Copyright by Timothy Wayne Chumley 2007 The Dissertation Committee for Timothy Wayne Chumley certifies that this is the approved version of the following dissertation: Phylogeny, Biogeography and Systematics of Menodora (Oleaceae) and The Chloroplast Genome of Pelargonium × hortorum Committee: Robert K. Jansen, Supervisor Donald A. Levin, Co-supervisor Jose L. Panero Beryl B. Simpson Alan M. Lloyd David C. Cannatella Phylogeny, Biogeography and Systematics of Menodora (Oleaceae) and The Chloroplast Genome of Pelargonium × hortorum by Timothy Wayne Chumley, B. 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 While there are many people deserving of recognition for their assistance and support during the process of completing this research, I can mention here only a few. First, without a doubt, I would like to thank Irene for her love and support over the years, and without whom this process might never have started, and certainly would not have ended. I thank my mother, Marilyn Chumley, for her love and support as well, especially after the death of my father, Don Chumley; I trust that he would be proud of this accomplishment. My advisor, Dr. Robert K. Jansen and my cohort of labmates deserve mention for providing a fun and challenging environment. Jan Barber, Romey Haberle, Barbara Goodson, and Micheal J. Moore all provided excellent advice, discussion or feedback in the lab or field. Everyone who went into the field with me needs a special award, particularly if the Land Cruiser decided to break down on that particular trip; Geoff Denny gets kudos for the Monterrey experience, when we, like an old submarine, ran only on batteries, and Mike gets some kudos for the Deerslayer episode, and the many, many beers and many, many miles, usually not at the same time of course. James Henrickson also provided me with miles of amusement, and discussions that were particularly instructive about the practice of systematics and helped shape my perceptions about Menodora. Early in this work, Eva Wallander provided advance access to her sequences of Menodora and the Oleaceae. Ricardo Vanni, Arturo Schinini, and Lazaro Novarra all provided invaluable assistance while I was collecting in their home ranges. Jerzy Rzedowski provided truly invaluable specimens in exchange, and tremendous botanical insight. I also extend my gratitude to the always helpful curators and staff of the many herbaria I’ve visited. Melica Muñoz of SGO in Santiago has been especially iv helpful in answering questions and providing information about the exciting rediscovery of Menodora linoides in Chile. Finally, I would like to thank the members of my committee for their advice and assistance (and patience), and to Jose Panero and Beryl Simpson in particular for taking time during their travels to collect plants for me as they found them. The major portion of this dissertation concerning research on the plant genus Menodora was supported by funding from a National Science Foundation Dissertation Improvement Grant, and by smaller grants from Sigma Xi, the American Society of Plant Taxonomists, the Botanical Society of America and the Graduate Program in Plant Biology at The University of Texas at Austin. This chloroplast genome portion of this work was supported by grant DEB­ 0120709 from the National Science Foundation to R. K. Jansen and J. L. Boore. Part of this work was performed under the auspices of the U.S. Department of Energy, Office of Biological and Environmental Research, by the University of California, Lawrence Berkeley National Laboratory, under contract No. DE-AC02-05CH11231. May, 2007 v Phylogeny, Biogeography and Systematics of Menodora (Oleaceae) and The Chloroplast Genome of Pelargonium × hortorum Timothy Wayne Chumley, Ph.D. The University of Texas at Austin, 2007 Supervisors: Robert K. Jansen, Donald A. Levin This dissertation presents the result of two separate research programs. The first elucidates the phylogeny, biogeography and systematics of the genus Menodora in the olive family. A phylogeny based on the internal transcribed spacer (ITS) of nuclear ribosomal DNA and the chloroplast rps16 and trnL introns and trnL-F intergenic spacer demonstrates that the genus is monophyletic. Within the genus, M. robusta of Patagonia is the first taxon to branch, followed by a monophyletic African clade and M. spinescens of California, though the placement of the latter does not have strong support. Most North American species are nested within the derived South Americans. A South American origin is hypothesized, with two independent dispersals to North America, and a single dispersal to Africa. The phylogeny provided new insights for the systematic treatment, where 24 species, one subspecies and six varieties are recognized, with major vi realignments of the intregrifolia and scabra species complexes, and a single new species described. In the second area of research, the chloroplast genome of Pelargonium × hortorum has been completely sequenced. At 217,942 base pairs (bp), it is both the largest and most rearranged land plant chloroplast genome yet sequenced. It features two copies of a greatly expanded inverted repeat (IR) of 75,741 bp each, and diminished single copy regions of 59,710 bp and 6,750 bp. Gene content is similar to other angiosperms, with the exceptions of a large number of pseudogenes, two open reading frames (ORF56 and ORF42), and the losses of accD, trnT-ggu, and possibly rpoA. The latter may be represented, however, by highly divergent set of rpoA-like ORFs. The IR expansion accounts for most of the size increase of the genome, but an additional 10% is related to the large number of repeats found. Most of these occur near rearrangement hotspots, and two different repeat associations (characterized by full or partial duplications of several genes) are localized in these regions. We propose simple models that account for the major rearrangements with a minimum of eight IR boundary changes and 12 inversions in addition to several sequence duplications. vii Table of Contents List of Tables ...........................................................................................................x List of Figures....................................................................................................... xii Chapter 1: Introduction...........................................................................................1 Chapter 2: Phylogeny and biogeography of Menodora (Oleaceae).........................2 Introduction.....................................................................................................2 Hypotheses of Species Relationships in Menodora...............................3 The Biogeography of Menodora............................................................5 Materials and Methods....................................................................................9 Sampling ................................................................................................9 DNA Isolation, PCR, and Sequencing.................................................10 Analysis................................................................................................12 Results...........................................................................................................14 ITS (nrDNA)........................................................................................14 rps16 intron and trnLF region (cpDNA) .............................................16 Combined Datasets ..............................................................................18 Testing Alternate Topologies...............................................................21 Biogeography.......................................................................................22 Discussion.....................................................................................................23 Phylogeny and Biogeography..............................................................23 Morphological Character Evolution ....................................................30 Systematic Implications.......................................................................33 Conclusions...................................................................................................36 Chapter 3: A systematic revision of Menodora Bonpl. (Oleaceae) ......................67 Introduction...................................................................................................67 Taxonomic history ...............................................................................67 viii Generic relationships ...........................................................................76 Species Relationships, Distribution and Speciation.............................78 Morphology..........................................................................................84 Ecology ..............................................................................................101 Ethnobotanical and Human Uses.......................................................105 Materials/Methods ......................................................................................106 Species Concept.................................................................................109 Systematic Treatment..................................................................................110