Novel approach to quantitative spatial gene expression uncovers cryptic evolution in the developing Drosophila eye

Robustness in development allows for the accumulation of cryptic variation, and this largely neutral variation is potentially important for both evolution and complex disease phenotypes. However, it has generally only been investigated as variation in the response to large genetic perturbations. Here we use newly developed methods to quantify spatial gene expression patterns during development of the Drosophila eye disc, and uncover cryptic variation in wildtype developmental systems. We focus on four conserved morphogens, hairy, atonal, hedgehog, and Delta, that are involved in specifying ommatidia in the developing eye. We find abundant cryptic variation within and between species, genotypes, and sexes, as well as cryptic variation in the regulatory logic between atonal and hairy and their regulators, Delta and hedgehog. This work paves the way for a synthesis between population and quantitative genetic approaches with that of developmental biology.