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A Phylogenetic Analysis of Species Diversity, Specificity, and Distribution of Mycodiplosis on Rust Fungi

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A Phylogenetic Analysis of Species Diversity, Specificity, and Distribution of Mycodiplosis on Rust Fungi Louisiana State University LSU Digital Commons LSU Master's Theses Graduate School 2013 A Phylogenetic Analysis of Species Diversity, Specificity, and Distribution of Mycodiplosis on Rust Fungi Donald Jay Nelsen Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_theses Part of the Plant Sciences Commons Recommended Citation Nelsen, Donald Jay, "A Phylogenetic Analysis of Species Diversity, Specificity, and Distribution of Mycodiplosis on Rust Fungi" (2013). LSU Master's Theses. 2700. https://digitalcommons.lsu.edu/gradschool_theses/2700 This Thesis is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Master's Theses by an authorized graduate school editor of LSU Digital Commons. For more information, please contact [email protected]. A PHYLOGENETIC ANALYSIS OF SPECIES DIVERSITY, SPECIFICITY, AND DISTRIBUTION OF MYCODIPLOSIS ON RUST FUNGI A Thesis Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Master of Science in The Department of Plant Pathology and Crop Physiology by Donald J. Nelsen B.S., Minnesota State University, Mankato, 2010 May 2013 Acknowledgments Many people gave of their time and energy to ensure that this project was completed. First, I would like to thank my major professor, Dr. M. Catherine Aime, for allowing me to pursue this research, for providing an example of scientific excellence, and for her comprehensive expertise in mycology and phylogenetics. Her professionalism and ability to discern the important questions continues to inspire me toward a deeper understanding of what it means to do exceptional scientific research. I would also like to thank my committee members for unfailing support and advice: Dr. Meredith Blackwell for her inspirational mycological expertise and suggestions which made this project a success, Dr. Christopher Clark for his broader understanding of the context of this research, and Dr. Marc Cohn for his technical advice and interest in my professional success. While working on this project I also was privileged to collaborate with two scientists in Japan. Dr. Tsuyoshi Hosoya at the National Museum of Nature and Science in Tsukuba, Japan provided lab space and equipment, collecting opportunities, and assisted in the identification of rust fungi that I collected while visiting his institution. Dr. Yuichi Yamaoka at the University of Tsukuba in Tsukuba, Japan gave his time to take me collecting for several days and also provided his expertise with the identification of rust fungi occurring in Japan. I am grateful to the Louisiana Board of Regents for providing funding in support of this effort. In the course of pursuing this project I have had the pleasure of discussing various aspects of the work with many faculty and fellow graduate students. I would like to extend my gratitude to Dr. Eric Achberger for his advice on PCR protocol development. I would also like to thank Drs. James Geaghan and Bin Li for their advice on appropriate statistical methods. A ii special thanks to Dr. Hector Urbina for advice on using MEGA and RAxML software as well as listening to my ideas regarding interpretation of the data. I am thankful for the advice and guidance in molecular techniques provided by the post doctoral researchers Alistair McTaggart, Merje Toome, and Gregory Heller. I’ve also had the pleasure to work alongside some wonderful graduate students without whom this work would not have been possible; to Sebastian Albu, Andrew Rodriguez, Tomas Rush, Rachel Koch, Youwen Gong, and Jorge Diaz I extend my heartfelt appreciation for their support and friendship. I would also like to thank Paige Muse and Catherine Perino for keeping the lab running so I could complete this work. I must also mention that I am so very grateful to my friends and family for their unfailing support and encouragement. I thank Britta Simonson for inspiring me to pursue my dream. I thank Chad Borgheiink for his lifelong friendship and interest in my research. To my sisters, Teri and Jodi, I extend special thanks for their willingness to listen and help me find my way back to the goal of this research. I would like to thank my mother and her husband, Dee and Dean Hoeft, for always listening and providing practical advice that has always kept me grounded. I also thank my father, Donald James Nelsen, for his kindness, patience and perspective. iii Table of Contents Acknowledgments........................................................................................................................... ii Abstract .......................................................................................................................................... vi Chapter 1. Introduction and Literature Review .............................................................................. 1 1.1 Pucciniales ............................................................................................................................. 1 1.2 Mycodiplosis ......................................................................................................................... 1 1.3 Host specialization and coevolution ...................................................................................... 4 1.4 Species concepts .................................................................................................................... 5 1.5 DNA based species identification ......................................................................................... 6 1.6 Objectives .............................................................................................................................. 9 Chapter 2. Materials and Methods ................................................................................................ 10 2.1 Collecting larvae for analysis .............................................................................................. 10 2.2 DNA extraction, amplification, and sequencing ................................................................. 11 2.2.1 DNA extractions .......................................................................................................... 11 2.2.2 PCR amplification and sequencing .............................................................................. 12 2.3 Phylogenetic analyses ......................................................................................................... 17 2.3.1 Sequence assembly, alignment, outgroup selection, and phylogenetic analysis ......... 17 2.3.2 Test analyses using comparable data sets .................................................................... 19 2.3.3 Phylogenetic analyses of 28S and COI sequences of Mycodiplosis ............................ 20 2.3.4 Phylogenetic analysis of concatenated sequences of Mycodiplosis ............................. 21 2.4 Geographical and host-specificity of Mycodiplosis larvae ................................................. 21 2.4.1 Collection of data ......................................................................................................... 21 2.4.2 PCA analysis of larval occurrence ............................................................................... 21 2.4.3 Clade level analysis of larval occurrence ..................................................................... 22 Chapter 3. Results ......................................................................................................................... 23 3.1 DNA extraction, amplification, and sequencing ................................................................. 23 3.2 Phylogenetic analyses ......................................................................................................... 23 3.2.1 Test analyses using comparable data sets .................................................................... 23 3.2.2 Phylogenetic analyses of 28S and COI sequence diversity in Mycodiplosis ............... 26 3.2.3 Concatenated phylogenetic analysis of sequence diversity in Mycodiplosis ............... 26 3.3 Distribution and specificity of Mycodiplosis larvae on rust fungi ...................................... 36 3.3.1 Data collection ............................................................................................................. 36 3.3.2 PCA analysis of larval occurrence ............................................................................... 36 3.3.3 Chi Square and Fisher’s exact test of the distribution of supported clades ................. 41 Chapter 4. Discussion ................................................................................................................... 43 4.1 Phylogenetic diversity estimates ......................................................................................... 43 4.2 Host Specificity and Distribution of Mycodiplosis ............................................................. 46 Chapter 5. Conclusions ................................................................................................................. 50 iv References ..................................................................................................................................... 52 Appendix A. Collection Survey Supplementary Data .................................................................. 57 Appendix B. Statistical Analyses Supplementary Data
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