The Neanderthals live on in us

The two naked men are a magnet for visitors to London’s Natural History Museum. Stars of a new exhibition, the life-sized models look electrifyingly real. One is grey-haired, tattooed and slim. He’s one of us, Homo sapiens, modelled on a 33,000-year-old skeleton found at Goat’s Hole, in Pembrokeshire, UK. The other is burly with a large, squashed nose, a noticeable brow-ridge, a matted beard and sporting a striped tattoo across his shoulders. He is a Neanderthal, Homo neanderthalensis, modelled from the remains of a 40,000-year-old skeleton found at Spy Cave in Belgium.

Squinting out at their audience, the two gnarly men represent an extraordinary meeting of two human species. Although these individuals never met, other members of their species certainly did, during thousands of years of co-existence in Europe. Then, 35,000 years ago, Neanderthals vanished from the face of the Earth.

The faces of the museum visitors are etched with the same question that has haunted us for a century and a half. What happened when the paths of these two Homo species crossed? Were we responsible for wiping them out? The audience gets an extraordinary answer to these questions when they visit the last display of the museum.

Here, in video displays in one corner of the exhibition’s main hall, an assortment of UK personalities from scientists to comedians, reveal the amounts of Neanderthal DNA that have been found in their genomes. Most are amused. Some are quite proud. All are quite matter of fact. Chris Stringer, the exhibition’s lead scientist tells us: “You can buy a test kit for under £150 (US$260) that can tell you the amount of Neanderthal DNA you possess.”

Not so long ago, the history of the Neanderthal seemed destined to remain as mysterious and fragmented as the occasional dusty bones dug from caves across Europe. Now Neanderthals’ DNA is not only writing the missing pages of their history, but our own.

How did we get to this extraordinary juncture?

Much of the credit would have to go to Svante Pääbo, the Swedish-born director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, whose name has become synonymous with Neanderthal DNA. “If you had asked me 20 years ago, I would have said that sequencing the genome of an extinct species like the Neanderthal was science fiction,” he reflects in his recently published book Neanderthal Man.

Pääbo embodies a rare mix of mad obsession, dogged determination and punctiliousness – everything it takes to turn the stuff of science fiction into reality. His obsession began with his quest to read the DNA of an Egyptian mummy. A passion for Egyptology had burned in him since the age of 13 when his mother took him on a trip to Egypt. But a short sojourn cataloguing pottery shards at a museum cured his ambitions for this type of academic career.

He opted instead for a medical degree and then a PhD at the University of Uppsala, where he was supposed to be probing the DNA secrets of a virus. Instead he began wondering what secrets DNA might reveal about mummies. Behind the scenes he began procuring mummy flesh from East Berlin museums to see if it retained any traces of DNA. In 1985, he published his successful results in Science.

Today many suspect it was contamination – perhaps the DNA of a person who handled the mummy, but at the time it didn’t matter. The electrifying paper made the front cover, featuring a mummy wrapped in threads of DNA, helping to spark the birth of the new discipline of ancient DNA science. It also provided a red carpet for Pääbo into the elite company of those who study humans that are way older than Egyptian mummies.

In the mid-1980s there were huge questions brewing about human origins that seemed destined to remain forever a matter of debate.

Darwin had predicted that, like every other animal, human beings would have fossil ancestors. And indeed in 1856 quarry workers blasting their way into a limestone cave in Germany’s Neander valley found a human-like skull with protruding brow ridges that seemed to fit the bill. But where did these “Neanderthals” fit in the family tree? Were they direct ancestors or more distant cousins that had evolved into a dead end? By the 1980s the question had grown much larger. Many fossil hominins – upright walking apes who shared part of our evolutionary path after we split from the common ancestor of humans and apes – were being found in Europe, Asia and Africa. They were different species whose bones ranged in age; some were hundreds of thousands of years old. But by 30,000 years ago, only one was left: us, Homo sapiens.

What happened? Had these different species all interbred to create modern humans? Or had an intrepid group of Homo sapiens spread out of Africa and simply exterminated other species they encountered along the way? It made for a fierce debate and Pääbo’s mummy paper catapulted him to its very epicentre – to the Berkeley, California lab of Allan Wilson who together with Chris Stringer was one of the primary architects of the “out of Africa” theory.

By 2001 “out of Africa” appeared to have won the debate after being adjudicated by the reading of the human genome. Once the first entire human DNA code was read, scientists started comparing the DNA of different populations. For instance they compared two different tribes of Africans, the San from South Africa and the Yoruban from West Africa, and found their DNA to be quite unalike. On the other hand when they compared DNA from a European and an Asian, they found it was much more similar. This is exactly what would be expected if a group of founders with limited variety in their DNA, had left Africa to colonise the rest of the world some 60,000 years ago. While the humans tree’s roots were in Africa and it produced many different offshoots, it seems it was the descendants of only one small branch who took off to populate the rest of the planet.

But if the picture had seemed all sewn up in the 2000s, by 2010 things began to unravel. Thanks, in no small measure, to Pääbo. Twenty-five years after his mummy paper, and after starting his own lab in Leipzig, he again had an electrifying paper in Science. This time the cover announced “The Neanderthal Genome”. The Neanderthal’s DNA was poised to deliver revelations far more profound than any Egyptian mummy. Neanderthals, as the two models standing proudly in the Natural History Museum show, were like us but not like us. They too were toolmakers, wore clothing, cooked their food, produced ornaments and buried their dead. Yet they were a different species. Their bones clearly differentiated them from ours. Their brow ridges, the shape of their brain cases, their short stocky limbs, even their inner ear bones, were different from anything seen in modern humans. And our tools and weapons were more sophisticated, we painted pictures on cave walls, we were intellectually a leap ahead. Comparing our DNA to theirs should provide the answer to what had given us that edge.

“This is what was immensely exciting – among the few differences one would expect to find in the Neanderthal genome, there must be those that set us apart,” says Pääbo.

Neanderthals also occupied an exceptional place when it came to filling in the story of human origins because at times they lived in colder,  drier parts of Europe. Unlike bones resting in the heat of Africa or southern Asia, which is unkind to DNA preservation, those in caves in Croatia and Siberia have delivered a bounty.

The 2010 Science paper reported the findings of a global consortium headed by Pääbo. They had read the genome sequence of three Neanderthal individuals obtained from bone fragments preserved in a cool, dry cave in Vindija, Croatia. It was a rough draft – each letter of their genetic code had been read only once on average. Greater accuracy would require multiple readings. But notwithstanding possible mistakes, it provided glimpses of some extraordinary secrets.

The DNA was very similar to that of a modern human. Gene for gene they match us. But although they carry the same genes, there are small “typos” – single-letter mutations in the genetic code. On average, one in every 700 letters was different. By comparison the difference between any two human beings is about one in every 1,000 letters. It may not sound like much of a difference but over the three billion letters of the entire DNA code, it adds up: three million typos between two humans, versus four million between a human and a Neanderthal.

The Neanderthal genomes offered tantalising glimpses of what they might have looked like. For instance, their DNA carried mutations in a gene for the melanocortin receptor that controls skin and hair pigmentation  and is responsible for producing red hair as well as pale skin. This was, presumably, an adaptation to the low sunlight conditions they encountered in Europe: fair complexions allow more sunlight through, which is needed to manufacture vitamin D.

The consortium also compared the rough Neanderthal genome to that of five modern-day people: a San bushman from South Africa, a Yoruban from West Africa, a New Guinean, a Chinese and a Frenchman. They found an occasional snippet of Neanderthal DNA sequence in the New Guinean, Chinese and French DNA – different snippets in each case. Overall those snippets accounted for around 2% of their total DNA. But they did not find any snippets of Neanderthal DNA in the African genomes.

It was no surprise that Neanderthal DNA was absent in the DNA of modern Africans – Neanderthals began to evolve in Europe at least 400,000 years ago, descendants of an earlier human group of African émigrés. That descendants of Europeans and Asians carried Neanderthal snippets suggested that, after modern humans left Africa some 60,000 years ago, they interbred with the Neanderthals they encountered, probably in the Middle East. But it was certainly not the only explanation for how modern humans could have ended up with a few distinctly Neanderthal genes.

The period following the publication of the Neanderthal genome was a controversial time, recalls Josh Akey, a population geneticist at the University of Washington in Seattle. While those in the Pääbo consortium argued for evidence of interbreeding, others, such as Andrea Manica from the University of Cambridge, argued for an alternative interpretation. The difference seen in Africans versus non-Africans could simply result from the fact that they inherited those differences from their common African ancestor, probably the sophisticated, big-brained Homo heidelbergensis who lived 500,000 years ago. Like any group today, there would have been slight variation in the DNA of H. heidelbergensis. And those variations would have been amplified in their descendants – those who spread to Europe to become Neanderthals and those who stayed in Africa to evolve into modern humans.

For a while all bets were off. But as more Neanderthal DNA was read, there was more certainty, especially thanks to David Reich’s lab at Harvard Medical School in Boston that specialises in the genetics of populations. The analysis was done by Sriram Sankararaman, a computer scientist who had turned his coding skills to analysing genomes. His mathematical models could test when the Neanderthal DNA actually appeared in the human genome.

The model looks at the size of the blocks of Neanderthal DNA sitting in modern human genomes. Say Neanderthal ‘Bob’ has a child with a modern human female. Because parental DNA is broken up and bits are swapped when it is passed on to the next generation – a bit like shuffling a pack of cards – the chunks of Bob’s DNA will grow smaller in each generation. By calculating the number of generations and estimating the time elapsed by the size of the remaining chunks, Sankararaman reckoned that Neanderthal DNA chunks had been kicking around in modern humans for between 37,000 and 86,000 years.

That means Neanderthal DNA was not an inherited relic from the common ancestor of 500,000 years ago, but had entered the modern human population quite recently. Perhaps it was time to rearrange the ancient family photographs. Alongside the many African great grandparents, there would be an odd Neanderthal, perhaps a sturdy lad with flaming red hair.

Fast forward to 2014 and the interbreeding debate has been largely won “by the slow accumulation of data”, says Akey. And the most detailed Neanderthal genome ever seen – of a young girl  – confirmed it. This individual is known not from her pronounced brow ridges or unusual ear bones, but entirely by her DNA. It was extracted from an otherwise unremarkable shard of toe bone found in the Denisova Cave in the Altai mountains, Siberia. The sample was the most uncontaminated and richest source of Neanderthal DNA ever found, enough to read the genome independently 50 times over.

Her genome also revealed another secret – she was inbred. Instead of carrying many differences in the DNA she had inherited from her father and mother, they were identical across large stretches. It would be consistent with her father being the half-brother of her mother, says Reich.

Overall Neanderthals are estimated to have been only one quarter as genetically diverse as we are – and,  as species go, our diversity is at the very low end: even endangered chimpanzees have more diversity.

It’s not hard to work out why this happened to Neanderthals. They eked out a living through the ice ages of Europe and central Asia when glaciers covered the continent every 100,000 years or so. Life would have been grim. By contrast, modern humans evolving in Africa were protected from the worst vicissitudes of climate change. Homo sapiens would have thrived there while at times, Neanderthals were only able to cling on in a few, small isolated, inbred groups in Europe, the Middle East and central Asia. Estimates suggest that across the Neanderthal’s entire range, from Spain to Siberia, the total population may have been as low as 3,000 breeding adults towards the end of their time on Earth.

One girl’s little toe bone has cast a new light on the whole drama. Severely inbred Neanderthals probably suffered debilitating genetic disorders and their low variability would have meant that microbes could easily devastate their numbers.

For 150 years, we’ve suspected that we had Neanderthal blood on our hands. Now maybe we are off the hook. “Their populations were already stressed and low in density and then, to make matters worse, they encountered members of Homo sapiens who began to exploit the same territories and the same animals and plants as the Neanderthals did,” says Stringer. “It was probably the final straw. Certainly there is no need to invoke a violent takeover by modern humans.”

We may not have made war with the Neanderthals but we certainly made love.

With the surety attached to the new Altai genome, scientists became  bolder. Fishing for Neanderthal DNA in a handful of humans had retrieved small bits – different bits in different people. It accounted overall for about 2% of their DNA. Now Akey at Washington, Sankararaman at Harvard, and their respective colleagues decided to cast their nets wider – to search the genomes of up to 1,000 people.

As Akey put it, “Our work asked the opposite question; not how much Neanderthal DNA looks human but how much human DNA looks Neanderthal?” The two groups used slightly different methods, but came up with similar answers.

Spread across their populations, the bits of Neanderthal DNA added up to 20% to 30% of the Neanderthal genome. The Neanderthal may be extinct but much of their DNA lives on in us. The question then is: what is special about the 20-30% of Neanderthal DNA that survives in our genome?

It was not just a random process, says Akey. A filter was at work: bad DNA was ditched while good DNA was not only tolerated, but there is evidence in some cases that it was selected during human evolution because it conferred an advantage.

The evidence for positive selection is visible in our genomes. It depends on the size of the inherited block of Neanderthal DNA and the frequency with which it appears in the population. The larger the block, the more recently it was inherited, and so the less frequently it should appear in the population. But sometimes a block appears more frequently than it should for its large size. That is a sign the DNA in that block has been selected by evolution. Akey and Sankararaman used different methods to find these signatures
of selection.

Akey and his graduate student Benjamin Vernot started blind. Without reference to Neanderthal DNA, they searched for “ancient-looking” large blocks of DNA across the genome. Then they restricted analysis to those blocks that were not found in African genomes, since they are devoid of Neanderthal DNA. In some cases, they found they had zeroed in on Neanderthal sequences.

Sankararaman’s group, on the other hand, started with Neanderthal sequences and looked for places in the human genome where these chunks were present in unexpectedly large blocks.

The two groups ended up zeroing in on chunks of Neanderthal DNA that bore the signature of being positively selected by human evolution.

These signature chunks contain hundreds of genes, so it is impossible to say which ones were providing the selective advantage, but there are some intriguing candidates. We know in broad strokes something of what these genes do. But what we have inherited from Neanderthals are typos in the DNA code of these genes, and as yet we cannot be sure what they mean. Nevertheless the scientists can make some educated guesses.

“One that really jumped out at us was the Basonuclin-2 (BNC2) gene,” says Sankararaman. “On average each European carries 2% Neanderthal DNA, but 60% of them carry the BNC2 gene inherited from their Neanderthal ancestor.”

What we know about the general function of the gene is that it is involved in pigmentation. Zebra fish lacking it do not form their stripes properly. And in humans, this gene has been associated with freckling. That doesn’t necessarily mean the Neanderthal version of BNC2 caused freckles in them or us. But amongst the genes that we seem to have selected from Neanderthals, there is a preponderance of those that play a role in skin and hair. Besides BNC2, variants of keratin, that determines the toughness of skin (we have lots in our fingernails for instance) also appear to have been selected.

Neanderthals had to survive 400,000 years that included ice-ages and limited sunlight. They adapted by evolving genes for distinctive pale pigmentation and other skin traits that are yet to be fully understood. But when troops of modern humans emerged from Africa some 300,000 years later, with darker skin to protect themselves from the strong African sun, they could take a genetic short-cut. “It was a very different environment from east Africa. This is a neat way to adapt – just pick up genes from people who’d been there for hundreds of thousands of years,” says Akey.

We also seem to have inherited some other intriguing Neanderthal genes that bear the signature of selection.

Long before anyone was talking about Neanderthal genes, these genes had come to the attention of medical researchers because they were associated with modern-day afflictions, including diabetes, Crohn’s disease and other autoimmune conditions where a patient’s own tissues are under attack from their immune system. People with Crohn’s disease for instance, a chronic inflammation of the lower bowel, are much more likely to carry a gene variant known as NOD2. It seems to make their immune system a little trigger happy. Now it seems they can thank their Neanderthal great grandparent for that.

But why would we have selected that gene and others like it?

Maybe in the close quarters of cave-living, a quick-acting immune system was helpful for fighting off microbes. There are lots of cases where gene evolution comes at a price. For instance, a haemoglobin gene variant that protects people against the malaria parasite in the tropics also leaves them more at risk of sickle-cell anaemia. The NOD2 gene variant increases the risk of Crohn’s disease but studies in Indian populations show it is slightly protective against leprosy. What diseases might it have protected Neanderthals and ancient humans against? “This is work that is going to go on for years,” say Pääbo.

But while there are parts of Neanderthal DNA we avidly took up, there are large bits we clearly rejected. These are stretches in the human DNA code that can never be substituted for Neanderthal. It is the DNA that lies here that may well provide what Pääbo anticipated, the key to what makes us Homo sapiens. And within one of these un-swappable bits, lies a gene that has long been touted to have that role: the FOXP2 gene.

People that carry two bad copies of this gene have profound difficulties with language. The gene seems to link the thinking centre of the brain to those parts that articulate thoughts. Inarticulate chimpanzees share 99% of our DNA but their FOXP2 gene is very different. Naturally as soon as the first Neanderthal genome became available, scientists zeroed in. At first glance, their version of the gene appeared very much the same as ours – a blow to the status of FOXP2 as the sapiens gene. But the more detailed readings have shown slight differences, not in those regions that encode the protein (a gene’s primary function) but in the so-called regulatory code that tweaks the way the protein is used.

It’s very likely that Neanderthals were able to communicate through speech given their sophisticated culture, a view supported by the similarity of their FOXP2 gene. But our version of the gene may have been used slightly differently. “Maybe we had richer articulations, more complex patterns of speech,” says Akey.

And finally we come to one more secret revealed by DNA. Neanderthals were a different species and yet we interbred, just as polar bears and brown bears sometimes do. But matings between different species are notoriously susceptible to fertility problems. There are hints that our trysts suffered the same fate. The evidence lies again with a stretch of modern human DNA that has largely rejected Neanderthal inheritance – the X chromosome. It is, says Reich, a pattern often seen in couplings between not-quite-compatible species, as the X chromosome carries genes that are crucial for sperm fertility. Reich hypothesises that this is why genes from the Neanderthal X were rejected.

As to which Neanderthal gender most contributed their genes, we cannot yet say. The Neanderthal Y chromosome is yet to be decoded; and the female Neanderthal lineage, usually traceable through mitochondrial DNA, has not been detected in modern humans. But Akey says that may be a reflection of the rarity of those matings.

Neanderthal DNA may have opened a new chapter in the history of human origins but clearly many of the pages remain to be filled in. We may be absolved of their extinction – indeed we may in a sense have rescued them from extinction by preserving 30% or so of their genome. And their DNA has in a very real sense brought Neanderthals back to life. George Church, a high profile geneticist at Harvard University, has even suggested, perhaps tongue in cheek, that we should do so, or at least bring their cells to life in the culture dish.

But there’s no doubt that Neanderthals live large in our imagination. Dozens of men have written to Pääbo claiming to be full Neanderthals. The only women to have written to him have done so to say that they thought their husbands were Neanderthals as well.