Phylogenetic analyses based on mitochondrial (mt) DNA have indicated that the cichlid species
flock of the Lake Victoria region is derived from a single ancestral species found in East
African rivers, closely related to the ancestor of the Lake Malawi cichlid species flock. The
Lake Victoria flock contains ten times less mtDNA variation than the Lake Malawi radiation,
consistent with current estimates of the ages of the lakes. We present results of a phylogenetic
investigation using nuclear (amplified fragment length polymorphism) markers and a wider coverage
of riverine haplochromines. We demonstrate that the Lake Victoria–Edward flock is derived from
the morphologically and ecologically diverse cichlid genus Thoracochromis from the Congo
and Nile, rather than from the phenotypically conservative East African Astatotilapia.
This implies that the ability to express much of the morphological diversity found in the
species flock may by far pre-date the origin of the flock. Our data indicate that the nuclear
diversity of the Lake Victoria–Edward species flock is similar to that of the Lake Malawi flock,
indicating that the genetic diversity is considerably older than the 15000 years that have
passed since the lake began to refill. Most of this variation is manifested in trans-species
polymorphisms, indicating very recent cladogenesis from a genetically very diverse founder
stock. Our data do not confirm strict monophyly of either of the species flocks, but raise
the possibility that these flocks have arisen from hybrid swarms.