Reconstructions of a Neanderthal man, left, and woman at the Neanderthal museum in Mettmann, Germany. (AP Photo/Martin Meissner)

One hundred thousand years ago, research suggests, a group of Homo sapiens — isolated from their own kind — came across a group of Neanderthals. The rest, as they say, is history — and the proof of their love affair has just been uncovered in ancient DNA.

It wasn't long ago that Neanderthals had a universal reputation for being hulking, idiotic cousins — brutal beasts who couldn't outsmart the modern humans we count as our ancestors. But that's been changing: Now we know that Homo neanderthalensis co-existed with Homo sapiens for thousands of years at a time. There's strong evidence that Neanderthals were more like us than we give them credit for, perhaps even producing art, and many of us carry the DNA signatures of generations of interbreeding between neanderthalensis and sapiensAccording to a study published Wednesday in Nature, that interbreeding may have started some 50,000 years earlier than previously assumed.

The new findings don't change the timestamp of Neanderthal interbreeding in our own history. Scientists can tell, based on the bits of Neanderthal DNA found in many humans today, that our ancestors met up with Neanderthals some 50,000 to 60,000 years ago.

But now there's evidence of at least one earlier event.

"I think our idea of these being really separate and highly distinct groups that had relatively little interaction, that is starting to change," Cold Spring Harbor Laboratory's Adam Siepel, one of the study's lead authors, told The Post. Siepel and his colleagues — an international group including several members of the Max Planck Institute for Evolutionary Anthropology — used new computer algorithms to analyze the genomes of ancient humans.

They were looking at the so-called Altai Neanderthal, a Siberian individual known only by a tiny, remarkably well-preserved toe fragment. It's the same Neanderthal that was used to sequence the species's genome for the first time, but Siepel and his team were looking at it through a new lens. Their algorithms were set to track patterns in tiny fragments of DNA to root out commonalities between species, painting a picture of migrations and meetings.

Their model confirmed several previous findings about Neanderthal and human history, which gave the researchers hope that their methods were working. But then they found that the Altai Neanderthal had modern humans in its genetic history.

"It was perplexing to see gene flow in the opposite direction," Siepel said.

The group also sequenced the genomes of two contemporary Neanderthals from Western Europe and found no traces of modern human DNA in their samples. That's not a huge surprise, because researchers had already suspected that Eastern and Western Neanderthals were fairly separate groups by the time modern humans came along. The new study also sequenced a Denisovan — another early human relative — found in the same cave as the Altai Neanderthal. No traces of modern humans showed up there, either.

But even more intriguing than this human-Neanderthal hybrid are the humans it descended from: Based on the story told by the DNA, the scientists believe these humans became separated from other modern humans some 200,000 years ago, not long after Homo sapiens first evolved. That suggests that there was a wave of very early migration out of Africa. Modern African humans lack the Neanderthal DNA found in Eurasian individuals, so researchers are fairly certain that the groups didn't meet up there.

There has been evidence of such a migration before — individual skeletons from 100,000 years ago and a set of human teeth found in China and dated back 80,000 years — but the story is still patchy. Did a group of intrepid Homo sapiens trek out of the cradle of humanity while our species was still in its infancy and actually survive? Where did they go, and how did they meet the Neanderthals?

What the scientists do know is that this separation from other modern humans took place about 100,000 years before the interbreeding event occurred. "It's hard to know what may have happened during that time," Siepel said.

It's even harder not to speculate. How long did the two species interact before they began to truly intermingle? Did they even think of one another as being so different? Maybe not, and that's something modern scientists are coming to terms with as well.

"It seems clear that there was a fair amount of interbreeding," Siepel said. "We now know of at least four events between different groups of archaic hominins, and we're probably going to keep discovering more."

Sriram Sankararaman, a post-doctoral researcher in genetics at Harvard Medical School who wasn't involved in the latest study, called it "quite convincing" and said that these kinds of events no longer come as a surprise.

"Admixture appears to be a very common phenomenon," Sankararaman told The Post. "Given the geographical range of Neanderthals, it was always plausible that the two populations overlapped and interbred."

This is more than just an interesting thought experiment on what it means to be a modern human. According to Siepel, this shift in thinking has practical applications in genome analysis.

"When you look at a modern European genome, you have to wonder whether mutations were passed down through early humans, or whether they were brought in by Neanderthals. Now we have to do the same thing with Neanderthal genomes, as well," he said.

Read More:

New study on Otzi the Iceman reveals humanity’s intimate affair with one microbe

How Roman toilets (and fish sauce) may have helped spread parasites across Europe

Human and Neanderthal love affair is traced back to Israel, 55,000 years ago

This weird worm is a surprisingly close cousin of ours

Surprising infant grave may solve the mystery of North American migration