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Thesis Preliminary Plan RELACIONES FILOGENÉTICAS EN LA TRIBU TIGRIDIEAE (IRIDACEAE) YOLANDA MARCELA CELIS PACHECO UNIVERSIDAD NACIONAL DE COLOMBIA FACULTAD DE CIENCIAS-ÁREA CURRICULAR DE BIOLOGÍA Bogotá, 2012 RELACIONES FILOGENÉTICAS EN LA TRIBU TIGRIDIEAE (IRIDACEAE) YOLANDA MARCELA CELIS PACHECO Tesis de Doctorado en Ciencias-Biología DIRECTOR LUIS FERNANDO GARCÍA PINZÓN Biólogo, Ph. D. UNIVERSIDAD NACIONAL DE COLOMBIA FACULTAD DE CIENCIAS-ÁREA CURRICULAR DE BIOLOGÍA Bogotá, 2012 ACKNOWLEDGEMENTS I want to acknowledge the support of the Department of Biology, the Institute of Natural Sciences, the National University of Colombia and its Doctoral program in Science, for their help in developing this research. I want to thank to Dr. Luis Fernando García, Departamento de Biología, Universidad Nacional de Colombia; Dr. Hervé Sauquet, Université Paris-Sud 11, Lab. Écologie, Systématique, Évolution (ESE); Dr. Peter Goldblatt, Missouri Botanical Garden, St. Louis, MO; M.S. Diego Bogarín, Jardín Botánico Lankester (Costa Rica); Dr. Aarón Rodríguez, Departamento de Botánica y Zoología, Universidad de Guadalajara (México); Dr. Vincent Savolainen and the team of Molecular Systematics Section, Royal Botanic Gardens, Kew; Imperial College, London, UK, for training and assistance in obtaining and analyzing molecular data. To Dr. Paula Rudall, Head of Micromorphology Section, Kew; Dr. Chrissie Prychid and Dr. Hannah Banks, Team of Micromorphology Section Royal Botanic Gardens, Kew; Dr. Shirley Graham, Missouri Botanical Garden, Dr. Sara Fuentes-Soriano St. Louis, MO For training and assistance in obtaining and analyzing data of pollen morphology. Dr. David Boggler, Lab Manager, Missouri Botanical Garden, for SEM training, and with support from NSF-MRI 0958873. To M.S. Angel Cruz and Dr. Fabio González, Bioingenium Research Group, National University of Colombia for assistance in managing and obtaining data from SEM images. Special thanks: Dr. Germán Roitman, Facultad de Agronomía, Universidad de Buenos Aires, Argentina for access to his living collection and for pictures of South American Tigridieae. To Dr. Luis Fernando García, M.S. Zachary Rogers and Dr. Sara Fuentes- Soriano for their comments, continuous support and encouragement they gave me to make and greatly improve this work. Finally I am grateful for the financial support to the following grants and institutions that made this work possible: Shirley Graham Fellowship, Missouri Botanical Garden, St. Louis, MO; Kew Latin American Research Fellowships Programme (KLARF), Royal Botanic Gardens, UK; Red de Macrouniversidades de América Latina yel Caribe (Universia, México); National PhD Support Program, Instituto Colombiano para el desarrollo de la Ciencia y la Tecnología (COLCIENCIAS), Colombia; Programa de Movilidad Universidad Nacional de Colombia, Bogotá, Colombia. CONTENT ACKNOWLEDGEMENTS ........................................................................................ 3 CONTENT................................................................................................................ 5 LIST OF FIGURES .................................................................................................. 8 LIST OF TABLES ................................................................................................... 10 LIST OF APPENDICES ......................................................................................... 11 GENERAL ABSTRACT ............................................................................................ 1 GENERAL INTRODUCTION ................................................................................... 3 LITERATURE CITED ............................................................................................... 7 Chapter 1. PHYLOGENETIC RELATIONSHIPS IN TIGRIDIEAE (IRIDACEAE) BASED ON PLASTID AND NUCLEAR ITS DNA SEQUENCES ........................... 11 Abstract .................................................................................................................. 12 Resumen ............................................................................................................... 13 1. Introduction ........................................................................................................ 15 2. Material and Methods ........................................................................................ 18 2.1. Taxa and genetic material ........................................................................ 18 2. 2. DNA extraction and amplification ............................................................ 19 2.3. DNA sequencing, and DNA alignment .................................................... 20 2.4. Phylogenetic analyses ............................................................................ 20 2.5. Ancestral area reconstruction .................................................................. 22 3. Results ............................................................................................................... 24 4. Discussion.......................................................................................................... 28 4.1. The ITS region ......................................................................................... 28 4.2. The chloroplast plus the ITS regions ....................................................... 29 4.3. Geographical distribution of Tigridieae and ancestral areas .................... 33 4. 4. Taxonomy and nomenclature ..................................................................... 36 5. Literature cited ................................................................................................... 39 6. TABLES ............................................................................................................. 46 7. FIGURES ........................................................................................................... 58 Chapter 2. POLLEN MORPHOLOGY OF THE TRIBE TIGRIDIEAE (IRIDOIDEAE, IRIDACEAE) AND ITS SYSTEMATIC IMPLICATIONS ....................................... 102 Abstract ................................................................................................................ 103 Resumen ............................................................................................................. 104 1. Introduction ...................................................................................................... 105 2. Materials and methods ..................................................................................... 107 2.1.Palynological analyses............................................................................ 107 2.2 Molecular phylogenetic analyses ........................................................... 108 2.3 Character evolution ................................................................................ 108 3. Results ............................................................................................................. 109 3.1. General description of Tigridieae pollen ................................................. 109 3.2. Pollen descriptions of genera of Tigridieae ............................................ 111 3.3 Pollen morphological variation: univariate, bivariate and multivariate analyses. A case study in Cypella species ................................................... 115 3.4 Character evolution ................................................................................ 116 4. Discussion and conclusions ............................................................................. 117 5. Literature cited ................................................................................................. 119 6. TABLES ........................................................................................................... 121 7. FIGURES ......................................................................................................... 134 8. APPENDICES .................................................................................................. 145 Chapter 3. ZYGELLA S. MOORE, A SYNONYM OF LARENTIA KLATT (IRIDACEAE) ....................................................................................................... 150 Abstract ................................................................................................................ 151 Acknowledgments ................................................................................................ 155 Literature cited ..................................................................................................... 156 General conclusions……………………………………………………………………157 LIST OF FIGURES Chapter 1. Figure 1-1: Phylogenetic relationships among members of the Tribe Tigridieae (Subfamily Iridoideae) based on nuclear sequences of the ITS region……………………………………………………………………………………...58 Figure 2-1: Phylogenetic relationships among members of the Tribe Tigridieae (Subfamily Iridoideae) based on plastid sequences from Combination 10 (genes MatK, psbA, TrnKK3, trnL-F, and trnL intron)…………………………………………59 Figure 3-1: Phylogenetic relationships among members of the tribe Tigridieae (Subfamily Iridoideae), based on sequences from Combination 7 (3 of 6 genes)……………………………………………………………………………………..60 Figure 4-1: Times of divergence for the main clades of Iridoideae based on Bayesian inference reconstruction……………………………………………….…….61 Figure 5-1 A: Geographical areas distribution of Tigridieae………………………..62 Figure 5-1 B: Geographical distribution of Tigridieae based on current classification of the subtribes
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