Evolutionary history of the cichlid assemblages of the Lake Victoria Region Superflock reconstructed using whole genome seqencing

Pilot project
KEAseq (Kivu Edward Albert whole genome sequencing
Maarten Van Steenberge & Jos Snoeks
JEMU partner: 
JEMU team
Project summary: 
Background: The cichlid species flocks of the East African Great Lakes form the most spectacular examples of adaptive radiation and explosive speciation in vertebrates. Hence, they have become well-established models in speciation research. This especially holds for those of the three largest lakes: Tanganyika, Malawi and Victoria, which hold an estimated 250, 1000 and 600 endemic cichlid species. However, the other great lakes that also hold endemic cichlid species, such as Albert, Edward and Kivu have remained largely overlooked. The endemic cichlids inhabiting these lakes, together with those of Lake Victoria, are very closely related and are collectively referred to as the Lake Victoria region Superflock (LVRS). In spite of them being well-established as model systems in evolutionary research, several basic biological characteristics of these cichlid assemblages have long remained unknown. As they evolved in an explosive way, and as hybridization often lied at the basis of cichlid radiations, traditional molecular markers have shown to be inadequate for species characterization or validation and for the reconstruction of phylogenies that can be considered species trees. This has changed through the emergence of next generation sequencing technology. For example, in 2018, phylogeny reconstructions of both the Lake Tanganyika and the Lake Malawi cichlid radiations have been published that, for the first time, agree with geological and morphological assumptions. We are confident that this approach may also allow the study of the youngest of the three cichlid assemblages. Firstly, it was recently shown that reduced representation sequencing data allowed to distinguish between selected Lake Victoria species (Wagner et al., 2013). Secondly, a recent study using the same techniques on a few representatives of the LVRS region suggested that this approach could be useful to reconstruct a detailed phylogeny of the LVRS. We propose to use next generation sequencing technology to answer the following questions: 1) Can next generation sequencing applications be used to identify species in Lake Edward? Can they be used to date the radiation? 2) Did the different cichlid radiations evolved in-situ? And therefore constitute true biological replicates of a similar evolutionary process? 3) Did the same genes contribute to similar phenotypes in the Lake Victoria Region Superflock?
Erik Verheyen (RBINS) Nathan Vranken (RMCA)
Lab work progress: 
In progress
Starting date: 
Project status: 
In progress
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith