Patterns of phenotypic similarity in the haplochromine cichlids of the Lake Victoria Region Superflock: an eco-morphological and genomic approach

Species that look very similar are not always closely related. Numerous examples of species that independently evolved similar structures have been reported: the flippers of penguins and dolphins, the wings of bats, birds, and insects, and the striking similarity between the eyes of humans and squids. Although structures look similar, the mechanisms of how they developed can be very different.

Lakes Albert, Edward, Kivu, and Victoria are inhabited by ~700 closely related species of cichlids, a family of perch-like fishes that evolved very rapidly. Each of these species inhabits a single lake, and many species look very similar, both within a lake and between lakes. How they are related to each other, however, remains mostly unknown. Their young age and many similarities make these cichlids a perfect system to investigate how similar forms arise. Are they more closely related to each other, or did they evolve independently from each other, and if so, which mechanisms underlie their similarity?

While the cichlids of most lakes are relatively well known, those from Lake Edward remained understudied. Hence, we performed a taxonomic revision of its species. We delineated 52 species from Lake Edward, including 19 species newly described to science. These species show a large variation, including piscivorous species with long oral jaws that are set with acutely pointed teeth, sardine-like filter feeders with an elongated body, species with rounded heads that scrape algae from rocks, and molluscivorous species with strong and blunt teeth that enable them to crush molluscs. Highly similar species inhabit all four lakes.

With the knowledge of the species that inhabit the different lakes, we could investigate their evolutionary relationships and unravel how similarities came about. For this purpose, external phenotypes were examined and the complete DNA was read out from 128 species from all four lakes. The DNA of the examined species from all lakes shows that they belong to three species flocks, which are groups of species that have evolved independently of each other. The first flock includes all species from Lake Albert, the second those from Lake Victoria, and the species from Lakes Kivu and Edward belong to a third species flock. Despite having evolved independently, we demonstrate a strong signal of the independent evolution of similar phenotypes between species flocks with numerous examples of species showing very strong similarities in their appearance, diet, and behaviour.

Several regions in the DNA (genes) were found to be associated with strong phenotypic similarities. These genes were found in cichlid species from different species flocks and show that many of the strong similarities evolved partially because they share the same genes. They inherited most of these genes from the common ancestor of all species flocks, while they acquired some others from distantly related species through hybridization (crossbreeding between different species). Because these cichlids retain or inherit candidate adaptive genes from distantly related species, species can significantly change many of their external features over just a few generations. We show that many genes across their genome contribute to the evolution of a large diversity of external features in species that evolved independently from each other.