Molecular Systematics of Selected Australian Brown Algae Nuttanun Soisup A thesis submitted in fulfillment of the requirements for the degree of Doctor of Philosophy School of Earth and Environmental Sciences University of Adelaide, Australia November 2014 Table of contents Thesis summary . . . . . . 5 Declaration of Authority of Access to Copying . . 6 Acknowledgements . . . . . . 7 Chapter 1 - Introduction . . . . . 10 1.1 Background . . . . . 11 1.2 Thesis structure and objectives . . . 14 1.3 Molecular phylogenetic background . . 18 1.4 Taxonomic description of the focal species and genera of this study . . . . . . . 28 Chapter 2 - Phylogenetics, DNA barcoding and phylogeographic discrimination within the Australian endemic brown macroalgal genera, Caulocystis and Acrocarpia (Sargassaceae, Phaeophyceae), based on ITS, cox1 and rbcL DNA sequences . . . . . . . . . 39 Statement of Authorship . . . . 40 Abstract . . . . . . 41 Introduction . . . . . . 43 Materials and Methods . . . . 48 Results . . . . . . . 52 Discussion . . . . . . 61 Taxonomic Changes . . . . . 67   2 Chapter 3 - Molecular Phylogenetics of the Australian endemic brown algal genus Cystophora (Sargassaceae, Phaeophyceae) based on cox1, rbcL and ITS DNA sequence analyses . . . . . . 69 Statement of Authorship . . . . 70 Abstract . . . . . . 71 Introduction . . . . . . 72 Materials and Methods . . . . 76 Results . . . . . . . 80 Discussion . . . . . . 93 Taxonomic changes . . . . . 100 Chapter 4 -: Unveiling species diversity of Australian Lobophora (Dictyotales) based on rbcL and cox1 DNA sequence analyses . . . 102 Statement of Authorship . . . . 103 Abstract . . . . . . 104 Introduction . . . . . . 105 Materials and Methods . . . . 108 Results . . . . . . . 113 Discussion . . . . . . 121 Chapter 5 -: General Discussion . . . . 110 5.1 Taxonomic revision and phylogenetic relationships of Acrocarpia, Caulocystis and Cystophora . . . . 128 5.2 Taxonomic changes . . . . 131 5.3. Unveiling cryptic diversity in Lobophora . 133 5.4 Phylogeographic inferences . . . 134 5.5 Significance of the thesis . . . . 136   3 References . . . . . . . 137 Appendices . . . . . . . . 160   4 Thesis Summary This thesis focuses on the molecular systematics of four selected Australian brown algal genera (Phaeophyceae); Acrocarpia, Caulocystis, Cystophora (Fucales) and Lobophora (Dictyotales). The thesis consists of five chapters. Chapter 1: General introduction; Chapter 2: The phylogenetics, DNA barcoding and phylogeographic discrimination of Caulocystis and Acrocarpia species; Chapter 3: The molecular phylogenetics of Cystophora; Chapter 4: An assessment of species diversity within Australian Lobophora based on rbcL and cox1 DNA sequence analyses, and Chapter 5: General discussion. The first chapter describes the marine floral biodiversity of Australia, the ecological importance of benthic brown algae, the development of taxonomic studies in macroalgae, and the aims and significance of this study. The second chapter is the first molecular taxonomic study specifically targeting two endemic Australian Fucales genera, Acrocarpia and Caulocystis, based on cox1, rbcL and ITS2 DNA sequence analyses. Results from molecular and morphological data suggest that two known Caulocystis species are conspecific, and hence should be merged into a single taxon. The third chapter aims to clarify taxonomic problems originating from the phenotypic plasticity of the Australian and New Zealand endemic genus Cystophora. Traditionally, Cystophora species identification has been based on morphological features alone. This study applies molecular phylogenetic analyses to reassess Cystophora taxonomy. Results demonstrate the competence of molecular phylogenetics for resolving species delineation problems and establishing evolutionary relationships within the genus. The fourth chapter reports on the true levels of species richness in the brown algal genus Lobophora based on rbcL and cox1 DNA sequences. Lobophora is found all over the world, from tropical to warm temperate waters, and wherever it is found, species in this genus are common and conspicuous members of the benthic flora. In Australia there have been only four species recognized so far. However, the molecular data generated from approximately 300 new specimens collected widely around Australia suggest the existence of at least 22 species. Consequently, the species diversity within the genus has been highly underestimated, worldwide. The last chapter is a summary of the findings, including new taxonomic changes and the   5 significance of molecular phylogenetics in both, solving long standing phylogenetic questions and uncovering hidden brown algal species diversity in Australia.   6 Declaration and Authority of Access to Copying This work contains no material which has been accepted for the award of any other degree or diploma in any university or other tertiary institution and, to the best of my knowledge and belief, contains no material previously published or written by another person, except where due reference has been made in the text. I give consent to this copy of my thesis when deposited in the University Library, being made available for loan and photocopying, subject to the provisions of the Copyright Act 1968. I also give permission for the digital version of my thesis to be made available on the web, via University’s digital research repository, the Library catalogue, the Australasian Digital Theses Program (ADTP) and also through web search engines, unless permission has been granted by the University to restricted access for a period of time. Nuttanun Soisup 26 July 2013   7 Acknowledgements I would like to thank my supervisors, Dr. C. Frederico D. Gurgel and Prof. Andrew Lowe, for their direction, encouragement and perseverance in guiding me to the completion of this work. I also would like to express my gratitude to members of the Fred and Andy labs: Rainbo Dixon, Gareth Belton, Tracey Spokes, Chelsea Tothill, Phyllis MacGillivray, Patricia Fuentes-Cross, Jolene Scoble, Kym Ottewell, Martin Breed and Maria Marklund for advice, support and encouragement. I also would like to thank Alison Jobling, Andy’s PA, for arranging the meetings and people in Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) for providing facilities and assistance. I extend my further gratitude to the staff at State Herbarium of South Australia, for providing access to specimens and collections. I thank Bob Baldock for providing me advice in species identification and morphological identification issues, Carolyn Ricci for lab assistance, advice and support. I also would like to thank people who provided me specimens and fieldtrip assistance, namely Dr. Gerald Kraft, John Huisman and Kyatt Dixon. I also thank members of Phycology Lab at the Faculty of Fisheries, Kasetsart University, namely Prof. Khanjanapat Lewmanomont, Assoc. Prof. Anong Chirapart, Dr. Jantana Priboon. I also would like to thank Narongrit Muanmai for support and important advice for the data analyses.   8 Additionally, I would like to thank all staffs at the Office of Educational Affairs, Royal Thai Embassy for providing me support and important information; and the Royal Thai Scholarship for providing me the opportunity to complete my degree at the University of Adelaide. Lastly, I would like to thank my family, my mom and my brother for support and understanding. I also would like to thank friends and people who gave me support and encouragement during the four years of my study. Nuttanun Soisup 26 July 2013   9 Chapter 1 Introduction   10