The Sixty-Million-Year Virus

How do we know that we are kin to chimpanzees and howler monkeys and the other primates? For one thing, it’s by far the best explanation for the fossil record. For another, our DNA shows signs of kinship to other primates, much like the genetic markers that are shared by people from a particular ethnic group. There’s a third line of evidence that I find particularly fascinating: the viruses carried by humans and other apes.

Every day, viruses traffic in and out of human bodies. They invade people’s cells, make new copies of themselves, and then, if they’re lucky, infect a new host. Some viruses do this by stapling themselves into our DNA, so that their own genes are read by our cells much as they read their own genes. In many cases, infected cells die as they manufacture hundreds of new viruses that burst out of them. But in some cases the viruses get stuck. They sit in the cell’s genome, and the cell goes on living. When the cell duplicates, it duplicates the virus DNA as well. Just because the virus spares the cell is not necessarily a good thing. The virus may still be able to pop out of dormancy and wreak havoc. It may also trigger its host cell to duplicate like mad–giving rise to cancer. One in five cancers is associated with these viruses.

Now imagine what might happen if one of these viruses happened to infect an egg. The egg might well die. Or not. And if it started to divide (as a fertilized embryo), the virus would be passed down to all the daughter cells. In other words, a baby would be born with the virus throughout its body.

Too freaky, I know. Put it in a sci-fi script, and a movie producer will say, “Forget it kid. That’s as crazy as the zombie cockroach story some lunatic came in here with this morning.” But it has happened, and many times over. Scientists can identify viruses lurking in our genome (known as endogenous retroviruses) by their distinctive DNA. A fully-functioning retrovirus sequence contains three genes–one for copying DNA, one for a shell, and one for escaping and invading cells. These genes are flanked by a series of repeating DNA, which allow viruses to be inserted or snipped out of their host’s genome. The human genome carries full-fledged retroviruses, as well as viruses in various state of decay. Scientists have identified 98,000 of these viruses, along with about 150,000 fragments of defunct viruses. All told, they make up 8 percent of the human genome. In many cases, the virus genes have disappeared altogether, leaving behind flanking repeats, which have been duplicated to millions of copies that take up about 40 percent of the genome. As a point of comparison, our “own” genes–in other words, those that encode proteins that make up our bodies and allow our bodies live–make up only about one percent of the genome.

Some of these endogenous retroviruses are only found in some people and not others. They must have invaded someone’s genome and then spread to his or her descendants, but have not yet spread throug our entire species. Others appear to be ubiquitous–meaning that they are ancient passengers that had already spread throughout an ancestral population.

Other vertebrates carry their own collections of endogenous retroviruses. Mice have a particularly lively collection that continues to spread through their genome with each generation. And you can trace their history through evolutionary time. Domesticated cats, for example, share many endogenous retroviruses with their wild cousins. But they also carry other endogenous retroviruses of their own. The same goes for pigs, and their wild boar cousins. As pigs and boars stopped interbreeding, they could no longer spread newly acquired retroviruses to future generations.

Now, if you really don’t enjoy reading about evidence that you are related to a chimpanzee, now’s the time to close your browser window. Because now I must write about the endogenous retroviruses in chimpanzees, macaques, and other primates. It turns out that most of the viruses we carry can also be found in these other species. Our retroviruses can be grouped into families. They carry the same families. Our retroviruses usually appear in the same position in the genome, no matter whose genome you look at. Many of theirs are in the same place. These are all the sorts of evidence you’d expect if retroviruses had been carried down from distant primate ancestors. A particular retrovirus is not identical from one host primate to the next, but you wouldn’t expect that. Once each host lineage branched off, the viruses could acquire mutations. But the different versions of these retroviruses are still similar enough that scientists can reconstruct the DNA of original virus that infected some long-gone primate.

Retroviruses appear to have invaded the primate genome in a series of waves, starting over 55 million years ago and continuing until just a couple million years ago. As a result, some of the retroviruses in our genome are found only in some primates and not others. It’s not completely random as to which primates share these retroviruses. In general, they are the same species that other studies have shown to be our closest relatives.

Once viruses get established in a genome, they can take any of a number of evolutionary paths. They may still be able to break out of their resident genome, become full-blown viruses, and invade another cell in the body. If they’ve lost the ability to become true viruses, their DNA can still get accidentally copied and inserted back into the genome. These copies may accidentally get swapped, producing drastic changes in their host’s genome. And most remarkble, sometimes genes from viruses become useful to their hosts. It appears that virus genes have become vital for the development of primate placentas, and to carry out other essential tasks. While these genes retain distinctive sequences seen only in retroviruses, they show signs of having been preserved by natural selection, even as the viral genes that surround them have mutated into uselessness.

There’s one more use these viruses have to offer: they have preserved a precious record of our evolutionary history.

(For more information, see talk.origins for a discussion of retroviruses and primate evolution from a few years ago.)