Plants possess sex chromosomes at all stages of sex chromosome evolution. Carica papaya has become a model for early stages of sex chromosome evolution. The papaya sex-determining region (SDR) spans the centromere and is approximately 10% the length of Chromosome 1. The objectives of this dissertation are to investigate which mechanisms have driven sex chromosome evolution in papaya by comparing the patterns of polymorphism in the male-specific region of the Y (MSY) and the corresponding X region to low-recombining autosomal regions in the genome.
In Chapter 2, patterns of nucleotide polymorphism were measured for regions of various levels of recombination within the papaya genome in order to determine whether strong patterns of selection are present within regions of low recombination. No significant correlations between nucleotide polymorphism (Watterson's theta) and divergence (KS [JC]) versus recombination rate (cM/Mbp) were found. This lack of relationship suggests little to no selection driving evolution of papaya regions of low recombination, inferred to be pericentromeric regions. From this, I concluded that levels of diversity and any patterns of selection occurring within papaya sex chromosomes are products of sex chromosome evolution, rather than their pericentromeric nature.
In Chapters 3 and 4, patterns of selection were assessed at 19 X/Y gene pairs and two pseudoautosomal loci. X-linked loci, in general, exhibited low nucleotide diversity. Two regions were identified that exhibit signatures of selective sweeps, indicated by an excess of rare alleles and low diversity. In contrast, Y-linked loci had an excess of diversity, which is localized within three regions of balancing selection. When the regions of selection for the X region and MSY are plotted against each other, the regions overlap, with the selective sweeps for the X coinciding with the sites of balancing selection along the Y. Together, these results suggest that X-driven meiotic drive may be occurring within the papaya sex chromosomes.