The haplochromine cichlid fish of the East African Great Lakes represent some of the fastest and most species-rich adaptive radiations known, but rivers in most of Africa accommodate only a few morphologically similar species of haplochromine cichlid fish. This has been explained by the wealth of ecological opportunity in large lakes compared with rivers. It is therefore surprising that the rivers of southern Africa harbour many, ecologically diverse haplochromines. Here we present genetic, morphological and biogeographical evidence suggesting that these riverine cichlids are products of a recent adaptive radiation in a large lake that dried up in the Holocene. Haplochromine species richness peaks steeply in an area for which geological data reveal the historical existence of Lake palaeo-Makgadikgadi. The centre of this extinct lake is now a saltpan north of the Kalahari Desert, but it once hosted a rapidly evolving fish species radiation, comparable in morphological diversity to that in the extant African Great Lakes. Importantly, this lake seeded all major river systems of southern Africa with ecologically diverse cichlids. This discovery reveals how local evolutionary processes operating during a short window of ecological opportunity can have a major and lasting effect on biodiversity on a continental scale.

Phylogenetic analyses based on mitochondrial (mt) DNA have indicated that the cichlid species flock of the Lake Victoria region is derived from a single ancestral species found in East African rivers, closely related to the ancestor of the Lake Malawi cichlid species flock. The Lake Victoria flock contains ten times less mtDNA variation than the Lake Malawi radiation, consistent with current estimates of the ages of the lakes. We present results of a phylogenetic investigation using nuclear (amplified fragment length polymorphism) markers and a wider coverage of riverine haplochromines. We demonstrate that the Lake Victoria-Edward flock is derived from the morphologically and ecologically diverse cichlid genus Thoracochromis from the Congo and Nile, rather than from the phenotypically conservative East African Astatotilapia. This implies that the ability to express much of the morphological diversity found in the species flock may by far pre-date the origin of the flock. Our data indicate that the nuclear diversity of the Lake Victoria-Edward species flock is similar to that of the Lake Malawi flock, indicating that the genetic diversity is considerably older than the 15 000 years that have passed since the lake began to refill. Most of this variation is manifested in trans-species polymorphisms, indicating very recent cladogenesis from a genetically very diverse founder stock. Our data do not confirm strict monophyly of either of the species flocks, but raise the possibility that these flocks have arisen from hybrid swarms.

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Despite African rivers containing high species diversity, continental-scale studies investigating the mechanisms generating biological diversity of African riverine faunas are limited compared with lacustrine systems. To investigate the build-up of diversity in a tropical aquatic continental radiation, we test different models of lineage diversification and reconstruct the biogeographic history in a species-rich siluriform genus, Synodontis (~130 species), with a broad distribution across all major tropical African drainage basins. The resulting robust species-level phylogeny (~60% complete, based on a multigene data set) exhibits a near constant rate of lineage accumulation throughout the mid-Cenozoic to recent, irrespective of missing species and despite the changing environmental conditions that were prevalent during this time period. This pattern contrasts with the findings for species-level diversification of large clades that commonly show an early burst of cladogenesis followed by declining rates through time. The identification of distinct biogeographic clades demonstrates a correlation between river hydrology and cladogenesis, although there is evidence of recent repeat dispersal into the southern range of the focal group. We conclude that diverse freshwater fish radiations with tropical continental distributions represent important organisms to test hypotheses of diversification and investigate the effects of palaeo-landscapes and climates on present day biodiversity.