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Novel Computational Tools and Utilization of the Gut Microbiota For Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2013 Novel computational tools and utilization of the gut microbiota for phylogeographic inference Sarah Michelle Hird Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Hird, Sarah Michelle, "Novel computational tools and utilization of the gut microbiota for phylogeographic inference" (2013). LSU Doctoral Dissertations. 3458. https://digitalcommons.lsu.edu/gradschool_dissertations/3458 This Dissertation 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 Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. NOVEL COMPUTATIONAL TOOLS AND UTILIZATION OF THE GUT MICROBIOTA FOR PHYLOGEOGRAPHIC INFERENCE A Dissertation 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 Doctor of Philosophy in The Department of Biological Sciences by Sarah Michelle Hird B.S., University of Idaho, 2005 M.S., University of Idaho, 2008 May 2013 Acknowledgments This document is years in the making and the effort of many people. First, my advisors, Dr. Robb Brumfield and Dr. Bryan Carstens, have my eternal gratitude for being the perfect yin and yang. Together, they have allowed me the space and the structure to work at my own pace yet push my boundaries. They were always there when I needed guidance of any kind. Bryan, in particular, first encouraged me to learn Perl and I can’t express how grateful I am that he did. Robb invested in me as a student and thus granted me access to the LSU Museum of Natural Science (LSUMNS). I’d also like to thank my Master’s advisor, Dr. Jack Sullivan, for teaching me good habits and starting me on this path in the first place. The NSF and LSU funded my degree and research and I very much appreciate that. My committee members, Dr. Brent Christner, Dr. Brygg Ullmer and Dr. Robert Rohli have all been available and informative whenever I asked. In particular, Dr. Christner introduced me to the world of microbial ecology and discussions with Dr. Ullmer helped solidify my interest in bioinformatics. The LSUMNS faculty, staff and students are a group of unbelievably amazing naturalists and scientists; they are directly responsible for the (comparatively very small) amount of natural history I know. The access to and support from the Bird Lunch group was integral in guiding my reasoning and justification for the bird gut chapters; a special thanks to the extremely helpful comments of Dr. J. Van Remsen and Dr. Fred Sheldon. I have been fortunate to work with many wonderful collaborators and post-doctoral researchers. Dr. Maggie Hanes (Koopman) was a generous friend, mentor and collaborator; I strive to be like her in more ways than one. Dr. John McCormack included me in many projects that were of great interest and value to me. He and Dr. Amanda Zellmer offered friendship, intellect and perspective on many issues. Dr. Erica Tsai provided a lot of useful advice regarding pursuing bioinformatics and thoughtfully answered any questions I had. Many other professionals had a strong positive influence on me and my education/research; thank you Dr. Jeremy Brown, Steve Cardiff, Donna Dittmann, Dr. Brian Smith, Dr. Brad Chapman and Daniel Ence. The chapters on bird gut microbiota would never have happened without the enthusiasm, encouragement and hard work of many museum graduate students. Cesar Sanchez conducted much of the fieldwork and contributed both physically and intellectually to the Neotropical bird project. Michael Harvey, Dr. Gustavo Bravo and all the other field assistants who collected many intestinal tracts for me and I appreciate their hard work more than I can write. Graduate students at the museum and in the Department of Biological Sciences contributed much to my education. I gratefully acknowledge the following individuals for friendship on top of help with reading groups, paper edits, talk critiques, good/bad ideas, etc., especially over coffee or cocktails: Melissa DeBiasse, Eric Rittmeyer, Verity Mathis, Lorelei Patrick, Cathy Newman, Clare Brown, Vivien Chua. All past and present members of both the Brumfield and Carstens labs provided an amazing work environment and helped me professionally by reading drafts of manuscripts, discussing ideas, critiquing talks, and much more. Thank you – Noah Reid, John McVay, Tara Pelletier, Jordan Satler, Dr. James Maley, Andres Cuervo, Caroline Duffie, Dr. Gustavo Bravo, Michael Harvey, Glenn Seeholzer, John Mittermeier. These people are also wonderful human beings and good friends. ii Emotional support and well-being can be attributed to my many good friends at LSU and beyond, especially Tara Pelletier, John McVay and Megan McVay. Nala is the four-legged definition of stress relief. My family is amazing and everything that I am is because of them. Joan Hopkins, my mother, is a paragon of efficiency and determination and a role model that I am grateful for every day. She and my sisters, Katie Hird and Stephanie Thompson, comprise my heart. Finally, none of this would exist without Noah Mattoon Reid, who makes everything in my life, including this dissertation, better. He is my best friend, my husband, my mentor, my sounding board, my advocate, my editor, my support and my sanity. Thank you, thank you, thank you. iii Table Of Contents Acknowledgments ........................................................................................................................... ii Abstract ............................................................................................................................................v Chapter 1. Introduction: High-Throughput Sequencing, Computational Tools and Host- Associated Microbiota .........................................................................................................1 Chapter 2. PRGMATIC: An Efficient Pipeline For Collating Genome-Enriched Second- Generation Sequencing Data Using A ‘Provisional-Reference Genome’ ...........................7 Chapter 3. LOCINGS: A Lightweight Alternative For Assessing The Suitability Of Next- Generation Loci For Evolutionary Analysis ....................................................................14 Chapter 4. Nature, Nurture And The Gut Microbiota Of The Brood-Parasitic Brown-Headed Cowbird (Molothrus ater) ..................................................................................................23 Chapter 5. Assessing The Use Of Gut Microbiota As A Marker For Phylogeographic Inference In Neotropical Birds ...........................................................................................................39 Chapter 6. Conclusions ..................................................................................................................58 References ......................................................................................................................................61 Appendix A. PRGMATIC README ..............................................................................................72 Appendix B. PRGMATIC: Guide To Common Errors ....................................................................79 Appendix C. LOCINGS README .................................................................................................85 Appendix D. Specimen Information For Birds Of Chapter 4 ........................................................94 Appendix E. Mammals And Insects Of Chapters 4 And 6 ............................................................96 Appendix F. Specimen Information For Birds Of Chapter 5 .........................................................98 Appendix G. Permissions From Cambridge University Press .....................................................105 Appendix H. Permissions For Portions of Chapter 1 ...................................................................106 Appendix G. Permissions For Chapter 2 .....................................................................................107 Appendix G. Permissions For Chapter 3 .....................................................................................108 Vita ...............................................................................................................................................109 iv Abstract Genetic data are frequently responsible for biological insight and recent advances in sequencing technology (high-throughput sequencing; HTS) have created massive DNA-sequence based datasets. While these technologies are invaluable, there are many analytical and application issues that need to be addressed. With these data we can ask and answer novel biological questions that were previously inaccessible. One major challenge in applying HTS to biological questions is data management: the file formats and sizes are foreign to many primary researchers. In the second and third chapters of this dissertation, I introduce two pieces of software that allow researchers to utilize HTS with minimal time investment. PRGMATIC (Chapter 2) is a pipeline that collates raw HTS data into a more traditional and useable format: two diploid alleles for a given locus. LOCINGS (Chapter 3) uses these loci, the alignments from which the loci
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