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Neutral and Adaptive Genetic Structure of the South American Species of Nothofagus Subgenus Lophozonia

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Neutral and Adaptive Genetic Structure of the South American Species of Nothofagus Subgenus Lophozonia NEUTRAL AND ADAPTIVE GENETIC STRUCTURE OF THE SOUTH AMERICAN SPECIES OF NOTHOFAGUS SUBGENUS LOPHOZONIA. NATURAL HISTORY, CONSERVATION, AND TREE IMPROVEMENT IMPLICATIONS By RODRIGO VERGARA A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2011 1 © 2011 Rodrigo Vergara 2 To my wife Tracy for her constant support and my kids Sofia and Nico for their unconditional smiles and love. 3 ACKNOWLEDGMENTS I would like to offer my most sincere gratitude to the people and institutions that have made this project possible. First, I thank my advisor Pam Soltis for her guidance, encouragement, and endless belief that one day I would finish this endeavor. I also thank my committee members Matt Gitzendanner, Dudley Huber, Doug Soltis, and Tim White for their advice throughout the development of my project and dissertation. Especial acknowledgment to my sources of funding including the Organization of American States (OAS/LASPAU) grant, the Florida Museum of Natural History fellowship, the Department of Biology scholarships, and the financial support from the Soltis Lab for laboratory supplies and sequencing. Thanks to my fellow students from the Soltis Lab for their friendship, willingness to share ideas and knowledge. Thanks to many members of the Instituto de Silvicultura at Universidad Austral de Chile for their valuable support in identifying sample sites in the field and providing the means for sampling processing. Thanks go to the genetics crew at the Instituto Forestal in Concepcion for offering me the progeny-provenance trials information and contacts, to Corporacion Nacional Forestal for granting me permission to collect samples in protected areas and for assisting me in the field, to Agricola y Forestal Taquihue for allowing me access to the trials planted in their land and providing me with shelter and field assistance, and to the people from the Genomics Core Facility in the Department of Biology at East Carolina University, for their kindness in providing me with hardward and softwere support in the last stages of my research. I also thank many people and friends that helped in different stages of this research: Diego Alarcon, Cesar Sepulveda, and Aristides Leiva helped in site 4 identification and accessibility; Felipe Schultz, Alvaro Aguilar, Oscar Reyes, Hector Reyes, and Victor Vera assisted in the field; Emilio Cuq, Ivo Cuq, Linsay Fernandez Salvador, and Claudia Paez, helped in sample processing and laboratory measurements. Special thanks go to my wife Tracy Van Holt for her unconditional support, love, and invaluable help with general logistics, field assistance, and in the elaboration of maps. 5 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 9 LIST OF FIGURES ........................................................................................................ 11 LIST OF ABBREVIATIONS ........................................................................................... 13 ABSTRACT ................................................................................................................... 16 CHAPTER 1 INTRODUCTION .................................................................................................... 18 2 POPULATION GENETIC STRUCTURE AND GENETIC DIVERSITY OF THE SOUTH AMERICAN SPECIES OF NOTHOFAGUS SUBGENUS LOPHOZONIA. NATURAL HISTORY INFERRED FROM MULTI-LOCUS NUCLEAR MICROSATELLITE DATA .................................................................... 22 Introductory Remarks.............................................................................................. 22 Materials and Methods............................................................................................ 27 Study Site, Sample Collection, and Storage ..................................................... 27 DNA Extraction ................................................................................................. 28 PCR Amplifications and Genotyping ................................................................ 29 Data Analysis ................................................................................................... 29 Detection of scoring errors ......................................................................... 29 Linkage disequilibrium analysis .................................................................. 30 Genetic diversity within populations ........................................................... 30 Genetic structure ........................................................................................ 31 Hybridization analysis ................................................................................ 33 Results .................................................................................................................... 33 Detection of Scoring Errors and Linkage Disequilibrium .................................. 33 Genetic Diversity within Populations ................................................................ 34 Genetic Structure Inferred from Bayesian Clustering ....................................... 36 Genetic Structure Inferred from AMOVA and Pairwise Genetic Distances ....... 37 Hybridization Analysis ...................................................................................... 39 Discussion .............................................................................................................. 40 Genetic Variation within Populations at Nuclear Microsatellite Loci ................. 40 Differences in within-Species Genetic Variation ............................................... 42 Outcrossing and Inbreeding ............................................................................. 43 Structure and Isolation by Distance (IBD)......................................................... 44 Structure in Nothofagus obliqua ................................................................. 45 Structure in Nothofagus alpina ................................................................... 46 6 Structure in Nothofagus glauca .................................................................. 47 Contribution to Genetic Variation from Hybridization ........................................ 48 Natural History and the Glacial Refugia Hypotheses ........................................ 50 Concluding Remarks ........................................................................................ 53 3 MORPHOLOGICAL GENETIC VARIATION WITHIN AND AMONG PROVENANCES OF NOTHOFAGUS OBLIQUA AND N. ALPINA GROWING IN CHILE. ADAPTIVE DIFFERENCES INFERRED FROM A PROVENANCE- PROGENY TRIAL ................................................................................................... 66 Introductory Remarks.............................................................................................. 66 Materials and Methods............................................................................................ 72 Study Area, Seed Collection, and Trials General Description .......................... 72 Experimental Design, Measurements, and Data Editing .................................. 73 Analysis of Variance ......................................................................................... 74 Analysis of variables from all five blocks .................................................... 75 Analysis of variables from block one .......................................................... 76 Genetic Parameter Estimation .......................................................................... 77 Estimates for variables from all five blocks ................................................ 77 Estimates for variables from block one ...................................................... 79 Among-Provenance Differentiation ................................................................... 79 Canonical Correlation, Discriminant, and Cluster Analysis ............................... 80 Analysis at the provenance level ................................................................ 80 Analysis at the family level ......................................................................... 81 Results .................................................................................................................... 81 Best Models for the Analysis of Variance ......................................................... 81 Genetic Parameter Estimates ........................................................................... 83 Among-Provenance Differentiation ................................................................... 84 Patterns of Variation Related to Single Environmental Variables ..................... 85 Multivariate Analysis ......................................................................................... 86 Multivariate association between morphological and environmental traits ........................................................................................................ 86 Group membership of provenances ........................................................... 87 Genetic similarities among provenances through morphological traits ...... 87 Provenance membership of families .......................................................... 88 Discussion .............................................................................................................
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