Neanderthals were much like us. Their brains were as large as ours, and they carried a lot of the same DNA we do.

They were good hunters, extremely well-adapted to the cold, and skilled craftspeople: they shared our ability to make sophisticated stone tools, for instance.

We were so alike, in fact, that when modern humans came face-to-face with Neanderthal groups in Europe and Asia, the two species interbred. We see evidence of this in all modern-day Europeans and Asians.

Combing through their DNA and comparing it to ours has already revealed that several disease-causing genes we carry today came from the Neanderthals via these inter-species romps.

But a new study proposes that disease transmission went the other way too. When modern humans met Neanderthals in Europe, we may have given groups of Neanderthals several harmful pathogens.

These could have included the herpes simplex 2 virus, which causes genital herpes, and Helicobacter pylori, a bacterium that causes stomach ulcers. We may even have given Neanderthals tuberculosis and tapeworms.

These diseases would not have killed Neanderthals quickly

Charlotte Houldcroft of the University of Cambridge and her colleague Simon Underdown from Oxford Brookes University, both in the UK, came to these conclusions after considering the fact that some of the most common Neanderthal DNA carried by living people has a role in fighting diseases. This suggests dealing with pathogens was an important fact of life in the Stone Age when the two species met.

They also looked at the genetic family trees of several pathogens, to establish when they first infected modern humans.

Many were initially thought to have spread from animals to humans in the last 8,000 years, after the dawn of agriculture. But it is now becoming clear that a number of human diseases were around thousands of years earlier.

That means they would have been carried by modern humans travelling out of Africa when they met Neanderthals, and might have passed between the two species.

The research is published in the American Journal of Physical Anthropology.

These diseases would not have killed Neanderthals quickly, says Houldcroft. "It would have been a slow progression into slightly worse health than they had before."

I don't think we'll ever find a single theory of what killed the Neanderthals

People today do not usually die from these ancient diseases – they only have a small impact on our general health. However, Neanderthals were facing other challenges when these diseases arrived on their doorstep.

Genetic evidence suggests their numbers were already low about 50,000 years ago. Adding some unwelcome pathogens to the mix would have put additional strains on the hunting and foraging ability of Neanderthal groups, each of which probably included between 15 and 30 individuals.

If any one group was wiped out, it would have been devastating for the Neanderthal population as a whole.

This influx of diseases, if it really happened, could provide another piece of an enduring puzzle: why our cousins went extinct while we thrived.

"I don't think we'll ever find a [single] theory of what killed the Neanderthals, but there is increasing evidence that lots of things happened over a period of a few thousand years that cumulatively killed off the Neanderthals," says Houldcroft.

"Our hypothesis is basically that each band of Neanderthals had its own personal disaster and over time you lose more and more groups. This is just one of many factors," she says.

We are able to reconstruct the challenges faced by our ancestors 40,000 years ago

Climate change may also have been a factor. It led to a dramatic reduction of the forested environment Neanderthals were used to, resulting in less food for them to hunt and gather.

While the Neanderthal genome does not show traces of modern human diseases, we might soon be able to infer their presence by looking for signs that gene variants known to be resistant to the pathogens were widespread in Neanderthal populations.

"We get a record of natural selection by looking at what genes are present and what genes are missing," says Underdown. "We are able to reconstruct the challenges faced by our ancestors 40,000 years ago, essentially using the genetic record to reconstruct their daily life."

A second new study is currently on the pre-print server bioRxiv and has not yet undergone peer review. It might explain why Neanderthals fared worse when exposed to diseases that modern humans had successfully survived for a long time.

This latest analysis shows that Neanderthals had extremely low genetic diversity in many genes important for disease resistance. Neanderthals all had pretty much the same variants of each of these genes.

Modern humans, on the other hand, show much more diversity. This means that, when faced with foreign diseases, Neanderthals had a weaker defence mechanism.

When populations have been separated for some time their diseases evolve separately as well

In other words, although there may have been a two-way exchange of diseases when modern humans and Neanderthals met, the modern humans would have been better able to deal with new infections than Neanderthals were.

George Perry of Pennsylvania State University in the US is co-author of this latest study. He says that, taken together, these analyses emphasise the important role the transmission of diseases has played in our evolution.

"When populations have been separated for some time, their diseases evolve separately as well," says Perry. "So when the populations come together and potentially exchange those diseases, there could be some effect on one or both populations."

Unfortunately for Neanderthals, it just so happens that we had a better genetic toolkit for dealing with that situation than they did.

Melissa Hogenboom is BBC Earth's feature writer. She is @melissasuzanneh on Twitter.

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