It turns out that clusters of these genes — sometimes called modules — tend to keep working together over the course of millions of years. But they get rewired along the way. They respond to new signals, and act to help build new traits.

In an influential 1997 paper, Sean B. Carroll of the University of Wisconsin, Neil Shubin of the University of Chicago and Cliff Tabin of Harvard Medical School coined a term for these borrowed modules: “deep homology.”

Since then, scientists have gotten a far more detailed look at many examples of deep homology. Dr. Carroll and his colleagues, for example, recently figured out how the spots on a fly’s wing evolved through rewiring modules. A tiny fly called Drosophila guttifera sports a distinctive pattern of 16 polka dots on its wings. Dr. Carroll and his colleagues discovered that the module of genes that sets the location of the spots is the same module that lays out the veins and sensory organs in the wings of many fly species. The module was later borrowed in Drosophila guttifera to lay down dots, too.

Our own eyes are also the product of deep homology. The light-sensing organs of jellyfish seem very different from our eyes, for example, but both use the same module of genes to build light-catching molecules.

Scientists are also discovering that our nervous system shares an even deeper homology with single-celled organisms. Neurons communicate with each other by forming connections called synapses. The neurons use a network of genes to build a complete scaffolding to support the synapse. In February, Alexandre Alié and Michael Manuel of the National Center for Scientific Research in France reported finding 13 of these scaffold-building genes in single-celled relatives of animals known as choanoflagellates.

Image EMBRYONIC In their quest for drugs that can kill tumors by stopping blood vessel growth, scientists use glass needles to fertilize frog embryos with genes from yeast that also make proteins found in developing human blood vessels. Credit... Ben Sklar for The New York Times

No one is sure what choanoflagellates use these neuron-building genes for. The one thing that is certain is that they don’t build neurons with them.