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Cambridge NERC Doctoral Training Partnerships

Graduate Research Opportunities

Lead supervisor: Richard Durbin, Genetics

Co-supervisor: Emilia Santos, Zoology

Brief summary: 
Use large scale genome sequencing and evolutionary genetics to identify and study genes involved in adaptation and speciation in an iconic evolutionary radiation.
Importance of the area of research concerned: 
The diversity of life is a consequence of the processes of speciation, which generates new species, and adaptation, which leads to divergence into new forms. Both these processes take place through an interplay between ecology and genetics. Understanding them is central to our understanding of biodiversity. The ~500 closely related species of cichlid fishes in Lake Malawi form perhaps the most dramatic recent evolutionary radiation in vertebrates, providing many outstanding examples of speciation and adaptation, with extensive parallelism to allow dissection of key processes. By studying the genome sequences of population samples from multiple species at different degrees of divergence, and correlating them with adaptive traits and other properties, we can gain insights into adaptive speciation that can be tested in an experimental setting. Recently we developed methods to extract quantitative information from 3-D X-ray scans of fish skulls. This study aims to identify genetic determinants of jaw and head shape and combine them with evolutionary genetics analyses to identify genes involved in the process of speciation in an iconic evolutionary system.
Project summary : 
This project will study whole genome sequence data from population samples of multiple cichlid species, in conjunction with quantitative data on jaw and head shape extracted from micro-CT scans of the same fish. From initial studies on over 2000 sequences, we are starting to understand the processes and genes involved in this dramatic radiation. Genome wide association studies (GWAS) on micro-CT data from a first set of ~120 fish have already suggested interesting candidate genes. The student will extend these studies, and correlate them to evolutionary genetic analyses so as to identify loci selected during speciation. There will be an opportunity for field work to collect new samples. Functional consequences will be tested in collaboration with the Santos group in laboratory crosses and experiments.
What will the student do?: 
The student will initially study samples for which preserved fish are available in Cambridge that have also been whole genome sequenced. Already over 1500 samples have been sequenced from over 200 Lake Malawi species, for about 20 of which we have population samples of 15-100; we are currently doubling these numbers. They will carry out further morphometric analyses from micro-CT data, then use association genetics and selection scans to identify variants that are associated with differences in head and jaw morphology within and between multiple species, and that also show evidence of adaptive selection. These loci will be analysed further for parallel differentiation across multiple species across the radiation for which we have additional sequence data, and strong candidates will be taken forward for functional experiments in collaboration with the Santos lab, potentially following genotypes and phenotype co-segregation within multiple interspecies crosses already under way, or directly manipulating the genotype to confirm functional predictions. After ~1 year a field trip will be taken to collect further samples to follow up initial findings
References - references should provide further reading about the project: 
Malinsky, M., Svardal, H., Tyers, A.M., Miska, E.A., Genner, M.J., Turner G.F. & Durbin R. 2018. Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nat Ecol Evol. vol. 2, pp.1940-1955. DOI 10.1038/s41559-018-0717-x
Malinsky, M., Challis, R.J., Tyers, A.M., Schiffels, S., Terai, Y., Ngatunga, B.P., Miska, E.A., Durbin, R., Genner, M.J. & Turner, G.F. 2015. Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake. Science vol. 350, pp. 1493-8. DOI 10.1126/science.aac9927
Albertson, R. C., and T. D. Kocher. 2006. “Genetic and Developmental Basis of Cichlid Trophic Diversity.” Heredity 97 (3): 211–21.
You can find out about applying for this project on the Department of Genetics page.