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Orchidaceae) from Indonesia, and Fungal Association of Goodyera Section Goodyera

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Orchidaceae) from Indonesia, and Fungal Association of Goodyera Section Goodyera Phylogenetic Analyses of subtribe Goodyerinae and Revision of Goodyera section Goodyera (Orchidaceae) from Indonesia, and Fungal Association of Goodyera section Goodyera Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Lina Susanti Juswara, MSc. Graduate Program in Evolution, Ecology, and Organismal Biology The Ohio State University 2010 Dissertation Committee: Paul Fuerst, Advisor Laura Kubatko Hans Klompen Copyright by Lina Susanti Juswara 2010 Abstract Phylogenetic analyses using morphological and molecular data of the orchid subtribe Goodyerinae were performed using parsimony, maximum likelihood, and Bayesian methods. Two hypotheses, proposed by Dressler (1993) and Szlachetko (1995), were tested. The results showed that neither hypothesis can be supported, and that there are no morphological characteristics that can define groups within the subtribe Goodyerinae. Monophyletic groups within the subtribe cannot be defined using molecular information from three genes. Systematic revision of Goodyera section Goodyera from Indonesia was investigated using phenetic analyses (cluster analysis, non-metric multidimensional scaling), and discriminant function analysis. The results showed that, of eight forms initially recognized, only three independent taxa can be recognized by these analyses. The independent taxa are Goodyera bifida, G. procera, and G. reticulata. Six subspecies are recognized under Goodyera reticulata. They are G. reticulata subsp. colorata, G. reticulata subsp. gibbsiae, G. reticulata subsp. gemmata, G. reticulate subsp. pusilla, and G. reticulata subsp. reticulata. ii Fungal associations with members of Goodyera section Goodyera from Indonesia were examined using data from the fungal nuclear ITS region. Indonesian species of Goodyera section Goodyera have a broader range of fungal associates than do other taxa from the subtribe that had been previously studied. Members of Goodyera section Goodyera from Indonesia are associated not only with fungi of the phylum Basidiomycetes, including Rhizoctonia-like forms and Russula,, but also with some species from the phylum Ascomycetes. In contrast, temperate species of the subtribe (Goodyera oblongifolia) showed the stricter association with previously defined fungal taxa (Rhizoctonia groups). iii Dedication Dedicated to the students at The Ohio State University iv Acknowledgments Thanks to my committee members: Dr. Paul Fuerst, Dr. Laura Kubatko, and Dr. Hans Klompen for providing scientific assistance during the process of finishing the dissertation. Also, thanks goes to Mr. Lyn Craven from The Australian National Herbarium for assistance in the taxonomic treatments of Goodyera section Goodyera from Indonesia. Thanks to the directors or the chiefs of several herbaria Bogor: Herbarium Indonesia (BO); Australian National Herbarium, Australia (CANB and QRS) Queensland Herbarium, Australia (BRI), New South Wales Herbarium, Australia (NSW); The British Museum, U.K. (BM), Kew Herbarium, U.K. (K); National Herbarium Nederland (Leiden Branch), The Netherlands (L); Museum National d’Histoire Naturelle, France (P); and Bishop Museum (BISH) Hawaii, The USA for lending herbarium specimens under their care. Thank you to funding institutes: Indonesian Institute of Sciences: Botany Division; Evolution, Ecology, and Organismal Biology: Beatley Funding; The Office of International Affairs: International Travel Funds; Linnean Society of London; The American Plant Taxonomy; The Ohio State University Graduate School: Alumni Grants v for Graduate Research and Scholarship; and others that have supported the research and other workshops need to complete the dissertation. I would like to thank to Jose Diaz, Barbara Shady, Alpana Chaudhuri, and Mesfin Tadesa for providing assistance in molecular techniques and herbarium specimens. Finally, I would like to thank many people anonymously to support my fieldwork in Indonesia (Java, Sumatra, Sulawesi, Irian Jaya, and Bali), and in the US (Wisconsin and Ohio), during the process of preparation of the projects, sending leaf samples, gathering data, and finishing up my dissertation during the process. vi Vita 1995 ………………………………. B.S. Agriculture, Brawijaya University Indonesia 2000 ………………………………. MSc Science, The Australian National University 2002-Present ……………………. Graduate Teaching Associate, Department of Evolution, Ecology, and Organismal Biology, The Ohio State University Publications: Juswara, L.S. and Craven, L.A. 2005. The Hibiscus panduriformis complex (Malvaceae) in Australia. Blumea 50: 389-405. Craven, L.A., Brown, G.K., and Juswara, L.S. 2005. Collection of Rhododendron Section Vireya in Sulawesi, Indonesia, for studies into their evolutionary relationships and biogeography. American Rhododendron Society Journal 59: 194-201. vii Field of Study Major Field: Evolution, Ecology, and Organismal Biology viii Table of Contents Abstract …………………………………………………………………………..……… ii Dedication ……………………………………………………………………….……… iv Acknowledgments ………………………………………………………………………. v Vita ……………………………………………….……………………………………. vii List of Tables ………………………………………………………………………… xviii List of Figures ………………………………………………………………………….xxii Chapter 1: Introduction ………………………………………………………………….. 1 1.1. Introduction to Goodyerinae ………………………………………………….. 6 1.2. Morphology of Goodyerinae.…………….……………………………………... 9 1.3. Geographic Distribution of Goodyerinae …………………………………..… 14 1.4. Systematic problems of Goodyerinae ……………………………………….. 15 1.5. The genus Goodyera ……………………………………………………….. 17 1.6. The Aims of the Research …………………………………………………… 22 ix Chapter 2: Phylogenetic Analysis of the Subtribe Goodyerinae ………………………. 23 2.1. Introduction ………………………………………………………………………... 23 2.1.1. Taxonomic History of Goodyerinae ……………………………………………. 25 2.1.2. The Association of the subtribe Goodyerinae with other subtribes within tribe Cranichideae .…………………..…………………………………………….. 29 2.1.3. Aims of the study ……………………………………………………………….. 30 2.2. Methods ……………………………………………………………………………. 31 2.2.1. Testing Phylogenetic Hypotheses: The Problem of Defining the Homology of Characters .………………..…………………………………………………..... 31 2.2.2. Collection of data ………………………………………………………………... 32 2.2.3. Homology of molecular characters ……………………………………………... 40 2.2.4. Molecular characters used ………………………………………………………. 40 2.2.4.1. Internal Transcribed Spacer (ITS) .………………………………………….. 41 2.2.4.2. trnL-F …………………………………………………………………………………… 43 x 2.2.4.3. rpl16 …………………………………………………………………………….44 2.2.5. Molecular Technique ……………………………………………………………. 47 2.2.5.1. DNA extraction ………………………………………………………………... 47 2.2.5.1.1. CTAB method ……………………………………………………………….. 47 2.2.5.1.2. CTAB extraction for Micro Samples ………………………………………... 48 2.2.5.1.3. Qiagen DNeasy Plant Mini Extraction Kit ………………………………….. 50 2.2.5.2. PCR Amplification and Sequencing …………………………………………... 50 2.2.6. Coding of Potentially Phylogeneticaly Informative Characters ………………… 50 2.2.7. Data Analyses …………………………………………………………………… 52 2.2.7.1. Sequence Alignment…………………………………………………………… 52 2.2.7.2. Analysis Using Parsimony……………………………………………………... 52 2.2.7.3. Maximum Likelihood: Parameters in Maximum Likelihood ………………… 53 2.2.7.3.1. ModelTest ………………………………………………………………….... 54 2.2.7.4. Bayesian Inference of Phylogeny………. …………………………………….. 56 xi 2.2.7.5. Combined Analyses …………………………………………………………….56 2.2.7.6. Statistical Support of Branching Order and Clades …………………………....57 2.2.7.6.1. The Use of Bootstrapping …………………………………………………… 58 2.2.7.6.2. The Use of Jackknifing ……………………………………………………….58 2.3. Results ………………………………………………………………………………59 2.3.1. Use of Molecular Characters to Infer Phylogenetic Relationships in the Subtribe Goodyerinae ………………………………………………………………… 60 2.3.1.1. Analyses Using Parsimony ……………………………………………………. 60 2.3.1.2. Analyses of ITS, trnL-F, rpl16, and Combined Data Sets Using maximum likelihood ………………………………………………………………………..71 2.3.1.3. Bayesian Analyses …………………………………………………………….. 83 2.4. Discussion and Conclusion ………………………………………………………... 90 Chapter 3: Fungal Association of Goodyera section Goodyera from Indonesia ……..…93 3.1. Introduction ………………………………………………………………………... 93 xii 3.1.1. Fungal Associations of Goodyera section Goodyera in Indonesia…………….. 100 3.1.2. Hypotheses about Orchid-Fungal Associations ………………………………... 102 3.2. Materials and Methods …………………………………………………………….104 3.2.1. Sampling Strategy ……………………………………………………………… 104 3.2.2. Fungal Cultures and DNA Extraction ………………………………………….. 106 3.2.3. Data Analyses ………………………………………………………………..… 108 3.2.4. Association between Orchids and Fungi ……………………………………….. 111 3.2.5. Statistical Tests for Co-speciation ……………………………………………... 113 3.2.6. Analysis of Fungal Association of Goodyera section Goodyera from Indonesia …………………………………………………………………………………..114 3.3. Results…………………………………………………………………………….. 114 3.3.1. Anatomical analysis of roots …………………………………………………… 115 3.3.2. DNA Analysis of Fungal Associations with Species within Goodyera section Goodyera in Indonesia ………………………………………………………... 117 xiii 3.3.3. Results of Parsimony…………………………………………………………… 119 3.4. Discussion ………………………………………………………………………... 122 3.5. Conclusion ……………………………………………………………………….. 124 Chapter 4: Multivariate Analysis of Goodyera section Goodyera from Indonesia ……126 4.1. Introduction ………………………………………………………………………. 126 4.1.1. Goodyera section Goodyera from Indonesia…………………………………… 126 4.1.2. Species Concepts ………………………………………………………………. 129 4.2. Methods…………………………………………………………………………….132 4.2.1. Sampling Strategy……………………………………………………………….
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