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Utilization of Phylogenetic Systematics, Molecular Evolution, and Comparative Transcriptomics to Address Aspects of Nematode and Bacterial Evolution Brigham Young University BYU ScholarsArchive Theses and Dissertations 2010-06-18 Utilization of Phylogenetic Systematics, Molecular Evolution, and Comparative Transcriptomics to Address Aspects of Nematode and Bacterial Evolution Scott M. Peat Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biology Commons BYU ScholarsArchive Citation Peat, Scott M., "Utilization of Phylogenetic Systematics, Molecular Evolution, and Comparative Transcriptomics to Address Aspects of Nematode and Bacterial Evolution" (2010). Theses and Dissertations. 2535. https://scholarsarchive.byu.edu/etd/2535 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Utilization of Phylogenetic Systematics, Molecular Evolution, and Comparative Transcriptomics to Address Aspects of Nematode and Bacterial Evolution Scott M. Peat A dissertation submitted to the faculty of Brigham Young University In partial fulfillment of the requirements for the degree of Doctor of Philosophy Byron J. Adams Keith A. Crandall Michael F. Whiting Alan R. Harker George O. Poinar Department of Biology Brigham Young University August 2010 Copyright © 2010 Scott M. Peat All Rights Reserved ABSTRACT Utilization of Phylogenetic Systematics, Molecular Evolution, and Comparative Transcriptomics to Address Aspects of Nematode and Bacterial Evolution Scott M. Peat Department of Biology Doctor of Philosophy Both insect parasitic/entomopathogenic nematodes and plant parasitic nematodes are of great economic importance. Insect parasitic/entomopathogenic nematodes provide an environmentally safe and effective method to control numerous insect pests worldwide. Alternatively, plant parasitic nematodes cause billions of dollars in crop loss worldwide. Because of these impacts, it is important to understand how these nematodes evolve, and, in the case of entomopathogenic nematodes, how their bacterial symbionts evolve. This dissertation contains six chapters. Chapter one is a review of DNA markers and their use in the phylogenetic systematics of entomopathogenic and insect-parasitic nematodes as well as a review of phylogenetic, co- phylogenetic, and population genetic methodologies. Chapter two characterizes positive destabilizing selection on the luxA gene of bioluminescent bacteria. Our data suggests that bacterial ecology and environmental osmolarity are likely driving the evolution of the luxA gene in bioluminescent bacteria. Chapter 3 examines relationships among bacteria within the genus Photorhabdus. Our analyses produced the most robust phylogenetic hypothesis to date for the genus Photorhabdus. Additionally, we show that glnA is particularly useful in resolving specific and intra-specific relationships poorly resolved in other studies. We conclude that P. asymbiotica is the sister group to P. luminescens and that the new strains HIT and JUN should be given a new group designation within P. asymbiotica. Chapter 4 characterizes the morphology of the head and feeding apparatus of fungal feeding and insect infective female morphs of the nematode Deladenus siricidicola using scanning electron microscopy. Results showed dramatic differences in head, face, and stylet morphology between the two D. siricidicola female morphs that were not detected in previous studies using only light microscopy. Chapter five utilizes comparative transciptomics to identify putative plant and insect parasitism genes in the nematode Deladenus siricidicola. Results from this study provide the first transcriptomic characterization for the nematode Deladenus siricidicola and for an insect parasitic member of the nematode infraorder Tylenchomorpha. Additionally, numerous plant parasitism gene homologues were discovered in both D. siricidicola libraries suggesting that this nematode has co-opted these plant parasitism genes for other functions. Chapter six utilizes a phylogenomic approach to estimate the phylogeny of the nematode infraorder Tylenchomorpha. Keywords: Photorhabdus, luxA, positive destabilizing selection, bioluminescent bacteria, phylogeny, Deladenus siricidicola, stylet, morphology, scanning electron microscopy, comparative transcriptomics, parasitism genes, phylogenomics, Tylenchomorpha ACKNOWLEDGEMENTS I would like to express my sincere appreciation to all of the individuals who have assisted and supported me in completing this dissertation. I would first like to thank my advisor, Byron Adams, for his advice, support, optimism, encouragement throughout this whole process. You were not just my advisor but also a mentor and a friend and I am forever greatful for the time I have been able to share with you and your family. To the members of my graduate committee, Keith Crandall, Michael Whiting, Alan Harker, and George Poinar, thank you for all of your feedback and guidance on each of my projects, and for pushing me to be a better scientist. I would like to thank Hilary Oldroy and Elaine Rotz for making sure I met all of my deadlines and for having an answer or solution to any issues I had regarding degree requirements and paperwork. I would like to thank Ed Wilcox for sequencing assistance and troubleshooting and Josh Udall and Peter Maughan for providing invalueable suggestions on cDNA library construction techniques. Additionally, I would like to thank Matthew Bendall, Tyler Collette, and Daniel Standage for invaluable bioinformatics assistance. To all of the members of the nematode evolution lab, thank you for all of your support and assistance over the last five years. I would like to thank the following agenecies for providing funding for this project: Brigham Young UniversityGraduate Studies, Department of Biology, Department of Molecular Biology and Microbiology, Charles Redd Center, United States Department of Agriculture, and the National Science Foundation. Finally, I would like to express gratitude to my family for their love and support thoroughout this whole process. I would especially like to thank my wife for her unwavering support, patience, and continuous encouragement, without which I would have never been able to make it through this process. Table of Contents Abstract ........................................................................................................................................... ii Acknowledgements ........................................................................................................................ iv Table of Contents ........................................................................................................................... vi List of Tables ............................................................................................................................... viii List of Figures ................................................................................................................................ ix Introduction ......................................................................................................................................1 Chapter 1: Phylogenetics and Population Genetics of Entomopathogenic and Insect-parasitic Nematodes ..................................................................................................................................7 Introduction ..........................................................................................................................7 Phylogenetics .......................................................................................................................8 Population Genetics ...........................................................................................................10 DNA Bar Coding ...............................................................................................................11 DNA Markers Considered for Phylogenetic and Population Genetics Studies ...............11 Ribosomal DNA.....................................................................................................11 Mitochondrial DNA ...............................................................................................16 Methodology ......................................................................................................................22 Alignment Strategies ..............................................................................................22 Multiple Alignments and Most Common Software ...............................................23 Phylogenetic Reconstruction Methods ................................................................27 Co-phylogenesis and Cospeciation ........................................................................35 Population Genetics Methods ................................................................................38 References .........................................................................................................................42 Chapter 2: Natural Selection on the luxA Gene of Bioluminescent Bacteria ................................56 Abstract ..............................................................................................................................56 Introduction ........................................................................................................................58 Materials and Methods .......................................................................................................62
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