SUMMARY A major question in modern biology is how gene mutations affect development and are translated into macroevolutionary changes in morphology. Variations in tooth number, a strategy used by many mammals to develop specialized dentitions, has been an important factor for species diversification. Changes in the number of teeth tend to occur in the reverse of the order teeth are formed during development, which also characterizes the general pattern of tooth loss observed during the evolution of placental mammals. To understand how changes at the molecular level affect the distinct stages of tooth development, we analyzed the ontogenesis of tooth growth arrest in sciurids and mice and in single and double knockout mutant mice. We show that the complexity of the genetic network that governs tooth development can change during ontogenetic trajectory, and these changes may be related to macroevolutionary changes. Furthermore, we show that the variation in tooth number in the affected members of human families bearing mutations in the MSX1 and PAX9 genes can help to understand how the genetic variations within a population can modulate evolutionary changes in dental patterning.