Abstract
A long history of research focused on the East Africa cichlid radiations (EAR) revealed discrepancies between mtDNA and nuclear phylogenies, suggesting that interspecific hybridisation may have been significant during the radiation of these fishes. The approximately 250 cichlid species of Lake Tanganyika have their roots in a monophyletic African cichlid assemblage, but controversies remain about the precise phylogenetic origin and placement of different lineages and consequently about L. Tanganyika colonization scenarios. 3312 AFLP loci and the mitochondrial ND2 gene were genotyped for 91 species representing almost all major lacustrine and riverine haplotilapiine east African cichlid lineages with a focus on L. Tanganyika endemics. Explicitly testing for the possibility of ancient hybridisation events, a comprehensive phylogenetic network hypothesis is proposed for the origin and diversification of L. Tanganyika cichlids. Inference of discordant phylogenetic signal strongly suggests that the genomes of two endemic L. Tanganyika tribes, Eretmodini and Tropheini, are composed of an ancient mixture of riverine and lacustrine lineages. For the first time a strong monophyly signal of all non-haplochromine mouthbrooding species endemic to L. Tanganyika (“ancient mouthbrooders”) was detected. Further, in the genomes of early diverging L. Tanganyika endemics Trematocarini, Bathybatini, Hemibatini and Boulengerochromis genetic components of other lineages belonging to the East African Radiation appear to be present. In combination with recent palaeo-geological results showing that tectonic activity in the L. Tanganyika region resulted in highly dynamic and heterogeneous landscape evolution over the Neogene and Pleistocene, the novel phylogenetic data render a single lacustrine basin as the geographical cradle of the endemic L. Tanganyika cichlid lineages unlikely. Instead a scenario of a pre-rift origin of several independent L. Tanganyika precursor lineages which diversified in ancient rivers and precursor lakes and then amalgamated in the extant L. Tanganyika basin is put forward as an alternative: the 'melting pot Tanganyika' hypothesis.
Highlights
The ‘Tanganyika Problem’, i.e. the question of the origin of the highly diverse and endemic fauna of Lake Tanganyika (LT), has remained a phylogenetic enigma since Moore (1903) [1]
It is clear today, that all LT cichlids have their roots in one subgroup of the monophyletic African cichlid assemblage [2], controversies remain about the precise phylogenetic placement and composition of different LT cichlid lineages, which directly reflect on proposed Tanganyika colonization scenarios [3,4,5,6]
Despite major uncertainties in the estimated timings of cichlid cladogenesis, as well as the tempo and mode of the tectonism that has reshaped landscapes across the LT region, it has been assumed that we can use an explicit, relatively parsimonious model to explain the origins and diversification of the LT cichlids, by linking the origin of these fishes to the first appearance of one substantial, ancient rift lake anchored in turn by straightforward geochronology
Summary
The ‘Tanganyika Problem’, i.e. the question of the origin of the highly diverse and endemic fauna of Lake Tanganyika (LT), has remained a phylogenetic enigma since Moore (1903) [1]. It is clear today, that all LT cichlids have their roots in one subgroup of the monophyletic African cichlid assemblage (austrotilapiines) [2], controversies remain about the precise phylogenetic placement and composition of different LT cichlid lineages, which directly reflect on proposed Tanganyika colonization scenarios [3,4,5,6] These controversies result from discordant phylogenetic signal in molecular data sets (e.g. mitochondrial vs nuclear DNA) and differences in taxon sampling, especially in those phylogenetic analyses that have not included all potentially important cichlid founder lineages of LT. The composition of all these groups is supported only to a limited extent on both mt and ncDNA data and many potential riverine founder species have not been evaluated; so the phylogenetic integrity of these groupings must still be regarded as preliminary [4]
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