Mitochondrial DNA haplotype diversity and frequency distribution were examined within and
among four narrowly endemic species and one cosmopolitan species of the rock-dwelling cichlid
fish species flock (mbuna) of Lake Malawi in East Africa. The endemics, restricted to very
small islands, appear to have originated less than 20,000 yr ago. Relative and absolute levels
of genetic diversity were used to examine the possibility that these endemics arose through
founder events, as has been suggested for the Hawaiian drosophiloids, to which the East African
cichlids have been compared. Three principal results emerged from this study. First, the
undescribed species Pseudotropheus zebra 'black dorsal' was found to be depauperate
of mtDNA haplotype diversity relative to sister taxa, suggesting a severe population bottleneck
during, or subsequent to, its recent origin. Second, significant differences in haplotype
frequency existed among all five closely related species examined here. Geologic evidence
and distributional limits indicate that this divergence in haplotype frequency occurred
rapidly, consistent with population bottlenecks. Paradoxically, in three of four species
examined there was no apparent reduction in genetic diversity, and two had haplotype
diversity values that were high relative to other freshwater fishes. Third, it was found
that replicate collections of single species at different sites within the same general
locations, without obvious barriers to gene flow, also exhibited significant differences
in haplotype frequency. Such apparent fine-scale genetic structuring, whether spatial or
temporal, has substantial implications for estimates of effective population size and modeling
of speciation processes.