SRP341862 PRJNA767561 Reconstructing the canalized developmental trajectories of superorganismal caste differentiation in ants An ant colony is a higher-level organism consisting of specialized germline and soma individuals that differentiate early in development, but whether developmental trajectories in metazoan bodies and colonial superorganisms are formally analogous has never been assessed. Here we reconstructed transcriptional trajectories for > 1400 individuals covering most developmental stages of two ant species. Our results show that caste differentiation is highly canalized from early development onwards, particularly in germline individuals (gynes). The canalized genes with gyne-biased expression were enriched in ovary and wing functions, while canalized genes with worker-biased expression were enriched in behavioural functions. Suppression of Freja, a top canalized gene expressed in gynes, reduced the expression of gyne-specific traits. Our results suggest caste differentiation can be understood as a Waddington epigenetic landscape process of developmental bifurcation and canalization towards terminally differentiated phenotypes. The parallels between organismal and superorganismal development that we retrieved were predicted a century ago. Pharaoh ant; Leaf-cutter ant; Frutfly