Conflict and competition in the evolution of sexual traits

The living world is dominated by competition and conflict. From genes to species, units of life prioritise their reproduction over those around them. This is notably evident in the study of sexual characteristics, where conflict may occur between the sexes over traits with shared genetics, within the sexes over access to mates, and across the genome when genes preferentially force their inheritance during meiosis. This thesis investigates and discusses these varying dimensions of conflict and their roles in shaping genomic and transcriptomic diversity. How we detect selection on these traits is complex for several reasons; sex-related traits are often located on the sex chromosomes that exhibit different evolutionary environments to the autosomes, and complex traits are often housed in inversions that physically link large portions of a chromosome. As such, transcriptomics is a powerful tool in understanding the evolution and consequences of conflict. Accordingly, Chapters 2 and 3 discuss advances in our understanding of intralocus sexual conflict and the evolution of the transcriptome respectively, whilst considering the nuances of sequencing methods and models for detecting regulatory evolution. Considering these findings I then investigate the patterns of genomic and transcriptomic evolution in the zebra finch and stalk-eyed fly, models for the study of sexual selection, genomic inversions, and sperm competition. In Chapter 4, I demonstrate that within-male competition via sperm competition can maintain large structural variation in the genome, a product of associative overdominance of an inversion polymorphism. Chapter 5 then characterises the single-cell transcriptomic landscape of the stalk-eyed fly and elucidates the consequences of meiotic drive on the transcriptome, whilst providing candidate mechanisms. Together, my work highlights the diverse outcomes of conflict in the genome and transcriptome, and provides important considerations for understanding the evolution of gene expression.