Author Summary Because embryonic development must proceed correctly for an animal to survive, changes in evolution are constrained according to their effects on development. Changes that disrupt development too dramatically are thus rare in evolution. While this has been long observed at the morphological level, it has been more difficult to characterize the impact of such constraints on the genome. In this study, we investigate the effect of gene expression over vertebrate developmental time (from early to late development) on two main features: the gravity of mutation effects (i.e., is removal of the gene lethal?) and the propensity of the gene to remain in double copy after a duplication. We see that both features are consistent, in both zebrafish and mouse, in indicating a strong effect of constraints, which are progressively weaker towards late development, in early development on the genome.