[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
References:
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:
http://www.ncbi.nlm.nih.gov/pubmed/12065836.
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:
107–132.
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:
102-16.
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:
1304-1312
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:
35-54.
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:
410-417.
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:
343-347.
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:
22.
--
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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