Twenty-two tilapiine cichlid species in the three major genera, Tilapia, Sarotherodon and Oreochromis, were electrophoretically examined at 43 different enzyme loci, providing a large allozyme data base for these species. A number of comparative data based on behavioural, biogeographical and morphological characters at the generic, subgeneric and specific levels of the same species were collected from the literature and were numerically coded. A number of molecular phylogenies were produced by a variety of different analytical methods utilizing various treatments of the allozyme data set. The theoretically most robust and least restrictive analytical techniques were then used to assess the morphological data set. The phylogenies generated from the different data sets, allozymes and morphological characters, were compared and a conclusive consensus phylogeny generated.

The electrophoretic data were interpreted in a number of ways. The banding pattern of each enzyme locus was described. Allozyme differences between genus, subgenus and species were recorded as inter- generic, subgeneric and specific discriminating loci, providing a large number of genetic markers for species/stock management in this group. The estimated heterozygosities (He) ranged between 0.008 – 0.122 (± 0.008 – 0.034). The highest He were found in the lacustrine species, especially the three chambo species, O. (Ny.) karongae, O. (Ny.) lidole and O. (Ny.) squamipinnis, from Lake Malawi 0.110 ± 0.032). The fixation index (F-statistics, Fgj) observed within different levels of the taxa studied ranged between 0.734 – 0.907 within genera, and 0.378 – 0.749 within subgenera. The chambo showed the lowest ^ST (O.OS 1) within any single species grouping, suggesting that very little genetic differentiation has occurred between these species. The observed genotypic frequencies in the various chambo species did not significantly deviate from Hardy-Weinberg expectations (X%2o.o5) allele frequencies observed between species were significantly different {yCpi.0.05) at most loci, suggesting large random mating populations with reproductive isolation of the chambo spiecies. The results support the hypothesis that spĂ©ciation in the Lake Malawi chambo was sympatric rather than allopatric.
Interspecific genetic distances ranged between 0.054 – 0.735 (arc distance of Cavalli-Sforza & Edwards, 1967) and 0.(X)2 – 0.786 (unbiased distance of Nei, 1978) from the most similar pair of T. (C.) tholloni and T. (C.) zillii to the least similar pair of T. (C.) rendalli and S. melanotheron (aquarium stocks). However the averaged genetic distances within a group showed that the chambo share the closest relationship to each other (0.128, arc distance; 0.010, unbiased distance). The small genetic distances found in the chambo also suggest their recent spĂ©ciation (estimated time since divergence about 100,000 – 250,000 y). The average inter-generic distances show that the two mouthbrooding genera were closer to each other than either were to the substrate spawning Tilapia.

Molecular and non-molecular phylogenies consistently supported the monophyly of the mouthbrooding taxa studied in relation to the substrate spawning Tilapia, supporting the classification proposed by Trewavas (1983). The relationships between two species pairs, O. (O.) mossamhicus & O. (O.) mortimeri and O. (O.) placidas & O. (O.) shiranus, were consistently shown by the molecular phylogenies as closely related sister-species or subspecies. All intra- and inter- generic, subgeneric and specific evolutionary relationships shown in the phylogenies were discussed and placed in the context of the biogeography and distribution of the species in this group.