Through adaptive radiation, ancestral species rapidly diversify into multiple species with different ecological adaptations. The haplochromine cichlid fishes of the East African Great Lakes are considered classic examples of adaptive radiation, but our understanding of the evolutionary origins of these radiations has been limited by inadequate taxonomic and genomic sampling [1] and [2]. Perhaps the largest of these radiations is from Lake Malawi, estimated to contain between 500 and 800 endemic species. Surprisingly, its monophyly - the origin from a single ancestral species - has never been critically tested. This is because river populations which could have seeded the radiation, with one very limited exception [3], have never been included in phylogenetic reconstructions. Moreover, phylogenies have relied heavily on mitochondrial DNA (mtDNA), which can be a misleading phylogenetic marker for species capable of hybridization [4] and [5] because its non-recombining nature means that transfer to other species can occur via asymmetric introgression and 'allele surfing' [6]. Here, we used broad taxonomic sampling and nuclear DNA markers with wide genomic coverage and find that the Lake Malawi radiation is not monophyletic, but instead contains genetic material from divergent riverine ancestors indicating multiple invasions and hybridization.
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