Migration rates among nine populations of the endemic Lake Malawi cichlid Melanochromis
auratus were estimated along a 42-km stretch of habitat in the southern end of the lake.
Allele frequencies were surveyed at four simple sequence repeat (SSR) loci. The data suggest
migration rates among populations are quite low. Exact tests indicate that statistically
detectable allele frequency differences exist between many adjacent populations in the study.
The Fs, value among all populations was estimated to be 0.151 (P < 0.0002). A biogeographic
survey suggests that the highest levels of genetic differentiation exist between populations
separated by stretches of deep water. Migration is more common between populations separated
by shallower water or with shoreline dispersal routes. Reduced allelic diversity was observed
at more recently created habitat patches, suggesting that either bottlenecks are associated
with the colonization of new habitat patches or that these shallower sites were all founded
by genetically depauperate ancestral populations. The extreme philopatry of M. auratus,
coupled with the patchy distribution and transient nature of its preferred habitat, provides
opportunities for both selection and genetic drift to produce genetic differentiation among
populations. Both processes may be important to the evolution of taxonomic diversity in the
East African cichlid species flocks.