As I posted yesterday, a lot of contributors gave their answers to the 2017 annual Edge Question, “What scientific term or concept ought to be more widely known?” (See all responses here.) In the last 24 hours Richard Dawkins has weighed in with his answer, “The genetic book of the dead,” which involves reverse-engineering our DNA sequences to reconstruct the ancestral environments of living species. While Dawkins has discussed this before, most notably in Unweaving the Rainbow, not everyone’s read that book. It’s worth considering that an organism’s genome may be a palimpsest of its ancestry, which in turn reflects in part the environments to which those ancestors were adapted.
You can read Richard’s piece for yourself; I’ll give one brief excerpt:
Given a key, you can reconstruct the lock that it fits. Given an animal, you should be able to reconstruct the environments in which its ancestors survived. A knowledgeable zoologist, handed a previously unknown animal, can reconstruct some of the locks that its keys are equipped to open. Many of these are obvious. Webbed feet indicate an aquatic way of life. Camouflaged animals literally carry on their backs a picture of the environments in which their ancestors evaded predation.
But most of the keys that an animal brandishes are not obvious on the surface. Many are buried in cellular chemistry. All of them are, in a sense which is harder to decipher, also buried in the genome. If only we could read the genome in the appropriate way, it would be a kind of negative imprint of ancient worlds, a description of the ancestral environments of the species: the Genetic Book of the Dead.
Naturally the book’s contents will be weighted in favour of recent ancestral environments. The book of a camel’s genome describes recent milennia in deserts. But in there too must be descriptions of Devonian seas from before the mammals’ remote ancestors crawled out on the land. The genetic book of a giant tortoise most vividly portrays the Galapagos island habitat of its recent ancestors; before that the South American mainland where its smaller ancestors thrived. But we know that all modern land tortoises descend earlier from marine turtles, so our Galapagos tortoise’s genetic book will describe somewhat older marine scenes. But those marine ancestral turtles were themselves descended from much older, Triassic, land tortoises. And, like all tetrapods, those Triassic tortoises themselves were descended from fish. So the genetic book of our Galapagos giant is a bewildering palimpsest of water, overlain by land, overlain by water, overlain by land.
We can already reconstruct the features of ancestors by looking at some bits of the genome, especially those “dead genes” that were useful to our ancestors but no longer to their descendants. For example, as I mention in WEIT, the human genome contains three dead genes that are very similar in sequence to active genes that make proteins in the egg yolks of living birds and reptiles. That’s almost irrefutable evidence that we descended from animals with yolked eggs. That says a bit about our ancestral environments, but we can do better. Humans also have a number of dead “olfactory receptor genes” that enabled our ancestors to smell particular molecules (one per gene). Those genes are still active in our relatives like dogs and mice. This tells us that our lineage experienced reduced selection for olfaction, almost certainly because our lineage became more dependent on vision and hearing.
In fact, whales have a huge set of olfactory genes, but every single one of them is inactive. That tells us that the environment of their ancestors was terrestrial.
Can we go further than that? Yes, in principle it’s possible. Richard suggests this solution:
I have a sort of dim inkling of a plan. For simplicity of illustration, I’ll stick to mammals. Gather together a list of mammals who live in water and make them as taxonomically diverse as possible: whales, dugongs, seals, water shrews, otters, yapoks. Now make a similar list of mammals that live in deserts: camels, desert foxes, jerboas etc. Another list of taxonomically diverse mammals who live up trees: monkeys, squirrels, koalas, sugar gliders. Another list of mammals that live underground: moles, marsupial moles, golden moles, mole rats. Now borrow from the statistical techniques of the numerical taxonomists, but use them in a kind of upside-down way. Take specimens of all those lists of mammals and measure as many features as possible, morphological, biochemical and genetic. Now feed all the measurements into the computer and ask it (here’s where I get really vague and ask mathematicians for help) to find features that all the aquatic animals have in common, features that all the desert animals have in common, and so on. Some of these will be obvious, like webbed feet. Others will be non-obvious, and that is why the exercise is worth doing. The most interesting of the non-obvious features will be in the genes. And they will enable us to read the Genetic Book of the Dead.
There are a few problems here, though. One is convergent evolution. A marsupial mole evolved its morphology and behavior independently from those of placental moles, and it’s very likely that the genetic signature of a fossorial life will differ at least somewhat between these two groups. Likewise for arboreal koalas and monkeys, and many desert animals. In such cases, looking at the genes might tell us very little about their ancestral environment of animals whose forebears lived underground, in trees, or in deserts. In other cases, genes no longer used will degrade, making it more difficult to decide what function they served. (That hasn’t happened for olfactory receptor genes or egg-yolk genes, though, telling us that useful genetic information can be preserved for millions of years.) Richard takes that into account when he says the reverse engineering is more effective for more recent ancestors.
Finally, there’s another genetic way to reconstruct ancestral environments: using DNA to make phylogenies, or “family trees” and combining that with the fossil record or the existence of vestigial features. Doing that, for instance, has told us that whales not only descended from terrestrial mammals, but fossils add that it’s probably descended from a deer-like artiodactyl called Indohyus. We can tell what the environment of Indohyus was from its morphology. And in many cases ancestral environments might be better reconstructed from fossils, which bear signs of their adaptations, than the DNA sequences themselves. Also, using DNA-based phylogenies can give us ideas of when certain characters appeared on the lineage: which are ancestral and which are derived. From that kind of reconstruction, for instance, we know that the one species ancestral to social bees was monogamous–singly mated–giving support to the notion that kin selection was an impetus for the evolution of eusociality (kin from single matings are more closely related to each other than kin from multiple matings). The reference is given below.
Regardless, it’s fascinating to see organisms as palimpsests of the past: a thing that we evolutionists have known for a while but that the layperson may not appreciate. Our many vestigial organs (like the muscles that I can use to move my ears) testify to that, and now, with DNA sequencing, we get more testimony from our genes.
Below are the three ear muscles that we inherited but (with some individual exceptions like me) can no longer use. The big muscle atop the ear, and the thin ones in front and back, are the three vestigial ones. In animals like dogs and horses they’re used to move the ear around for hearing; in humans they have no use—except to amuse my students.
Hughes, W. O. H., B. P. Oldroyd, M. Beekman, and F. L. W. Ratnieks. 2008. Ancestral monogamy shows kin selection is key to the evolution of eusociality. Science 320:1213-1216.