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Ecological and Biological Studies of New Zealand Lichens in Genus Usnea

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Ecological and Biological Studies of New Zealand Lichens in Genus Usnea Lincoln University Digital Thesis Copyright Statement The digital copy of this thesis is protected by the Copyright Act 1994 (New Zealand). This thesis may be consulted by you, provided you comply with the provisions of the Act and the following conditions of use: you will use the copy only for the purposes of research or private study you will recognise the author's right to be identified as the author of the thesis and due acknowledgement will be made to the author where appropriate you will obtain the author's permission before publishing any material from the thesis. Ecological and Biological Studies of New Zealand Lichens in the Genus Usnea A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University by Arash Rafat Lincoln University 2014 Abstract of a thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy Abstract Ecological and Biological Studies of New Zealand Lichens in the Genus Usnea by Arash Rafat Due to its complicated taxonomy, the ecology and evolution of the lichen genus Usnea has been understudied by lichenologists in New Zealand and around the world. To address this, almost 450 specimens of Usnea were collected in this study from 42 different sites around the North and South Islands of New Zealand. Molecular data (ITS rDNA) were generated for both the mycobiont and photobiont symbionts using specific algal and fungal primers. For the first time, the phylogenetic positions of the specimens within the genus Usnea in New Zealand and their associated photobionts were studied using Bayesian phylogenetic analysis of the molecular data. The reliability of some of the most important phenotypic characters, which usually are used in specimen identification to species, were evaluated by mapping the characters onto the mycobiont phylogenetic tree. Patterns of codiversification within New Zealand Usnea were investigated by examining phylogenetic congruence for the mycobiont and photobiont symbionts using three independent, geographically-referenced molecular datasets, which varied in phylogenetic diversity and spatial extent. In vitro culture protocols for symbiont isolation and synthetic relichenisation were optimised for Usnea specimens in New Zealand and some of the culturable endolichenic microorganisms associated with these specimens were identified. Algal and fungal ITS rDNA regions were successfully generated for both the mycobionts and photobionts from 367 samples. The Bayesian mycobiont and photobiont phylogenetic trees revealed the first view of the phylogenetic position of Usnea specimens in New Zealand and some within-genus groupings are proposed based on the results of sequence-similarity BLAST searches, morphologically identified specimens, and the available Usnea species ITS sequences in GenBank. All photobionts associated with Usnea were from the genus Trebouxia and their phylogenetic tree suggested the presence of many different species including Trebouxia jamesii, T. brindabellae, and T. australis. Analyses of phylogenetic congruence between the mycobiont and photobiont genetic distances revealed very strong patterns of codiversification exist for the genus Usnea lichen in New Zealand at three spatial scales, from within one kilometre to across New Zealand. There was, however, some ii variation in these codiversification patterns, which is likely to be driven by both intrinsic and extrinsic factors, such as the specificity of both partners towards each other, environmental conditions, and the availability of symbionts and their habitat preferences. In vitro protocols successfully produced axenic cultures of both the mycobionts and photobionts and provided an opportunity to compare the morphology and structure of both symbionts in their non-lichenised forms. These cultures of the Usnea mycobiont and the Trebouxia photobiont were used to successfully create a synthetic relichenisations, which had very different morphology compared to the parental thalli. Numerous algal, bacterial, and fungal endolichenic microorganisms living within Usnea thalli were cultured and identified. Of these, a relichenisation experiment showed that the alga Coccomyxa spp. is proposed to be a potential second photobiont associated with some Usnea mycobionts. The results of this thesis have improved our understanding of Usnea biology, phylogenetics and ecology and provide a foundation for further studies of this genus. Keywords: Usnea, Trebouxia, Lichen, Symbiosis, Phylogenetic, Mycobiont, Photobiont, Codiversification, In vitro Culture, Endolichens. iii Acknowledgements All praises to the Almighty God for affording me the strength and determination to complete this study. It is my pleasure to express my sincere gratitude and appreciation to my supervisor Dr. Hannah Buckley for her guidance and valuable advice, her constant encouragement, and the freedom that she provided to work and think throughout my research. She was following my research progress during our regular meeting and her great ideas were always helpful. I am grateful to Dr. Rob Cruickshank as my associate supervisor for his valuable suggestions and useful discussions during my research. The academic meetings at the Department of Ecology arranged by him, especially the molecular ecology meeting, were also very helpful during my research. I would also like to thank him for useful information he provided during the molecular systematic course. I am also grateful to Dr. Hayley Ridgway as my associate supervisor for her useful comments and suggestions about proper molecular biology methods and in vitro culture techniques. I would also like to thank Dr. Allison Knight and Jennifer Bannister for their help in the sampling and identification of specimens. However, the valuable effort of many other people (Hugh Wilson, Elizabeth Bargh, Dan Blanchon, Lars Ludwig, Brad Case, Mike Bowie, John Marris, Ben Wiseman, Ursula Brandes, Hamish Maule, Ben Myles, Natalie Scott) is greatly appreciated here for collecting and sending samples for this study. Many thanks are due to Dr. Tina Summerfield (University of Otago) for helping me to investigate the presence of cyanobacteria within my lichen samples and to Dr. Marie Hale (University of Canterbury) for her valuable suggestions for preparing suitable DNA sample for pyrosequencing and establishing microsatellite markers. Special thanks to Dr. Brad Case and Sam Brown for helping me with data analyses. I would also like to acknowledge the Allen Herbarium for providing valuable sample vouchers and the Department of Conservation for land access permission. Special thanks to Brain Mason for providing research funding and to Lincoln University for providing research funding, the use of laboratory facilities, and for a Doctoral Scholarship. It's my pleasure to offer my thanks to all my laboratory mates, colleagues and friends especially Saman Berenji, Thomas Maxwell, Johnathon Ridden, Maelle Pannetier, Suhaizan Lob, Wendy Liu, Heng Wee Tan, Dalin Brown, and Anusara Herath Mudiyanselage for maintaining a pleasant research atmosphere and making my stay at Lincoln University an enjoyable one. iv Last but not least, it is difficult to word my gratitude towards my family members for their encouragement and support during this period. v Table of Contents Abstract ....................................................................................................................................... ii Acknowledgements ..................................................................................................................... iv Table of Contents ........................................................................................................................ vi List of Tables ................................................................................................................................ x List of Figures .............................................................................................................................. xi Chapter 1 Introduction ...........................................................................................................15 Chapter 2 Literature Review....................................................................................................18 2.1 Lichens ................................................................................................................................... 18 2.2 The genus Usnea .................................................................................................................... 18 2.3 Taxonomy of lichens .............................................................................................................. 18 2.4 Taxonomy and the species concept in Usnea ........................................................................ 19 2.4.1 Morphological characteristics of Usnea spp. .............................................................20 2.4.2 Usnea chemotaxonomy .............................................................................................21 2.4.3 Systematics and taxonomy based on fungal molecular data ....................................22 2.4.4 Combining genetic and phenotypic information to address taxonomic and evolutionary questions in lichens ..............................................................................25 2.5 Photobiont ............................................................................................................................. 27 2.5.1 Identification and
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