AN ABSTRACT OF THE THESIS OF David S. Gernandt for the degree of Doctor of Philosophy in Botany and Plant Pathology presented on May 7, 1998. Title: Phylogeny, Cospeciation, and Host Switching in the Evolution of the Ascomycete Genus Rhabdocline on Pseudotsuga and Larix (Pinaceae). Abstract Approved: Redacted for Privacy Jeffrey K. Stone The relative role of cospeciation and host switching in the phylogenetic history of ascomycete foliar symbionts is addressed in the orders Leotiales and Rhytismatales, fungi associated predominantly with Pinaceae (Coniferales). Emphasis is placed on comparing the evolution of the sister genera Pseudotsuga and Larix (Pinaceae) with that of the pathogenic and endophytic fungi in the genus Rhabdocline. Pinaceae evolved during the Mesozoic and divergence of all extant genera and several infrageneric lineages (esp. in Pinus) occurred prior to the Tertiary, with subsequent species radiations following climatic changes of the Eocene. The youngest generic pair to evolve from Pinaceae, Larix and Pseudotsuga, diverged near the Cretaceous-Tertiary boundary in East Asia or western North America. Rhabdocline is comprised of seven species and subspecies, six known from two species of Pseudotsuga and one, the asexual species Meria laricis, from three species of Larix. Evidence from host distributions and from nuclear ribosomal DNA suggests that Rhabdocline speciated in western North America and has been involved in several host switches. The ancestor ofMeria laricis appears to have switched from P. menziesii to its current western North American hosts, L. occidentalis, L. lyallii, and very recently may have extended its host range to the European species, L. decidua. The occurrence of two lineages of R. weirii ssp. weirii on both North American species of Pseudotsuga is also probably the result of a recent host switch. Evidence of host- mediated divergence is seen in R. parkeri, which has different internal transcribed spacer types in the geographically isolated coastal and interior forms of P. menziesii. The wide host ranges of fungal genera closely related to Rhabdocline indicates that host switching is a prevalent pattern in the evolution of foliar symbionts in Leotiales and Rhytismatales. The prevalence of host switching in this group relative to other endosymbiotic organisms can probably be attributed to differences in dispersal mechanisms. Spores of foliar fungi are dispersed horizontally by wind and rain, rather than vertically from parent to offspring. Over evolutionary time, this provides more opportunities to shift to new hosts, particularly when the hosts are closely related and have overlapping distributions. ©Copyright by David S. Gernandt May 7, 1998 All Rights Reserved Phylogeny, Cospeciation, and Host Switching in the Evolution of the Ascomycete Genus Rhabdocline on Pseudotsuga and Larix (Pinaceae) by David S. Gernandt A THESIS submitted to Oregon State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Completed May 7, 1998 Commencement June 1998 Doctor of Philosophy thesis of David S. Gernandt presented on May 7, 1998 APPROVED: Redacted for Privacy Major Professor, repiesenting Botany and Plant Pathology Redacted for Privacy Chair of Department of Bot ny and Plant Pathol.:41 Redacted for Privacy Dean of Graduate, chool I understand that my thesis will become part of the permanent collection of Oregon State University libraries. My signature below authorizes release of my thesis to any reader upon request. Redacted for Privacy David S. Gernandt, Author Acknowledgments It is with great pleasure that I extend my thanks to the many people who assisted and sometimes participated in the creation of this work. First and foremost, I thank my major professor, Jeffrey K. Stone for his countless hours of training that started while I was an undergraduate at the University of Oregon, continued throughout graduate school and which I hope will continue with future mycological collaborations. Jeffs confidence in me and willingness to guide my education have been critical in the positive graduate experience I had at Oregon State University. I thank the members of my graduate studies committee, Aaron Liston, Joseph Spatafora, Steven Strauss, and Patrick Breen. It was Aaron Liston who first introduced me to both the theoretical and practical aspects of molecular systematics. I have thoroughly enjoyed participating in the several collaborations that we have pursued together. Since his arrival at Oregon State University, Joseph Spatafora has been an excellent mentor to me in both molecular systematics and fungal evolution. I thank Patrick Breen for being my graduate school representative and for letting me off the hook towards the end of my preliminary oral exams. Steven Strauss kindly agreed to sit on my committee as a replacement member for the last hurdle of my graduate school career. I would also like to extend my thanks to former committee member Everett Hansen, who had to be replaced when he took a sabbatical in France. Everett served as a co-advisor with Jeff in the early stages of my graduate studies. Everett was very patient with me and was indispensible in planning my graduate program. Everett gave me room to roam in the laboratory, and in what was certainly a selfless desire to broaden my mycological education, provided me with ample opportunities to assist in his research on Basidiomycetes and Oomycetes. George Carroll and Howie Bonnett served as my undergraduate thesis advisors at University of Oregon. I thank them for first introducing me to the life of a research scientist. Along with Aaron Liston, fellow student Ankie Camacho gave me my first training in DNA isolation, PCR, sequence analysis, and several other molecular methods that have proved invaluable. Over the years I have studied specimens generously provided from researchers around the world. Thanks are due to Ernest Ash III, Brenda Callan, George Carroll, Greg DeNito, John Dennis, Martin Gardner, Everett Hansen, Ottmar Holdenrieder, Dan Jones, Alan Kanaskie, Rolf Kehr, Blakey Lockman, Bill Merrill, Jim Oliphant, Catherine Parks, Miguel Soto, Yoshihiko Tsumura, Craig Schmitt, and Gerard Verkley. I also extend my gratitude to the American Type Culture Collection and Centraalbureau voor Schimmelcultures. Over the years my labmates have given me useful advice on everything from biological theory to technical support to lab courtesy. My sincerest thanks (approximately in order of appearance), to Tina Dreisbach, Marion Murray, Jerry Hefner, Mike McWilliams, Brennan Ferguson, Deborah Clark, Ankie Camacho, Wes Messinger, John Wheeler, Jim Oliphant, Susan Massey, Pablo Rosso, Koren Dennis, Aleta Groenig, Lori Trummer, Lori Winton, Kimberly Davis, and Bryan Capitano. Although I have not worked side-by-side with members of the Spatafora lab, they too have been availed themselves to me on countless occassions. Thanks to Jamie Platt, Lisa Grubisha, and Eric Peterson in that regard. Funding for this project has come from discretionary funds of Jeff Stone, and from personal contributions by David Miller Sr. and David Miller Jr. at Moore Mill and Lumber Company in Bandon, Oregon and by my grandmother, Frances Cavoretto. The Mycological Society of America awarded me several travel grants to their annual meetings as well as the Backus award. Sigma Xi contributed a grant in aid of research. The last several months of writing and analyses for this thesis were done in Mexico City. I thank my future wife Sol Ortiz Garcia for her love and support during that time. I also thank her brother Salvador Ortiz Garcia for providing critical computer support. Finally, I would like to thank my parents, and once again, my grandmother, for all the extra little things they did to help me reach this point in my life. This thesis is dedicated to the loving memory of my grandmother, Frances Cavoretto. CONTRIBUTION OF AUTHORS Chapter three was coauthored with Aaron Liston, who advised in the design and analysis, provided laboratory resources, and reviewed several drafts. Jeffrey K. Stone advised in the sampling, participated in acquisition of fungal isolates, provided laboratory resources, and edited several drafts for chapters one, four, five, six, and seven. Despite its placement in this thesis, chapter five was the first chapter written. Francisco J. Camacho kindly trained me in the molecular techniques and sequence analysis that were used in this and several other chapters. He also participated in the benchwork necessary for sequencing Meria laricis and Rhabdocline parker!. TABLE OF CONTENTS Page CHAPTER ONE: INTRODUCTION AND LITERATURE REVIEW 1 1.1 Abstract 1 1.2 Introduction 2 1.3 Strengthening hypotheses regarding the evolution of Pseudotsuga and Larix 4 1.4 Phylogenetic reconstruction of inoperculate discomycetes 6 1.5 Speciation of Rhabdocline on Douglas-Fir and Larch 9 1.6 Literature Cited 12 CHAPTER TWO: A PHYLOGENETIC RECONSTRUCTION OF PINACEAE BASED ON RBCL AND THE FOSSIL RECORD 16 2.1 Abstract 16 2.2 Introduction 17 2.3 Materials and Methods 22 2.4 Results 25 2.5 Discussion 34 2.6 Literature Cited 35 CHAPTER THREE: INTERNAL TRANSCRIBED SPACER REGION EVOLUTION IN LARIX AND PSEUDOTSUGA (PINACEAE) 39 3.1 Abstract 39 3.2 Introduction 40 3.3 Materials and Methods 42 3.4 Results 49 3.5 Discussion 63 3.6 Acknowledgements 70 3.7 Literature Cited 70 CHAPTER FOUR: A PHYLOGENETIC RECONSTRUCTION OF INOPERCULATE DISCOMYCETES INFERRED FROM PARTIAL SMALL SUBUNIT SEQUENCES OF NUCLEAR RIBOSOMAL DNA 76 4.1 Abstract 76 4.2 Introduction