In this thesis, I use transcriptomic and genomic data from multiple bird species to investigate the genetic architecture of sexual dimorphism and to understand how sex-specific selection shapes genome evolution. I consider two routes to sexual dimorphism. Firstly, due to their unequal pattern of inheritance, sex chromosomes are hypothesised to facilitate the evolution of sexual dimorphisms by navigating functional constraints that shared regions of the genome are subject to. However, the sex chromosomes have differences in mutation rate, effective population size and recombination rate relative to the autosomes, which may act to reduce the efficacy of selection acting on them. Consistent with this, in Chapter 2, I show that the avian Z chromosome is not a hotspot of sexual conflict relative to the autosomes. Additionally, in Chapter 3, I reveal that a combination of adaptive and purifying selection are the dominant modes of evolution of the avian W chromosome. Secondly, I examine the role of differential regulation of the parts of the genome that are shared equally between males and females in the evolution of phenotypic dimorphisms. In Chapter 4, I discover an abundance of autosomal genes with sex differences in expression level and alterative splicing and suggest that differential alternative splicing evolves under sex-specific selection and facilitates sex-specific adaptation when differential expression level is limited by pleiotropic constraints. Together, my findings shed light on the role of sex-specific selection on the sex chromosomes and the autosomes in the evolution of intraspecific genetic diversity
