Phylogenetic and Population Genetic Studies in Grindelia (Asteraceae: Astereae) By Abigail Jane Moore A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology in the Graduate Division of the University of California, Berkeley Committee in Charge: Professor Bruce G. Baldwin Professor Brent D. Mishler Professor David D. Ackerly Professor Roger Byrne Fall 2010 Abstract Phylogenetic and Population Genetic Studies in Grindelia (Asteraceae: Astereae) by Abigail Jane Moore Doctor of Philosophy in Integrative Biology University of California, Berkeley Professor Bruce G. Baldwin, Chair Grindelia is among the most taxonomically challenging groups of North American composites. The genus as a whole has an amphitropical distribution, with approximately half of the species native to North America and Mexico and the remainder native to South America. I used DNA sequence data from the nuclear ribosomal ITS and ETS and chloroplast psaI-accD regions to revisit hypotheses on biogeographic history across the genus. Grindelia as a whole is well- supported and is composed of two sister clades, one native to South America and the other native to North America, including Mexico. The South American taxa are much more diverse in habit than the North American taxa. The North American taxa constitute two clades that largely occur on different sides of the Continental Divide. The diverse radiation of Grindelia in the California Floristic Province (CA-FP) appears to be most closely related to species from the Great Basin and Colorado Plateau and evidently descended from drought-adapted ancestors. Although Steyermark’s hypotheses about the relationships of North American Grindelia are not all supported, I did recover a clade corresponding to his Pacific radiation and many of the Mexican and Texan species that he hypothesized to be basal in the genus represent early diverging lineages in my trees. Polyploid complexes have long been a source of confusion to taxonomists due to their combination of morphological and ecological variability with a lack of obvious boundaries between putative species. Grindelia (Asteraceae) in the CA-FP provides a prime example of both of these attributes. Both diploid and tetraploid plants occur within the CA-FP, with tetraploids predominating along the coast and diploids in the interior. Although phylogenetic analysis shows that CA-FP Grindelia form a clade, relationships within the clade remain unresolved due to a lack of sequence divergence. Complex ecological and morphological variation within CA-FP Grindelia has been interpreted as being indicative of either extensive or no taxonomic diversity. I have chosen to follow an intermediate approach, recognizing what I consider to be the most morphological and ecologically distinctive ecotypes or clusters of ecotypes as taxa. In addition, I emphasized putative taxa that appear to maintain their morphological distinctiveness when growing sympatrically or peripatrically in the field. 1 Most of the morphological and ecological diversity in CA-FP Grindelia is present in the tetraploids, which appear to be autotetraploids based on cytogenetic data from prior studies. I used data from six nuclear microsatellites to examine 439 individuals from ten populations (nine tetraploid and one diploid) of Grindelia collected in and near the San Francisco Bay Area. I wanted to assess whether any genetic structure was evident across populations or taxa or both. Each of the ten populations was genetically distinct from the others and gene flow among populations appeared to be low. Although the plants grouped more strongly according to population than according to taxon, it was possible to classify > 90% of the individuals according to taxon using discriminant analysis of the microsatellite data. 2 I would like to dedicate my dissertation to my parents, Jane Ehardt Moore and William Loyd Moore, and to my brother, John Loyd Moore, for all of their love, support, and good humor throughout my graduate career. i Table of Contents Chapter 1, a taxonomic revision of California Grindelia. 1 Chapter 2, a phylogeny of Grindelia reconstructed from nuclear ribosomal 17 and chloroplast sequence data. Chapter 3, population structure in autotetraploid Grindelia of the California 65 Floristic Province. References Cited 94 ii Acknowledgements I would like to thank my major professor, Bruce Baldwin, for all the help and encouragement he has given me over the years I have been in Berkeley. His deep knowledge of the California flora and of botany in general are an inspiration to me. The remaining members of my committee, David Ackerly, Roger Byrne, and Brent Mishler, have been given me valuable suggestions in their areas of expertise throughout the course of my research and made comments that greatly improved this manuscript. John Strother of the U.C. Herbarium instigated my work on Grindelia, despite his and Bruce’s best efforts to discourage me from working on the genus. I have profited from his advice, good humor, and knowledge of all things relating to botanical nomenclature. The other graduate students in the Baldwin Lab during my time there, Matt Guilliams, Danica Harbaugh Reynaud, Chris Hobbs, Ruth Kirkpatrick, Mike Park, Doug Stone, Genevieve Walden, and Elizabeth Zacharias have provided much needed perspectives when I was lacking in perspectives, as well as help with everything I needed and many good times in the field. I have also enjoyed sharing the enthusiasm of the undergraduates who have worked in our lab: Mary Guo, Nairi Hartooni, Gracie Martin, and Monica Neff. Many of the specimens I collected for these projects and others were collected with Mike, and without him I would not have visited nearly as many interesting localities as I did in the course of my time in Berkeley. My understanding of the California flora and of phylogenetic theory has been much improved through our discussions. I would not have survived my first year at Berkeley without the guidance of Elizabeth. The current graduate students in the Baldwin Lab, Matt, Chris, Mike, and Genevieve have given me much help, encouragement, and friendly conversation throughout the process of writing this dissertation. Bridget Wessa, the lab manager of the Baldwin Lab, runs the most organized lab in Integrative Biology. It has been a pleasure working with her over the years, learning from her lab-related wisdom, and attempting to absorb some of her calmness in the face of lab-related mistakes and failed PCRs. Dean Kelch has shared with me and the other graduate students in the Baldwin Lab his wisdom, perspectives, and humor, all three of which were necessary at various times to remind me why I was here and what I was doing. He has also been a model of how one can be successful as a botanist and lead a balanced life. The members of the Mishler Lab have been like labmates to me as well: Ben Carter, Eric Harris, Bier Kraichak, Anna Larsen, Tom Madsen, Andy Murdock, Bianca Knoll Nakayama, Sonia Nosratinia, Susan Tremblay, and Rebecca Welch. Rebecca has been a calming influence and we have eaten many delicious meals together (as well as a few things that I burnt). The other graduate students in Integrative Biology are good friends as well as valued colleagues: Theresa Grieco, Becca Lutzy, Jenny McGuire, Erin Meyer, Tracy Misiewicz, Veronica Morris, Brody Sandel, Michal Schuldman, Jess Shade, and Steph Stuart. The other members of my dissertation writing support group listened to my tales of difficulty and reminded me that I was not alone: Sarah Amugongo, Katie Brakora, and Lorraine Cassaza. The people who work in the UC and Jepson Herbaria have been most helpful with questions about all things related to botany and many have become my friends as well: Sue iii Bainbridge, Andrew Doran, Barbara Ertter, John Game, David Gowen, Kim Kersh, Dan Norris, Ana Penny, and Cecile Shohet. Mei Greibenow, the graduate student affairs officer for Integrative Biology, has helped keep me on track throughout my years as a graduate student and helped me navigate the Berkeley bureaucracy. The plants in this dissertation have come from many different places. First and foremost, I would like to thank Adriana Bartoli and Roberto Tortosa, experts in Grindelia at the Universidad de Buenos Aires. I went in the field with them and Carlos Gonzalez in Argentina and they subsequently sent me many specimens and leaf material for my phylogenies. I would also like to thank the others with whom I went in the field, in addition to those listed above: John Anderson of Hedgerow Farms, Don Canestro of the University of California’s Kenneth S. Norris Rancho Marino Reserve, Hubert Jr., Kathy Koehler of the University of California Natural Reserve System's Donald and Sylvia McLaughlin Reserve, Steve Laymon of the Bureau of Land Management, Andrea Pickart of the Humboldt Bay National Wildlife Refuge, Lewis Reed of the Livermore Area Regional Parks, Joe Silviera of the Sacramento National Wildlife Refuge, and Pam Williams of the Kern National Wildlife Refuge. In addition, I like to acknowledge the California Department osf Fish and Game, California State Parks, the East Bay Regional Park District, the Humboldt Bay National Wildlife Refuge, the Kern National Wildlife Refuge, Livermore Area Regional Parks, the Sacramento National Wildlife Refuge, the San Francisco Bay National Wildlife Refuge Complex, and the Welder Wildlife Refuge for permission to collect and help in the field. This work was also performed in part at the following University of California Natural Reserve System Reserves: Bodega Marine Reserve, Coal Oil Point Natural Reserve, Jepson Prairie Reserve, Donald and Sylvia McLaughlin Reserve, Kenneth S. Norris Rancho Marino Reserve, Santa Cruz Island Reserve, and Sedgwick Reserve. I received funding to support my work from the Lawrence R. Heckard Endowment Fund of the Jepson Herbarium, the Department of Integrative Biology, the American Society of Plant Taxonomists, and the East Bay Chapter of the California Native Plant Society. My friends in the Bay Area outside of science, especially Rebecca Auerbach, Esther Cardona, Nancy Kerr, Kyle Sessions, Steph Whitesides, and Mark Wilde reminded me that life did not have to be all about Grindelia and DNA sequences if I did not choose for it to be. The vendors at the Berkeley Farmers Markets have kept me well fed and in good health throughout my time in Berkeley. I would especially like to thank Full Belly Farm, Guru Ram Das Orchards, Hodo Soy, Morrel’s Bread, La Tercera Farm, and Three Twins Ice Cream. The diverse wildlife of North Berkeley kept me amused and distracted while I was writing and analyzing data in my apartment: bushtits; chestnut-backed chickadees; American crows; black-tailed deer; mourning doves; northern flickers; red-tailed and Cooper’s hawks; Anna’s and Allen’s hummingbirds; salamanders; fox, golden-crowned, and white-crowned sparrows; hermit thrushes; plain titmice; California towhees; cedar waxwings; yellow-rumped and Townsend’s warblers; and, especially, the scrub jays who lived outside my kitchen window. My plants provided calming green-ness while I was writing and put up with my absences for field work. Ann Kelsey and Lynn Bohs from the University of Utah saw a beginning undergraduate who was interested in botany and encouraged me throughout my entire undergraduate career. Ann Kelsey gave me a job and a home away from home at the Garrett Herbarium. Lynn Bohs offered to hire me in her lab the day she met me and encouraged me through all difficulties, iv failed lab work, and bad writing until I graduated and published two papers with her. I would not have come to Berkeley without the influence of these two women. Finally, I would like to thank my family. My parents, Jane and Bill Moore, have provided both moral and financial support throughout my time in graduate school. They helped me collect and press a large proportion of the plants analyzed in Chapter Three when I would have had great difficulties doing the field work on my own due to a broken arm. My father also was my collaborator for the analyses presented in Chapter Three. My brother, John Moore, has given me much sage advice over the course of my time in Berkeley. We have also had many discussions of Grindelia, botany, fossils, geology, grammar, and other random topics. My understanding of these topics would have been much poorer and my enjoyment of them much less if I had not been able to talk about them with John. In addition, John was a good-humored field companion for the trips in which I collected many of the plants discussed in Chapter Two. v Chapter One A taxonomic revision of California Grindelia. GENERAL INTRODUCTION Grindelia is a New World genus, with approximately 75 species. It has an amphitropical distribution, with the North American and South American species forming sister clades in phylogenies based on ITS and ETS sequence data (Chapter Two). Within the North American clade, the species native to the Pacific states form a well-supported clade along with G. howellii from Montana and Idaho. This clade (called the Pacific Clade in Chapter Two) corresponds to a group hypothesized by Steyermark (1937) to have radiated rapidly in newly-created habitats along the Pacific Coast of North America. The Pacific Clade also corresponds to a group of species found by Dunford (1964) to have the same chromosomal arm arrangement, which he called the Hallii Genome (Dunford 1970). Most of the species in California belong to this Pacific Clade. The relationships among the plants in this clade were generally poorly resolved in the molecular phylogenies, consistent with a lack of sequence divergence among members of the group. The individuals collected in the California Floristic Province did form a subclade within the Pacific Clade that was supported in the Bayesian analyses. There are two species of Grindelia in California that are not part of the Pacific Clade. Both of these species occur mainly outside of California: Grindelia squarrosa occurs throughout most of the western and central United States and Canada; G. fraxinipratensis occurs in the Mojave Desert in the vicinity of Ash Meadows in south-eastern Nevada and adjacent California. TAXONOMIC OVERVIEW The genus Grindelia was described in 1807 by Willdenow, based on plants of G. inuloides that were being grown in the Royal Botanical Garden in Berlin. These plants were grown from seed collected in Mexico by Humboldt and Bonpland (Edwards 1817). The first specimens of Grindelia to be described from California were collected on the Beechey Expedition and described by Hooker and Arnott (1833). Douglas also collected early specimens of Grindelia in California, which were described by de Candolle (1836). De Candolle recognized 11 species in his treatment of worldwide Grindelia. He noted that the species were difficult to delimit, stating “Genus naturalissimum etiamsi ab auctoribus etiam gravissimus variè vexatum” (1836, p. 316). Throughout the remainder of the 1800s and early 1900s, the trend was to recognize more species of Californian Grindelia. Gray (1884) recognized seven species in California in his treatment of North American Grindelia. Jepson (1925) recognized six species of Grindelia in California and seven additional varieties. However, only three of Jepson’s six species were the same as those recognized by Gray. Steyermark (1934) recognized 14 species and 23 additional infra-specific taxa in his revision of North American Grindelia. 1