Fig. 3.

Reconstruction of ancestral character states for habitat in Lake Tanganyika and Lake Malawi using phylogenies estimated from control region (A) and NADH-2 (B). In both cases, the model selected by the AIC assumed equal transition rates between rock-dwelling and benthic species and between pelagic and benthic ones, whereas the transition rate between rock-dwelling and pelagic was assumed to be zero. The Inset below each tree shows typical probabilities of transitions among the three habitats after exponential transformation of the rate matrix for a time scale typical of the trees estimated (0.01). Transition between rock-dwelling and pelagic habitats is made possible via the benthic habitat. Both neighbor-joining trees are in agreement with recent phylogenetic analyses of the Great Lakes cichlids (14).