The classical methods of molecular phylogenetic investigation, allozyme electrophoresis and
mtDNA restriction or sequence analysis, have failed to resolve relationships among members
of rapidly evolving species flocks such as the mbuna (Cichlidae) of Lake Malawi.
Several classes of nuclear DNA markers may, however, provide greater resolution; most promising
are microsatellite markers. The extremely high mutation rates at these loci render them
fundamentally different from other nuclear DNA polymorphisms, as changes in allele frequency
are influenced by mutation as well as genetic drift. Analysis of two microsatellite loci in
three congeneric pairs of mbuna species strongly suggests that these markers can
provide phylogenetic information relevant to these recently diverged taxa.