Copyright by Taylor Sultan Quedensley 2012 The Dissertation Committee for Taylor Sultan Quedensley Certifies that this is the approved version of the following dissertation: MOLECULAR SYSTEMATICS OF THE MEXICAN TUSSILAGINIOID GROUP (ASTERACEAE: SENECIONEAE) Committee: Beryl Simpson Co-Supervisor Robert Jansen Co-Supervisor C. Randall Linder David Hillis James Mauseth MOLECULAR SYSTEMATICS OF THE MEXICAN TUSSILAGINIOID GENERA (ASTERACEAE: SENECIONEAE) by Taylor Sultan Quedensley B.S. Agr. Sci., M.S. Biology 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 Philospohy The University of Texas at Austin August 2012 Dedication This dissertation is dedicated to Don Mahoney and Dennis Breedlove. Their love for plants has inspired me for many years. Acknowledgements I am so grateful to Bob Jansen and Beryl Simpson for enabling me to be a botanist at The University of Texas at Austin and to pursue my academic and career goals. I thank Mario Véliz (Universidad de San Carlos de Guatemala) for his support in the field and for the use of the BIGU Herbarium. In Mexico, I thank Jose Luis Villaseñor (Universidad Nacional Autónoma de México), Jose Angel Villareal (Universidad Autónoma Agraria Antonio Narro), M. Socorro González-Elizondo (Instituto Politécnico Nacional), and Mario Ishiki (Colegio de la Frontera Sur) for assistance with fieldwork and specimen transport and export. I am grateful to Timmy Buxton (Cabrillo College) for his assistance in the field during multiple collecting trips. I also thank Taylor Nyberg and Nicholas Wilhelm (The University of Texas at Austin) for assistance with laboratory components of this project, and Thomas Payne (CIMMYT) for providing lodging during research visits to Mexico City. Leaf fragments for molecular studies were taken with permission from the following herbaria: BIGU, F, MEXU, TEX, US. I thank Beryl Simpson, Lindsay Woodruff, and Thomas Wendt of the Plant Resource Center for their support at the herbarium of The University of Texas at Austin. I am grateful to Donald Mahoney, David Kruse-Pickler, and Mona Bourell of the San Francisco Botanical Garden for sending live material to The University of Texas at Austin and for allowing us to make voucher specimens from their garden. I am thankful to Robert Kowal (University of Wisconsin- v Madison) and David Sutherland (University of Nebraska at Omaha) for sending living material to The University of Texas at Austin. Lastly, I thank Larry Gilbert and John Crutchfield at the Brackenridge Field Laboratory for providing greenhouse space for growing living specimens included in this project. I am very grateful to the following graduate students for all of their support over the past six years with my research and personal matters: Chris Blazier, Michael Gruenstaeudl, Amanda Kenney, Scott Meadows, Teofil Nakov, Sandra Pelc, Erica Schwarz, Roxi Steele, and Mao-Lun Weng. I thank David Des Marais with guidance on some aspects of the phylogenetic analyses and Eli Meyer for help with genome assembly and analysis. Funding was provided by The University of Texas at Austin Graduate School, College of Natural Sciences, Plant Biology Graduate Program, Sidney and Doris Blake Professorship, and the Mexican Center. Additional funding was provided by the American Society of Plant Taxonomists, the American Philosophical Society Lewis and Clark Field Scholarship, the University of Hawaii at Manoa Department of Botany, and the National Museum of Natural History at the Smithsonian. I thank Dr. Billie Turner for his friendship and encouragement and for always believing in me. Without you my graduate school experiences would have had an empty feeling. I will always remember our coffee chats that meant so much to me for six years. Finally, I wish to thank my mom Cindy, my wife Marnie, and my daughters Nomi Xela and Lucille Xilone, for their unwavering support and love while I have been in graduate school. vi SYSTEMATICS OF THE MEXICAN TUSSILAGINIOID GENERA (ASTERACEAE: SENECIONEAE) Taylor Sultan Quedensley, Ph.D. The University of Texas at Austin, 2012 Supervisors: Beryl Simpson & Robert Jansen The Mexican tussilaginioid group consists of 13 diverse genera of sunflowers (Asteraceae: Senecioneae) distributed from the USA to Panama, with most species occurring in montane regions from Central Mexico to Guatemala. Presently, 140 species in 13 genera are recognized with many of these species considered to be endemic to threatened pine-oak forest or cloud forest ecosystems. Sixty-two species within the study group were included in a combined phylogenetic analysis of two regions of the nuclear ribosomal repeat, the internal and external transcribed spacers. Fifty-two of these taxa were analyzed in a phylogenetic framework for the first time. The results from the combined nrDNA analysis (62 species in 12 genera in the combined analysis) strongly support the monophyly of the Mexican tussilaginioid group, however, the topology and hypothesis testing using constraint models indicate that the genera Pittocaulon, Psacaliopsis, and Roldana are not monophyletic. Telanthophora s.s. is monophyletic, although this genus is nested within Roldana s.s. Endemism is abundant among the clade with over half of the species restricted to relatively small geographic areas. Moreover, vii most members of the group (ca. 120 species, or 87%) are present in montane regions under immense pressure from human land use practices at or above 1500 meters in Mexico and Guatemala. Two of the genera from my study group, Pippenalia and Psacaliopsis were taxonomically assessed based on their morphological characters and the nrDNA results. A single species, Psacaliopsis purpusii, remains in the genus, while Pippenalia delphinifolia, Psacaliopsis macdonaldii, and P. pudica are transferred to Psacalium. Funstonia gen. nov. is here erected a new genus encompassing a single species with two varieties. Chloroplast genomes of Arnoglossum atriplicifolium, Roldana aschenborniana, R. barba-johannis, and Telanthophora grandifolia were sequenced with next generation sequencing in order to identify regions of variation and to compare the assemblies produced via de novo and reference-based methods. The reference-based assemblies were more complete than the de novo assemblies, and therefore the former sequences were utilized for phylogenetic analyses. viii Table of Contents List of Tables .… ................................................................................................... xi List of Figures . ..................................................................................................... xii List of Illustrations . ............................................................................................. xiii List of Appendices . ............................................................................................. xiv Chapter 1: Introduction to the Mexican tussilaginioid group (Asteraceae: Senecioneae) ........................................................................................ 1 Chapter 2: Molecular phylogenetics of the endemic montane Mexican tussilaginioid group (Asteraceae: Senecioneae) ...................................................... 10 Introduction .................................................................................................. 11 Materials and Methods…..............................................................................12 Taxon sampling and DNA isolation .............................................. ….12 DNA amplification, sequencing, and alignment ............................ ….13 Phylogenetic analyses .................................................................... ….15 Congruence between ETS and ITS ................................................ ….16 Alternative hypothesis testing ........................................................ ….16 Results .......................................................................................................... 17 Phylogenetic analysis of ITS and ETS data .................................. ….17 Congruence test……………………………………………………...18 Combined data analysis ................................................................ ….18 Hypothesis testing ......................................................................... ….19 Discussion .................................................................................................... 20 Psacaliopsis purpusii, Robinsonecio (Clade 1) ............................. ….21 Psacaliopsis pinetorum/paneroi (Clade 2) .................................... ….22 Digitacalia (Clade 3) ..................................................................... ….23 Arnoglossum, Barkleyanthus, Yermo (Clade 4) ............................. ….24 Pippenalia, Psacaliopsis macdonaldii/pudica, Psacalium (Clade 5) .24 Roldana ‘Pericalia’ (Clade 6) ....................................................... ….26 Pittocaluon bombycophole (Clade 7) ............................................. ….26 Pittocaulon praecox/vellatum, Villasenoria (Clade 8) .................. ….27 Roldana petasitis complex (Clade 9) ............................................. ….28 Roldana sundbergii complex (Clade 10) ....................................... ….29 Roldana platanifolia complex (Clade 11) ...................................... ….30 Roldana mixtecana/reticulata (Clade 12) ...................................... ….30 Telanthophora (Clade 13) .............................................................