Phylogeny and development of Diptera. (A) Simplified phylogenetic tree displaying the relationships among the species used in this study, with respect to drosophilids and mosquitoes. The position of Clogmia albipunctata is controversial (see our Results). (B) Schematic representation of the dipteran life cycle, expanded view showing stages of embryo development. Transcriptomes were obtained from embryos at the following developmental stages: cleavage, blastoderm, gastrulation, and early germband extension. Image sources: Culiseta longiareolata and Episyrphus balteatus pictures by Joaquim Alves Gaspar; Clogmia albipunctata by Sanjay Acharya; Drosophila melanogaster picture by André Karwath (images publicly available through Wikimedia commons); Megaselia abdita picture taken by Karl R. Wotton; embryo, larvae, and fly drawings by Victor Jiménez-Guri.