Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals


Only 17% of 111 reef-building coral genera and none of the 18 coral families with reef-builders are considered endemic to the Atlantic, whereas the corresponding percentages for the Indo-west Pacific are 76% and 39%1,2. These figures depend on the assumption that genera and families spanning the two provinces belong to the same lineages (that is, they are monophyletic). Here we show that this assumption is incorrect on the basis of analyses of mitochondrial and nuclear genes. Pervasive morphological convergence at the family level has obscured the evolutionary distinctiveness of Atlantic corals. Some Atlantic genera conventionally assigned to different families are more closely related to each other than they are to their respective Pacific ‘congeners’. Nine of the 27 genera of reef-building Atlantic corals belong to this previously unrecognized lineage, which probably diverged over 34 million years ago. Although Pacific reefs have larger numbers of more narrowly distributed species, and therefore rank higher in biodiversity hotspot analyses3, the deep evolutionary distinctiveness of many Atlantic corals should also be considered when setting conservation priorities.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Phylogenies for corals in the suborder Faviina and related families (Oculinidae, Meandrinidae).
Figure 2: Illustrations of wall structures based on thin sections.


  1. 1

    Veron, J. E. N. Corals in Space and Time (UNSW Press, Sydney, 1995)

    Google Scholar 

  2. 2

    Veron, J. E. N. Corals of the World (Australian Institute of Marine Science, Townsville, 2000)

    Google Scholar 

  3. 3

    Roberts, C. M. et al. Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295, 1280–1284 (2002)

    ADS  CAS  Article  Google Scholar 

  4. 4

    Budd, A. F. Diversity and extinction in the Cenozoic history of Caribbean reefs. Coral Reefs 19, 25–35 (2000)

    Article  Google Scholar 

  5. 5

    Romano, S. L. & Cairns, S. D. Molecular phylogenetic hypotheses for the evolution of scleractinian corals. Bull. Mar. Sci. 67, 1043–1068 (2000)

    Google Scholar 

  6. 6

    Veron, J. E. N., Odorico, D. M., Chen, C. A. & Miller, D. J. Reassessing evolutionary relationships of scleractinian corals. Coral Reefs 15, 1–9 (1996)

    ADS  Article  Google Scholar 

  7. 7

    Chen, C. A., Wallace, C. C. & Wolstenholme, J. Analysis of the mitochondrial 12S rRNA gene supports a two-clade hypothesis of the evolutionary history of scleractinian corals. Mol. Phyl. Evol 23, 137–149 (2002)

    CAS  Article  Google Scholar 

  8. 8

    Cuif, J.-P., Lecointre, G., Perrin, C., Tillier, A. & Tillier, S. 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 (2003)

    Article  Google Scholar 

  9. 9

    Vaughan, T. W. & Wells, J. W. Revision of the suborders, families, and genera of the Scleractinia. Geol. Soc. Am. Spec. Pap. 44, 1–363 (1943)

    Google Scholar 

  10. 10

    Stolarski, J. & Roniewicz, E. Towards a new synthesis of evolutionary relationships and classification of Scleractinia. J. Paleontol. 75, 1090–1108 (2001)

    Article  Google Scholar 

  11. 11

    Wells, J. W. The recent solitary mussid scleractinian corals. Zool. Meded. 39, 375–384 (1964)

    Google Scholar 

  12. 12

    Paulay, G. in Life and Death of Coral Reefs (ed. Birkeland, C.) 298–353 (Chapman & Hall, New York, 1997)

    Book  Google Scholar 

  13. 13

    Wallace, C. C. Journey to the heart of the centre—origins of high marine faunal diversity in the central Indo-Pacific from the perspective of an acropologist. Proc. 9th Int. Coral Reef Symp. 1, 33–39 (2002)

    Google Scholar 

  14. 14

    Shearer, T. L., van Oppen, M. J. H., Romano, S. L. & Wörheide, G. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol. Ecol. 11, 2475–2487 (2002)

    CAS  Article  Google Scholar 

  15. 15

    Mace, G. M., Gittleman, J. L. & Purvis, A. Preserving the tree of life. Science 300, 1707–1709 (2003)

    ADS  CAS  Article  Google Scholar 

  16. 16

    Pandolfi, J. M. et al. Global trajectories of the long-term decline of coral reef ecosystems. Science 301, 955–958 (2003)

    ADS  CAS  Article  Google Scholar 

  17. 17

    Gardner, T. A., Côté, I. M., Gill, J. A., Grant, A. & Watkinson, A. R. Long-term region-wide declines in Caribbean corals. Science 301, 958–960 (2003)

    ADS  CAS  Article  Google Scholar 

  18. 18

    Williams, S. T., Knowlton, N., Weight, L. A. & Jara, J. A. Evidence for three major clades within the snapping shrimp genus Alpheus inferred from nuclear and mitochondrial gene sequence data. Mol. Phyl. Evol. 20, 375–389 (2001)

    CAS  Article  Google Scholar 

  19. 19

    Lopez, J. V. & Knowlton, N. Discrimination of sibling species in the Montastraea annularis complex using multiple genetic loci. Proc. 8th Int. Coral Reef Symp. 2, 1613–1618 (1997)

    CAS  Google Scholar 

  20. 20

    Swofford, D. L. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), Version 4.0b10 (Sinauer, Sunderland, MA, 2002)

    Google Scholar 

  21. 21

    Kimura, M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120 (1980)

    ADS  CAS  Article  Google Scholar 

  22. 22

    Posada, D. & Crandall, K. A. Modeltest: Testing the model of DNA substitution. Bioinformatics 14, 817–818 (1998)

    CAS  Article  Google Scholar 

  23. 23

    Kimura, M. Estimation of evolutionary distances between homologous nucleotide sequences. Proc. Natl Acad. Sci. USA 78, 454–458 (1981)

    ADS  CAS  Article  Google Scholar 

  24. 24

    Tamura, K. & Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512–526 (1993)

    CAS  PubMed  Google Scholar 

Download references


We thank J. Jara, E. Gomez, M. Hatta and staff of the Palau International Coral Reef Center for their assistance in the field and laboratory, and J. Jackson and R. Grosberg for comments on the manuscript. Financial support came from the National Science Foundation, the Smithsonian Institution, the Scripps Institution of Oceanography, and the Conselho Nacional de Pesquisas (CNPq). Authors' contributions. H.F. performed the collections and genetic analyses, A.F.B. the morphological and palaeontological interpretations, C.A.C. the coral molecular systematics and collections in Taiwan, G.P. the coral systematics and collections in Palau, A.S.-C. the molecular systematics and collections in Brazil, K.I. the collections in Okinawa, and N.K. the coral systematics, financial/logistic support and manuscript preparation.

Author information



Corresponding author

Correspondence to Nancy Knowlton.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Information 1

List of the species analyzed in this study and location of coral skeletons (in laboratories of respective authors). For photos of these corals, send requests to corresponding author. (DOC 32 kb)

Supplementary Information 2

50% majority-rule consensus tree of the first 10000 equally maximum-parsimonious trees inferred from MP analysis using 305 bp of the 5’-end of the nuclear 28S rRNA gene (primers from Romano and Cairns5). DNA sequences are available in DDBJ (Accession Nos. AB126702-AB126751). (PDF 1648 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Fukami, H., Budd, A., Paulay, G. et al. Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals. Nature 427, 832–835 (2004).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing