| The cichlid species flocks of East Africa offer powerful models in which to study explosive speciation and adaptive radiation. However, the phylogenetic history and population structure of the fishes of the Lake Victoria Region (LVR) have been problematic, due to a lack of appropriately variable genetic markers. Previous studies of the LVR cichlids using mitochondrial DNA sequences showed little interspecific divergence. To determine whether low mtDNA variation was due to small sample sizes, or is a characteristic of the LVR cichlids, a 432 base pair mtDNA region was sequenced from 35 individuals of a LVR widespread species, Astatoreochromis alluaudi, from six localities. Very little phylogenetically informative variation was detected, and no significant relationship was observed between mtDNA haplotype and the geographical source of samples. The results indicate that mtDNA sequence data are not useful for phylogenetic inferences of LVR cichlids.; To develop new genetic markers to study the problematic phylogeny of the LVR cichlids, a partial genomic library was constructed from A. alluaudi, and was screened for microsatellite DNA markers. Nine microsatellite DNA markers revealed significant regional differentiation among the same six population samples of A. alluaudi studied using mtDNA. Measures of genetic differentiation based on microsatellites are consistent with patterns predicted by both the biogeography and the jaw morphology of the six populations.; In sharp contrast to allozyme markers and mtDNA sequences, 14 microsatellite markers detected substantial amounts of genetic variation within samples from each of 24 cichlid species from the LVR. Phylogenetic analyses indicated that microsatellite markers, as a group, contain phylogenetic signals that confirmed taxonomic relationships of some, but not all, morphologically defined congeners. Microsatellites data also revealed a geographical component to the pattern of cichlid divergence in the LVR. The microsatellite based phylogeny is consistent with the hypothesis that many of the present-day LVR cichlid species may be derived from a group of species from Lake Edward. However, a robust and reliable phylogeny of these fish requires additional data from more microsatellite markers, as well as the inclusion of additional genera and additional sets of congeners from different lakes. |
