Systematics of Buddleja (Scrophulariaceae): Phylogenetic Relationships, Historical Biogeography, and Phylogenomics
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Systematics of Buddleja (Scrophulariaceae): phylogenetic relationships, historical biogeography, and phylogenomics John H. Chau A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2017 Reading Committee: Richard G. Olmstead, Chair Verónica S. Di Stilio Adam D. Leaché Program Authorized to Offer Degree: Department of Biology ©Copyright 2017 John H. Chau University of Washington Abstract Systematics of Buddleja (Scrophulariaceae): phylogenetic relationships, historical biogeography, and phylogenomics John H. Chau Chair of the Supervisory Committee: Professor Richard G. Olmstead Department of Biology Plants display incredible diversity, in morphology and spatial distribution, which can best be understood in an evolutionary context. The reconstruction of how this diversity has evolved can illuminate patterns and trends in the evolution of functionally and ecologically important traits and on how modern plant communities have formed around the globe. Case studies of individual taxa that encompass such diversity allow for thorough taxonomic sampling and detailed analysis of traits and distribution. The tribe Buddlejeae in Scrophulariaceae comprises 108 species of trees and shrubs in five genera: Buddleja, Chilianthus, Emorya, Gomphostigma, and Nicodemia. They are variable in flower color and shape, inflorescence architecture, fruit type, leaf shape and texture, and habitat preference, among other traits. They also have a wide distribution in tropical montane and subtropical regions of Africa, Madagascar, Asia, North America, and South America. Prior phylogenetic studies including the group have had limited taxonomic sampling, and evolutionary relationships between species and genera remained unknown. In Chapter 1, I infer a phylogeny for tribe Buddlejeae with extensive taxonomic sampling from all five genera and all major areas of distribution, using multiple nuclear and plastid markers. Buddleja and Chilianthus were resolved to be non-monophyletic, with Buddleja paraphyletic with respect to the other four genera. A new classification is proposed in which the other four genera are combined with Buddleja and seven sections in Buddleja are erected. Ancestral character state reconstructions show that some traits, including stamen exsertion, corolla shape, and inflorescence type, converged on similar states multiple times. The plesiomorphic trait states in Buddlejeae include capsular fruits, included stamens, white and tube-shaped corollas, and paniculate inflorescences. In Chapter 2, I infer a time-calibrated phylogeny for Buddleja, reconstruct ancestral distributions, and test for shifts in diversification rate dynamics. We found that from an ancestral distribution on continental Africa, Buddleja expanded its range to the New World, Asia, and Madagascar, one time each, in the mid to late Miocene. Long-distance dispersal or migration through northern high-latitude corridors may have allowed for these range expansions. An increase in speciation rate early in the diversification of the New World clade suggests conditions conducive to speciation in the American cordilleras. In Chapter 3, I use phylogenomic methods to infer a better-supported phylogeny for Buddleja, with particular focus on the Asian clade. Four locus sets were identified as targets for sequence capture and high-throughput sequencing. A “taxon-specific” locus set was developed using genomic and transcriptome data from two species of Buddleja. Three “general” locus sets were chosen from previous studies that used genomic data from several distantly related angiosperms. A greater number of loci were developed for the “taxon-specific” set. All sets had a very high proportion of target loci with assembled sequences for Buddleja species, but “general” sets had greater assembly for outgroup taxa. The “taxon-specific” and PPR loci had the highest average percentage of variable sites. A fully resolved and highly supported phylogeny for the Asian Buddleja clade can serve as a framework for future evolutionary studies. ACKNOWLEDGEMENTS I am grateful to my committee for all their support and advice over my time at UW. I especially thank my advisor, Dick Olmstead, for his encouragement of my work, for the independence he has given me, and for being a role model to me as a scholar and person. I also thank Adam Leaché and Verónica Di Stilio for their helpful suggestions and critiques of my work and for their generosity in sharing their lab resources. I am thankful to Sarah Reichard for reminding me to think more broadly about Buddleja’s place in the natural world, and to Eric Turnblom for his openness and interest as I was finishing my dissertation. I thank Eliane Norman for all her work with Buddleja and insights shared through our conversations. My research rests on the foundations she and other plant systematists laid. I thank Nataly O’Leary for her invaluable contributions to this research in procuring specimens and generating plastid sequence data and for her patience. I thank Sun Wei-Bang for facilitating collaborations with his lab in Kunming, which allowed me to have nearly complete sampling of Asian taxa and to experience these plants in the field. I thank the graduate students in the Olmstead lab, past and present, for our conversations about science, for passing on to me ancient lab knowledge, and for being a constant source of humor and support: Valerie Soza, Yuan Yaowu, Ryan Miller, Pat Lu-Irving, Laura Frost, Audrey Ragsac, and Ana Maria Bedoya. I also thank the many undergrads I have had the opportunity to work with, who have helped me generate data for this project: Bailey Craig, Anna O’Brien, Shulamit Harkavy, Ben Meersman, Calvin Lee, and Georgia Seyfried. I give special thanks to Wolf Rahfeldt for his programming expertise and excellent companionship. I thank the herbarium (WTU), especially David Giblin, for facilitating my work with specimens and for their financial and personal support. I also thank the Botany Greenhouse, especially Jeanette Milne and Doug Ewing, and the Medicinal Herb Garden and Keith Possee for allowing me to grow Buddleja in Seattle and see some in flower for the first time, for making teaching about plants immensely more interesting, and for many enjoyable and enlightening hours spent with plants. The staff of the UW Biology department has helped me tremendously in various ways through my years here. I especially thank Karen Bergeron for her guidance when I submitted my proposal for the NSF DDIG and for her affability. I thank the many institutions that have provided sources of plant specimens for my research: CAS, DAV, GH, GRA, K, KUN, LPB, MO, NBG, NY, SI, TEX, UC, WTU, Arnold Arboretum, Hoyt Arboretum, Kunming Botanical Garden, Kirstenbosch Botanical Garden, Los Angeles County Arboretum, Rancho Santa Ana Botanic Garden, San Francisco Botanical Garden, and University of California-Davis Arboretum. I especially thank the University of Washington Botanic Gardens for accepting into their collections the Buddleja specimens I have started and grown. Systematics and biodiversity research would be vastly more difficult without these important collections and records of life on Earth. I thank the many people who have made my fieldwork immeasurably easier and more enjoyable: Segundo Leiva and Mario Zapata Cruz in Peru; Dave Tank and Diego Morales- Briones in Bolivia; the Organization for Tropical Studies and Ricardo Kriebel in Costa Rica; Alistair Barker, Tony Dold, and Nigel Barker in South Africa; Sun Wei-Bang, Xin Zhang, and the other members of Prof. Sun’s lab in China; and especially Simon Uribe-Converse in Peru and Bolivia, who I explored beautiful Peru with on my first field trip and who inspired me to be a better field botanist and scientist. I thank the sources of financial support that have made this research possible: the Graduate Research Fellowship and Doctoral Dissertation Improvement Grant from the National Science Foundation; the Sargent Award, Giles Botanical Field Research Award, Washington Research Foundation and Benjamin Hall Fellowship, and Melinda Denton Writing Fellowship from the UW Department of Biology; and student research grants from the Botanical Society of America, American Society of Plant Taxonomists, and Society of Systematic Biologists. I thank my friends, in Seattle and beyond, who have provided camaraderie and welcome distractions from graduate school. Finally, I am grateful for my education in the public school system of the United States, in the Los Angeles Unified School District, Cornell University, University of California-Davis, and University of Washington, for the opportunities it has given me to engage in the pursuit and sharing of knowledge. CONTENTS CHAPTER 1. Phylogenetic relationships in tribe Buddlejeae (Scrophulariaceae) based on multiple nuclear and plastid markers ………………………………………………………….. 1 CHAPTER 2. Origins and timing of intercontinental disjunctions in the widely-distributed plant genus Buddleja (Scrophulariaceae) …………………………………………………………... 32 CHAPTER 3. Comparison of taxon-specific versus general locus sets for targeted sequence capture for plant phylogenomics ……………………………………………………………... 84 CHAPTER 1: Phylogenetic relationships in tribe Buddlejeae (Scrophulariaceae) based on multiple nuclear and plastid markers Citation: Chau JH, O’Leary N, Sun W-B, & Olmstead RG. 2017. Phylogenetic relationships in tribe Buddlejeae (Scrophulariaceae) based on multiple nuclear and plastid markers. Botanical Journal of the Linnean