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Copyright by Sarah Elizabeth Taylor 2012 The Dissertation Committee for Sarah Elizabeth Taylor Certifies that this is the approved version of the following dissertation: Molecular Systematics and the Origins of Gypsophily in Nama L. (Boraginaceae) Committee: Beryl B. Simpson, Supervisor Robert K. Jansen Donald A. Levin Jose L. Panero Ulrich G. Mueller Molecular Systematics and the Origins of Gypsophily in Nama L. (Boraginaceae) by Sarah Elizabeth Taylor, B.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 May 2012 Dedication For my son Graeme, who reminds me to greet every day with an inquisitive mind and an open heart. Acknowledgements I would like to thank my advisor, Beryl Simpson, for suggesting that I consider Nama as a possible research organism; for her calm guidance as I navigated classes, teaching obligations, and research; for her patience in my dissertation-writing process; and for her support of my personal and academic endeavors throughout my graduate school years. I would also like to thank my committee members, Bob Jansen, Jose Panero, Don Levin, and Ulrich Mueller, for their encouragement and wisdom. I have learned so much from each of them and am grateful that they have guided me through my graduate career. The past and present members of the Simpson, Jansen, Linder, and Theriot labs have been wonderful friends and colleagues. From teaching me the ropes in lab and helping me to understand phylogenetic analyses, to exploring Austin together and traveling to meetings across the country, each of these people has helped me along the way. Many thanks to Heidi Meudt, Andrea Weeks, Leah Larkin, Joanne Birch, Ruth Timme, Anneke Padolina, Cate Bergman, Josh McDill, Elizabeth Ruck, Mary Guisinger, Roxi Steele, Anushree Sanyal, Xiao Wei, Sandra Pelc, and Scott Meadows, for the ways in which they’ve helped me both in and out of lab, and for the friendship that we’ve shared. I would especially like to thank my friend Debra Hansen, without whom I would not be finishing this dissertation. Debra has taken care of administrative tasks for me on campus, traveled with me to Mexico, helped me run analyses on lab computers while I was away from Austin, and, with her husband Doug Dorst, welcomed me into her home on my visits to Austin. I would like to acknowledge the generous assistance provided by the Plant Resources Center staff. Tom Wendt and Lindsay Woodruff coordinated loans for me, helped me track down nomenclatural literature, and were always available to answer questions. Tom permitted me to sample numerous herbarium sheets in order to isolate DNA from leaf material and to obtain SEM images of seeds. Many thanks to Amber v Schoneman, who cheerfully made high-resolution scans of several specimens for me. I am also grateful to Bob Harms for demonstrating how to use the dissecting scope camera, explaining how to process the image files, and then emailing images to me. I’ve greatly enjoyed discussing the Chihuahuan Desert flora with Jim Henrickson and Billie Turner. I’m grateful to Fred Barrie of the Field Museum for helping me to determine the appropriate gender to apply to species of Nama – it’s always fun to find someone as interested in untangling these puzzles as I am. I also thank the herbaria at GH, NY, UC, US, and MO for loaning specimens. I was fortunate to have the opportunity to visit UC, NY, and MERL in my travels and appreciate the hospitality of the staff at each of those institutions. I also acknowledge the valuable assistance provided by the staff of the ICMB core facility at the University of Texas, especially Cecil Harkey in the DNA sequencing facility and Dwight Romanovicz in the microscopy facility. In support of this research I undertook field trips to California, west Texas, Mexico, and Argentina. From beating off swarms of mosquitoes in the Sierra Nevadas with Bob Patterson and his students from the University of California at San Francisco as well as Simpson Lab members, to the unforgettable adventures marking my first trip to Mexico with Mike Moore and Geoff Denny, each trip has resulted in my development as a botanist and given me many fond memories. I enthusiastically thank every person who has helped make these trips possible, including Beryl Simpson, Jack Neff, Lyn Headley, Kate Conley, Debra Hansen, Tim Chumley, George Hinton, Joshua McDill, Billie Turner, and Kenneth Jackson. Because I left Austin in order to accompany my husband to his postdoctoral appointments in England and Canada, and then to a permanent position in Colorado, I would like to acknowledge several online resources that I used to read original literature and perform analyses. Google Books (books.google.com) and Botanicus (www.botanicus.org) are extraordinary resources for finding and reading literature from Linnaeus forward when an academic library is inaccessible. The CIPRES Science Gateway (www.phylo.org/sub_sections/portal) is a free resource for researchers to run a variety of analyses; their help desk staff provided much-needed assistance. In addition, I vi obtained records of Nama collections from the REMIB database (Red Mundial de Información Sobre Biodiversidad; www.biosci.utexas.edu/prc/mexicanPlantDatabase.html) via the Plant Resources Center website, accessing the XAL, IEB, LL, TEX, and UNAM nodes. I wish to express my gratitude to my friends and family, who have never wavered in their support over this long endeavor. My parents, Ken and Eileen Jackson, have been my constant cheerleading squad, keeping me smiling through frequent phone calls and Skype chats and, in the case of my father, flying across the country to assist me on a collecting trip in the Mojave Desert. My husband’s parents, Thomas and Margaret Taylor, have been constant sources of encouragement. I am especially grateful to Margaret for traveling to Austin and Denver to care for our son full-time while I have worked on my thesis. My siblings, Doug Jackson and Laura DeLibero, and their spouses Molly Jackson and Tony DeLibero, have been ever ready with kind words and troubleshooting. If laughter is the best medicine, then my good health is entirely due to my clever, funny, loving little boy Graeme, who lights up my every day. Finally, this dissertation would not have been possible without the love, encouragement, and selflessness of my husband, Thomas Taylor. From helping me look for Nama in west Texas, to cooking almost all our dinners, to solo parenting on the weekends while I was at the library, to proofreading my drafts, he has been by my side at every step. Thomas believed in me when I doubted myself, and I am deeply grateful that he is my partner in life. This work was funded in part by a Dissertation Improvement Grant from the National Science Foundation and by grants from the Plant Biology Graduate Program at the University of Texas at Austin. vii Molecular Systematics and the Origins of Gypsophily in Nama L. (Boraginaceae) Sarah Elizabeth Taylor, Ph.D. The University of Texas at Austin, 2012 Supervisor: Beryl B. Simpson Nama L. is a genus of approximately 50 species of herbs and subshrubs that occurs in habitats ranging from arid deserts to mesic woodlands in the New World and the Hawaiian Islands. The group has historically been divided into five or six subgeneric groups based on habitat as well as on the morphology of the anthers, styles, leaves and seeds. At least 14 species of Nama from the Chihuahuan Desert Region are either facultatively or obligately endemic to gypsum deposits. This dissertation examines interspecies relationships within Nama from a molecular phylogenetic perspective in order to evaluate historic morphology-based subgeneric classification systems of the genus and to examine the origins of facultative and obligate gypsophily within the genus. DNA sequence data from the chloroplast regions matK and ndhF and from the nuclear ribosomal region ITS were collected from 46 species of Nama as well as from four new species and several outgroups. Data were analyzed using maximum likelihood and Bayesian methods. Phylogenetic analyses recover seven strongly supported major lineages within Nama. These lineages do not correspond to traditionally recognized subgenera, although they are largely congruent with an informal system based on ultrastructural observations of seeds. Four of the seven major lineages include gypsophilous species; these range from two lineages that include a single facultative gypsophile each, to one lineage that is almost entirely comprised of gypsophiles. viii Gypsum endemism in general, as well as facultative and obligate gypsophily in particular, has arisen multiple times in Nama. Parametric bootstrapping rejected the hypothetical monophyly of gypsophiles across the genus as a whole and within each of the two clades that contain multiple gypsophiles. Because approximately 20 species have been described since the last major revision of Nama nearly 80 years ago, detailed morphological observations of herbarium specimens were made in order to produce a comprehensive key to the species of Nama as well as the revision of a lineage comprising eight gypsophiles and one limestone endemic. ix Table of Contents List of Tables ....................................................................................................... xiii List of Figures ........................................................................................................xv