Evolution and Genetics of Plant Sex Chromosomes

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 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.Ph.D