DIVERSIFICATION AND EVOLUTION OF TOWNSEND’S DAISIES (TOWNSENDIA- ASTERACEAE): A PHYLOGENETIC AND NICHE MODELLING PERSPECTIVE by CHRISTOPHER LEE B.Sc., The University of British Columbia, 2007 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Botany) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) August 2015 Christopher Lee, 2015 i ABSTRACT Townsendia is a genus of the sunflower family (Asteraceae) flush with species that frequently specialize in marginal habitats limited by various abiotic factors (e.g., soil, temperature, precipitation), particularly in higher elevation habitats. Although species are well defined geographically and morphologically, the evolutionary relationships in the genus remain unclear. This thesis investigates the evolutionary relationships of Townsendia species through phylogenetic inference, and also uses an ecological niche modelling (ENM) approach to better understand the processes that have lead to inter- and intra-specific variation of the genus. Phylogenetic analysis of plastid DNA regions and the internal transcribed spacer (ITS) establishes the monophyly of the group, and also recovers a large core polytomy in Townsendia and two clades sister to the rest of the genus. The presence of this core polytomy suggests that the diversity in Townsendia may be the result of a recent and rapid process of adaptive radiation. Further evidence for an adaptive radiation in the genus may appear as greater rates of ecological niche divergence between related species, relative to expectations based on a process of random diversification under background environmental conditions. Looking at interspecific variation, ENMs presented varying levels of niche divergence between related species, suggesting that a combination of niche conservatism and divergence played a role in the evolutionary history of the genus. Niche modelling is also used to better understand the variation present within one species, particularly one with discrete population subsets such as diploid sexuals and polyploid asexuals. Polyploid asexual populations of T. hookeri tend to have a wider and more northerly distribution than their diploid counterparts, though the role of this pattern on the speciation of Townsendia is unclear. Such unequal distributions may arise from differences in dispersal ability, or in abiotic preferences between reproductive types. Comparisons of ii ENMs between these groups find evidence for intraspecific niche variation, and also predict the role of competitive exclusion, as factors that drive and maintain this distributional pattern. Overall, the combined use of phylogenetic analysis and ecological niche modelling in this thesis improves our understanding regarding the distribution patterns, evolutionary history and speciation pathways of Townsendia. iii PREFACE All of the research presented in this thesis was conducted in the field or in the Whitton Lab at the University of British Columbia, Point Grey campus. I was the lead investigator for all of the projects in Chapters 2 to 4, where I was primarily responsible for the formation of concepts, data collection and analysis, as well as for the composition of the manuscripts. Undergraduate students, Scott Black, Beryl Zhuang, Erica Li-Leger and Alberto Ruiz-Larrera, each contributed in the georeferencing of species localities used in Chapter 2 and 3. Then undergraduates, Kate McGrath and Ryan Godfrey were involved in a portion of the sequencing results in Chapter 2 as part of their lab skills training. Alice Garani (graduate student), Alberto Ruiz-Larrera, Erica Li-Leger and Ryan Godrey contributed many of the ploidy determinations via flow cytometry or pollen counting that were used in Chapter 4. Sean Graham, Loren Rieseberg and Wayne Maddison contributed through manuscript edits and in data interpretation. Jeannette Whitton was the supervisory author on this thesis and was involved in the project from the early stages of concept formation, through data analysis and interpretation, to manuscript edits. iv TABLE OF CONTENTS Abstract .................................................................................................................................... ii Preface ..................................................................................................................................... iv Table of Contents ..................................................................................................................... v List of Tables ......................................................................................................................... vii List of Figures ....................................................................................................................... viii Acknowledgements .................................................................................................................. x Dedication ............................................................................................................................... xi CHAPTER 1: Introduction ...................................................................................................... 1 General Introduction .................................................................................... 1 Thesis Outline and Objectives ................................................................... 10 CHAPTER 2: Testing the Role of Niche Divergence in Geographical Parthenogenesis within Townsendia hookeri (Asteraceae) ............................................................. 18 Summary .................................................................................................... 18 Introduction ............................................................................................... 19 Ecological Niche Modelling: Model Building ............................ 30 Ecological Niche Modelling: Niche Overlap Comparisons ........ 34 Materials and Methods .............................................................................. 36 Ecological Niche Modelling ........................................................ 37 Niche Comparisons ..................................................................... 39 Results ....................................................................................................... 42 Ploidy Assessment ....................................................................... 42 Ecological Niche Modelling ........................................................ 43 Discussion .................................................................................................. 44 Conclusion ................................................................................................. 48 CHAPTER 3: Phylogenetic, Life History and Morphological Evidence for Rapid Diversification of Townsendia (Asteraceae) ............................................. 58 Introduction ............................................................................................... 58 Materials and Methods .............................................................................. 64 Sampling Strategy ....................................................................... 64 DNA Extraction, Amplification and Sequencing ........................ 65 Sequence Assembly and Phylogenetic Analysis ......................... 69 Haplotype Network Estimation ................................................... 70 Results ....................................................................................................... 71 Sequencing .................................................................................. 71 Phylogenetic Analysis: ITS Region ............................................ 71 Phylogenetic Analysis: Plastid DNA .......................................... 72 Haplotype Network Analysis ...................................................... 73 v Discussion .................................................................................................. 73 Core Polytomy ............................................................................. 75 Genetic Differentiation ................................................................ 76 Hybridization ............................................................................... 77 Lineage Sorting and Ancestral Polymorphism ............................ 79 Adaptive Radiation ...................................................................... 84 Conclusion ................................................................................................. 86 CHAPTER 4: Patterns of Niche Evolution and Speciation in Townsendia ......................... 106 Introduction ............................................................................................. 106 Materials and Methods ............................................................................ 116 Selection of Species ................................................................... 116 Occurrence Data ........................................................................ 116 Ecological Niche Modelling ...................................................... 116 Niche Comparisons ................................................................... 118 Results ..................................................................................................... 119 Discussion ................................................................................................ 121 Conclusion ..............................................................................................