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Summary In the absence of processes regulating morphogenesis and growth, phenotypic variance of a population experiencing no selective mortality should increase throughout ontogeny. To determine whether it does, we measure variance of skull shape using geometric morphometrics and examine its ontogenetic dynamics in the precocial cotton rat (Sigmodon fulviventer) and the altricial house mouse (Mus musculus domesticus). In both species, variance of shape halves between the two youngest samples measured (between 1 and 10 days postnatal and 10 and 15 days postnatal, respectively) and thereafter is nearly constant. The reduction in variance did not appear to result from a general regulation of skull size or developmental timing, although skull size may also be regulated and developmental timing is an important component of the variation in skull shape of young house mice. The ontogenetic dynamics of variance suggest two possible scenarios. First, variation generated during fetal or early postnatal growth is not immediately compensated and therefore accumulates, whereas later in growth, variation is continually generated and rapidly compensated. Second, variation generated during fetal and early postnatal growth is rapidly compensated, after which no new variance is produced. Based on a general model for bone growth, we hypothesize that variance is generated when bone grows under the direction of disorganized muscular movements and decreases with increasing neuromuscular control. Additionally, increasing coherence of signals transmitted by the growing brain and sensory organs, which exert tensile forces on bone, may also canalize skull shape.