If you think about fossils, you probably picture a piece of bone or shell, turned to stone and buried in the ground. You visit them in museums; some of you may even have found some. But your closest fossils are inside you, scattered throughout your genome. They are the remains of ancient viruses, which shoved their genes among those of our ancestors. There they remained, turning into genetic fossils that still lurk in our genomes to this day.
We’ve known about our viral ancestors for 40 years, but a new study shows that their genetic infiltration was far more extensive than anyone had realised. The viral roots of our family tree have just become a lot bigger.
The two-toed sloth is a walking hotel. The animal is so inactive that its fur acts as an ecosystem in its own right, hosting a wide variety of algae and insects. But the sloth has another surprise passenger hitching a ride inside its body, one that has stayed with it for up to 55 million years – a virus.
In the Cretaceous period, the genes of the sloth’s ancestor were infiltrated by a “foamy virus“, one of a family that still infects humans, chimps and other mammals today. They are examples of retroviruses, which reproduce by converting an RNA genome into a DNA version and inserting that into the genome of whatever animal they’re infecting. If these hitchhikers become permanent tenants, as so often happens, they become known as endogenous retroviruses or ERVs.
ERVs act as a sort of viral fossil record, telling us about the ancient viruses that infected ancestral animals. In the sloth’s case, its ERVs tell us that foamy viruses must have been doing the rounds among ancient mammals over 100 million years ago, back when the dinosaurs still ruled the planet.
Despite the passing of a geological age, their descendants still circulate today and are astonishingly unchanged. The modern viruses look very similar to the one that inserted its genetic material into the sloth’s ancestors. That’s especially amazing because retroviruses – take HIV as an example – have a reputation for mutating at incredibly high rates.
The world of genetics is filled with stories that are as gripping as the plot of any thriller. Take the IRGM gene – its saga, played out over millions of years, has all the makings of a classic drama. Act One: setting the scene. By duplicating and diverging, this gene thrived in the cells of most mammals as a trinity of related versions that played vital roles in the immune system.
Act Two: tragedy strikes. About 50 million years ago, in the ancestors of today’s apes and monkeys, the entire IRGM cluster was practically deleted, leaving behind a sole survivor. Things took a turn for the worse – a parasitic chunk of DNA called Alu hopped into the middle of the remaining gene, rendering it useless. IRGM was, for all intents and purposes, dead and it remained that way for over 25 million years of evolution.
Act Three: the uplifting ending. The future looked bleak, but IRGM’s fortunes were revived in the common ancestor of humans and great apes. Out of the blue, a virus inserted itself into this ancient genome in just the right place to resurrect the long-defunct gene. A fall from grace, a tragic demise and an last-minute resurrection – what more could you ask for from a story?
This twisting tale lies hidden in the genomes of the world’s mammals and it was discovered and narrated by Cemalettin Bekpen from the University of Seattle. To reconstruct the evolutionary story of the IRGM gene, Bekpen searched for it in a variety of different species.
(Oh come on – you try to find an image to illustrate this story!)