[Coral-List] List of species-level DNA studies

Zac Forsman zforsman at gmail.com
Tue Nov 22 20:41:09 EST 2011

Dear coral listers,
   I am working on compiling a list for a review of genus and
species-level phylogenetic (DNA sequence data) studies on reef
building corals.  If any of you are aware of any studies that I have
not included on this list, I would really appreciate it if you let me
know (I'll make sure you are properly credited and I'll disseminate
the final list to coral-list).  I know that there are additional
studies out there that I am missing, or that are in press.  Thanks for
your help.

All the best, Zac


Odorico DM, Miller DJ. 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.  Molecular Biology and
Evolution 14: 465–473.

Hatta,  M.,  Fukami,  H.,  Wang,  W.Q.,  Omori,  M.,  Shimoike,
K.,Hayashibara, T., Ina, Y., and Sugiyama, T. 1999. Reproductive and
genetic  evidence  for  a  reticulate  evolutionary  history  of
mass-spawning corals. Mol. Biol. Evol. 16: 1607–1613.

van Oppen MJH, Willis BL, van Vugt HWJA, Miller DJ. 2000.  Examination
 of  species  boundaries  in  the  Acropora cervicornis  group
(Scleractinia,  Cnidaria)  using  nuclear DNA sequence analyses.
Molecular Ecology 9: 1363–1373.

Fukami, H., Omori, M., & Hatta, M. 2000. Phylogenetic relationships in
the coral family acroporidae, reassessed by inference from
mitochondrial genes. Zoological science 17: 689-96.

van Oppen, M. J. H., Mcdonald, B. J., Willis, B., & Miller, D. J.
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? Molecular biology and evolution 18: 1315-1329.

van  Oppen  MJH,  Willis  BL,  van  Rheede  T,  Miller  DJ. 2002.
Spawning  times,  reproductive  compatibilities  and genetic
structuring in the Acropora aspera group: evidence for   natural
hybridization   and   semi-permeable   species boundaries in corals.
Molecular Ecology 11: 1363–1376.

Vollmer, Steven V, and Stephen R Palumbi. 2002. “Hybridization and the
evolution of reef coral diversity.” Science (New York, N.Y.)
296(5575): 2023-5. Available at:

Wolstenholme  JK,  Wallace  CC,  Chen  CA.  2003.  Species boundaries
within  the  Acropora  humilis  species  group (Cnidaria;
Scleractinia):  a  morphological  and  molecular interpretation    of
  evolution.    Coral    Reefs    22:    155–166

Richards   ZT,   van   Oppen   MJH,   Wallace   CC,   Willis
BL,Miller   DJ.   2008.   Some   Rare   Indo-Pacific   Coral
SpeciesAre  Probable  Hybrids.  PLoS ONE 3:e3240.

Gittenberger, A., Reijnen, B. T., & Hoeksema, B. W. 2011. A
molecularly based phylogeny reconstruction of mushroom corals
(Scleractinia: Fungiidae) with taxonomic consequences and evolutionary
implications for life history traits. Contributions to Zoology 80:

Huang, D., Meier, R., Todd, P. a, & Chou, L. M. 2009. More evidence
for pervasive paraphyly in scleractinian corals: systematic study of
Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular
and morphological data. Molecular phylogenetics and evolution 50:

Chan, Y. L., Pochon, X., Fisher, M. a, Wagner, D., Concepcion, G. T.,
Kahng, S. E., Toonen, R. J., & Gates, R. D. 2009. Generalist
dinoflagellate endosymbionts and host genotype diversity detected from
mesophotic (67-100 m depths) coral Leptoseris. BMC ecology 9: 21.

Pillay, KRM  Asahida, Takashi,Chen, CA. 2006. ITS ribosomal DNA
distinctions and the genetic structures of populations of two
sympatric species of Pavona (Cnidaria: Scleractinia) from Mauritius.
Zoological 45: 132-144.

Mangubhai S, Souter P, Grahn M. 2007. Phenotypic variation  in  coral
Platygyra  daedalea  in  Kenya:  morphometry and genetics. Marine
Ecology Progress Series 345: 105–115.

Combosch, DJ; Guzman, HM; Schuhmacher, H; Vollmer, SV (2008)
Interspecific Hybridization and Restricted Trans-Pacific Gene Flow in
the Tropical Eastern Pacific Pocillopora. Molecular Ecology 17:

Flot, J.-F., Magalon, H., Cruaud, C., Couloux, A., & Tillier, S. 2008.
Patterns of genetic structure among Hawaiian corals of the genus
Pocillopora yield clusters of individuals that are compatible with
morphology. Comptes rendus biologies 331: 239-47.

Souter, P. 2010. Hidden genetic diversity in a key model species of
coral. Marine Biology 157: 875-885.

Pinzón, J. H., & LaJEUNESSE, T. C. 2010. Species delimitation of
common reef corals in the genus Pocillopora using nucleotide sequence
phylogenies, population genetics and symbiosis ecology. Molecular
Ecology: no-no.

Flot, J.-F., Couloux, A., & Tillier, S. 2010. Haplowebs as a graphical
tool for delimiting species: a revival of Doyleʼs “field for
recombination” approach and its application to the coral genus
Pocillopora in Clipperton. BMC Evolutionary Biology 10: 372.

Hunter, C.L., Morden, C.W., and Smith, C.M. 1997. The utility of ITS
sequences  in  assessing  relationships  among  zooxanthellae and
corals.  In  Proceedings  of  the  8th  Coral  Reef  Symposium,
Panamá, 24–29 June 1996. Vol. 2. Edited by H.A. Lessios and I.G.
Macintyre.  Smithsonian  Tropical  Research  Institute,  Balboa,
Panamá. pp. 1599–1602.

Forsman ZH, Wellington GM, Hunter CL G.E. Fox. (2006) Is the ITS
Region the Solution to the ‘Species Problem’ in corals? Intragenomic
Variation, and Alignment Permutation in Porites, Siderastrea and
Outgroup Taxa.  10th Int. Coral Reef Symp.14-23

Forsman, Z. H., Barshis, D. J., Hunter, C. L., & Toonen, R. J. 2009.
Shape-shifting corals: molecular markers show morphology is
evolutionarily plastic in Porites. BMC evolutionary biology 9: 45.

Benzoni, F., Stefani, F., Pichon, M., & Galli, P. 2010. The name game:
morpho-molecular species boundaries in the genus Psammocora (Cnidaria,
Scleractinia). Zoological Journal of the Linnean Society: no-no.

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 Scripta 37:71–91.

Benzoni F, Stefani F, Stolarski J, Pichon M, Mitta G, Galli P. 2007.
Debating phylogenetic relationships of the scleractinian Psammocora:
molecular and morphological evidences. Contributions to Zoology 76:

Benzoni, F., Stefani, F., Pichon, M., & Galli, P. 2010. The name game:
morpho-molecular species boundaries in the genus Psammocora (Cnidaria,
Scleractinia). Zoological Journal of the Linnean Society: no-no.

Benzoni, F., Arrigoni, R., & Stefani, F. 2011. Phylogeny of the coral
genus Plesiastrea (Cnidaria, Scleractinia). Contributions to Zoology
80: 231-249.
Diekmann, O;R, Bak;W, Stam;J, O. 2001. Molecular genetic evidence for
probable reticulate speciation in the coral genus Madracis from a
Caribbean fringing reef slope. Marine Biology 139: 221-233.

Frade, P. R., Reyes-Nivia, M. C., Faria, J., Kaandorp, J. a,
Luttikhuizen, P. C., & Bak, R. P. M. 2010. Semi-permeable species
boundaries in the coral genus Madracis: Introgression in a brooding
coral system. Molecular phylogenetics and evolution 57: 1072-1090.

Medina, M., Weil, E., & Szmant, A. 1999. Examination of the
Montastraea annularis Species Complex (Cnidaria: Scleractinia) Using
ITS and COI Sequences. Marine biotechnology (New York, N.Y.) 1: 89-97.

Fukami, H., Budd, A. F., Levitan, D. R., Jara, J., Kersanach, R., &
Knowlton, N. 2004. Geographic differences in species boundaries among
members of the Montastraea annularis complex based on molecular and
morphological markers. Evolution; international journal of organic
evolution 58: 324-37.

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:

van Oppen, M. J. H. , Koolmees, E., & Veron, J. 2004. Patterns of
evolution in the scleractinian coral genus Montipora (Acroporidae).
Marine Biology 144: 9–18.

Forsman, Z. H., Concepcion, G. T., Haverkort, R. D., Shaw, R. W.,
Maragos, J. E., & Toonen, R. J. 2010. Ecomorph or Endangered Coral?
DNA and Microstructure Reveal Hawaiian Species Complexes: Montipora
dilatata/flabellata/turgescens & M. patula/verrilli (R. C. Fleischer,
Ed.). PLoS ONE 5: e15021.

Forsman, Z. H., Guzman, H. M., Chen, C. a, Fox, G. E., & Wellington,
G. M. 2005. An ITS region phylogeny of Siderastrea (Cnidaria:
Anthozoa): is S. glynni endangered or introduced? Coral Reefs 24:

Flot JF, Licuanan WY, Nakano Y, Payri C, Cruaud C, Tillier  S.  2008.
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: 789–794.

Stefani, F., Benzoni, F., Yang, S.-Y., Pichon, M., Galli, P., & Chen,
C. A. 2011. Comparison of morphological and genetic analyses reveals
cryptic divergence and morphological plasticity in Stylophora
(Cnidaria, Scleractinia). Coral Reefs: 1-17-17.

Flot, J.-F., Blanchot, J., Charpy, L., Cruaud, C., Licuanan, W. Y.,
Nakano, Y., Payri, C., & Tillier, S. 2011. Incongruence between
morphotypes and genetically delimited species in the coral genus
Stylophora: phenotypic plasticity, morphological convergence,
morphological stasis or interspecific hybridization? BMC ecology 11:

Zac H. Forsman,  Ph.D.
Hawaii Institute of Marine Biology -
Papahānaumokuākea Marine National
Monument Postdoctoral Fellow

Hawaii Institute of Marine Biology
P.O. Box 1346 (regular post)
46-007 Lilipuna Rd. (FedEx or other shipping)
Kaneohe, HI 96744
808-236-7428 (ph)
808-236-7443 (fax)

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