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Morphological and Molecular Systematics of Resupinatus (Basidiomycota)

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Morphological and Molecular Systematics of Resupinatus (Basidiomycota) Western University Scholarship@Western Electronic Thesis and Dissertation Repository 8-24-2015 12:00 AM Morphological and Molecular Systematics of Resupinatus (Basidiomycota) Jennifer McDonald The University of Western Ontario Supervisor Dr. R. Greg Thorn The University of Western Ontario Graduate Program in Biology A thesis submitted in partial fulfillment of the equirr ements for the degree in Doctor of Philosophy © Jennifer McDonald 2015 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Other Life Sciences Commons Recommended Citation McDonald, Jennifer, "Morphological and Molecular Systematics of Resupinatus (Basidiomycota)" (2015). Electronic Thesis and Dissertation Repository. 3135. https://ir.lib.uwo.ca/etd/3135 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Morphological and Molecular Systematics of Resupinatus (Basidiomycota) (Thesis format: Integrated Article) by Jennifer Victoria McDonald Graduate Program in Biology A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy The School of Graduate and Postdoctoral Studies The University of Western Ontario London, Ontario, Canada © Jennifer V. McDonald 2015 i Abstract Cyphelloid fungi (small, cup-shaped Agaricomycetes with a smooth spore-bearing surface) are, compared to their gilled relatives, poorly studied and understood. Within the tribe Resupinateae (which has included the genera Resupinatus, Stigmatolemma, Aphyllotus and Stromatocyphella), little is known about the evolution of the cyphelloid fruit body form. How many times has this reduced morphology evolved within the group? Do all cyphelloid members that are currently treated in this group belong there? Are there other described species of cyphelloid fungi currently treated in other genera that belong within the Resupinateae? This study presents phylogenies of the cyphelloid and small lamellate members of the Resupinateae based on rDNA sequences (ITS1, 5.8S, ITS2 and the D1/D2 region of the nuclear large subunit rRNA gene) to illustrate the evolution of reduced basidiomata in the Resupinateae. This study also provides an analysis of traditional morphological characters used to distinguish species (fruit body colour and size, and spore size, shape, ornamentation and colour) and compares morphological and DNA-based classifications. A total of 10 species new to science (representing approximately 20% of herbarium specimens examined) were discovered as a result of this study, and 24 species belonging in the Resupinateae were “rediscovered” (species previously described but forgotten since their initial description) amongst herbarium collections and in the literature. Based on the phylogenetic analysis of the group, all members of the Resupinateae fall into a single genus, Resupinatus, including Stigmatolemma and Stromatocyphella as synonyms, whereas the genus Aphyllotus is excluded from the group based on morphology. The cyphelloid fruit body morphology has evolved at least four separate times within the group. This study highlights the significance of herbaria as repositories of unknown and undocumented biodiversity, and shows that the evolution of different fruit body morphologies in the Fungi is not a linear pattern of simple to complex. Keywords Systematics, Molecular Systematics, Taxonomy, Fungi, Basidiomycota, Resupinatus, Agaricales, Fruit Body Morphology, Herbarium Specimens, Natural History ii Acknowledgments First I would like to thank my supervisor, Dr. Greg Thorn, for his invaluable assistance over the last eight years. Without his support, this work would not have been possible. I would also like to thank my advisors, Dr. André Lachance and Dr. Nusha Keyghobadi for their assistance and guidance. When The Beatles sang the songs “With a Little Help from My Friends” and “All You Need Is Love” they were obviously thinking about the graduate students I share an office with (Sarah Allan, Sara Asmail, Asma Asemaninejad, Michael Del Vasto, Chris Hay, Jason Lehrer, and Nimalka Weerasuriya), as well as all of the current and past graduate students with whom I have shared a lab. You have all helped keep me sane over my time here, and for that I thank you very much. I have also shared a lab with work-study and volunteer students too numerous to name, but I would like to officially acknowledge one: Terry Dongkeun Kim. You got me excited to do lab work again. Thank you. Last but certainly not least, I would like to thank my family for supporting me during my time in graduate school: my parents, grandparents, aunts, uncles, cousins, and those that I lost along the way. To Dorothy Saunders: I wish you were still here to share in the joy of my accomplishments. I know you would have been so proud. I dedicate this thesis to you. iii Table of Contents Abstract……………………………………………………………………………………ii Keywords………………………………………………………………………………….ii Acknowledgments.............................................................................................................. iii Table of Contents ............................................................................................................... iv Statement of Co-Authorship .............................................................................................. ix List of Tables ...................................................................................................................... x List of Figures .................................................................................................................... xi List of Appendices ........................................................................................................... xiv List of Abbreviations ........................................................................................................ xv Preface.............................................................................................................................. xix Chapter 1 ............................................................................................................................. 1 1 General Introduction and Literature Review.................................................................. 1 1.1 Overview and Broad Classification of Macrofungi ................................................ 1 1.2 Historical Classification of the Agaricales ............................................................. 3 1.2.1 Defining the Agaricales using molecular techniques ................................. 5 1.2.2 Species concepts in Agaricales and other Fungi......................................... 6 1.3 A Synopsis of the Resupinateae ............................................................................. 8 1.3.1 Resupinatus (including Asterotus) .............................................................. 8 1.3.2 Stigmatolemma .......................................................................................... 12 1.3.3 Stromatocyphella ...................................................................................... 14 1.3.4 Aphyllotus ................................................................................................. 15 1.4 Goals of this work ................................................................................................. 15 1.5 References ............................................................................................................. 18 Chapter 2 ........................................................................................................................... 26 iv 2 The Resupinateae Singer: Resupinatus Gray ............................................................... 26 2.1 Introduction ........................................................................................................... 26 2.2 Materials and Methods .......................................................................................... 29 2.2.1 Herbarium samples ................................................................................... 29 2.2.2 Analysis of herbarium samples ................................................................. 29 2.2.3 Fresh collections ....................................................................................... 31 2.2.4 Media and cultures .................................................................................... 31 2.2.5 DNA extraction and amplification ............................................................ 32 2.2.6 Sequencing of PCR products .................................................................... 33 2.2.7 Phylogenetic analysis ................................................................................ 34 2.3 Results and Discussion ......................................................................................... 35 2.3.1 Stigmatolemma is polyphyletic and a synonym of Resupinatus ............... 49 2.3.2 The lamellate Resupinatus species............................................................ 49 2.3.3 Excluded species ....................................................................................... 50 2.3.4 Stromatocyphella conglobata ................................................................... 50 2.4 Taxonomy ............................................................................................................. 52 2.4.1 The tribe
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