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By Josh Hough a Thesis Submitted in Conformity with the Requirements for the Degree of Doctor of Philosophy Department of Ecolog

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By Josh Hough a Thesis Submitted in Conformity with the Requirements for the Degree of Doctor of Philosophy Department of Ecolog EVOLUTION AND GENETICS OF PLANT SEX CHROMOSOMES by Josh Hough A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Ecology and Evolutionary Biology University of Toronto © Copyright by Josh Hough 2016 EVOLUTION AND GENETICS OF PLANT SEX CHROMOSOMES Josh Hough Doctor of Philosophy Department of Ecology and Evolutionary Biology University of Toronto 2016 ABSTRACT Sex chromosomes have evolved multiple times independently in different lineages and the parallel changes that have occurred during their formation suggest that there are general processes driving their evolution. In this thesis I used a variety of approaches, including genetic crossing experiments, mathematical modeling, and statistical analysis of DNA sequence data to study the evolution and genetics of sex chromosomes, focusing on the recently evolved X and Y chromosomes in the plant Rumex hastatulus. I developed methods to identify sex-linked genes using segregation analysis and transcriptome sequencing, and found that both ancestral and neo-Y chromosomes in R. hastatulus have started to genetically degenerate, causing ∼28% and ∼8% hemizygosity of ancestral and derived X chromosomes, respectively. Genes remaining on Y chromosomes also accumulated more amino acid replacements, contained more unpreferred changes in codon use, and exhibited significantly reduced gene expression compared with their X-linked alleles. This genetic degeneration is consistent with ii theoretical predictions of reduced Y-linked selection efficacy caused by suppressed recombination. My results indicate that the magnitude of genetic degeneration depends on the time since X-Y recombination became suppressed. I also found that diversity on the Y was 40-fold lower than on the X, and nearly 50-fold lower than on autosomes, indicating that selective interference has played a significant role in reducing nucleotide polymorphism during the early stages of X-Y divergence. I also developed a theoretical model to investigate the interactions between sex chromosomes, haploid-phase selection, and selection on the sex ratio. The model’s results indicate that biased sex ratios can be evolutionarily stable when there is a trade-off between Fisherian selection on the sex ratio and selection for purging deleterious mutations in the haploid phase. This finding provides a novel evolutionary explanation for biased sex ratios in dioecious plants, where haploid-phase selection is widespread. In conclusion, my analyses indicate that the evolution of sex chromosomes from autosomes can result in significant changes to effective population size, recombination rate, and patterns of gene expression, all of which have important implications for DNA sequence evolution, including the effectiveness of natural selection, rates of molecular evolution, and patterns of genetic diversity. iii ACKNOWLEDGMENTS I would first like to thank my supervisors, Spencer Barrett and Stephen Wright, whose mentorship, encouragement, and supportive engagement with my research made my time as a graduate student both intellectually stimulating and personally enjoyable. I am grateful to Spencer for sharing his extensive knowledge of evolutionary biology, for helping me to become a better writer, and for the incredible wealth of advice, both scientific and professional, that he has shared with me over the years. I thank Stephen also for his support and mentorship, and for the countless arguments and debates that we have had. I will look back on these fondly, and I have learnt a lot from you. My experience working with both of you has been fantastic, and I cannot thank you enough. I also thank the members of my supervisory committee, Aneil Agrawal and Asher Cutter, for providing critical advice, criticism, and valuable discussion throughout the development of my thesis. Their expertise in evolutionary genetics, thoughtful suggestions, and encouragement has been inspiring and has helped me to improve the work presented here. I am also grateful to Locke Rowe and Judith Mank for serving on my examination committee and for providing valuable comments on my research. I thank all of my colleagues and peers in the Department of Ecology and Evolutionary Biology at the University of Toronto, especially Arvid Ågren, Nathaniel Sharp, Alison Wardlaw, Alethea Wang, Jesse Hollister, Lucia Kwan, Emily Josephs, Robert Williamson, and to the many members of the Agrawal, Barrett, Cutter, Stinchcombe, and Wright labs. You have all made my experience at U of T memorable, and I am grateful to have had the pleasure of learning with you, and also from you. I also extend my thanks to Deborah Charlesworth, who provided me with a wealth of research advice, answered many of my questions, and helped to clarify much of my thinking about the evolution and genetics of sex chromosomes. Finally, I thank Professor Mark O. Johnston (Dalhousie University), who taught my first undergraduate course in evolutionary biology, allowed me to tinker in his laboratory and read his books during my undergraduate years, and was a critical inspiration leading to my ambition to conduct research in the field of evolutionary genetics. iv TABLE OF CONTENTS ABSTRACT ....................................................................................................................... ii ACKNOWLEDGEMENTS ............................................................................................... v TABLE OF CONTENTS .................................................................................................. vi LIST OF TABLES ............................................................................................................. x LIST OF FIGURES .......................................................................................................... xi LIST OF APPENDICES ................................................................................................. xiv CHAPTER 1: INTRODUCTION...................................................................................... 1 Summary ..................................................................................................................... 1 Origin of sex chromosomes ........................................................................................ 1 Effects of recombination suppression on Y-chromosome evolution .......................... 4 Rates of molecular evolution and patterns of genetic diversity .................................. 6 Gene movement between X chromosomes and autosomes ........................................ 7 Sex chromosomes and sexual dimorphism ................................................................. 9 Young plant sex chromosomes: the early stages of X-Y divergence ....................... 10 Rumex hastatulus: a model system for sex chromosome evolution ......................... 11 Thesis outline ............................................................................................................ 14 CHAPTER 2: PATTERNS OF SELECTION IN PLANT GENOMES ........................... 15 Summary ................................................................................................................... 15 Introduction ............................................................................................................... 15 Genome-wide selection in models systems .............................................................. 16 Positive and negative selection in plants .................................................................. 20 Effective population size ........................................................................................... 21 Population structure, selection on standing variation, and polygenic adaptation ..... 24 Recombination rate ................................................................................................... 26 v Mating system ........................................................................................................... 28 Ploidy ........................................................................................................................ 30 Conclusions and future directions ............................................................................. 33 Acknowledgments ..................................................................................................... 34 CHAPTER 3: GENETIC DEGENERATION OF OLD AND YOUNG Y CHROMOSOMES IN THE DIOECIOUS PLANT RUMEX HASTATULUS ........................ 35 Summary ................................................................................................................... 35 Introduction ............................................................................................................... 36 Results and Discussion ............................................................................................. 37 Phylogenetic relationships and evolutionary divergence of sex-linked genes .......................................................................................... 39 Y chromosome gene loss and loss of expression ............................................ 41 Molecular evolutionary tests for deleterious mutations and codon usage bias ....................................................................................... 46 Conclusions ............................................................................................................... 48 Methods ....................................................................................................................
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