Levantines and Arabians Have Different Origins, Middle East Genomic Study Finds

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The peoples of the Middle East: 'Peace panel' from the Sumerian city of Ur.
The peoples of the Middle East: 'Peace panel' from the Sumerian city of Ur.Credit: Juan Carlos Fonseca Mata
Ruth Schuster
Ruth Schuster

Apparently, it is so: Anatomically modern humans have been leaving Africa for almost a quarter million years, but they all went extinct until an exit around 50,000 to 60,000 years ago. A new study of genomes in the Middle East shores up this hypothesis, finding no trace of the early humans in any of the genomes tested.

One of the routes out of Africa for hominins going back 2 million years, and later, for humans too, was the Levant, Iraq and Arabia. Indeed, researchers have found evidence of human and hominin exits in various places, including Israel and Saudi Arabia: stuff like the odd bone or a batch of stone tools.

The prevailing belief is that the groups taking part in the earliest migrations went extinct (though not before encountering other hominins in Eurasia). Then about 50,000 to 60,000 years ago, anatomical humans left Africa – and survived. They met and mixed with Neanderthals and heavens knows who else, and begat modern humanity.

Camels in Saudi Arabia, capable of crossing sandy lands.Credit: AHMED YOSRI / REUTERS

This belief that the early exiters did not survive is now bolstered by an international team led by Mohamed Almarri of the Wellcome Genome Campus in Britain. In their study, published in Cell, they looked at the genomic history of the Middle East and concluded that present-day populations in Arabia, the Levant including Israel, and Iraq have no signals from those early modern humans.

“We used a new whole genome sequencing technology to study human populations from the Levant [Lebanon, Syria, Jordan, Israel and the West Bank], Iraq and Arabia, and we reconstruct the population history of the region from over 125,000 years ago up to the last millennium,” Almarri says. “We show how changes in lifestyle and climate have affected the demography of human populations in the region.”

How does one test latter-day DNA for signals older than 60,000 years? By the density of mutations, he explains: “The more mutations there are, the older the segments will be.”

That’s a generalization; some genetic sequences are more evolutionarily conserved than others. If you check the sequence for the protein ubiquitin, it will be the same from a human to a tree frog and obviously, for earlier humans. But if a given segment has a ton of mutations (that didn’t kill the bearer), we may assume it’s old.

Also, obviously modern humans didn’t descend from newly-created beings who sprang up some 60,000 years ago; we will have some very, very ancient DNA. But, Almarri explains, when a population expands, the migrants are a tiny percent of the original population. The same would have applied to the African exit.

And indeed, genomic studies of today’s non-African populations show a genetic bottleneck around that time, Almarri says. Non-Africans all descend from exiters around 50,000 to 60,000 years ago and are much less genetically diverse than sub-Saharan Africans, who suffered no bottleneck.

The Neanderthals and the Levantines

Moving on, Levantines and Iraqis share the same Neanderthal signals as Eurasians, the team found. Arabians on the other hand have less Neanderthal DNA.

The reason apparently lies in origins. Levantines have more ancestry (than Arabians) from Europe and Anatolia. The Arabians have more ancestry (than Levantines) from Africans, who didn’t mix with Neanderthals, and from Natufians, who were the prehistoric inhabitants of the Levant, including Israel.

The peoples of the Middle East didn't necessarily like one another: Assyrian relief.Credit: Krikkiat/Shutterstock

The Natufians were prehistoric peoples living about 11,000 to 16,000 years ago in what is today Israel, Jordan and Lebanon. It’s possible that they also reached Arabia, but their remains haven’t been found.

Also, present-day Africans are believed to have a contribution from Neanderthals after all, a very small one, conferred by early humans who trekked in reverse – from Europe back to Africa – after mixing with Neanderthals.

Anyway, the Arabians of today apparently didn’t arise from early Levantine farmers but from Natufian hunter-gatherers who preceded these farmers and Africans, the study shows. Nor do the findings support the theory that Levantine farmers later replaced the indigenous Arabian population.

A Natufian burial, Rakefet Cave, Israel.Credit: Danny Nadel

It bears stressing that human fossil remains are incredibly rare; from the deep prehistoric past Saudi Arabia has so far produced one finger bone from 85,000 years ago, but it has also produced tools that may have been special to humans (as opposed to other hominins) from 125,000 years ago. In Israel there are a lot more very ancient human remains, starting with the 200,000-year-old jawbone found in Misliya, and there are more when you get to the Natufian period but they’re still very rare.

Desertification and population collapse

Another difference the genomic analysis indicated relates to the Neolithic Revolution – the “invention” of agriculture.

But here it bears stressing that the Middle East, Arabia and North Africa weren’t always baking-hot deserts. Sometimes, depending on planetary orbital cycles, they “greened.” Hippos and crocodiles cavorted in lakes and rivers, and hominins – and later, modern humans – could comfortably roam.

When the Neolithic Revolution – the gradual transition from a life of hunting and gathering to agriculture and animal husbandry – began over 10,000 years ago, Arabia and the Sahara were in such a lush period. The Arabian Desert as we know it today, the biggest sand desert in the world, didn’t exist. It began to form sometime between 6,000 to 8,000 years ago. (That might help explain the paucity of prehistoric human remains.)

Upper left jawbone of a modern Homo sapiens found in Misliya cave on Mount Carmel and dated to nearly 200,000 years ago, the oldest human remains out of Africa.Credit: Israel Hershkovitz

The Neolithic Revolution drove a massive population increase in the Levant and Iraq, but not in Arabia. The team even postulates that the small population groups of ancient Arabians may have perpetuated or descended from the local epipaleolithic hunting-gathering groups.

But as the Arabian Desert was forming, about 6,000 years ago its population imploded. The same would happen in the Levant about 4,200 years ago, commensurate with an intense aridification event.

“We find that prehistorical aridification and desertification events have resulted in population crashes a few thousands of years ago,” the team says – a warning for today, with all due respect to desalination technology.

Say it in Semitic

Current-day peoples the team studied in the Levant, Arabia and Iraq turned out to form distinct core clusters: Populations from the Levant and Iraq (Lebanese, Syrians, Jordanians, Israeli Druze, and Iraqi Arabs) clustered together. The Iraqi Kurds clustered with central Iranians.

Iraqi Kurds celebrate the Noruz spring festival, in 2015.Credit: SAFIN HAMED/AFP

The Arabians (Emiratis, Saudis, Yemenis and Omanis) clustered with Bedouin – who are from Israel, too. “These samples were collected by the Human Genome Diversity Project and were sequenced by us,” Almarri notes.

Fascinatingly, both the Iraqi Kurds and Iranians, who clustered together, speak Indo-Iranian languages – Kurdish isn’t Arabic or Semitic, it’s Indo-Iranian. All the other people sampled in the study speak Arabic, a Semitic language.

“The clustering patterns we find reflect the historical ancestries present in modern-day populations. In the Levant [and Iraqi Arabs], all the populations we tested have higher Anatolian-like ancestry, which is much rarer in Arabia. Arabian populations in contrast have higher Natufian-like ancestry,” Almarri says.

Apropos language, the team also suggests that a Bronze Age population in the Levant (meaning from about 5,000 years ago) plausibly was responsible for spreading Semitic languages to Arabia and East Africa.

A glass of milk and thou

Marc Haber of the University of Birmingham notes that the study detected positive selection for lactose digestion – the ability to drink and eat dairy products without experiencing socially repulsive and painful consequences.

“In the last 8,000 years this variant increased to a frequency of 50 percent in Arabians, coinciding with the transition from a hunter-gatherer to herder-gatherer lifestyle. This variant is much rarer in the Levant, and almost absent outside the region,” Haber says.

A woman walks past shops at the main market of the Kurdish-majority city of Qamishli, Syria, last year.Credit: DELIL SOULEIMAN / AFP

For this study, researchers at the Wellcome Sanger Institute collected 137 samples from people in eight Middle Eastern populations for sequencing. The genomic data was then analyzed at Wellcome Sanger and the University of Birmingham to look for variations in the genomes that could help map out human evolution from 100,000 years ago to today, the researchers explain.

It bears adding that apparently the domestication of the sheep, goats and cows wasn’t driven by a desire to exploit their milk but to eat the whole animal, instead of hunting for toothsome herbivores.

What have we learned? That we thrived after the advent of agriculture but were brought low by climate change. That we did not thrive in the Arabian Desert but did when it was wetter and greener. Did we do that?

We did not – the greening and aridification of North Africa and Arabia were due to planetary cycles, not human impact. Today Arabia contains the largest sand desert in the world (though not the largest desert), but by the next time the cycle swings and the area should, theoretically, turn green again, it may not happen, and that’s on us.

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