A multi-marker perspective on the evolutionary history of East African cichlid fishes

The East African cichlids, more precisely the cichlid fishes of Lake Tanganyika, Lake Victoria and Lake Malawi, are among the most famous textbook examples of adaptive radiations. Both hybridization and incomplete lineage sorting explain the high degree of shared gene lineages within these species-flocks. Considerable effort has been put into the understanding of the relationships between and among the main lineages as this is essential to establish the phylogenetic backbone of the East African cichlid radiations, which in turn is crucial to formulate and validate hypotheses about the patterns and processes underlying this unparalleled species diversification. So far, we know that the radiations within the three Great Lakes started at different time points and with a different set of seeding lineages; the radiations thus differ with respect to the number and diversity of species. The oldest of the lakes, Lake Tanganyika, harbors around 250 species from 12 to 16 different cichlid lineages, whereas the younger Lakes Malawi and Victoria contain a recent radiation of one lineage, namely the haplochromines. These two lakes are home to more than 1,200 cichlid species. Lake Tanganyika, although comprising less variety in number of species, is considered as the source of the East African cichlid radiation, as the modern haplochromines in Lake Malawi and Lake Victoria are derived from the Lake Tanganyikan haplochromines. Hence, Lake Tanganyika cichlids play a crucial role for the onset of the two other enormous radiations. However, the mainly mitochondrial DNA based phylogenies for the Lake Tanganyika cichlids lack resolution for some lineages as support values are low and phylogenetic positions are not consistent within the different tree estimates. It is unknown if this lack of resolution can be only found on the level of single gene trees or if it is reflected on the species level as a real biological polytomy.
In my thesis I mainly aimed to generate a solid phylogenetic framework for the cichlid tribes of Lake Tanganyika and hence to get insights to macroevolutionary processes. I developed a broad range of primers and applied next generation sequencing methods, resulting in the most comprehensive sequence-based multi-marker set for Lake Tanganyikan cichlids so far. Further I applied phylogenetic inferences and other methods based on the theory of molecular evolution to phylogeographic and other evolutionary questions (e.g. gene diversity).
The first two chapters of this thesis were driven by the question if more information from different genes would help to resolve the phylogenetic relationship of the major tribes within Lake Tanganyika. Based on the resulting dataset we could propose new hypotheses for the evolutionary history of the East African cichlids.
In the third chapter we report the occurrence of a new cichlid species, found in Lake Tanganyika. Using two nuclear and two mitochondrial markers and conducting different phylogenetic analyses, we detected its genetic affiliation to the haplochromine cichlids of the Lake Victoria superflock. We hypothesize that faunal exchange across in East African watersheds and, hence, between isolated ichthyofaunas, is more common than previously thought.
In the fourth chapter I contributed to the study of the molecular basis of the egg spots, which are a novel phenotypic color trait within the most species-rich lineage of the haplochromines. To investigate the underlying genetics of the egg spots it was crucial to have a proper phylogenetic hypothesis at hand. To this end, I generated a new phylogeny of the haplochromines, thus providing a solid basis for the assumptions of the trait emergence and consequently the experiments.
In the last chapter I present ongoing work, in which we explore the covariations of trophic morphology, trophic level, diet, body shape, macro-parasitism and MHC genes to investigate the contribution of parasite-mediated selection in this adaptive radiation. We showed that the trophic-morphological axis of diversification in Lake Tanganyika cichlids is strongly correlated with infection levels of metazoan macroparasites. We further detect correlation between these parasites and MHC constitution. This gives insights to the potential influence of parasitism and immunogenetic adaptations to the Lake Tanganyika cichlid radiation.