Abstract
The most variable segment of the mitochondrial control region were sequenced from several isolated populations of the genus Tropheus from different localities of Lake Tanganyika. Populations from opposite shores situated at shallow border sections of the lake basins were closely related to each other. Individuals from the eastern and western shoreline differed by a minimum of 1–2 point mutations in the very north and south of the lake; identical genotypes among individuals from the eastern and the western shorelines were found in the lake’s central region. Since Tropheus is strictly confined to rock habitats and is unable to cross larger distances of open water, the observed complete DNA sequence identity in the mitochondrial control region can be explained only by a dramatic drop of the lake level, forming a continuous band of shallow rock habitats across the lake. The consistently low amount of genetic variation suggests that this event must have happened more recently than indicated by geology-based estimations, probably around or even less than 10 000 years ago. Populations of several other stenotopic rock cichlids must have also been affected similarly.