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.

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Lake Tanganyika contains the oldest and most complex flock of cichlid fishes counting about 200 endemic species. It is comprised of 16 ecologically, morphologically and genetically highly distinct tribes. Many species are further subdivided into arrays of geographic morphs, each colonizing particular sections of the shore line. The genus Tropheus represents the most spectacular and best studied example for this phenomenon, counting more than 100 distinctly colored populations and sister species, some living in sympatry. Their present distribution and genetic structure was shaped by a series of lake level fluctuations which caused cycles of isolation and secondary admixis. The present study extends previous work on the phylogeography of Tropheus and aims at the fine-scale reconstruction of the origin and spread of lineages in the central and southern basin of the lake. The previously defined mtDNA lineages were evaluated on the basis of statistical parsimony networks. Haplotype networks were created for each lineage and related to their centers of diversity in terms of present distribution. A linearized tree analysis and a mismatch distribution analysis corroborate two of the three radiation waves suggested in earlier works, but the new data suggest a different primary colonization scenario for the southern basin.

Lake Tanganyika harbors an enormous diversity of cichlid fish that stem from eight distinct ancestral lineages, which colonized the lake after its formation 9 to 12 million years ago. Six of twelve currently described tribes are assigned to the "H-lineage," an assemblage of exclusively mouthbrood-ing cichlids, all of which evolved during a short period of time during the course of the primary radiation of lacustrine species. Our study focuses on the deepwater tribe Limnochromini, comprising bi-parental mouthbrooders, and is based on phylogenetic analysis of two mitochondrial gene segments. We confirm the polyphyletic origin of the Limnochromini as they are defined to date, in that Gnathochromis pfefferi is placed among the Tropheini, whereas the genus Benthochromis is presented as an independent lineage. The remaining nine species were unambiguously resolved as monophyletic and should be redefined as the tribe Limnochromini. Concerning generic assignments, the genus Greenwoodochromis appeared as monophyletic, Limnochromis as paraphyletic, and the genera Reganochromis and Baileychromis as monophyletic sister genera. The linearized tree analysis and the comparison of average sequence divergences to that of the remaining tribes of the H-lineage revealed a relatively recent but simultaneous proliferation of the Limnochromini, suggesting that the same environmental changes triggered the radiation of particular deepwater, benthic, pelagic, and littoral lineages. By using a preliminary calibration of a molecular clock based on gamma-corrected amino acid distances of the NADH2 gene, the diversification of the Limnochromini could tentatively be dated to 2.9-3.5 MYA, coinciding with a period of aridification in East Africa between 2.5 and 3 MYA. The lack of geographic color morphs and the structural uniformity and resource scarcity of deepwater habitats suggest that competition and resource partitioning leading to differential trophic specialization promoted speciation within the Limnochromini, rather than an allopatric model.