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Copyright by Ruth Evangeline Timme 2006 Copyright by Ruth Evangeline Timme 2006 The Dissertation Committee for Ruth Evangeline Timme Certifies that this is the approved version of the following dissertation: Reticulate Evolution in Helianthus (Asteraceae) Committee: C. Randal Linder, Supervisor Beryl B. Simpson, Co-Supervisor Robert K. Jansen Thomas E. Juenger David M. Hillis Reticulate Evolution in Helianthus (Asteraceae) by Ruth Evangeline Timme, B.S.; M.A. Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin August 2006 Acknowledgements First, I want to thank both of my advisors: Randy Linder for his funding for my project and providing me with an RAship for two years, and both Randy Linder and my co-advisor, Beryl Simpson, for all their helpful advise and support during my time at UT. They both have been so willing to help at a moments notice and have been excellent advisors. I also want to thank Bob Jansen who advised my on my fourth chapter and has served as an informal third advisor for my dissertation. My other two committee members, Tom Juenger and David Hillis were also very accommodating throughout the years in scheduling committee meetings and in giving insightful comments and feedback to my research. I am also grateful to Sheri Church and Eric Baack for sending me leaf material and allowing me to use a molecular marker they had developed in the Rieseberg lab. Also Sherri Church performed two plates of sequences for the polyploids and has been very helpful in discussions regarding my project. My time at UT was most influenced by the other graduate students that I interacted with everyday. I chose to attend UT because of the community I sensed between the graduate students and that definitely proved to be true during my time here. I thank all the follow members in the Simpson and Linder labs along with the graduate iv students in the Jansen and Theriot labs: Josh McDill, Cate Bergman, Simone Capellari, Juanita Choo, Debra Hansen, Anneke Padolina, Sara Taylor, Heidi Meudt, Joanne Birch, Andrea Weeks, Geoff Denny, Jennifer Tate, Sarah Simmons, Leah Larkin, Andy Alverson, Elisabeth Ruck, Michael Moore, Tim Chumley, Mary Guisinger, Roxi Steele, Mary McGovern, and Anushree Sanyal. Derrick Zwickl and Tracy Heath were also extremely helpful with computational assistance. I would also like to thank all of the undergraduates that assisted me with lab work: Alex Moffet, Justin Rogers, Megan Noel, Kathryn Turner, Katie Golder, Sheila Shapori, Anandita Agarwala, and Sandra Pelc. I am deeply grateful to my parents, especially my father who was so encouraging, supportive and inspirational though the tougher times in my graduate education. I also thank him for being my collecting partner for several long collecting trips, which made them so enjoyable and productive. His support can only be matched by my partner, Jenny, who kept my sanity in check throughout this whole process. This work was funded in part through generous grants from the National Science Foundation (through a Dissertation Improvement Grant, ITR grant, and IGERT fellowship), PEO Scholar Award, and the Plant Biology Graduate Program at the University of Texas. v Reticulate Evolution in Helianthus (Asteraceae) Publication No._____________ Ruth Evangeline Timme, Ph.D. The University of Texas at Austin, 2006 Supervisors: C. Randal Linder and Beryl B. Simpson Many plants have a net-like or reticulate phylogenetic history caused by hybrid speciation or introgression. These more complex histories require additional methods and data for their reconstruction and Helianthus provides an ideal system for which to uncover these past events. Reconstructing the phylogeny of Helianthus is important for two reasons: it contains two economically important crop plants (H. annuus and H. tuberosus) and its annual species have formed an important model system for studying speciation genetics. To reconstruct the reticulate evolution of Helianthus in this study, multiple independent gene phylogenies were collected for the genus: four nuclear regions (rRNA external transcribed spacer (ETS), an actin gene, pistillata and 1548 EST) and four plastid regions (trnY-rpoB spacers, trnL-rpl32 spacer, ndhC-trnV spacer and a portion of ycf1) Each of the five independent datasets were analyzed separately (the four plastid regions were concatenated into one dataset). vi The resulting ETS phylogeny revealed for the first time a resolved gene tree for Helianthus. Phylogenetic analysis of these data allowed the determination of a monophyletic annual H. sect. Helianthus, a two-lineage polyphyletic H. sect. Ciliaris, and the monotypic H. sect. Agrestis, all of which are nested within the large perennial and polyphyletic H. sect. Divaricati. Previously collected secondary chemistry characters were mapped onto this phylogeny for examination of their character evolution. Supported incongruences between the five gene-trees were identified as possible reticulation events (hybrid speciation and/or introgression). One of these led to the discovery of a new undescribed species, H. ‘Newhall Ranch’, which our molecular data shows was formed via an allopolyploid reduction event. Two complete chloroplast genomes in the Asteraceae were sequenced, Helianthus annuus (sunflower) and Lactuca sativa (lettuce), which belong to the distantly related subfamilies, Asteroideae and Cichorioideae, respectively. Pair-wise sequence divergence across all both plastid genomes resulted in the discovery of new, fast-evolving DNA sequences for use in species-level phylogenetics in Asteraceae. The complete annotated genome sequences also enabled a novel analysis of repeat patterns (thought to be involved in genome rearrangement) in the genomes and of RNA editing by comparison to available EST sequences. vii Table of Contents List of Tables ..................................................................................................... xi List of Figures................................................................................................... xii Chapter 1. Introduction.........................................................................................1 Chapter 2. External transcribed spacer provides phylogenetic resolution in sunflowers, Helianthus (Asteraceae): implications for the evolution of secondary chemistry ....................................................................................6 Introduction.................................................................................................6 Materials and Methods ..............................................................................10 Results.......................................................................................................15 Features of ETS in Helianthus ..........................................................15 Phylogenetic Analysis.......................................................................16 Character Evolution. .........................................................................20 Discussion.................................................................................................21 Phylogenetic relationships of non-hybrids.........................................21 Hybrid species ..................................................................................25 Secondary chemistry.........................................................................30 Tables........................................................................................................31 Figures ......................................................................................................33 Chapter 3: Multi-gene analyses for Helianthus reveal imprints of reticulation in the midst of recent rapid radiation. ..................................................................40 Introduction...............................................................................................40 Methods ....................................................................................................43 Samples. ...........................................................................................43 Identifying low-copy genes for phylogenetic use...............................44 Amplification and sequencing...........................................................45 viii Phylogenetic analyses .......................................................................46 Tests for recombination ....................................................................47 Results.......................................................................................................48 Phylogenetic results - plastid.............................................................48 Phylogenetic results - Actin ..............................................................49 Phylogenetic results - 1548 EST .......................................................51 Phylogenetic results - Pistillata .........................................................52 Discussion.................................................................................................52 Supported clades recovered by all gene trees.....................................54 Supported incongruences between the gene trees: evidence of reticulation .................................................................................................55 Conclusions...............................................................................................62
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