a, Observed relationship between evolution and development. Divergence (horizontal distance) can be morphological or molecular. b, Transcriptome similarity between three species pairs throughout development (matched stages) using 11,439 1:1 orthologues. Similar trends were obtained using all species pairs. The weighted average Spearman correlation coefficients are −0.81 (P = 1 × 10−12) for the mouse–rat comparison, −0.69 (P = 2 × 10−11) for mouse–human and −0.42 (P = 0.0004) for mouse–opossum. At the bottom are the Spearman correlations between transcriptome correlation coefficients and matched developmental time for each organ and species pair (**P < 0.02, *P < 0.05). Lines were estimated through linear regression and the 95% confidence interval is shown in the shaded areas. c, The pLI score for genes with different developmental trajectories in human (top) and mouse (bottom). Lower values mean less tolerance. The pLI scores used for mouse genes are from their human orthologues. The P values refer to early versus late comparisons, two-sided Wilcoxon rank-sum test. Box plots are as in Fig. 3e. d, Percentage of lethal and subviable genes expressed throughout development among a set of 2,686 neutrally ascertained mouse knockouts (top) and the same after excluding housekeeping genes (bottom). Spearman correlations at the bottom of each plot. Lines were estimated through linear regression and the 95% confidence interval is shown in grey.