Embryo polarity in moth flies and mosquitoes relies on distinct old genes with localized transcript isoforms.

Unrelated genes establish head-to-tail polarity in embryos of different fly species, raising the question of how they evolve this function. We show that in moth flies (, ), a maternal transcript isoform of is localized in the anterior egg and adopted the role of anterior determinant without essential protein change. Additionally, lost maternal germ plasm, which contributes to embryo polarity in fruit flies (). In culicine (, Aedes) and anopheline mosquitoes (Anopheles), embryo polarity rests on a previously unnamed zinc finger gene (), or (), respectively. These genes also localize an alternative transcript isoform at the anterior egg pole. Basal-branching crane flies () also enrich maternal transcript at the anterior egg pole, suggesting that functioned as ancestral axis determinant in flies. In conclusion, flies evolved an unexpected diversity of anterior determinants, and alternative transcript isoforms with distinct expression can adopt fundamentally distinct developmental roles.