Purdue University Purdue e-Pubs Open Access Theses Theses and Dissertations Summer 2014 Refining phylogenetic hypotheses using chloroplast genomics and incomplete data sets in Lasthenia (Madieae, Asteraceae) Joseph Frederic Walker Purdue University Follow this and additional works at: https://docs.lib.purdue.edu/open_access_theses Part of the Biology Commons, Botany Commons, and the Ecology and Evolutionary Biology Commons Recommended Citation Walker, Joseph Frederic, "Refining phylogenetic hypotheses using chloroplast genomics and incomplete data sets in Lasthenia (Madieae, Asteraceae)" (2014). Open Access Theses. 701. https://docs.lib.purdue.edu/open_access_theses/701 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. REFINING PHYLOGENETIC HYPOTHESES USING CHLOROPLAST GENOMICS AND INCOMPLETE DATA SETS IN LASTHENIA (MADIEAE, ASTERACEAE) A Thesis Submitted to the Faculty of Purdue University by Joseph Frederic Walker In Partial Fulfillment of the Requirements for the Degree of Master of Science August 2014 Purdue University West Lafayette, Indiana ii ACKNOWLEDGMENTS First of all I would like to thank Dr. Nancy Emery. I would not have accomplished what I have and would not be headed to a PhD program at Michigan if it was not for her. Her mentoring allowed me to design and lead my projects, but at the same time she has always been there when I need help. I am thankful that I have had an opportunity to work with an advisor who puts her students first and always makes sure what happens is in their best interest. With that in mind, I would also like to thank Dr. Michael Zanis, who has also profoundly impacted my career. Not only has he been a supportive committee member, but he was also my undergraduate mentor for four years. He is the person who originally sparked my interest in research and has continued to provide me guidance throughout my scientific career. I cannot thank Dr. Zanis enough for all the time and effort he put into helping me develop my scientific career. I would also like to thank my other committee members, Dr. Stephen Goodwin and Dr. Kevin Gibson, who have challenged me to think critically about my project and have provided me with an invaluable skill set for the future. I have been very fortunate to have had many mentors in science who have shaped my thought process and my way of approaching problems over the years. One last mentor who I have to thank is Dr. Antónia Monteiro, who, despite working in her ii lab for only a short internship, always made time to meet with me and helped shape the way I approach problems. I would also like to thank Dr. Peter Goldsbrough and the rest of the Botany Department staff. Dr. Goldsbrough might be the department head but he always makes time to provide students with advice and as he knows I have often times been in need of that. The entire office staff has always been exceptionally helpful and made sure that my graduate experience has run smoothly. Especially Dave Kniola, and although we lost him this year, he will forever be remembered for his sense of humor, his hard work with graduate students, and I will always remember him for making my greenhouse experience amazing. Finally, I would like to thank my family, friends, labmates and most of all, the one combination of all of those, my original mentor Sheryl Walker. Not only has she put up with me for my entire life, but she is the one who first encouraged me to join a lab at Purdue and started my scientific career. It was a pleasure to learn lab techniques from her and it is truly incredible that after all these years she is still willing to proofread grants and papers that I write. I'd like to thank Alan Clinton, who is probably the only undergraduate to come in during a polar vortex and do volunteer lab work. Thank you so much for all that you have made possible Alan, and no matter where you end up you're going to be highly successful. Thank you to the entire Emery lab, it has definitely been a journey and it has been wonderful to be around such a supportive group. I am going to miss everyone at Purdue and to all thank you so much, keep in touch and good luck with everything you pursue! iii " You do not really understand something unless you can explain it to your grandmother." --Albert Einstein "How someone can call themselves a soybean expert but be unable to grow the plant, is beyond me." ~Dave Kniola iv TABLE OF CONTENTS Page LIST OF TABLES..............................................................................................vi LIST OF FIGURES............................................................................................vii ABSTRACT..........................................................................................................viii CHAPTER 1. COMPARATIVE ANALYSIS OF COMPLETE CHLOROPLAST GENOME SEQUENCE AND INVERSION VARIATION IN LASTHENIA BURKEI (MADIEAE, ASTERACEAE)..................................................................................1 1.1 Introduction..........................................................................................1 1.2 Materials and Methods.........................................................................3 1.3 Results................................................................................................6 1.4 Discussion............................................................................................8 1.5 References.....................................................................................12 CHAPTER 2.RESOLVING EVOLUTIONARY RELATIONSHIPS IN GOLDFIELDS THROUGH MODERN PHYLOGENETIC METHODS AND INCOMPLETE DATA MATRICES.......................................................................19 2.1 Introduction....................................................................................19 2.2 Materials and Methods..................................................................22 2.3 Results...........................................................................................25 2.4 Discussion.....................................................................................31 2.5 References....................................................................................38 v LIST OF TABLES Table Page Table 1.1 G+C content of Plastomes……......……............................................18 Table 2.1 Sections of Lasthenia…...................................................................48 Table 2.2 Primer Sequences.............................................................................49 Table 2.3 ETS Genbank Accessions…….....................................................50-53 Table 2.4 ITS Genbank Accessions…….....................................................54-57 Table 2.5 3'trnK Genbank Accessions...............…......................................58-61 Table 2.6 Newly Obtained Samples...................…......................................62 vi LIST OF FIGURES Figure Page Figure 1.1 Chloroplast Map..................................................................................15 Figure 1.2 Sliding Window Analysis.....................................................................16 Figure 1.3 Asteraceae Phylogeny........................................................................17 Figure 2.1 Composition of Datasets...................................................................41 Figure 2.2 Phylogenetic Recreation of Dataset 1..........................................42-44 Figure 2.3 Phylogenetic Recreation of Dataset 2…….........................................45 Figure 2.4 Phylogenetic Recreation of Dataset 3…….........................................46 Figure 2.5 Phylogenetic Recreation of Dataset 4................................................47 vii ABSTRACT Walker, Joseph Frederic. M.S., Purdue University. August 2014. Refining Phylogenetic Hypotheses Using Chloroplast Genomics and Incomplete Data Sets in Lasthenia (Madieae, Asteraceae). Major Professor: Nancy C. Emery. The genus Lasthenia (Madieae, Asteraceae), consists of predominantly annual plant species that are largely endemic to the California Floristic Province of western North America and occupy a large range of habitat types. With high levels of morphological and ecological diversity, Lasthenia is a robust tool, capable of providing a natural non-model organism for answering a diverse array of ecological and evolutionary questions. Future studies would benefit greatly from a strong phylogenetic hypothesis and more molecular resources, such as the whole plastome sequence for a representative species in the genus. Over a decade ago there was a study that laid a strong foundation for a molecular phylogenetic hypothesis, however, many critical nodes still remained ambiguous. Since that study was conducted, there have emerged new statistical and biological methods to maximize the information obtained from the sequence data. With the advent of next-generation sequencing, it is now simpler than ever to obtain molecular resources for a genus, and it is possible to apply some of those molecular resources to resolving the phylogenetic relationships in viii Lasthenia. My research has two specific outcomes: 1) I have provided the first whole plastome in the tribe Madieae of the Asteraceae and used the plastome to analyze rates of evolution across the regions of other sequenced plastomes in the Asteraceae, and 2) Through the use of modern phylogenetic methods and incomplete data sets consisting of freely