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A comparison of the pattern and timing of development of cranial lateral line canals and canal neuromasts in three species of Lake Malawi cichlids, Labeotropheus fuelleborni and Metriaclima zebra (narrow lateral line canals), and Aulonocara baenschi (widened lateral line canals) was used to test the hypothesis that the evolution of widened canals (thought to be an adaptive phenotype in the lateral line system) from narrow canals is the result of heterochrony. Using histological analysis and scanning electron microscopy, this study has provided the first detailed and quantitative description of the development of widened lateral line canals in a teleost, and has demonstrated that: 1) canal neuromast number and the pattern of canal morphogenesis are conserved among species with different adult canal phenotypes, 2) heterochrony (“dissociated heterochrony” in particular) can explain the evolution of widened canals and variation in morphology between canals within a species with respect to canal diameter and neuromast size, and 3) the morphology of the lateral line canals and the dermal bones in which they are found (e.g., the mandibular canal the dentary and anguloarticular bones of the mandible) can evolve independently of each other, thus requiring the addition of another level of complexity to discussions of modularity and integration in the skull of bony fishes