGoogle Scholar
  88. You EM, Chiu TS, Liu KF, Tassanakajon A, Klinbunga S, Triwitayakorn K, de la Peña LD, Li Y, Yu HT (2008) Microsatellite and mitochondrial haplotype diversity reveals population differentiation in the tiger shrimp (Penaeus monodon) in the Indo-Pacific region. Anim Genet 39:267–277PubMedCrossRefGoogle Scholar
  89. Zvuloni A, Mokady O, Al-Zibdah M, Bernardi G, Gaines SD, Abelson A (2008) Local scale genetic structure in coral populations: a signature of selection. Mar Pollut Bull 56:430–438PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Fabrizio Stefani
    • 1
    Email author
  • F. Benzoni
    • 1
    • 2
  • S.-Y. Yang
    • 3
  • M. Pichon
    • 4
  • P. Galli
    • 1
  • C. A. Chen
    • 3
    • 5
  1. 1.Department of Biotechnology and BiosciencesUniversity of Milano-BicoccaMilanItaly
  2. 2.Institut de Recherche pour le Développement (IRD), UMR227 Coreus2Nouméa, New CaledoniaFrance
  3. 3.Biodiversity Research Centre, Academia SinicaTaipeiTaiwan
  4. 4.Museum of Tropical QueenslandTownsvilleAustralia
  5. 5.Institute of OceanographyNational Taiwan UniversityTaipeiTaiwan

Personalised recommendations