Copyright by Barbara Elizabeth Goodson 2007
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Copyright by Barbara Elizabeth Goodson 2007 The Dissertation Committee for Barbara Elizabeth Goodson certifies that this is the approved version of the following dissertation: Molecular Systematics and Biogeography of Descurainia Webb & Berthel. (Brassicaceae) Committee: Robert K. Jansen, Supervisor C. Randal Linder Alan M. Lloyd Beryl B. Simpson Tandy J. Warnow Molecular Systematics and Biogeo graphy of Descurainia Webb & Berthel. (Brassicaceae) by Barbara Elizabeth Goodson, B.S., M.C.S., M.S 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, 2007 Acknowledgements I would like to thank my advisor, Robert Jansen, for his direction, financial support, and encouragement during all stages of my graduate study at the University of Texas, and Randy Linder, Alan Lloyd, Beryl Simpson, and Tandy Warnow for serving on my dissertation committee. I am also greatly indebted to Ihsan Al -Shehbaz for his adv ice and suggestions, and his knowledge and general enthusiasm for all things Brassicaceae. Many people helped me obtain plant material. These include César Gomez - Campo and Jay McKendrick, who provided seeds of various Canarian Descurainia species and D. so phioides , respectively, and Tim Chumley, Romey Haberle, José Panero, Bonnie Crozier, Ali Dönmez, and Arnold Santos -Guerra who collected specimens in the United States, Chile, Turkey or the Canary Islands for me. I am grateful to Mark Beilstein for providin g DNA of Ianhedgea , Robeschia , and D. sophia , and to Robert Price for sharing unpublished ITS sequences of Tropidocarpum . For assistance with field work in Bolivia, I thank Carolina Garcia, Jorge Jácome, Ivan Jimenez, Cynthya Jurado, Mauricio Ocampo, Jorge Uzquiano, and Carlos Zambrana. I am extremely grateful to those helping me with collecting permits, logistics and advice for the Bolivia collecting trip, including Carolina Garcia, Stephan Beck, Rosa Isela Meneses, Gisela Carrasco, Monica Zepallos, Maximo Liberman, Franz Guzmán, Eustaquio Marca, Peter Jorgensen, Mauricio López, Martín Timana, and Tom Wendt. For help in the field in Argentina I thank Matías iv Morales, Lázaro J. Novara, Silvia Perfetti, Mónica Stronati, Tim Chumley, and Mike Moore, and gratefu lly acknowledge the advice and assistance of Iris Peralta, Eduardo Méndez, Robert Kiesling, Osvaldo Morrone, Gabriel Rua, and especially Renee Fortunato and Silvia Perfetti. For help in Chile, I thank Mélica Muñoz -Schick, Carmen Cristóbal, and Clodomiro Ma rticorena. I thank the curators of herbaria who supplied loan material and/or allowed me to sample specimens for DNA material, namely BAA, GH, LPB, MO, NY, UNM, OSC, SI, and TEX, as well as those who allowed me to examine material, namely BAB, LIL, MCNS, M ERL, RM, and SGO. At the University of Texas, I would like to acknowledge the following people for their assistance. Sumaiyah Rehman helped with lab work, including amplifying and sequencing the ndhF -rpl32 chloroplast region for a large number of accession s. Alan Lloyd, Anneke Padolina, José Panero, and Ruth Timme offered suggestions for chloroplast or nuclear primers, and Dena Sutton assisted me in growing plants in the UT greenhouse. A number of people answered software questions including Andy Alverson, Jeff Austen, Tim Chumley, Romey Haberle, Mary Guisinger, Leah Larkin, Andrea Weeks, and Derrick Zwickl. Tom Wendt and Lindsay Woodruff of the UT Plant Resources Center did a fantastic job handling loan requests, processing material from loans and collectin g trips, and answering innumerable questions. Most importantly, I would like to thank the members of the Jansen and Theriot labs who offered their friendship, advice, and help during my graduate study at the University of Texas. I am grateful to Javier Fra ncisco -Ortega, Klaus Mummenhoff, Joey Shaw, and Ruth Timme for sharing pre -prints of journal articles. A huge thank you to Romey Haberle, Heidi Meudt, and Jennifer Tate for reading most of this dissertation and making many helpful and insightful comments, and also to Javier Francisco -Ortega and an v anonymous reviewer for their critical comments on the publication based on Chapter 4 of this dissertation. Funding from a National Science Foundation IGERT fellowship and UT botany program research and travel supp ort, including Lorraine I. Stengl endowment and Linda Escobar memorial funds, is gratefully acknowledged. Thanks are extended to Tim Chumley and Irene Thien, who housed my children while I was gone on South American collecting trips. For generously sharing their homes during my final back -and -forth years in Austin, I thank Lori Cooper and especially Mary Guisinger and her family. Finally, I will always be indebted to my husband Jeff Austen and our children Martha and Jesse for putting up with my long absen ces from their lives and all the vacations that morphed into Descurainia collecting expeditions. vi Molecular Systematics and Biogeography of Descurainia Webb & Berthel. (Brassicaceae) Publication No._____________ Barbara Elizabeth Goodson, Ph.D. The Uni versity of Texas at Austin, 2007 Supervisor: Robert K. Jansen Descurainia is a genus in the Brassicaceae distributed throughout temperate areas of the Old and New World. The genus is well -known for its taxonomic complexity, especially within New World s pecies, on account of its numerous intergrading forms coupled with circumscriptions dependent upon inconsistent and overlapping characters. Descurainia is most diverse in western North America and western South America, with a smaller center of distributio n in the Canary Islands and three additional Old World species. This distribution makes the genus well -suited for addressing biogeographical issues related to New World intercontinental dispersal and evolution in island systems. A molecular -based analysis of Descurainia was conducted using DNA sequences from nuclear ribosomal internal transcribed spacer (ITS), single -copy nuclear Target of Rapamycin (TOR), and non -coding chloroplast regions. The genus, with the inclusion of the monotypic genera Hugueninia a nd possibly Robeschia , is strongly supported as monophyletic, and appears to be of Old World origin with recent diversification within vii the Canary Islands and the New World. A phylogeny recovered from combined ITS and chloroplast data is not well -resolved w ith respect to relationships between some major New World lineages, but suggests that multiple independent dispersals of Descurainia have taken place between North and South America. Substantial incongruence between ITS, chloroplast, and TOR phylogenies, a s well as the presence of mixed ITS and TOR sequences, point to a complex evolutionary history involving extensive gene flow and hybridization for North American Descurainia . The molecular data highlight possible problems with current species circumscripti ons, especially within North American taxa such as D. incisa , D. obtusa , and D. pinnata . ITS and chloroplast data indicate that species of Descurainia in the Canary Islands are derived via a single colonization event, most likely from southwestern Europe o nto the lowland scrub zone on Tenerife. Both intra -island adaptive radiation and inter -island colonization have played a prominent role in the evolution of this genus in the islands. The results presented in this dissertation represent the first comprehens ive molecular study of Descurainia, and may serve as a phylogenetic framework for future research on the genus as well as phenomena such as speciation and hybridization in recently -evolved groups. viii Table of Contents List of Tables ................................ ................................ ................................ ........ xii List of Figures ................................ ................................ ................................ ...... xiii Chapter 1: Introduction ................................ ................................ ............................ 1 Chapter 2: Molecular s ystematics of Descurainia Webb & Berthel. (Brassicaceae) based on nuclear ITS and non -coding chloroplast DNA .............................. 13 Introduction ................................ ................................ ................................ ... 13 Materials and Methods ................................ ................................ .................. 20 Sampling ................................ ................................ .............................. 20 PCR amplification and DNA sequencing ................................ ............ 22 Phylogenetic analyses ................................ ................................ .......... 24 Estimates of divergence times ................................ ............................. 27 Results ................................ ................................ ................................ ........... 30 Analys is of ITS and trnL data to assess the monophyly of Descurainia ................................ ................................ ................. 30 Analysis of ITS data to assess relationships within Descurainia ........ 33 Chloroplast data ................................ ................................ ................... 35 Tests for inco ngruence ................................ ................................ ......... 38 Analysis of combined data ................................ ................................ ... 39 Optimization of New World