Charles Darwin was interested not just in how new things evolve, but also in how old things disappear. Often, they don’t disappear completely without a trace. We don’t have a visible tail like our primate ancestors did, but we still have a series of little bones tucked away at the bottom of the spine. While it may not function like a full-blown tail, it still anchors muscles around the pelvis. Blind cavefish may not have eyes of the sort found on their cousins in the outside world, but they still start to develop eyes as larva, before the cells start to die away.
Sometimes, though, the only place to look for vestiges of a lost trait is in a genome.
In the journal PLOS Genetics, Mark Springer of the University of California and his colleagues have published an intriguing study of how teeth–and the genes for teeth–have faded away over the past 50 million years. In particular, they looked at enamel, the tough covering that caps the teeth of humans and other vertebrates.
Enamel has three advantages for this kind of study: one is that it fossilizes well. For a lot of species, enamel is often the only thing left behind. Another advantage of enamel is that scientists also have a good understanding of the genes that build it–genes that are similar across a wide range of species. And the third advantage of enamel is that certain lineages of mammals have lost it. Baleen whales, anteaters, and pangolins have all lost their teeth entirely. (Baleen whales grow tooth buds, like cave fish grow eyes, but the buds die back without ever forming enamel.) Sloths, armadillos, pygmy sperm whales, and aardvarks still have teeth, but have no enamel left. This pattern suggests that enamel has been lost independently in several lineages of mammals.
In each lineage, these mammals have lost enamel as they’ve shifted away from depending on hard teeth. As I wrote about here, baleen whales descend from ancestors with formidable teeth for catching prey. But then their ancestors evolved a new way to eat, growing baleen–frond-like sheets of tissue that can filter out krill and other small animals from sea water. As anteaters came to only eat insects, the teeth of their ancestors became not just pointless but a hindrance. Their mouth became finely adapted for shooting a long tongue forward into ant nests. Big teeth would just get in the way.
So where did the enamel go? The scientists decided to test the possibility that the genes for enamel were still in the genomes of toothless mammals, but they had been shut down. In each species’s genome, scientists find a number of so-called pseudogenes, which can no longer encode a protein because of a crippling mutation. A mutation may, for example, insert a “stop” command, so that cells can no longer read the full sequence of a gene and make a full protein. Other mutations can shift a big chunk of DNA over a couple positions, garbling the code. Imagine shifting all the spaces in a sentence to the left. Y ouwou ldg etsomethi ngli kethis.
Despite these devastating mutations, pseudogenes often manage to retain a strong resemblance to their working counterparts. We, for example, have hundreds of pseudogenes that show a striking resemblance to hundreds of other genes that encode a variety of receptors in our noses. So Springer and his colleagues sequenced an enamel-building gene called ENAM in 49 mammal species, including toothless or enamel-less ones to see what happened to the gene along the way.
Their results were pretty much what they expected, but they’re still pretty amazing. There were no frameshift mutations in ENAM among the mammals with teeth. But 17 out of 20 species without teeth or enamel had at least one. In all 20 enamel-free species, a stop command (known as a stop codon) was present. These genes are shot.
The scientists then probed the evolution of the ENAM genes by taking advantage of the fact that only some letters in a gene encode a protein and others are ignored. Mutations that change the structure of a protein may have serious effects on an animal. They may be good effects or really bad ones–in either case, they may change the overall reproductive success of individuals who carry the mutation. On the other hand, silent mutations may have no effect (or at least just a small one).
It turns out that in mammals with teeth, the ENAM gene has experienced something call purifying selection. In other words, very few protein-changing mutations have endured for millions of years because tinkering with the recipe for enamel is a really bad thing to do if you need hard teeth to survive. In mammals without enamel, on the other hand, the ENAM gene evolved in a different way. It experienced what’s known as neutral evolution: the silent mutations and the protein-changing ones have occurred at about the same rate. It just doesn’t matter to the mammals anymore, because the genes are, as I mentioned before, shot.
These genomic vestiges don’t just provide evidence of how teeth were lost. They also provide some clues to when they were lost. By comparing closely related species that don’t have enamel, the scientists could tally up the mutations that had arisen since their last common ancestor. And since neutral mutations tend to pile up at a fairly steady rate, the scientists were able to estimate how long ago the ENAM gene turned from an essential gene to a useless one. In some cases, the scientists predict, paleontologists will find toothless members of these lineages millions of years older than the oldest known fossils without teeth–such as with pangolins, as this figure illustrates.. It is a remarkable convergence, of traces of history recorded in molecules tucked away in anteater cells, and skulls that have managed to turn to stone. But from them, a single picture emerges.