We’ve seen that Pax6 from vertebrates and eyeless from flies are remarkably similar in sequence and function, but what about our other visionaries — the squid and the flatworm? Despite the major differences in their eyes, they all have genes similar to Pax6. Here are corresponding sections of the Pax6-like eye-building genes for our visionaries. Similarities to the mouse gene are highlighted in green:

But why are these genes so similar when the animals from which they come, and the eyes that they develop, are so different? As discussed earlier, there are two basic evolutionary explanations for similarities: homology and analogy. Are these genes homologous (i.e., were they passed down from the common ancestor of all these different organisms) or analogous (i.e., did they all evolve independently through convergent evolution)?

Based on the observations that all of these gene versions are remarkably similar in sequence, have related functions, and are incredibly widespread (animals all across the tree of life have them), scientists have concluded that they must be homologous and must have been inherited from the common ancestor of all these animals. It is just too unlikely that all these different animal lineages happened to independently evolve remarkably similar genes that do remarkably similar jobs. The most parsimonious explanation is that the gene evolved just once long ago and was then passed down to all these different modern animal lineages.

The original Pax gene — the ancestral version of eyeless, mouse Pax6, and the eye-building genes of all the different animal lineages we’ve studied here — probably evolved more than 500 million years ago. That animal’s descendants evolved into all the diverse organisms alive today that carry eye-building genes. As these descendent lineages further evolved, the basic eye-building gene was modified in different ways in the different lineages, giving rise to the diversity of Pax6-like genes seen in modern animals.