Canalized gene expression during development mediates caste differentiation in ants

Abstract Ant colonies are higher-level organisms consisting of specialized reproductive and non-reproductive individuals that differentiate early in development, similar to germ-soma segregation in bilateral Metazoa. Analogous to diverging cell lines, developmental differentiation of individual ants has often been considered in epigenetic terms, but the sets of genes that determine caste phenotypes throughout larval and pupal development remain unknown. Here we reconstruct the individual developmental trajectories of two ant species after obtaining > 1400 whole-genome transcriptomes. Using a novel backward prediction algorithm, we show that caste phenotypes can be accurately predicted by genome-wide transcriptome profiling. We find that caste differentiation is increasingly canalized from early development onwards, particularly in germline individuals (gynes/queens), and that the juvenile hormone signalling pathway regulates this process with feedback from diverging larval body mass. We quantified gene-specific canalization levels and found that canalized genes with gyne/queen-biased expression were enriched for ovary and wing functions while canalized genes with worker-biased expression were enriched in brain and behavioural functions. Suppression in gyne larvae of Freja, a highly canalized gyne-biased ovary gene, disturbed pupal development by inducing non-adaptive intermediate phenotypes between gynes and workers. Our results indicate that the life cycle ontogeny of colonial superorganisms is maintained by strong purifying selection.