Our ancestors found their Neanderthal cousins to be particularly adept in the bed – er, cave – room. According to a new paper published in Cell, Neanderthals and Homo sapiens interbred at least twice in the last 100,000 years, exchanging both viruses and the genetic tools to fight against them. And we have the evidence in our genomes to prove it. In modern Asian and European populations, around 2 to 3 percent of DNA can be traced back to Neanderthals. Bow chicka.  

Modern humans diverged from Neanderthals between 500,000 and 800,000 years ago, but they interbred at least twice before the latter mysteriously died out some 40,000 years back. When the two first made contact, Neanderthals had already been living outside of Africa for hundreds of thousands of years, giving their immune systems time to evolve in response to infectious diseases. Having not been exposed to these types of viruses, modern humans emigrating to Europe and Asia would have been particularly vulnerable to the diseases they caused. Rather than wait thousands of years to evolve defenses against them, they did what any moderately intelligent being would do – “borrow” these genetic defenses from Neanderthals through mating.

Researchers at Stanford University are calling it a classic case of the “poison-antidote model”, where gene swapping between the two species meant Neanderthals were giving modern humans infectious diseases (poison) but also the genetic toolkit to fight against them (antidote).

"Our research shows that a substantial number of frequently occurring Neanderthal DNA snippets were adaptive for a very cool reason," said Stanford evolutionary biologist Dmitri Petrov in a statement. "Neanderthal genes likely gave us some protection against viruses that our ancestors encountered when they left Africa."

To see where this cross-section happened, the team built a catalog of more than 4,500 human proteins known to interact with at least one virus and then checked these against a database of sequenced Neanderthal DNA. A total of 152 were found to also occur in modern humans and interact with modern-day RNA-based viruses such as HIV, influenza A, and hepatitis C.

The researchers say their work shows that it’s possible to comb through genomes and find evidence of ancient diseases even after those viruses are long gone.

"It's similar to palaeontology," said study co-author David Enard. "You can find hints of dinosaurs in different ways. Sometimes you'll discover actual bones, but sometimes you find only footprints in fossilized mud. Our method is similarly indirect: Because we know which genes interact with which viruses, we can infer the types of viruses responsible for ancient disease outbreaks." 

Noted in the paper is the fact that the poison-antidote scenario is preliminary even though the statistics behind it are relatively strong.

“Indeed, although the enrichments we describe are rigorously defined, they represent only statistical associations,” wrote the authors. “We believe that more functional work will be required to establish the causal impact of the virus-host interactions on the detected patterns of adaptive introgression.”