The fly’s eye retains a common genetic core after 90 million years of evolutionary drift

A study by the CABD analyzes how two flies, Drosophila and Episyrphus—separated by 90 million years of evolution—use information from their genomes to build their eyes, revealing the similarities and differences resulting from evolution

The study sheds light on the formation of compound eyes in insects—the most common type of visual organ in nature—and also provides empirical evidence of “regulatory fluidity.”

A team from the Andalusian Center for Developmental Biology (CABD)—a joint center of the Spanish National Research Council (CSIC), Pablo de Olavide University, and the Regional Government of Andalusia—has compared the mechanisms that control eye formation in two species of flies separated by 90 million years: Drosophila melanogaster, the fruit fly, and Epysirphus balteatus, the jam fly.

The comparison reveals both the existence of a core set of genes common to both species and significant variation in the genomic elements that control the expression of those genes over the course of this evolutionary period.

“What we have seen is that the ‘tools’ for building eyes in both species have been conserved, but the ‘instructions’ for using them have varied considerably.” “This suggests that preserving function does not require preserving exactly the same regulatory architecture: the network can be ‘rewired’ significantly without losing its core logic,” summarizes Fernando Casares, a CSIC researcher at the CABD and senior author of the study.  “In fact, we believe that it is possibly this phenomenon—which we call ‘regulatory fluidity’—that enables evolution,” he adds.

The finding, published in PLOS Genetics, provides a better understanding of how the compound eye—the most common type of eye in nature (found in the most diverse and numerous animal groups on Earth, crustaceans and their terrestrial relatives, the insects)—forms. Furthermore, it sheds light on how evolution modifies the mechanisms underlying the construction of complex organs and broadens our understanding of the rules governing organ formation during embryonic development.

A Common Genetic Core

Until now, Drosophila was the primary model organism for studying the compound eye in insects, but it was unclear to what extent its gene regulatory network was representative of the rest of the group.

By comparing it with Episyrphus, a fly whose lineage diverged from that of Drosophila 90 million years ago, the researchers have been able to confirm that, although differences exist, they still share a common genetic core that has been preserved throughout this entire period.

Specifically, the results show a core set of 106 genes associated with eye development that are common to both species, including 22 transcription factors (proteins that bind to DNA and activate or inhibit protein production from other genes).

“With this study, we have increased the number of known genes essential for compound eye formation nearly tenfold. But above all, we have reconstructed the gene regulatory network of the eye for each species—that is, the set of relationships that explains how some genes control others during the development of this organ. And this gives us a better understanding of the mechanisms by which nature generates the different forms and functions of organs,” adds Tomás Navarro, the study’s first author and a researcher in the group.

“Regulatory fluidity,” the recipe for successful evolution

At the same time, the study reveals that, despite this common core, many of the connections that regulate the expression of these genes differ between the two species. This is what the researchers call “regulatory fluidity”—proof that nature can drastically reconfigure an organism’s internal genetic circuitry without altering the final anatomical outcome, ensuring that the eye forms correctly despite mutations accumulated over millennia.

In this regard, the study provides empirical evidence that, in evolutionary processes, there is a distinction between functional conservation and exact structural conservation. In other words, an organ (in this case, the eye) continues to develop correctly because a set of key regulatory factors is maintained, but the specific way in which those regulatory factors interact with one another can vary greatly.

“Our work shows that the evolution of complex organs can be better understood not just by looking at which genes are present, but also at how they connect and how that connectivity changes,” Casares concludes.

Reference

Navarro T, Torres J, Sáez-Moreno R, Guerrero G, Almudí I, Iannini A, Figueras J, Wotton K, Aerts S, Casares F. (2026). Expanding the fly eye gene regulatory network: From Drosophila to the hoverfly Episyrphus balteatus. PLoS Genet.  https://doi.org/10.1371/journal.pgen.1011864