Evolutionary genomics of the zebra finch Z chromosome inversion polymorphism

A large (~60-70Mbp) inversion polymorphism found on the Z chromosome of the model organism Taeniopygia guttata (the zebra finch), has previously been shown to have profound effects on sperm traits. There are three main haplotypes for this polymorphism (A, B & C). However, relatively little is known about how gene sequence and selection pressures vary between these inversion haplotypes or the phylogenetic relationship between them. In this thesis I explore the structure and molecular evolution of this inversion polymorphism. I produced a list of diagnostic single nucleotide polymorphisms (SNPs) which were used to determine the inversion karyotype of zebra finch Z chromosome sequence. This list was used to show that the male bird used to construct the zebra finch reference genome is heterozygous for the inversion polymorphism. However, I demonstrated that the two inversion haplotypes on the reference genome have not been successfully assembled or accurately phased. I used publicly available zebra finch sequence data to show evidence for a relaxation of purifying selection within the inversion region, particularly on the B haplotype, which has allowed sequence divergence between the haplotypes to occur. Finally, I showed, using phylogenetic inferences, that the inversion polymorphism emerged less than 1 million years ago, and the ancestral form is likely to be Haplotype A, with the other two haplotypes derived from separate inversion mutations. Multiple sub-regions of the inversion region were identified, which may indicate the locations of each of the inversions that established the derived haplotypes. The work presented in this thesis adds to the existing literature on supergenes, which are of increasing interest due to their dramatic impact on phenotypic variation and adaptive evolution in a wide variety of species.