Animals that live underground inhabit a lightless environment. Some aspects of vision in this context might not be useful, particularly those that facilitate vision in bright light. If a species has lived underground for millions of years, we would expect that many genes tied to vision have become pseudogenes, just like in animals that live in the dim-light conditions of the deep ocean.
I conducted a study  in which I investigated 65 vision genes across three different species of subterranean mammals, including the Cape golden mole (Chrysochloris asiatica), a member of the African golden moles (Chrysochloridae)
the naked mole-rat (Heterocephalus glaber), an African mole-rat (Bathyergidae)
and the star-nosed mole (Condylura cristata), a true mole (Talpidae).
You’ll notice that the naked mole-rat has tiny eyes, and you’ll see the same thing if you examine other pictures of the star-nosed mole. The golden mole has no external eyes; they’re completely covered with skin and fur! You can imagine that vision is not terribly important for these three mammals, especially golden moles.
What I discovered is that the golden mole has 17 vision pseudogenes uniquely derived in its lineage, the naked mole-rat has 12 and the star-nosed mole has 6. Interestingly, this corresponds with the amount of light each species likely experiences. Star-nosed moles frequently foray above ground and often swim; naked mole-rats are entirely subterranean but have an exposed eye; and golden moles are entirely subterranean but have eyes underneath their skin. By contrast, in the above-ground mammals that I used for comparison (e.g., elephants, cows, mice), nearly all of the vision genes were functional.
I then used a method to estimate when these genes might have been inactivated, and compared that to estimations of when these species might have invaded a subterranean habitat. The fossil record and molecular phylogenetics suggests that subterranean mammals descended from above-ground species, suggesting that these vision genes might have become pseudogenes as a result of this transition underground.
As described in my first post, the earliest golden mole, a transitional fossil, dates to 33.9-28.4 million years ago. However, we only have jaw fragments of this species, so we are unable to discern if it was subterranean. The next oldest species, Prochrysochloris miocaenicus (23-16 million years ago), has modifications to its skull to suggest that it lived underground. Of the 16 genes I was able to date, I estimated 13 were inactivated after the earliest date for Prochrysochloris.
African mole-rats are all subterranean, so their last common ancestor is inferred to have lived underground as well. Molecular clock methods estimate that this ancestor dates to approximately 28 million years ago. The earliest fossils don’t appear until 23 million years ago. Regardless, all 10 of the genes I was able to estimate inactivation times for post-dated both of these dates.
True moles vary in their mode of locomotion. Some are diggers, some live above ground, some spend a lot of time in the water, and star-nosed moles both dig and swim. Nonetheless, the oldest fossils of true mole limb bones show modifications for digging, and these date to 33.9-28.4 million years ago. I estimated that 4 of the 5 pseudogenes I found were inactivated after these fossils appeared.
I also examined two published vision pseudogenes in the Mediterranean blind mole-rat
and a single vision pseudogene in the marsupial mole.
These represent two more subterranean lineages, and both happen to have eyes beneath their skin.
The earliest digging blind mole-rat fossils date to 11.6-5.3 million years ago, and I estimated that both gene inactivation events took place after blind mole-rats invaded the underground habitat.
Finally, the only marsupial mole fossil dates to 23-16 million years ago and shows modifications for living underground. The pseudogenization event post-dates the fossil.
Put together, I estimated that 30 of the 35 vision genes across these five underground mammal lineages became inactivated after they became subterranean.
Questions for Creationists
Why would God create mammals with eyes covered by skin and fur? Why would He also give them nonfunctional vision genes? Is it a coincidence that these genes were estimated to have been inactivated after their fossils appear? Do you think these results are consistent with mammals evolving from above-ground ancestors to underground species?