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Is There a Neanderthal Lurking in Your Genes?

Those of us of European or Asian ancestry probably wouldn’t exist today, at least not in our present form, if it were not for those open-minded Neanderthals who mated with our ancient Homo sapiens ancestors

When I was a teenager in Israel, I once hiked on Mount Carmel with a bunch of my buddies. We came to the site of a cave, the Tabun cave, that contained the skeleton of a woman that lived there about 120,000 years ago. But, she wasn’t human, by which I mean the Homo sapiens species. She was a Neanderthal (Homo neanderthalensis). Practically next door, there was another cave, where many other skeletons were found, only they were not Neanderthals, but rather an early version of Homo sapiens (aka archaic H. sapiens). 

The Nahal Me’arot cliff, Mount Carmel, Israel, showing the prehistoric caves of el-Wad, Jamal and Tabun | by R Yeshurun | CC by SA 3.0

As unruly teenagers, we couldn’t resist making the obvious jokes about humans having sex with Neanderthals? Of course, we were scolded by our youth movement guide who told us, first of all, we were disrespectful, and second, we were stupid because by the time humans made Aliyah ( i.e. migrated to Israel) from Africa, all the Neanderthals had migrated to Europe. There was no overlap.

It turns out we weren’t stupid (or at least not that stupid), we were just ahead of our time. A few months ago, a group of archaeologists writing in the journal Nature, described finding a human skull that dated back to 55,000 years ago in a cave by the Sea of Galilee—the same place where Jesus plied his trade 53,000 years later.

Not only did Neanderthals live in the Middle East at that time, but several caves in the vicinity of Mount Carmel were inhabited by them. They lived at the same time and in the same vicinity as ancient humans. So again, I ask the question: Did they have sex with each other?

We no longer do we have to resort to the fevered imagination of Israeli teenagers to get to the answer. Genome studies of Neanderthals and of both ancient and contemporary H. sapiens suggest that the two species interbred somewhere in the Middle East between 50,000 and 60,000 years ago.


Is there a Neanderthal lurking in your genes?

If you are of European or Asian descent then, in all likelihood, you are part Neanderthal. Although Neanderthal genes are only a small part of our genome to be sure (about 2-4%), it could actually be making an important contribution to who we are.

Bonobo photo: By Psych USD (CC BY-SA 3.0)

Bonobo | via Psych USD | CC BY-SA 3.0

Consider this: Only about 1-4% of our genome makes us modern humans. The rest of our genome is identical to lower primates. We are 96% identical to the chimpanzees and 99% to the bonobos. Look at what a huge difference this small percent has made, for better or for worse.

But wait, what we now know is, for some people, 2-4% of the 1-4% difference between us and lower primates is actually Neanderthal! And, that’s the contribution from only one closely related species of humans, the Neanderthals.


What about other human species?

Denisovans or Denisova hominins are another extinct species of human in the genus homo. In March 2010, scientists announced the discovery of a finger bone fragment from a juvenile female who lived about 41,000 years ago. It was found in the remote Denisova cave in the Altai mountains in Siberia, a cave that has also been inhabited by Neanderthals and modern humans

The family history of the human species doesn’t look like a tree, but rather like a bush, with as yet undiscovered stems and branches

So, again I ask: was there interbreeding? How could there not be? About 17% of the Neanderthal genome from skeletons found there is Denisovan. Tests comparing the Denisova hominin genome with those of six modern humans showed that between 4% and 6% of the genome of Melanesians derives from a Denisovan population. This DNA was possibly introduced during the early migration to Melanesia.


Melanesians may not be the only modern-day descendants of Denisovans. Population geneticist David Reich of Harvard, in collaboration with Mark Stoneking of the Planck Institute team, found genetic evidence that Denisovan ancestry is shared by Melanesians, Australian aboriginals, and smaller scattered groups of people in Southeast Asia. Their genome is 5% Denisovan. The data places the interbreeding event in mainland Southeast Asia, and suggests that Denisovans once ranged widely over eastern Asia.

These examples are only the tip of the iceberg. More discoveries of cousin hominins are sure to come because evidence is accruing that the family history of the human species doesn’t look like a tree, but rather like a bush, with as yet undiscovered stems and branches.


How Neanderthal and other hominin genes helped our species survive

This post would have ended here if that was all to the story. But as it happens, these slivers of “alien” DNA have an outsize effect on our biology. An article in Nature reviews some of those effects.

Take something as basic as our immune response. Everybody is familiar with adaptive immunity, in which, after exposure to pathogens, we develop antibodies and lymphocytes programmed to specifically attack them. But that takes time, a minimum of 7-10 days if the pathogen has never been encountered before. To be left defenseless during that period would result in certain death.

To the rescue comes an immune system, called innate immunity. How does it work? We have 10 variants of a peptide called TLR (Toll-like Receptor). This peptide does not recognize specific organisms, but it recognizes certain molecular patterns that don’t exist in humans. When such a molecular pattern binds to the TLR, it activates white cells to go on the attack against the organism, be it bacteria or virus, and annihilate it. And here is the surprise: genomic analysis revealed that we have to give thanks to our Neanderthal relatives for making a major contribution toward development of this first line of defense.

Neanderthals even helped us with adaptive immunity. As macrophages engulf and digest dangerous invaders, they chew them up and spit out the broken down peptides of the pathogen’s proteins. On their membrane, these macrophages have proteins called HLA (Human Leukocyte Antigens) which perform the most basic thing the immune response does: recognize self from non-self. If they bind a pathogen’s broken down peptide and don’t recognize it as self, they set in motion synthesis of antibodies to that particular pathogen. So far, four families of HLA peptides, each containing about 1000 variants, have been identified. One of those families, present in 75% of Europeans, is Neanderthal!

What about non-immunological genetic contributions? As we lost our pigmentation coming out of Africa, we became exposed to the harmful effects of UV radiation. How could the new immigrants to the Middle East and Europe adapt quickly enough before being completely wiped out by the sun’s radiation? The welcoming local Neanderthals made sure that we’d survive the old fashion way: they made love to us, and in the process transferred a gene protective of UV-B radiation. They also saw us suffering from hitherto unfamiliar cold temperatures of Europe and gave us a series of genes involved in the inner workings of cells called keratinocytes, which make up most of the outer layer of human skin and produce hair.


And what about the Denisovan contributions?

Tibetans in the clouds | by darcym | CC BY-NC-ND

Tibetans in the clouds | by darcym | CC BY-NC-ND

Denisovan’s also made significant contributions to the human genome? Here’s a striking example. Tibetans adapted to living in high altitudes that would make you and me gasp for air. It turns out they have a variant of a gene, EPAS1, that allows them to function at such altitudes. The source of the gene? Their Denisovan ancestors.

So why don’t the Han Chinese have this gene variant? A tiny minority of them do have it, but because of natural selection, it largely disappeared in the majority of Han because, at lower elevations, it had no survival advantage.


Was it all fun and games?

As you read this post, you might think that it was written by a Neanderthal advocate. Far from it. There are a whole lot of Neanderthal genes that are not found in humans. There are long stretches of DNA where you don’t have a trace of Neanderthal genes. Why is that? Most likely, because these genes were actually deleterious and those unfortunate individuals who inherited them were “bred out” by natural selection. Case in point: the X chromosome is totally devoid of Neanderthal genes, most likely because they reduced fertility. The obvious consequence was rapid elimination from the gene pool.


Let us give thanks

So all you Europeans and Asians (myself included), take note. We probably wouldn’t exist today, at least not in our present form, if it were not for those open-minded Neanderthals who mated with our ancient Homo sapiens ancestors. The result of these interspecies liasons was the transfer to our species of the genes that now protect us from unfamiliar pathogens, UV irradiation, and bitter cold. We owe them a debt of gratitude and, for sure, we should be proud of their contributions to our well-being.

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