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Cambridge NERC Doctoral Training Partnerships

Graduate Research Opportunities

Lead supervisor: Emilia Santos, Zoology

Co-supervisor: Richard Durbin, Genetics

Brief summary: 
Here, we will determine the genetic and developmental mechanisms underlying novel trait emergence - haplochromine egg-spots in Malawi cichlid fishes - using a combination of population genomics, developmental genetics tools and field work.
Importance of the area of research concerned: 
We are interested in understanding the genetic and developmental basis underlying organismal diversification using cichlid fish species as a model system. Cichlids are one of the most species rich vertebrate families (~2500 species) showing extreme diversity in their colour patterns. Despite this morphological diversity, they are genetically very similar allowing for in depth comparative developmental studies between closely related species. They are a well characterised model in evolutionary ecology, phylogenetics and genomics and are an emerging model system for developmental biology. This is mostly due to the recent increase in genomic resources, the viability of hybrid crosses and the application of the genome modification method - CRISPR/Cas9. Using all of these tools we are currently focusing on the study of variation of sexually dimorphic pigmentation patterns - eggspots. These are circular pigmentation markings present on the anal fins of cichlid fishes and show variation in colour, number and arrangement, both within and between species.
Project summary : 
Egg-spots are circular pigmentation markings present on the anal fins of approximately 1500 species of cichlid fishes -eggspots. They are a highly variable trait, varying in colour, number and arrangement, both within and between species. They function as badges of status, being sexually selected via female choice in some species and via male-male competition in others. We are interested in understanding which genes and developmental processes underlie variation in this iconic sexually selected trait. The project will use whole genome sequence data from population samples of multiple cichlid species (>2000 genomes from over 250 species) in conjunction with genomic data from F2 individuals deriving from several inter-specific crosses to map the genetic architecture of trait variation within and between species. Candidate genes will be validated using genome editing tools.
What will the student do?: 
The student will make use of natural variation present within and between species to identify the genes, cells and developmental mechanisms generating variation. The three aims of the project are: 1) To identify the genetic basis of eggspot variation by performing association studies using whole genome data from: a) several cichlid populations (~10 species) and; b) F2 individuals deriving from several inter-specific hybrid crosses with different eggspot morphologies. Two preliminary genome wide association studies using population data from two cichlid species (Astatotilapia calliptera and Maylandia zebra) already suggested interesting candidates. 2) To characterise trait development and candidate gene function using crispr/cas9 and different imaging techniques. This will to determine the specific role of candidate genes in trait development; 3) To characterise candidate loci evolution across the cichlid phylogeny (e.g. selection scans and further association studies) using hundreds of cichlid species genomes (>2000 genomes from over 250 species). After a ~1 year (covid permitting) a field trip will take place to collect further samples to follow up initial findings.
References - references should provide further reading about the project: 
Santos et al. (2014) The evolution of cichlid egg-spots are linked with a cis-regulatory change. Nature Communications, 5, 5149.
Malinsky et al. (2018) Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nature, Ecology & Evolution, 2, 1940-1955.
You can find out about applying for this project on the Department of Zoology page.