Evolution of transcriptional regulation as motor of morphological diversification in cichlid fishes

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One of the ultimate goals of evolutionary biology is to understand the genetic basis of phenotypically diverse traits. Evolutionary alterations to genomic regulatory landscapes have the power to generate adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. There is growing evidence supporting the hypothesis that changes in non-coding DNA constitute a major catalyst for phenotypic evolution. Once relegated the name >>junk DNA<<, the role of non-coding DNA has only begun to be explored. It has recently been suggested that non-coding DNA indeed constitute a major catalyst for phenotypic evolution by controlling gene expression patterns and levels. They might explain many or even most phenotypic differences within and between species. My research project aims to investigate changes in transcriptional regulation that have been suggested to drive phenotypic evolution. I use cichlid fishes as a model since they are considered as one of the most diverse and species-rich families of vertebrates. Cichlids are famous for their astonishing rate of phenotypic diversification, making them excellent models for the investigation of the evolutionary role of coding regions but also non-coding elements such as cis-regulatory elements. Their extreme rate of speciation and diversification are still puzzling. Therefore, cichlids are a suitable model in which to analyze the genetic bases of evolution. By comparative analyses of gene expression levels using RNA-sequencing (RNA-seq) and abundance of active regulatory elements using Chromatin-immuno-precipiation with high-throughput sequencing (ChIP-seq) I aim to reveal the evolutionary dynamics of gene regulation and transcriptomes. To functionally explore the importance of cis-regulatory elements in an evolutionary context, I take advantage of transgenic approaches I will perform within cichlids to analyze the activity of regulatory elements in vivo.