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Evolution of regulatory elements in lake Malawi cichlid fishes

Supervisors: Dr Emília Santos

Project summary:

Regulatory evolution is a major mechanism underlying organismal diversification. Despite this, genome-wide patterns of regulatory evolution remain largely unknown, e.g.: A) How do regulatory sequences evolve? B) What is the impact of structural variation on gene regulation? C) What is the level of pleiotropy of these sequences? Cichlid fishes of lake Malawi are an ideal system to address these questions. There are ~700 species in lake Malawi, they are genetically very similar (~0.3%), but phenotypically very distinct, exhibiting extreme diversity in body shape, colour, trophic morphology and behaviour. The cichlid genome project revealed that coding sequence alone cannot explain this diversity. Conversely, regions situated upstream of coding regions show fast rates of evolution and a high number of transposable element insertions suggesting that changes in gene regulation has played a major role in cichlid diversification.

What the student will be doing:

In this project the student will analyse ATAC-seq and RNA-seq datasets derived from three developmental stages of three cichlid species that differ in pigmentation and craniofacial phenotypes - Astatotilapia calliptera, Rhamphochromis sp. chillingali and Tropheops sp. red cheek. The objective is to identify enhancer regions, test if these are associated with structural variation and determine if regions are active across stages to use it as a proxies for their pleiotropic state. This will lay the foundation for functional experiments and comparative genomics using hundreds of cichlid genomes to infer patterns of regulatory evolution across the cichlid phylogeny. The regulatory regions showing patterns of variation across species will be studied further (expression and function) throughout development to understand the impact of regulatory changes in phenotypic evolution and species diversification.

References:

Cichlids: Santos ME & Salzburger Science 2012

Structural variation and morphological diversity: Santos ME, et al. Nature Communications 2014

Genomes from Lake Malawi Cichlids: Malinsky M, et al. Nature Ecology and Evolution 2018

Funding:

Available for research costs.