The evolution and breakdown of self-incompatibility in Leavenworthia: insights from the S-locus Adam C. Herman Department of Biology McGill University, Montréal, Quebec, Canada July 2015 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Doctor of Philosophy © Adam Herman, 2015 DEDICATION To Otis and Louis Herman What you’ll find in here is some of what I did when you guys were little. Crazy, huh? I love you both so much. Call your mother and me. 2 TABLE OF CONTENTS DEDICATION ................................................................................................................................ 2 TABLE OF CONTENTS ................................................................................................................ 3 LIST OF TABLES .......................................................................................................................... 5 LIST OF FIGURES ........................................................................................................................ 6 PREFACE ....................................................................................................................................... 8 Thesis format ............................................................................................................................................ 8 Contributions of authors ........................................................................................................................... 9 Statement of originality .......................................................................................................................... 11 Acknowledgements ................................................................................................................................ 13 ABSTRACT .................................................................................................................................. 15 RÉSUMÉ ...................................................................................................................................... 17 General Introduction and Literature Review ................................................................................ 20 References .............................................................................................................................................. 28 Chapter 1: Phylogeny of Leavenworthia S-alleles suggests unidirectional mating system evolution and enhanced positive selection following an ancient population bottleneck. ............. 36 Abstract ................................................................................................................................................... 37 Introduction ............................................................................................................................................ 38 Materials and Methods ........................................................................................................................... 41 Results .................................................................................................................................................... 48 Discussion ............................................................................................................................................... 52 Conclusions ............................................................................................................................................ 59 Tables ..................................................................................................................................................... 61 Figures .................................................................................................................................................... 63 References .............................................................................................................................................. 69 Linking Statement................................................................................................................................... 77 Chapter 2: Secondary evolution of a self-incompatibility locus in the Brassicaceae genus Leavenworthia............................................................................................................................... 79 Abstract ................................................................................................................................................... 80 Introduction ............................................................................................................................................ 81 Materials and Methods ........................................................................................................................... 84 Results .................................................................................................................................................... 92 Discussion ............................................................................................................................................. 104 Figures .................................................................................................................................................. 112 References ............................................................................................................................................ 124 Linking Statement................................................................................................................................. 131 Chapter 3: Strong, recent selection for self-compatibility in a population of Leavenworthia alabamica .................................................................................................................................... 133 Abstract ................................................................................................................................................. 134 Introduction .......................................................................................................................................... 135 3 Materials and Methods ......................................................................................................................... 138 Results .................................................................................................................................................. 143 Discussion ............................................................................................................................................. 146 Conclusions .......................................................................................................................................... 151 Tables ................................................................................................................................................... 152 Figures .................................................................................................................................................. 155 References ............................................................................................................................................ 162 General Conclusions and Summary ............................................................................................ 170 References ............................................................................................................................................ 174 Appendix I .................................................................................................................................. 176 Supplemental results for Chapter 1....................................................................................................... 176 References ............................................................................................................................................ 185 Appendix II ................................................................................................................................. 186 Supplemental tables and figures for Chapter 2 ..................................................................................... 186 Appendix III ................................................................................................................................ 206 Supplemental Methods for Chapter 3 ................................................................................................... 206 References ............................................................................................................................................ 217 4 LIST OF TABLES CHAPTER 1: Table 1. Diversity statistics for the SRK alleles studied ............................................................... 61 Table 2. Number, identity and average for sites identified as evolving under positive selection in the taxa studied, according to Model M8 implemented in CODEML ............................. 62 CHAPTER 3: Table 1. Summary statistics for loci included in this study .. ..................................................... 152 5 LIST OF FIGURES CHAPTER 1: Figure 1. Sliding window analysis of nucleotide diversity (π) in the portion of the S-domain of SRK encompassing hypervariable regions 2 and 3............................................................... 63 Figure 2a. Majority-rule (50%) consensus phylogeny for Leavenworthia SRK alleles ............... 64 Figure 2b. cpDNA phylogeny of the genus Leavenworthia