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The cichlid fish of Lake Tanganyika in Eastern Africa are a celebrated example of both ecological and species diversification. Because population subdivision is likely to play an important role in the speciation process, understanding how habitat features interact with species' demographic, behavioral and ecological attributes to influence gene flow and population divergence may help explain the causes of high species richness in this and other systems. Here, we test the roles of isolation-by-habitat and isolation-by-distance in generating fine-scale population genetic structure in three sympatric species of habitat-restricted cichlids in Lake Tanganyika. Using multilocus microsatellite genotypes, we contrast patterns of population differentiation in these habitat specialists along a mosaic coastline of both favorable and unfavorable habitat. Despite their close phylogenetic relationship and shared habitat affinity, these species show striking differences in their pattern of genetic subdivision within the same geographical region, suggesting substantially different patterns of gene flow. In particular, two trophically specialized species exhibit much more restricted gene flow over sandy habitat than a trophically opportunistic species. This result suggests that ecological and behavioral traits have a strong influence on the scale and degree of population subdivision, a finding that has potentially important implications for understanding differential propensities for diversification among lineages and phylogenetic patterns of diversity.

Fishes of the genus Semionotus diversified in the rift lakes of eastern North America during the Mesozoic (Newark Supergroup). Like the well-known cichlid fishes of the African great lakes, diverse complexes of semionotids were apparently endemic to a number of different lakes. Semionotid fishes show considerable morphological diversity in body shape and in a modified row of scales termed "dorsal ridge scales." A number of distinct dorsal-ridge-scale patterns characterize groups of species from the Newark Supergroup. Interestingly, about 5.5% of individuals examined have anomalous scales mixed in with otherwise stereotypic dorsal-ridge-scale patterns. In this study, I take advantage of nearly annual stratigraphic resolution to determine whether dorsal-ridge-scale anomalies are concentrated stratigraphically in the early phase of lake formation and colonization by semionotids. More than 1,700 specimens of semionotid fish were collected from a single lake deposit (cycle P4), representing approximately 21,000 years, in the Early-Jurassic Towaco Formation of the Newark Basin. Dorsal-ridge-scale anomalies are significantly more frequent in older than in younger lake sediments, which I interpret as being the result of relaxed selection during the early colonization of the lake. Anomalous variation parallels variation in dorsal ridge scales between species-groups. Some anomalies are atavisms, while others are unique or foreshadow future evolutionary events. One type of anomaly is incorporated into the dorsal-ridge-scale series of two new species that gave rise to a radiation in a subsequent lake filling the same topographic basin. Because both novelties and atavisms occur in the dorsal-ridge-scale series of single individuals, I argue that the disruptions of the same "developmental program" produced both atavistic and novel traits.