Exploring phenotypic plasticity and gene co-expression networks in the jaw apparatus of speciating cichlid fishes

A major goal in evolutionary biology is to understand the molecular basis of phenotypic divergence during speciation. Given their high species richness, short evolutionary timescale coupled with exceptional ecological diversity, East African cichlid fishes represent model candidates for such investigations. Research for this thesis focuses on populations of the haplochromine cichlid Astatotilapia calliptera, in Lake Masoko, Tanzania, which are currently undergoing sympatric speciation into a shallow-water littoral ecomorph and deep-water benthic ecomorph. In Chapter 1 the study system is introduced, and genetic and epigenetic influences on phenotypic divergence are broadly summarised. In Chapter 2 I compare jaw morphology of wild-caught individuals of A. calliptera. I also quantify the jaw morphology of both ecomorphs when reared on divergent diets in common garden conditions. The results help to further our understanding of the extent that these phenotypes are determined by phenotypic plasticity. In Chapter 3 I link transcriptomic (RNA sequencing) and epigenetic (DNA methylation; whole genome bisulphite sequencing) data, to explore the potential for epigenetic mechanisms to promote divergent expression of functional genes during the early stages of ecological diversification. Specifically, I use a network analysis to identify co-expressed genes associated with ecologically relevant traits such as oral and lower pharyngeal jaw apparatus, and determine the overlap with those regions of the genome that are differentially methylated between the ecomorphs. In Chapter 4, I summarise the key insights provided by the study, and discuss research opportunities by this remarkable study system