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Phylogenetics of Stelis (Orchidaceae: Pleurothallidinae)

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Phylogenetics of Stelis (Orchidaceae: Pleurothallidinae) Phylogenetics of Stelis (Orchidaceae: Pleurothallidinae) and closely related genera By: Adam P. Karremans Based on: Molecular Data, Morphological Characteristics and Geographical Distribution In the Mesoamerican and Andean Cordilleras MSc Thesis Plant Breeding & Genetic Resources Plant Sciences Group / Biosystematics Group Wageningen University July 2010 “Systematics is a lonely voice speaking on behalf of an interest in diversity in Biology” (Robinson 1901 cited in Constance 1964). Supervised by: Freek Bakker Nationaal Herbarium Nederland–Wageningen Branch, Biosystematics Group, Wageningen University, Wageningen, The Netherlands. Email: [email protected]. Franco Pupulin Jardín Botánico Lankester, Universidad de Costa Rica, Apdo. 1031–7050, Cartago, Costa Rica, CA; Marie Selby Botanical Gardens, Sarasota, FL, USA; Harvard University Herbaria, Cambridge, MA, USA; ‘‘Angel Andreetta’’ Andean Orchid Research Center, University Alfredo Pérez Guerrero. Ecuador. Email: [email protected] Rene Smulders Plant Research International, Wageningen UR. P.O. Box 16, NL‐6700 AA Wageningen. The Netherlands. Email: [email protected]. With the collaboration of: Diego Bogarín Jardín Botánico Lankester, Universidad de Costa Rica, Apdo. 1031–7050, Cartago, Costa Rica. ‘‘Angel Andreetta’’ Andean Orchid Research Center, University Alfredo Pérez Guerrero, Ecuador. Email: [email protected]. Robert L. Dressler Jardín Botánico Lankester, Universidad de Costa Rica, Apdo. 1031–7050, Cartago, Costa Rica. Email: [email protected]. Eliecer Duarte Observatorio Vulcanologico y Sismologico de Costa Rica. OVSICORI‐UNA. Heredia, Costa Rica. Email: [email protected]. Melania Fernández Jardín Botánico Lankester, Universidad de Costa Rica, Apdo. 1031–7050, Cartago, Costa Rica. Email: [email protected]. Eric Hágsater Herbario AMO, Montañas Calizas 490, México, D.F. 11000, México. Email: [email protected]. Stephen Kirby U.S. Geological Survey, 345 Middlefield Road, Menlo Park, California 94025, USA. Email: [email protected]. Christina Smith Jardín Botánico Lankester, Universidad de Costa Rica, Apdo. 1031–7050, Cartago, Costa Rica. Email: [email protected]. Rodolfo Solano Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Oaxaca, Instituto Politécnico Nacional. Hornos 1003, Santa Cruz Xoxocotlan, 71230, Oaxaca, México. Email: [email protected]. Mark Wilson Biology Department, the Colorado College. 14 East Cache, La Poudre, Colorado Springs. CO 80903. USA. Email: [email protected]. I I am thankful to the staff at Lankester Botanical Gardens for all their cooperation and support, especially to Jorge Warner the general director, the researchers Robert Dressler, Franco Pupulin and Diego Bogarín and the research assistants Melania Fernández and Christina Smith, for everything they have done and made possible. I am also thankful to the staff at Wageningen University and Research Center, from the Biosystematics Department to Mark Sosef, Jan Wieringa and Freek Bakker and from the Plant Sciences Department to Rene Smulders and Clemens van de Wiel for their extended involvement, and the Plant Breeding lab staff who made the molecular studies possible, especially Linda Kodde. I am grateful to all the external collaborators, Eric Hágsater, Stephen Kirby, Rodolfo Solano and Mark Wilson for their contributions, and to Arjen and Wesley. Last, but not least, I am very much in dept to my parents and girlfriend for the continuing support and feedback. II Table of Contents Summary ..................................................................................................................................... VI 1. Introduction .......................................................................................................................... 6 1.1. Taxonomical History of Stelis ................................................................................................ 8 1.2. Phylogenetic Analyses ......................................................................................................... 10 1.3. The Present Study ............................................................................................................... 14 1.3.1. Main Hypothesis ............................................................................................................... 15 1.3.2. Secondary Hypotheses ...................................................................................................... 15 2. Materials and Methods ....................................................................................................... 16 2.1. Field Work ........................................................................................................................... 16 2.1.1. Species Selection ............................................................................................................... 16 2.1.2. Documentation ................................................................................................................. 17 2.1.3. Sample Collection ............................................................................................................. 18 2.1.4. Scoring Morphology .......................................................................................................... 18 2.2. Laboratory Work ................................................................................................................. 18 2.2.1. DNA Extraction .................................................................................................................. 19 2.2.2. Primer Selection ................................................................................................................ 19 2.2.3. Amplification ..................................................................................................................... 19 2.2.4. Sequencing ........................................................................................................................ 20 2.3. Building the data sets .......................................................................................................... 21 2.3.1. Sequence Editing ............................................................................................................... 21 2.3.2. Sequence Alignment ......................................................................................................... 21 2.4. Analyzing the data Sets ....................................................................................................... 22 2.4.1. Parsimony ......................................................................................................................... 22 2.4.2. Maximum Likelihood......................................................................................................... 22 2.4.3. Bayesian Analysis .............................................................................................................. 22 2.4.4. Testing the model ............................................................................................................. 23 2.4.5. Concatenation ................................................................................................................... 23 2.4.6. Consensus Networks ......................................................................................................... 24 2.4.7. Quality of the Analyses ..................................................................................................... 24 2.4.8. Morphological Matrix ....................................................................................................... 25 III 2.4.9. Geographical Trends ......................................................................................................... 25 3. Results ................................................................................................................................ 26 3.2. Phylogenetic Reconstruction .............................................................................................. 26 3.1.1. DNA Extraction and Amplification .................................................................................... 26 3.1.2. Analysis of ITS ................................................................................................................... 26 3.1.3. Analysis of matK ................................................................................................................ 27 3.1.4. Analysis of trnH‐psbA ........................................................................................................ 27 3.1.5. Concatenated Analysis ...................................................................................................... 27 3.3. Clade Descriptions .............................................................................................................. 31 3.2.1. First Level Clades ............................................................................................................... 32 3.2.2. Second Level Clades .......................................................................................................... 34 3.2.3. Third Level Clade ............................................................................................................... 35 3.4. Consensus Networks ........................................................................................................... 36 3.5. Morphology ........................................................................................................................
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