Visual systems as “magic traits” and their role in the evolution of biodiversity

Project background

Magic traits are phenotypic traits that have a particular function according to the environment, while also acting as a cue for reproductive isolation via assortative mating. This means magic traits have the potential to be an important driver of speciation, because relatively small changes in the genome could rapidly lead to population divergence. This divergence could be further enhanced by sexual selection.

Magic traits also have particular potential to cross species boundaries via hybridisation, so their role in generating biodiversity could be far reaching. But making predictions about how magic traits could lead to speciation in changing environments is difficult without being able to experimentally test evolutionary processes. In order to understand their role, we need to be able to confer magic traits on “non-magic” species and examine the consequences for reproductive isolation. We could then test how far their consequences could extend across species boundaries.

This PhD project will explore the role of visual systems as magic traits, using haplochromine cichlid fishes as a model system. The tropical freshwater lakes of East Africa are home to several thousand endemic species of cichlid, characterised by hybridization, and shaped by both natural and sexual selection. We have a detailed understanding of the genetic basis of their visual systems, which in turn influence their ecology and mate choice behaviour. Visual proteins can therefore act as magic traits and we are now in a position to be able to test specific predictions about the ability of magic traits to drive evolution via hybridization and/or sexual selection. We are also able to use CRISPR/cas9 to genetically modify haplochromine cichlid fish, and thus can experimentally test and advance ideas about the importance of magic traits in generating biodiversity in nature using this system.

What the project involves

As a PhD student on this project, you will benefit from an existing mRNA expression dataset designed to quantify gene expression in deep water cichlids. Using this, and published information about the specific changes to the opsin DNA sequence that alter colour perception, we will be able to genetically modify fish so that we can test predictions about how fish will behave in different light environments, depending on their genetic make-up. We will also be able to make interspecific crosses so that we can assess the performance of magic traits in hybrid genetic backgrounds. We have a large purpose built tropical cichlid aquarium that can be used for making and raising crosses, and for behavioural assays.

During the course of the PhD, you will be able to 1) identify specific adaptations to deep water 2) use CRISPR/cas9 to confer new visual traits on species 3) test how behaviour is affected in individuals with and without the conferred visual traits, including mate choice behaviour. You will therefore have the opportunity to develop a suite of biological skills during your studies, which will include bioinformatics, behaviour, animal husbandry and genetic modification. Although the project has some specific aims, there is also some flexibility so that you can take the work in the direction that most interests you. The data we collect will enable us to better understand the possible consequences of increased turbidity as a result of environmental pollution changing the light environment of fish, as well as the evolutionary role that hybridization may have played in enabling these visual magic traits to cross species boundaries and generate new species.

Interested in applying?

If you’re interested in applying for this PhD, please contact me, Dr. Domino Joyce directly so that I can offer application advice and give you more information about the project and Department, and answer any questions you may have. In the meantime you can have a look at this video of me explaining why I love using cichlids for researching evolution:


Your ideal background would include an honours degree and/or Masters in a topic relating to Biology, Zoology, Ecology, Genetics, Biodiversity, Evolution, Bioinformatics, Maths & Biology etc. An interest in genetics and behaviour is desirable, as well as an interest in developing skills in bioinformatics. Any prior experience in these would be advantageous.


Training will be provided in husbandry, behaviour, population and evolutionary genetics/genomics, bioinformatics and statistical modeling in R. In addition the student will also benefit from wider general skills training provided within the framework of the Leeds-York-Hull DTP.

Research context and environment

The project will be in partnership with Dr. Emilia Santos at Cambridge University, and benefit from the expertise of Prof. Martine Maan at the University of Groningen, and Prof. Ole Seehausen at the University of Bern. The majority of the work will be carried out at the University of Hull, where we have a large and friendly post-graduate research community, access to VIPER (super computing cluster) and extensive, purpose built tropical aquarium facilities which you can see here using the virtual tour

Further reading

Hahn, C. et al. (2017) ‘The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi’, Evolution letters. Available at:

Hofmann, C. M. et al. (2009) ‘The eyes have it: regulatory and structural changes both underlie cichlid visual pigment diversity’, PLoS biology, 7(12), p. e1000266.

Maan, M. E. and Seehausen, O. (2012) ‘Magic cues versus magic preferences in speciation’, Evolutionary ecology. Available at:

Malinsky, M. et al. (2018) ‘Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow’, Nature ecology & evolution. doi: 10.1038/s41559-018-0717-x.

Meier, J. I. et al. (2019) ‘The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes’, Nature communications, 10(1), p. 5391.

Nichols, P. et al. (2015) ‘Secondary contact seeds phenotypic novelty in cichlid fishes’, Proceedings. Biological sciences / The Royal Society, 282(1798), p. 20142272.