Genetic sex-determination is one of the most prevalent systems by which the sex of an organism can be established. The genes that determine sex reside on chromosomes that experience a unique pattern of evolutionarily processes, which often leads to the degradation of genes surrounding these sex-determination loci. The widespread degradation of sex chromosomes has been noted in the relatively old and heteromorphic sex chromosomes of therian mammals and birds. However, with the advent of next-generation sequencing, it is now possible to study the earliest stages of sex chromosome evolution in relatively homomorphic sex chromosomes.

African cichlid fishes are a powerful model system for studying the early stages of sex chromosome evolution because of the diversity and young age of their sex chromosomes. This dissertation develops methods for studying young sex chromosomes and employs these approaches to evaluate the sex chromosomes within tilapia and Lake Tanganyika cichlid fishes. Furthermore, this research demonstrates a

method for identifying the ancestral state for species sharing a common sex chromosome system and a process for evaluating the functional significance of these shared mutations. Lastly, this dissertation proposes a mechanism for the diversity of sex chromosome systems observed within African cichlid fishes.

This analysis not only characterizes the decay of several known young sex chromosomes, but also reveals multiple previously undiscovered sex chromosome systems within the African cichlid fishes. These novel sex chromosome systems likely represent only a fraction of the true variety of sex chromosome systems within this group, and therefore push forward the argument for characterizing the sex chromosome systems of more cichlid species in order to better understand the early stages of sex chromosome evolution.