The species flocks of cichlid fishes in the largest East African Lakes, Victoria,
Malawi and Tanganyika, are well-known examples of adaptive radiations and "explosive
speciation." These species assemblages are the most species-rich and the most diverse,
morphologically, ecologically and behaviorally among vertebrates. Phenotypic and
genotypic data sets are expected to provide concordant phylogenetic information about
these species assemblages, since both share identical evolutionary histories.
Molecular data however have some advantages for phylogeny reconstruction over
morphological data. Our understanding of the phylogenetic relationships among East
African cichlid fish species flocks has increased rapidly since the recent invention
of the polymerase chain reaction (PCR) which dramatically facilitated the collection
of molecular data. Phylogenetic analyses of recent molecular data in the context of
the geological history of the East African lakes helped to elucidate some aspects of
the evolutionary history and evolutionary processes that might have led to the origin
of these extraordinary fish faunas. The molecular studies on the whole confirm many
previous morphology-based hypotheses.