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Morphological and Molecular Systematics of Scleractinian Corals (Cnidaria, Anthozoa), with Emphasis on Deep-Water Species

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Morphological and Molecular Systematics of Scleractinian Corals (Cnidaria, Anthozoa), with Emphasis on Deep-Water Species ResearchOnline@JCU This file is part of the following reference: Kitahara, Visentini Marcelo (2011) Morphological and molecular systematics of scleractinian corals (Cnidaria, Anthozoa), with emphasis on deep-water species. PhD thesis, James Cook University. Access to this file is available from: http://researchonline.jcu.edu.au/39370/ The author has certified to JCU that they have made a reasonable effort to gain permission and acknowledge the owner of any third party copyright material included in this document. If you believe that this is not the case, please contact [email protected] and quote http://researchonline.jcu.edu.au/39370/ To Michelle F. de O. Kitahara and Isadora Kitahara This page is intended to be blank ii Statement of Access I, the undersigned author of this thesis, understand that James Cook University will make it available for use within the university library and by electronic digital format, via the Australian digital theses network, for use elsewhere. I understand that, containing unpublished work, a thesis has significant protection under the Copyright Act. Therefore, all users consulting this work should agree with the following statement: “In consulting this thesis, I agree not to copy or partially paraphrase it in whole or in part without the written consent of the author, and to make proper written acknowledgement of any assistance which I have obtained from it” Beyond this, I do not place any restriction on access to this thesis. Marcelo Visentini Kitahara, April 2011 iii Statement of Sources I declare that this thesis is my own work and has not been submitted in any form for another degree or diploma at any university or other institution of tertiary education. Information derived from the published or unpublished work of others has been acknowledged in the text or in the Statement of Contribution of Others and a list of references is given. Marcelo Visentini Kitahara, April 2011 iv Statement on the Contribution of Others Scientific Contributions I gratefully thank the following people and organisations for providing resources and scientific/technical assistance to me during my candidature: • Dr Stephen D. Cairns (Smithsonian Institution), Dr Philippe Bouchet (Muséum National d’Histoire Naturelle), Dr Carden Wallace (Museum of Tropical Queensland), Ms Felicity McEnnulty (Commonwealth Scientific and Industrial Research Organisation), Dr Jane Fromont (Western Australian Museum) and Dr Karen Miller (University of Tasmania) for generously providing deep-water scleractinian samples. • Dr David J. Miller (James Cook University), Dr Stephen D. Cairns (Smithsonian Institution), Dr David Blair (James Cook University) and Dr Jaroslaw Stolarski (Instytut Paleobiologii) for providing critical reviews on my research and writing. • Dr Jaroslaw Stolarski (Instytut Paleobiologii) for providing SEMs, microstructural / microarchitectural data. • Dr David Blair (James Cook University) for assisting in the phylogenetic reconstructions. • Dr Tracy Ainsworth (ARC Centre of Excellence for Coral Reef Studies) for providing materials and guidance during histological studies, and Ms Sue Reilly (James Cook University) for embedding coral samples in paraffin. • Mr Paul Greenhall (Smithsonian Institution), Mrs Barbara Done (Museum of Tropical Queensland), Dr Carden Wallace (Museum of Tropical Queensland), Dr Pierre Lozouet (Muséum National d’Histoire Naturelle), Dr Aude Andouche (Muséum National d’Histoire Naturelle), Ms Felicity McEnnulty (Commonwealth Scientific and Industrial Research Organisation) for logistic v help with loans, CITES permission acquisition and/or providing institutional catalogue numbers for the specimens examined. • Mr James Robinson (University of Tasmania) and MSc Dustin Edge for technical assistance in laboratorial work and graphical design of maps respectively. • Dr Hironobu Fukami (Kyoto University) for providing unpublished CO1 sequences from 11 species of shallow-water scleractinian species used in the chapter 5. • Dr Chaolun A. Chen (Academia Sinica) and MSc Mei-Fang Lin (Academia Sinica) for providing unpublished universal mitochondrial primer sequences that resulted in the amplification of nearly 70% of the mitochondrial genome of Gardineria hawaiiensis as well as unpublished mitochondrial genome data from many hexacorallians. • Dr Sylvain Forêt (ARC Centre of Excellence for Coral Reef Studies) for assisting the gene annotation of the mitochondrial genome of Gardineria hawaiiensis and providing support for the phylogenetic analyses. • Dr Marcos Barbeitos (National Museum of Natural History) for providing personnal protocols for amplification of the nuclear 28S rDNA. • Dr Jen Whan (James Cook University) for gold coating and assisting the acquisition of SEM images. • Dr Joel Stake (Rivier College) for providing SEMs of Agaricia undata and Helioseris cucullata. Financial Assistance This research project was funded by Coordination for the Improvement of Higher Education Personnel and James Cook University as detailed below: • Coordination for the Improvement of Higher Education Personnel PhD scholarship (12/2006 - 10/2010). vi • School of Pharmacy and Molecular Sciences PhD scholarship (11/2010 - 04/2011). • James Cook University Research Graduate Scheme Grant (2008). vii Publications Arising from Thesis At the time of thesis submission, five papers describing the research findings of Chapters 2, 4 and 5 were already published, one manuscript arising from chapter 8 is under review, and other six manuscripts are currently in preparation. The complete taxonomic review arising from chapter 2 will be published as a volume of the book series Tropical deep-sea benthos. Details of each manuscript and talks presented during my PhD candidature are provided below: Manuscripts • Janiszewska, K., Stolarski, J., Benzerara, K., Meibom, A., Mazur, M., Kitahara, M. V. & Cairns, S. D. 2011. A unique skeletal microstructure of the deep-sea micrabaciid scleractinian corals. Journal of Morphology 272: 191-203. (Chapters 2 and 5) • Kitahara, M. V., Cairns, S. D. & Miller, D. J. 2010. Monophyletic origin of the Caryophyllia (Scleractinia; Caryophylliidae), with description of six new species. Systematics and Biodiversity, 8: 91-118. (Chapters 2 and 4) • Kitahara, M. V., Cairns, S. D., Stolarski, J., Blair, D. & Miller, D. J. 2010. A comprehensive phylogenetic analysis of the Scleractinia (Cnidaria, Anthozoa) based on mitochondrial CO1 sequence data. Plos One, v. 5, p. e11490. (Chapter 5) • Kitahara, M. V. & S. D. Cairns. 2008. New records of the genus Crispatotrochus (Scleractinia; Caryophylliidae) from New Caledonia, with description of a new species. Zootaxa, 1940: 59-68. (Chapter 2) • Kitahara, M. V. & Cairns, S. D. 2009. Revision of the genus Deltocyathus (Cnidaria, Scleractinia), with a description of a new species from New Caledonia. Zoosystema, 31(2): 233-249. (Chapter 2) • Stolarski, J., Kitahara, M. V., Miller, D. J. Cairns, S. D., Mazur, M. & Meibom, A. Submitted – BMC Evolutionary Biology. An ancient evolutionary origin of Scleractinia revealed by azooxanthellate corals. (Chapter 8) viii • Kitahara, M. V. & Cairns, S. D. In advanced stage of preparation - Invited to be published as a volume of the Tropical Deep-sea Benthos by the Museum National d’Histoire Naturelle. Deep-water azooxanthellate Scleractinia from New Caledonia. (Chapter 2) • Kitahara, M. V., Miller, D. J., Cairns, S. D., Stolarski, J. & Wallace, C. In advanced stage of preparation - Target: Nature. Was climate change the driving force for deep-water colonization by scleractinian corals? (Chapter 10) • Kitahara, M. V., Stolarski, J., Cairns, S. D. & Miller, D. J. In advanced stage of preparation - Target: Coral Reefs. Reciprocal illumination between molecular phylogeny and morphological characters supports the transfer of Dactylotrochus cervicornis (Moseley, 1881) to the Agariciidae (Anthozoa, Scleractinia). (Chapter 6) • Kitahara, M. V., Cairns, S. D. & Connoly, S. In preparation - Target: Journal of Biogeography. Diversity of deep-sea corals from New Caledonia: a central Pacific “hot spot” for azooxanthellate scleractinians. (Chapter 3) • Kitahara, M. V., Stolarski, J., Cairns, S. D. & Miller, D. J. In advanced stage of preparation - Target: Zoologica Scripta. Towards the second unification step between classical taxonomy and molecular phylogeny of Caryophylliidae (Anthozoa, Scleractinia): the elevation of Deltocyathus to family rank (Deltocyathiidae fam. nov.). (Chapter 7) • Mei-Fang, L., Kitahara, M. V., Yong, Y., Fôret, S., Fukami, H., Tracey, D., Miller, D. J. & Chen, C. A. In advanced stage of preparation - Target: Proceedings of the National Academy of Science, US. Anthozoa phylogeny based on 50 entire mitochondrial genomes. (Chapter 9) Talks • Kitahara, M. V. & Cairns, S. D. 2008. Diversity of deep-sea corals (Cnidaria, Scleractinia) from New Caledonia and adjacent waters: a central Pacific hot- spot for azooxanthellate scleractinians. Presented at the 4th International Symposium of Deep-sea Corals (NIWA - Wellington). • Kitahara, M. V. 2009. Global list of cold-water corals (Scleractinia, Filifera, Octocorallia, Antipatharia) from waters deeper than 200 m, vulnerable species, relevant references, list of experts, and draft recommendations for the ix production of identification guides. Presented at the Food and Agriculture Organization (FAO - Rome), the United Nations (UN). • Kitahara, M. V., Miller, D. J., Cairns, S. D. & Stolarski, J. 2009. How do azooxanthellate deep-water Scleractinia fit into the evolutionary history
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