Clark, Frances ElizabethB chromosomes (Bs) are selfish genetic elements known to manipulate various cellular processes. These manipulations increase their transmission to the next generation, a process known as drive. After the recent discovery of Bs in African cichlid fish, sequence amplification methodologies were used to quantify B chromosome distribution in 7 species of Lake Malawi cichlids. In these species, Bs are limited to females and are haploid in the diploid genome. Considering various possible drive mechanisms, I propose this B chromosome drives by manipulating meiosis I in females. Genetic crosses quantifying B transmission in Metriaclima lombardoi confirmed transmission above Mendelian expectations. The transmission of this B also skews the sex ratio among progeny towards females. M. lombardoi individuals lacking Bs were shown, via a genetic linkage analysis, to have a male heterogametic (XY) sex determination system. A similar linkage analysis of families segregating B chromosomes indicated only the progeny lacking a B were influenced by this XY system. This substantiates the hypothesis that this B is a female sex determiner. Individuals of all 7 species were re-sequenced with short-reads and read coverage across the genome was compared in a coverage ratio analysis that resulted in the detection of 1.37 Mb in the reference genome with copies on the B, shared by all 7 species. Accounting for copy number of each sequence, 12-44 Mb of shared B sequence was identified. Amongst this sequence were 144 loci containing genes and gene fragments. A differential expression analysis found hundreds to thousands of differentially expressed loci between individuals with and without Bs, biased towards decreased expression in B individuals. Transcriptomes were analyzed for B-specific SNPs revealing 53 loci transcribed from the B chromosome and six candidate genes that might contribute to drive. I have described the distribution and behavior of the Lake Malawi cichlid B as well as captured a large portion of its sequence. This, combined with the genomic resources available for cichlids, makes this model system a valuable tool for future studies of the molecular mechanisms of drive, sequence structure and evolution of B chromosomes, and the association between B and sex chromosomes.enDissertationGeneticsEvolution & developmentAfrican CichlidsB ChromosomesEvolutionary GeneticsGenomicsSex ChromosomesSupernumerary Chromosomes