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Elaeocarpaceae) in Australasia ResearchOnline@JCU This file is part of the following reference: Baba, Yumiko (2013) Evolution, systematics and taxonomy of Elaeocarpus (Elaeocarpaceae) in Australasia. PhD thesis, James Cook University. Access to this file is available from: http://researchonline.jcu.edu.au/38321/ 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/38321/ Evolution, systematics and taxonomy of Elaeocarpus (Elaeocarpaceae) in Australasia Thesis submitted by Yumiko Baba BSc (Hons) Tokyo University of Agriculture MSc The University of Edinburgh in July 2013 for the degree of Doctor of Philosophy Australian Tropical Herbarium and the School of Marine and Tropical Biology James Cook University Cairns, Australia STATEMENT ON THE CONTRIBUTION OF OTHERS The chapters of this thesis are also manuscripts that have been published or are in preparation for submission. Several researchers have made contributions to these manuscripts as follow: Chapter 1: P. Bannink produced a distribution map. Chapter 3: M. Rossetto supplied primer sequences of microsatellite markers utilised in this chapter and technical guidance for genotyping and analyses. C.D. Kilgour provided assistance in collecting the samples. P. Bannink produced a distribution map. C. Micheneau assisted in the data analysis and provided theoretical background. Technical support for running the statistical program R was provided by A. Lechner. Chapter 4: C.D. Kilgour provided assistance in collecting the samples. Chapter 5: This chapter has been published as Baba, Y. and Crayn, D. (2012) Elaeocarpus hylobroma (Elaeocarpaceae): a new species endemic to mountain tops in north-east Queensland, Australia. Kew Bulletin, 67, 1–8. D. Crayn and P. Bostock provided technical and theoretical background. Assistance for production of line drawing was gained from W. Cooper. P. Bannink produced a distribution map. C.D. Kilgour supplied a picture for a figure. M. Coode contributed for the improvement of manuscript. Permission for reproduction of the article as a chapter in this thesis was obtained from Springer with a license number 3165350580769. Herbarium Loans were obtained for all the chapters from Queensland Herbarium (BRI). Land access and permissions for the scientific collection were granted from Council of Northern Peninsula Area, a chairman of Lama Lama National Park (CYPAL), Kuku Yalanji People, other National Park rangers, Australian Wildlife Conservancy Picaninny Plain, the owners of Bromwell Station and Mackay Botanic Garden. Scientific collections were made under WISP05391710 and WITK04740210, issued by the Queensland Department of Science, Information Technology, Innovation and the Arts. I was supported financially by an Australian Biological Resources Study (ABRS) scholarship, which funded me the second half of this study, came from the ABRS Grant No. 211-42 to D.M. Crayn, S.-N. Phoon and Y. Baba, titled Systematic studies in the Polystachyus-XIB group complex of Elaeocarpus L.. The Skyrail Rainforest Foundation provided two consecutive funding rounds to carry out Chapters 3, 4 and 5. The Australian Tropical Herbarium (ATH) made available significant in-kind and logistical support for this project. Every reasonable effort has been made to gain permission and acknowledge the owners of copyright material. I would be pleased to hear from any copyright owner who has been omitted or incorrectly acknowledged. STATEMENT ON THE PUBLICATION OF NEW TAXONOMIC NAMES Under Article 30.7 (reproduced below) of the International Code of Botanical Nomenclature, Melbourne Code (McNeill et al. 2012), taxonomic names proposed in this thesis are not considered effectively published. Article 30.7. Publication on or after 1 January 1953 of an independent non-serial work stated to be a thesis submitted to a university or other institute of education for the purpose of obtaining a degree does not constitute effective publication unless the work includes an explicit statement (referring to the requirements of the Code for effective publication) or other internal evidence that it is regarded as an effective publication by its author or publisher. ACKNOWLEDGMENTS Special thanks are due to my principal supervisor, Professor Darren M. Crayn for the support, training and encouragement he gave me throughout my candidature. I also express my gratitude to co-supervisors, Professor Paul A. Gadek and Dr. Mark Harrington. I could not have wished for more enthusiastic, patient and inspiring supervisors. I gratefully acknowledge the grant bodies, my parents and Australian Biological Resource Study for the generous financial support and for the academic tuition fees and living stipend; Skyrail Rainforest Foundation for research funding; Australian Systematic Botany Society and Australian Biological Resources Study for the support to attend conferences. My candidature would have been impossible without the support of these people and organizations. My colleagues at the Australian Tropical Herbarium in Cairns are some of the most wonderful people to have shared the journey of my candidature with. Many thanks are due to Dr. Caroline Puente Lelievre, Kaylene Bransgrove, Lalita Simpson, Sook-Ngoh Phoon, Agustina Arobaya, Gary Wilson, the co-occupants of the post graduate room; Drs. Claire Micheneau, Katharina Schulte, Ashley Field for sharing their extensive knowledge of systematics, patient guidance and discussions; Andrea Lim, Frank Zich and the team of ATH for logistic and moral support. These people provided me with a great deal of personal and professional support. These people are acknowledged for providing technical assistance in the various subjects, in field and sharing their invaluable knowledge of NE Queensland: Wendy and William Cooper, Rigel Jensen, Andrew Ford, Mark Coode, Stuart Worboys, Dr. Fanie Venter, Dr. David Rentz, Melissa Harrison, Dr. Soraya Gaze, Dr. Alex Lechner, Peter Bannink, Dr. Tapio Linderhaus, Charlie and Lewis Roberts, Dr. Craig Costion, Tony Roberts, Bruce Gray, Fay Adams and Irene Champion. Many thanks to the following people for criticising chapter drafts: Dr. Claire Micheneau, Gary Wilson, Dr. Chris Quinn, Cameron Kilgour, Kaylene Bransgrove, Dr. David Rentz, Dr. Fanie Venter. I really appreciated the constructive comments and advice. Lastly and most importantly, I would like to express my greatest gratitude to my family Cameron Kilgour, Kayoko and Eiji Baba, and friends I acquired over the years, especially Dr. Caroline Puente Lelievre, Kaylene Bransgrove and Barbara Forster. We went through some long and hard times together but they were most significant and fun time in my life, and cannot thank you enough for sharing it with me from the beginning until, the very end. GENERAL ABSTRACT An important role of taxonomy is to document the biological world by discovering and determining the relationships of, and formally describing, organisms. This not only enhances our knowledge of biodiversity, but also provides fundamental information for other disciplines. The aim was to increase the understanding of the hierarchical relationships within the rainforest tree genus Elaeocarpus as the basis for a better understanding of the evolutionary processes that have given rise to the extant diversity. An hierarchical approach using different methods and datasets for different taxonomic questions was employed: phylogenetics, population genetics, morphometrics and traditional descriptive taxonomy. The phylogenetic relationships of Elaeocarpaceae were investigated using nucleotide sequences of two plastid intergenic spacers, trnL-trnF and trnV-ndhC, and the nuclear encoded Internal Transcribed Spacer region. Maximum parsimony and Bayesian analyses of the combined plastid and nuclear data with enhanced taxon sampling produced a more detailed estimate of relationships within Elaeocarpaceae than previous studies. Monophyly of all the genera of Elaeocarpaceae except Elaeocarpus, Aceratium and Sericolea was confirmed. Elaeocarpus, Aceratium and Sericolea formed a strongly supported clade in the multigene tree in the Bayesian analysis but the determination of taxonomic rank for each group requires further investigation. Some morphological groups such as Group V Subgroup A, Group VI Subgroup B and part of Group XI subgroup B proposed by Coode (1984) were each strongly supported as monophyletic based on the separate marker data sets as well as the combined data set. Additionally, samples of the Elaeocarpus obovatus species complex (Group V D + E. coorangooloo) formed a monophyletic group strongly supported in most analyses. Some clades showed correlation with geography. These areas are New Caledonia-Pacific and Asia. The phylogenetic study provided an evolutionary framework within which to place the undescribed taxa in Australia. The undescribed taxa sampled for this study now have their positions in their respective groups confirmed: E. sp. Mt Misery was nested in Group VI B; E. Mt. Windsor Tableland was placed in Group XI Subgroup B. Further investigation of these entities was beyond the scope of this study, partly because insufficient material was available for a thorough analysis. With the aim to solve long-standing problems of taxonomic delimitation within the E. obovatus species complex (Group V D + E. coorangooloo), genetic variation, diversity and relatedness were
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