Archaeologists digging in a cave in northern Israel have found the oldest remains of a modern human outside Africa, confirming theories about how and when our direct ancestors left their evolutionary cradle.

The discovery of a partial skull from the cave of Manot, detailed in an article published this week in the science journal Nature, shows that the region was the first stop for humans leaving Africa tens of thousands of years ago.

The discovery also suggests that it was here that humans created history's first melting pot when they encountered Neanderthals, the other hominid species that inhabited the Earth at the time of the last Ice Age. What's for sure is the two species existed in this area at about the same time.

Quarter-million-year old time capsule

As is often the case with science and archaeology, the discovery was helped by dumb luck. In 2008, a bulldozer laying a sewage line for the Western Galilee village of Manot, just south of Israel's border with Lebanon, punched a hole through the roof of a large underground space.

Amateur speleologists rappelling into the darkness found a large active cave filled with dripping water that had formed spectacular stalagmites and stalactites over a period of half a million years. But even more astounding was seeing an abundance of prehistoric artifacts, flint tools and animal bones strewn around the cave, often just sticking out of the muddy floor.

The cave turned out to be something of a prehistoric time capsule. The entrance collapsed between 15,000 to 30,000 years ago, sealing in and protecting a record of habitation that may go as far back as 250,000 years.

So far, the most important find to emerge from this treasure trove is "Manot 1," a human calvaria, or the top part of a skull, that was found lying on a ledge in a small side chamber of the cave.

The Nature article, authored by a team of two dozen researchers from universities and institutes across Israel and abroad, says the remains belong to a young adult and date to around 55,000 years ago.

"It's the earliest evidence of anatomically modern humans outside of Africa," said Omry Barzilai, one the directors of the project and the head of the prehistory branch at the Israel Antiquities Authority. "It supports the theory that modern humans left Africa around 60,000 years ago through this region."

Support for the Out of Africa theory

Geneticists and paleontologists have been building support for the so-called "Out of Africa" theory since the 1980s. While several hominid species are known to have emigrated north from the continent over the last hundreds of thousands of years, DNA analysis has traced the genome of all humans alive today to a small group of people who left East Africa some 60,000 years ago and ended up colonizing the rest of the world.

Human remains from this period are extremely rare in the Middle East and usually belong to other hominid species, said Tel Aviv University anthropologist Israel Hershkovitz, another director of the dig and the lead scholar on the study. The Manot skull looks completely different from other groups that inhabited the region at that time or in the previous millennia, but bears a striking resemblance to specimens found in Africa and, in later periods, in Europe, Hershkovitz said.

The skull is in the right place, from the right time and has the right features to have belonged to one of those early explorers from Africa whose descendants later spread into Asia and Europe, Hershkovitz said.

"This is the smoking gun that confirms what geneticists have been predicting," he said. "We had finds from Africa and from Europe but we were missing the connection between them; it's like finishing a puzzle and finding that a piece is missing: it drives you crazy. This is the missing connection between the older African populations and the later European populations."

Hershkovitz told Haaretz that the presence of modern humans at Manot also supports the idea that Homo sapiens sapiens left Africa through the Nile valley, Sinai and what is today known as Israel, striking a blow at competing theories that see our ancestors crossing the Red Sea into contemporary Yemen or the Mediterranean at the Straits of Gibraltar.

Meet the neighbors

The find also suggests that the region could have been the stage for the first encounter between modern humans and Neanderthals, the Nature article says.

Our stocky and sturdy evolutionary cousins did not live in Africa, proliferating mainly in the colder climate of Europe and Northwestern Asia. But they did reach the Middle East. Neanderthal remains dating to the same period as the Manot skull have been found in several caves throughout the Galilee and the Carmel mountain range.

"Neanderthals were flourishing here 50,000 to 60,000 years ago," Hershkovitz said. "Then, anatomically modern humans arrived from Africa and created a melting pot of evolution."

So what exactly happened when the African newcomers met their neighbors?

Scholars have long been puzzling over the relationship between humans and Neanderthals, questioning whether the two species interbred, and whether we had a hand in their ultimate disappearance. For years the debate focused on Europe, even though there are doubts as to whether Neanderthals even survived long enough to witness our arrival there some 40,000 years ago.

Recently, a different scenario has emerged. In 2010, a team in Germany sequenced the Neanderthal genome, discovering that between 1 percent to 4 percent of the DNA of non-African populations derived from Neanderthals.

Because the mixture is quite uniform among all groups outside Africa, the researchers postulated that humans and Neanderthals did the deed somewhere in the Middle East, before the ancestors of Asians and Europeans went their separate ways.

This was further supported last year by the analysis of DNA extracted from a 45,000-year-old human femur found in Siberia, which concluded that the inflow of Neanderthal genes must have occurred 7,000 to 13,000 years before that individual's life. That puts the likely interbreeding event smack in the dating range of the Manot 1 skull.

Was this young adult from the Galilee – researchers are unsure about the person's sex – the offspring of a prehistoric Romeo and Juliet who bridged the gap between two species?

Mosaic skull

The skull does exhibit some archaic features that were common in Neanderthals, such as occipital bunning – a characteristic bulge in the back of the skull, the study says.

"We call it a mosaic skull," Hershkovitz said. "This could be a hybrid of Neanderthals and modern humans." But he cautioned that scientists have so far been unable to extract DNA from the bone to confirm this hypothesis and the archaic features could have also been inherited from the Manot people's original ancestors in Africa.

Whether or not this individual was the result of interbreeding, the presence of modern humans at Manot some 55,000 years ago is hard evidence that confirms the theories of geneticists and makes the green limestone hills of the Western Galilee the most probable set for this key event in human history.

"It must have occurred in one place around 55,000 ago," Hershkovitz said. "Manot fits this description."

Five seasons of digging in the 1,000-square-meter cave have turned up thousands of artifacts used in the everyday lives of its prehistoric inhabitants: flint axes, scrapers and points, exquisite bone tools, animal remains left over from meals and seashells used for decoration. Ofer Marder, co-director of the dig and an archaeologist at Ben-Gurion University, said researchers have also located the burnt out remains of at least six hearths, dated to more than 35,000 years ago, that were used for warmth and to cook food.

But the project – a collaboration of the Israel Antiquities Authority, Tel Aviv University and Ben-Gurion University – has barely scratched the surface.

Barzilai, the IAA archaeologist, said that so far they have mostly excavated the later layers, deposited just before the cave was sealed. Researchers got lucky with the skull because it was found lying above ground, but they hope to find more remains from the same key period, and even earlier, once they reach the most ancient layers of the cave, he said.

The artifacts found, including the skull, are being kept for study at the various institutions involved. Barzilai hopes that the spectacular but fragile Manot site will be opened to the public for limited visits in the coming years.

"We don't want it to become just another tourist attraction," he told Haaretz. "We want it to be a living museum, with small guided groups visiting while researchers continue to work in the cave."