Genome Analyses Reveal Diverse Riverine Genetic Contributions to the Lake Malawi Cichlid Radiation

Comparative studies of whole genomes have increasingly shown that genetic introgression between closely related species is surprisingly common across the tree of life, making the description of biodiversity and understanding the process of speciation complex and challenging. The adaptive radiation of cichlid fishes in Lake Malawi, that is characterised by hybrid origins and cases of recent introgression, provides a valuable model system to study the evolutionary implications of introgression. However, many potential sources of introgression into the radiation have not yet been investigated. Here we use whole genome data from 239 species from Lake Malawi and 76 species from surrounding African river and lake systems to identify previously unknown introgression events involving the Malawi radiation. Computing genome-wide excess allele sharing (ABBA-BABA statistics) and window-based statistics, we find that three independent riverine cichlid lineages show significantly higher allele sharing with the Malawi radiation than expected, suggesting historical genetic exchange. Introgressed haplotypes are distributed relatively uniformly across the Malawi radiation, indicating that most hybrid-derived polymorphism was acquired and sorted before the formation of the contemporary Malawi radiation. Our results point towards several previously unknown contributors to the Malawi cichlid hybrid swarm and show that the history of one of the largest vertebrate radiations is more complex than previously thought.