Early Humans Slept Around with More than Just Neanderthals

Early Humans Slept Around with More than Just Neanderthals


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It’s been known for some time that our modern human ancestors interbred with other early hominin groups like the Neanderthals. But it turns out they were even more promiscuous than we thought.

New DNA research has unexpectedly revealed that modern humans (Homo sapiens) mixed, mingled and mated with another archaic human species, the Denisovans, not once but twice—in two different regions of the ancient world.

All we know about the mysterious Denisovans comes from a single set of human fossils found in a cave in the Altai Mountains of Siberia. In 2008, scientists first discovered a bone from a pinky finger in the cave, and concluded it belonged to a previously unknown ancient hominin who lived between 30,000 and 50,000 years ago. They called the species the Denisovans (pronounced “De-NEE-soh-vens”) after the cave where the fossilized finger was found.

After the genome of the finger’s owner, a young girl, was published in 2010, researchers went on to discover traces of the Denisovan ancestry in two groups of modern-day humans. Some Melanesians (who live in Papua New Guinea and other Pacific islands) were found to have around 5 percent of Denisovan ancestry, while some East and South Asians have around 0.2 percent. One particular gene mutation, which the Denisovans are thought to have passed to modern Tibetans, allows them to survive at high altitudes.

Researchers assumed the Denisovan ancestry found in Asia was due to migration from Oceania, the larger region containing Melanesia. But recently, scientists from the University of Washington in Seattle stumbled on something surprising: evidence for a second, distinct instance of humans getting hot and heavy with Denisovans.

In their analysis of more than 5,600 whole-genome sequences from individuals from Europe, Asia, the Americas and Oceania, the research team looked for ancient DNA, which stands out due to the larger number of mutations that have developed over hundreds of thousands of years. When they found the ancient genetic information, they compared with Denisovan DNA and Neanderthal DNA to determine its origin.

VIDEO: Neanderthals: Did Cro Magnons, the ancestors of early humans, cause the Neanderthal extinction?

What they found was a distinct set of Denisovan ancestry among some modern East Asians—particularly Han Chinese, Chinese Dai and Japanese—ancestry not found in South Asians or Papuans. According to the study’s findings, published in the journal Cell this week, this Denisovan DNA is actually more closely related to the sample taken from the girl in the Siberian cave.

“Although the Papuans ended up with more Denisovan ancestry, it turns out to be less similar to the sequenced Denisovan,” Sharon Browning, a research professor of biostatistics at the University of Washington School of Public Health and senior author of the study, told New Scientist. “Our research demonstrates that there were at least two distinct populations of Denisovans living in Asia, probably somewhat geographically distant.”

Browning and her colleagues assume that modern humans mixed with the Denisovans shortly after migrating out of Africa, around 50,000 years ago. While they’re not sure of the location, they believe the interbreeding occurred in at least two places: eastern Asia, and further south, in Indonesia or Australia.

While the new study confirms that modern humans interbred at least three times with ancient hominins—once with Neanderthals, and twice with the Denisovans—it also raises the possibility of even more extensive intermixing on the part of our ancient ancestors. As reported in New Scientist, one-quarter of the ancient DNA that the researchers found in living humans didn’t match up with either Denisovan or Neanderthal DNA, suggesting there may be other mystery mates out there to find.


Did Neanderthals have a society?

Neanderthals had sophisticated tools, a playful childhood and a place they could call home.

Published: 01st September, 2020 at 00:00

What do you think of when you read the word “Neanderthal”? Is it clunky cavemen, with tools made of little more than hunks of rock, wandering the landscape aimlessly? Or is it something intriguing, but confusing: another kind of human which you’ve heard gave us some of their DNA, and perhaps weren’t as stupid as long proposed?

In truth, while Neanderthal discoveries are always guaranteed headlines, the things that make it into the media can only convey a fraction of the incredible new understanding archaeologists have produced in the past three decades.

Aside from the fact that some of the most amazing stuff never gets seen outside scientific journals, new findings often come buffed up in press releases, and crucially they lack the Big Picture context.

In reality, our entire view on who and what Neanderthals were has been revolutionised. The seismic discovery that they were our direct ancestors, contributing to somewhere around 2 per cent of the genome to most living humans, happened a decade ago.

Read more about Neanderthals:

That fact has forever changed not only what we know was going on tens of millennia ago – potentially six or more different phases of baby-making – but also how we feel about them. Yet beyond ancient genetics, ‘slow science’ in archaeology has also radically altered understanding of their lives. Years and years of work goes into excavating a site, sometimes going down barely a hand’s breadth in a single season.

Then there’s pain-staking 3D recording by laser, recording and bagging up of finds before they’re digitally immortalised in gigantic databases. And that’s just the fieldwork: once the season is over, a smorgasbord of analytical methods are available that can extract astonishing amounts of information, whatever the object in question. But all this trouble is more than worth it.

In my book Kindred: Neanderthal Life, Love, Death and Art, all the fascinating details that haven’t had so much public attention are teased out and woven together to produce a stunning new view of their lives: a tapestry more rich and varied than we ever dreamed. And one of the biggest transformations has come in what we think Neanderthal society itself might have been like.


We did not invent clothes simply to stay warm

Clothes are not a necessity for everyone, so why do we bother wearing clothes at all?

Stephen Gough likes to be naked so much so, it has cost him his freedom. He has spent a combined total of 10 years in prison for showing too much skin in public, having been arrested multiple times.

Gough, also known as the "naked rambler", prefers to get naked when temperatures warm up. He is not a danger to the public, but when he walked naked from John o'Groats to Lands' End in the UK in 2003, he caused outcries around the country.

Some hunter-gatherer societies still choose to live mostly naked

When he attempted the journey again he was quickly arrested. In prison he was often put into solitary confinement for his refusal to wear clothes.

And yet, nobody can argue with the fact that we are all born, like Gough, without clothes. The difference is that most of us go on to cover up in our public lives.

There are good reasons to do so: in colder climes we would freeze to death without some extra padding, and in intense heat clothing can also shield us from the Sun. However, some hunter-gatherer societies still choose to live mostly naked, which suggests that clothing is not vital for our survival.

So if being naked is so natural, when did our obsession with clothing begin, and why?

Clothes do not fossilise, so we cannot get direct evidence for the time when our early human &ndash "hominin" &ndash ancestors stopped wandering about naked, and started draping their bodies with animal furs and skins.

Instead, anthropologists largely rely on indirect methods to date the origin of clothes. A 2011 study on lice suggested that it was only 170,000 years ago when it all began. Researchers found that head lice and lice that live in our clothes separated at around this time. The idea is that, once we started wearing clothes, some lice started living in them and evolved into a separate species.

Simple protection may not have been the only reason we started wearing clothes

At this time our own species, Homo sapiens, already walked the Earth in Africa. They no longer had much body hair, which had helped more archaic hominins keep warm at night and offered some protection from the heat of the Sun.

It is possible we started wearing clothes to compensate for the loss of fur, says Ian Gilligan of the University of Sydney in Australia.

Several modern-day hunter-gather societies, such as the Nuer people in southern Sudan, wear minimal clothing. This suggests that simple protection may not have been the only reason we started wearing clothes. Conceivably people were beginning to feel "modest" and wanted to cover up, but it is hard to find direct evidence of that.

Historical accounts suggest that other hunter-gatherer societies, such as the Fuegians from South America, wore simple clothes some of the time, but also walked around naked. Perhaps early humans only covered up when it was cold.

Outside of Africa, it is easy to see that clothes were vital to protect against the cold. Another human species, the Neanderthals, walked the Earth in much colder climes, and would certainly have needed to cover up.

Neanderthals existed in Europe long before modern humans arrived. We both evolved from a common ancestor, thought to be Homo heidelbergensis. It follows that, if Neanderthals also wore clothes, clothes were invented more than once and the Neanderthals invented them before we did.

Neanderthals did not have to make tight-fitting clothes that completely covered them up

The two hominin species seem to have had different approaches to clothing. "There does seem to be a distinction between Neanderthal and human [clothes]," says Nathan Wales of the Natural History Museum of Denmark.

In a study published in 2012, Wales estimated that Neanderthals must have covered 70-80% of their bodies during the winter months, in order to successfully live in some of the climates we know they inhabited. To figure this out, Wales compared what modern hunter-gathers wear in different environments, and cross-referenced this with historical climatic conditions.

Modern humans needed to cover themselves up slightly more, up to 90%, Wales argues. This means, he says, that Neanderthals did not have to make tight-fitting clothes that completely covered them up.

We now know a little bit about what type of clothes they might have worn.

The Neanderthals probably donned simple fur cloaks, according to a study published in August 2016. The researchers propose that the typical Neanderthal probably draped the fur of one animal around herself.

Meanwhile, modern humans made clothes that were slightly more complex, perhaps by stitching several pieces together.

The study's lead author Mark Collard, of Simon Fraser University in Burnaby, Canada, realised that modern humans tended to hunt animals that would have helped them make thicker, snugger furs. The wolverine is a prime example. It would have made excellent trimming near the neck or at the edge of sleeves.

Rather than having to evolve the ability to live there, you can simply create better clothing

Collard found that, even today, wolverines are preferentially targeted by groups such as the Inuit. "There was a real desire for those sorts of pelts, and it's something to do with structure of hairs, they don't frost up as badly as other furs," he says. "They are more effective than military cold-weather clothing."

For Wales, these findings confirmed that modern humans behaved differently to Neanderthals. "That technology really helped out humans, they could very quickly go into new habitats," he says. "So rather than having to evolve the ability to live there, you can simply create better clothing."

Despite this, Neanderthals, with their shorter and stockier bodies, were actually better adapted to Europe's colder weather than modern humans. They came to Europe long before we did, while modern humans spent most of their history in tropical African temperatures.

Paradoxically, the fact that Neanderthals were better adapted to the cold may also have contributed to their downfall.

If that sounds like a contradiction, to some extent it is.

Modern humans have leaner bodies, which were much more vulnerable to the cold. As a result, our ancestors were forced to make additional technological advances. "We developed better clothing to compensate, which ultimately gave us the edge when the climate got extremely cold [about] 30,000 years ago," says Gilligan.

We may have learned a thing or two from the Neanderthals

There is archaeological evidence to suggest that humans had better technology for making their garments. We had already developed specialised cutting tools, like blades and eventually needles. These helped us cut animal hide in shapes like rectangles and squares, which could then be joined together.

In contrast, Neanderthals seem only to have had simple scrapers. In 2007, Gilligan proposed that this contributed to their downfall, by leaving them with lower-quality clothes during the coldest periods of the last ice age.

"When they began to struggle, that could be the reason why they went extinct, they didn't have the technology for complex clothing that modern humans had already developed earlier in Africa," says Gilligan.

While modern humans had more sophisticated tools and clothes, Neanderthals were not the dumb brutes once depicted, and there is no reason to believe they were generally less sophisticated than us. They may simply not have needed to cover up completely, and when eventually they did, their technology failed them.

In fact, when it came to preparing animal hides, we may have learned a thing or two from the Neanderthals.

In 2013, a team led by Marie Soressi of the University of Leiden in the Netherlands found that Neanderthals were the first to use tools made out of bone, rather than stone. They did so about 40-60,000 years ago.

These "Lissoir tools" were rib fragments from deer. They were used to work animal hide to make it softer, possibly for clothes.

After the Neanderthals went extinct, similar bone tools turned up at Homo sapiens sites.

"This type of bone tool is very common in the upper Palaeolithic record, so it's very common in any sites used by modern humans after the demise of the Neanderthals," says Soressi. "For me, it's potentially the first evidence of something being transmitted from Neanderthals to modern humans."

Learning the Neanderthals' tricks for dealing with the cold would have been enormously useful for modern humans, who could then combine the bone tools with their other repertoire of tools to make even better clothes.

If this is true, it raises the question of why the Neanderthals did not copy the modern humans' more sophisticated technologies. It may be that modern humans simply found the Neanderthals' bone tools lying around, rather than through actually meeting with Neanderthals.

Humans were probably decorating themselves long before clothes even existed

A little more recently, perhaps around 30,000 years ago, Stone Age clothes became more sophisticated still.

In the Dzudzuana Cave in Georgia, researchers have discovered coloured flax fibres in areas where humans lived. These could have been used to make linen clothes in a range of colours.

This suggests that clothes were becoming more than just useful. They also served decorative purposes. In other words, clothes were becoming symbolic.

Gilligan points out that humans were probably decorating themselves long before clothes even existed. "When you look at contemporary hunter-gatherers who don't use clothing, they decorate themselves brilliantly with body painting. You don't need clothing in order to do that."

There is evidence to suggest that Neanderthals painted themselves with red ochre pigment too, with the oldest evidence dating to over 200,000 years ago. Of course, the pigment might also have been used to tan hides, for ritual burials, or for cave art.

The truth about clothes is more complex than you might have imagined

When it got too cold to show off painted bodies, early humans were forced to cover up. "That decorative function gets transferred onto clothing," proposes Gilligan. "Once that happens, humans need clothing for that social purpose as well as any thermal purpose."

This could explain how the use of clothing has become such an integral aspect to many people's identity. Similarly, a lack of clothing is crucial to the identity of some hunter-gatherer tribes, and to that of the naked rambler.

The truth about clothes is therefore more complex than you might have imagined. Without them we might not have survived, but today we use clothes for more than keeping warm.

They are a part of our identity, our culture and our social norms. Clothes set us apart from other species, and from nature, says Gilligan. What's more, by signaling that we belong to particular social or political groups, they can also set us apart from one another.

Melissa Hogenboom is BBC Earth's feature writer. She is @melissasuzanneh on Twitter.

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Twisted roots

While the analysis completes a few chapters in the Neanderthal story, there are still some cliffhangers. For one, despite the similarity of Neanderthal nuclear DNA though space and time, the mitochondrial DNA from the Hohlenstein-Stadel femur is unlike that of any other Neanderthals yet studied, says study author Stéphane Peyrégne, who conducted this work as part of his Ph.D. research at the Max Planck Institute for Evolutionary Anthropology in Germany.

The mysterious mitochondrial DNA was previously pointed out in a 2017 study in Nature. For this latest work, the team confirmed the accuracy of that analysis and employed numerical tests that showed the genetic variation isn’t just random chance. But they still can’t explain how it happened.

Perhaps it originated from another group of ancient Neanderthals that broke away from the rest of the population long ago. Or perhaps, the researchers posit, the ancestors to ancient humans had a hand in early Neanderthal genetics. Though members of this lengthy European line of Neanderthals are long gone, we know they interbred with the modern humans that left Africa around 55,000 years ago, leaving behind up to two percent Neanderthal DNA in modern people who are not of African descent. (Learn more about the many groups of ancient humans that interbred with us.)

It pieces together some history that we have absolutely no way to piece together in any other form.

But perhaps the opposite also took place, and an earlier group of modern humans passed DNA to Neanderthals. In this case, the modern humans would have bestowed at least two different types of mitochondria to Neanderthals, Prüfer explains. One developed into the sequence found in the Hohlenstein-Stadel femur, while the other gave rise to all other Neanderthal mitochondrial sequences yet found.

This discrepancy in the results between the nuclear and mitochondrial DNA is surprising—but perhaps it shouldn’t be, adds Qiaomei Fu of the Chinese Academy of Sciences in Beijing, who specializes in ancient DNA but was not part of the study team.

“Since this also happened in the Denisovan, with more of this kind of evidence, I think more and more [we’re learning] that admixture in hominin history is quite complex and may have occurred quite often,” Fu says via email.

Even with these lingering mysteries, the latest find continues to refine the story of an ancient human relative that we’ve only recently gotten to know, but that seems more familiar with every fresh discovery.

“I think it changes our perception to a certain degree,” Prüfer says, "to understand that there was really a cousin that might have been not unlike ourselves that . inhabited the same regions that we are living in now.”


Why are we the only human species still alive?

Two million years ago in Africa, several species of human-like creatures roamed the landscape. Some looked surprisingly similar to each other, while others had distinct, defining features.

In September 2015, another species was added to the list. Hundreds of bones discovered in a South African cave are now believed to belong to a new species, known as Homo naledi. There may well be many more extinct hominin species waiting to be uncovered.

Our own species appeared around 200,000 years ago, at a time when several others existed. Yet today, only we remain. Why did we manage to survive when all of our closest relatives have died out?

To start with, it's worth pointing out that extinction is a normal part of evolution. In that sense it may not seem surprising that human-like species &ndash known as "hominins" &ndash have died out.

There is no evidence they were systematically preying on large animals

But it is not obvious that the world only has room for one species of human. Our closest living relatives are the great apes, and there are six species alive today: chimpanzees, bonobos, two species of gorilla and two species of orangutan.

There are some clues that reveal why some of our forebears were more successful than others.

Several million years ago, when a great many hominin species lived side-by-side, they mainly ate plants. "There is no evidence they were systematically preying on large animals," says John Shea of Stony Brook University in New York, US.

But as conditions changed, and hominins moved from the forests and trees to the drier open savannahs, they became increasingly carnivorous.

Until quite recently, we still shared the planet with other early humans

The problem was, the animals they hunted also had fewer plants to eat, so overall there was less food to go around. That competition drove some species extinct.

"As human evolution pushed some members to be more carnivorous, you would expect to see less and less of them," says Shea.

But while the switch to meat-eating clearly took its toll, it did not come close to leaving Earth a one-human planet. Until quite recently, we still shared the planet with other early humans.

Rewind to 30,000 years ago. As well as modern humans, three other hominin species were around: the Neanderthals in Europe and western Asia, the Denisovans in Asia, and the "hobbits" from the Indonesian island of Flores.

The Neanderthals were displaced very soon after modern humans encroached on their habitat

The hobbits could have survived until as recently as 18,000 years ago. They may have been wiped out by a large volcanic eruption, according to geological evidence from the area. Living on one small island will also leave a species more vulnerable to extinction when disaster strikes.

We do not know enough about the Denisovans to even ask why they died out. All we have from them is a small finger bone and two teeth.

However, we know a lot more about the Neanderthals, simply because we have known about them for much longer and have many fossils. So to get at why we are the only human species left standing, we must rely on figuring out why they died out.

The archaeological evidence strongly suggests that the Neanderthals somehow lost out to modern humans, says Jean-Jacques Hublin of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. The Neanderthals were displaced very soon after modern humans encroached on their habitat, which Hublin says can't be a coincidence.

Neanderthals were better adapted to hunting in woodland environments than modern humans

Neanderthals evolved long before us, and lived in Europe well before we arrived. By the time we got to Europe, just over 40,000 years ago, Neanderthals had been successfully living there for over 200,000 years, ample time to adapt to the chilly climate. They wore warm clothes, were formidable hunters and had sophisticated stone tools.

But when Europe began experiencing rapid climate change, some researchers argue, the Neanderthals may have struggled.

The temperature was not the main issue, says John Stewart of Bournemouth University in the UK. Instead, the colder climate changed the landscape they lived in, and they did not adapt their hunting style to suit it.

Neanderthals were better adapted to hunting in woodland environments than modern humans.

But when Europe's climate began fluctuating, the forests became more open, becoming more like the African savannahs that modern humans were used to. The forests, which provided most of Neanderthals' food, dwindled and could no longer sustain them.

Modern humans also seemed to hunt a greater range of species.

As well as large game, they also hunted smaller animals like hares and rabbits.

In contrast, there is little evidence that Neanderthals hunted similar small ground mammals according to analyses of archaeological sites in Iberia where the Neanderthals clung on the longest.

We had a greater range of innovative and deadly tools

Their tools were better suited for hunting bigger animals, so even if they tried, they may not have been successful at catching small animals. Though there is evidence they ate birds, they may have lured them in with the remains of other dead animal carcasses, rather than actively hunting them in the sky.

All in all, "modern humans seemed to have a greater number of things they could do when put under stress," says Stewart. This ability to innovate and adapt may explain why we replaced Neanderthals so quickly.

"Faster innovation leads to better efficiency and exploitation in the environment and therefore a higher reproductive success," says Hublin.

He believes that there is something intrinsic to modern humans that helped us adapt so quickly. There is some evidence for that.

We know Neanderthal tools were remarkably efficient for the tasks they used them for, but when we arrived into Europe ours were better. The archaeological evidence suggests that we had a greater range of innovative and deadly tools.

But tools are not the only things modern humans made. We also created something else, which helped us outcompete every other species on Earth: symbolic art.

Our extinct relatives may have been able to speak

Genetic analysis suggests that Neanderthals and Denisovans both had the capacity for language. They carried the genes that allow us to finely control how our tongues move.

However, our heads were shaped differently to theirs, says Shea. That suggests we are better at making certain sounds.

Our face is situated directly under our brain, allowing us to break up sounds in short segments.

In contrast, Neanderthals and other ancient hominins had their faces further to the front of their skulls. "This makes it difficult to sort out particular sounds, like vowels," says Shea.

That does not necessarily mean they could not talk. Instead, it may indicate their language was more like song.

Shortly after modern humans left Africa, there is ample evidence that they were making art. Archaeologists have found ornaments, jewellery, figurative depictions of mythical animals and even musical instruments.

"When modern humans hit the ground [in Europe], their populations went up quickly," says Nicholas Conard at the University of Tübingen in Germany, who has discovered several such relics. As our numbers swelled, we began living in much more complex social units, and needed more sophisticated ways to communicate.

By 40,000 years ago, humans in Europe were making things any of us would recognise as art. One of the most striking is a wooden carving of a lion-human statue, called the Löwenmensch, found in a cave in Germany. Similar sculptures from the same period have been found elsewhere in Europe.

They didn't need a whole arsenal of symbolic artefacts to get the job done

This suggests that we were sharing information across cultural groups from different areas, rather than keeping knowledge to ourselves. It seems art was a critical part of our identity, helping to bring different groups together.

In other words, symbols were a kind of social glue. They could "help people organise their social and economic affairs with one another," says Conard.

In stark contrast, Neanderthals didn't seem to need art or symbols. There is limited evidence they made some jewellery, but not to the extent we did. "They did their hunting, cooking, sleeping, eating, sex and recreation. They didn't need a whole arsenal of symbolic artefacts to get the job done."

For humans, the sharing of symbolic information has been crucial to our success. Every new idea we pick up has the chance to become immortal by being passed down through the generations. That is how language spread, for example.

They found a rut and were stuck in it

The fact that we made any art at all, using the same hands that made all those tools, also points to our unique capacity for behavioural variability, says Shea.

"We do everything more than one distinct way," he says. "Often, the solutions we devise for one problem, we can repurpose to solve a different one. This is something we do exclusively well."

Other ancient hominins seemed to do the same thing over and over again. "They found a rut and were stuck in it."

Did we have a superior brain to thank for this?

That has long been a popular view. Illustrations of human evolution like the one above often show a progression from ape-like creatures to modern humans, with ever bigger brains as things went on.

Most Europeans only developed a tolerance to lactose when our ancestors started to eat more dairy produce

In reality, our evolutionary story is more complicated than that. Homo erectus survived for a long time and was the first hominin species to expand out of Africa &ndash before even the Neanderthals &ndash but its brain was quite small.

As a result, some anthropologists are uncomfortable with the idea that big brains were the solution. Our big brains may have played a role in our success, but Neanderthals had equally large brains compared to their body size.

Hublin says there is a more refined explanation.

We know that our behaviour, or the circumstances in which we find ourselves, can change our genetic make-up.

There are important differences between us and our Neanderthal and Denisovan relatives

For instance, most Europeans only developed a tolerance to lactose when our ancestors started to eat more dairy produce. Genetic changes can also occur when large populations are faced with devastating diseases such as the Black Death in the 14th Century, which changed the genes of survivors.

In a similar vein, Hublin proposes that modern humans, at some point, benefited from key genetic changes.

For the first 100,000 years of our existence, modern humans behaved much like Neanderthals. then something changed. Our tools became more complex, around the time when we started developing symbolic artefacts.

We now have genetic evidence to suggest that our DNA changed at some point after we split from the common ancestor we shared with Neanderthals.

When peering into our genetic make-up, there are important differences between us and our Neanderthal and Denisovan relatives. Geneticists have identified several dozen points in our genome that are unique to us, and several of them are involved in brain development.

Before we developed these abilities, modern humans and other hominins were fairly evenly matched

This suggests that while Neanderthals may have had a similar brain size to ours, it may have been the way our brains developed over our lifetimes that was key to our success.

We don't know what benefits these genetic changes had. But others have suggested that it is our hyper-social, cooperative brain that sets us apart. From language and culture to war and love, our most distinctively human behaviours all have a social element.

That means it could be our propensity for social living that led to our ability to use symbols and make art.

For tens of thousands of years, before we developed these abilities, modern humans and other hominins were fairly evenly matched, says Conard. Any other species could have taken our place.

But they did not, and eventually we out-competed them. As our population exploded, the other species retreated and eventually disappeared altogether.

If that's true, we might have our creativity to thank for our survival.

But there is one other possibility, which we can't entirely ignore. Maybe it was pure chance. Maybe our species got lucky and survived, while the Neanderthals drew the short straw.

Melissa Hogenboom is BBC Earth's feature writer. She is @melissasuzanneh on Twitter.


Denisovans: Another Human Relative

Scientists have also found DNA from another extinct hominin population: the Denisovans. The only remains of the species that have been found to date are a single fragment of a phalanx (finger bone) and two teeth, all of which date back to about 40,000 years ago (Reich 2010). This species is the first fossil hominin identified as a new species based on its DNA alone. Denisovans are relatives of both modern humans and Neanderthals, and likely diverged from these lineages around 300,000 to 400,000 years ago. You might be wondering: If we have the DNA of Denisovans, why can’t we compare them to modern humans like we do Neanderthals? Why isn’t this article about them too? The answer is simply that we don’t have enough DNA to make a comparison. The three specimen pool of Denisovans found to date is statistically far too small a data set to derive any meaningful comparisons. Until we find more Denisovan material, we cannot begin to understand their full genome in the way that we can study Neanderthals.

Neanderthals and modern humans shared habitats in Europe and Asia

We can study Neanderthal and modern human DNA to see if they interbred with modern humans

We can study the DNA of Neanderthals because we have a large enough Neanderthal sample size (number of individual Neanderthals) to compare to humans


Africans carry surprising amount of Neanderthal DNA

For 10 years, geneticists have told the story of how Neanderthals—or at least their DNA sequences—live on in today’s Europeans, Asians, and their descendants. Not so in Africans, the story goes, because modern humans and our extinct cousins interbred only outside of Africa. A new study overturns that notion, revealing an unexpectedly large amount of Neanderthal ancestry in modern populations across Africa. It suggests much of that DNA came from Europeans migrating back into Africa over the past 20,000 years.

“That gene flow with Neanderthals exists in all modern humans, inside and outside of Africa, is a novel and elegant finding,” says anthropologist Michael Petraglia of the Max Planck Institute for the Science of Human History. The work, reported in this week’s issue of Cell, could also help clear up a mysterious disparity: why East Asians appear to have more Neanderthal ancestry than Europeans.

As members of Homo sapiens spread from Africa into Eurasia some 70,000 years ago, they met and mingled with Neanderthals. Researchers knew that later back-migrations of Europeans had introduced a bit of Neanderthal DNA into African populations, but previous work suggested it was a just a smidgen. In contrast, modern Europeans and East Asians apparently inherited about 2% of their DNA from Neanderthals.

Previous efforts simply assumed that Africans largely lacked Neanderthal DNA. To get more reliable numbers, Princeton University evolutionary biologist Joshua Akey compared the genome of a Neanderthal from Russia’s Altai region in Siberia, sequenced in 2013, to 2504 modern genomes uploaded to the 1000 Genomes Project, a catalog of genomes from around the world that includes five African subpopulations. The researchers then calculated the probability that each stretch of DNA was inherited from a Neanderthal ancestor.

The researchers found that African individuals on average had significantly more Neanderthal DNA than previously thought—about 17 megabases (Mb) worth, or 0.3% of their genome. They also found signs that a handful of Neanderthal genes may have been selected for after they entered Africans’ genomes, including genes that boost immune function and protect against ultraviolet radiation.

The results jibe with as-yet-unpublished work by Sarah Tishkoff, an evolutionary geneticist at the University of Pennsylvania. She told Science she has also found higher-than-expected levels of apparent Neanderthal DNA in Africans.

The best fit model for where Africans got all this Neanderthal DNA suggests about half of it came when Europeans—who had Neanderthal DNA from previous matings—migrated back to Africa in the past 20,000 years. The model suggests the rest of the DNA shared by Africans and the Altai Neanderthal might not be Neanderthal at all: Instead, it may be DNA from early modern humans that was simply retained in both Africans and Eurasians—and was picked up by Neanderthals, perhaps when moderns made a failed migration from Africa to the Middle East more than 100,000 years ago.

Akey’s study might help explain another “head scratcher,” says computer biologist Kelley Harris of the University of Washington, Seattle. Studies had suggested East Asians have 20% more Neanderthal DNA than Europeans, she notes. “Europe is where Neanderthal remains are found, so why wouldn’t Europeans have more Neanderthal ancestry than any other group?”

By suggesting that Europeans introduced Neanderthal sequences into Africa, the new study points to an explanation: Researchers previously assumed that Neanderthal sequences shared by Europeans and Africans were modern and subtracted them out. After correcting for that bias, the new study found similar amounts of Neanderthal DNA in Europeans and Asians—51 and 55 Mb, respectively. It’s a “convincing and elegant” explanation, Harris says.


RELATED ARTICLES

An international team of researchers have revealed the first genetic evidence of a scenario in which early modern humans left the African continent and mixed with now-extinct members of the human family in the Near East.

DO ALL NEANDERTHALS HAVE DNA FROM MODERN HUMANS?

The study has revealed modern humans passed their genes to the Neanderthal population.

Modern humans and Neanderthals cross-bred on at least two separate occasions, 100,000 years ago and around 50,000 years ago.

But the findings only comes from one Neanderthal bone found in Russia.

Neanderthal remains found in Croatia and north Spain showed no fragments of Homo sapien DNA, showing they did not breed with early humans.

'Perhaps these Neanderthal groups did not coincide with H. sapiens, or, if they did, they did not have any offspring' said CSIC researcher, Carles Lalueza.

And astonishingly, this was before our ancestors are thought to have made the mass migration 'out of Africa' less than 65,000 years ago.

Antonio Rosas, of the Spanish Natural Science Museum, said: 'Over 100,000 years ago, anatomically modern humans ventured out of Africa for the first time.

'These modern humans met and interbred with a group of Neanderthals, which later may have moved to the south of modern day Siberia, carrying the genes of Homo sapiens.'

The finding, reported in the journal Nature, puts back the previously first-known case of a human-Neanderthal hybrid produced by the two species by 50,000 years.

'It's been known for several years, following the first sequencing of the Neanderthal genome in 2010, that Neanderthals and humans must have interbred,' quantitative biologist Professor Adam Siepel of Cold Spring Harbor Laboratory (CSHL) explained.

'But the data so far refers to an event dating to around 47,000 to 65,000 years ago, around the time that human populations emigrated from Africa.

This diagram shows the scenario of interbreeding between humans and Neanderthals. Neanderthal DNA in present-day humans outside Africa originates from interbreeding that occurred 47,000 - 65,000 years ago (green arrow). Modern human DNA is likely a consequence of earlier contact 100,000 years ago (red arrow)

The modern human ancestor who contributed genes to this particular Neanderthal individual (dorsal bone pictured) known as the Altai Neanderthal must have migrated out of Africa long before the main migration that led Homo sapiens into Europe and Asia 60,000 years ago, the scientists claimed

WHAT DO THE FINDINGS MEAN FOR MIGRATION MODELS?

Antonio Rosas, of the Spanish Natural Science Museum, said: 'These discoveries have direct implications on the evolutionary model.'

For decades experts have known that there was an early migration of H. sapiens out of Africa, because of the remains that were found at the archaeological sites at Skhul and Qafzeh in Israel.

But without palaeontological data, this movement was seen as a failed attempt at migration, since it went no farther than the Near East.

This study adds to evidence supporting an early migration out of Africa, some 200,000 years ago, such as the presence of Homo sapiens in China around 100,000 years ago.

Likewise, stone tools found in the south of the Arabian Peninsula have been attributed to this early H. sapiens journey out of Africa.

Both pieces of evidence could well tie in with those modern humans who passed their genes on to the branch of Neanderthals who migrated east.

'The event we found appears considerably older than that event.'

Professor Siepel added: 'One very interesting thing about our finding is that it shows a signal of breeding in the 'opposite' direction from that already known.

'That is, we show human DNA in a Neanderthal genome, rather than Neanderthal DNA in human genomes.'

The team of experts from Cold Spring Harbor Laboratory (CSHL), Spanish National Research Council (CSIC) Cornell University and the Max Plank Institute for Evolutionary Anthropology, used several kinds of computer modelling algorithms to compare the complete genomes of hundreds of contemporary humans with complete and partial genomes of four archaic humans.

Contemporary Europeans, Eurasians and Asians, carry two per cent genetic sequences from Neanderthals, which is proof of interbreeding that followed the 'out of Africa' human migration some 60,000 years ago.

This implies children born from Neanderthal-modern human pairings outside of Africa were raised among the modern humans and ultimately bred with other humans, explaining how fragments of Neanderthal DNA remain in human genomes.

Contemporary Africans, however, do not have detectable traces of Neanderthal DNA in their genomes.

This indicates that whatever sexual contact between modern humans and Neanderthals occurred among humans who had already left the African continent.

'It's been known for several years, following the first sequencing of the Neanderthal genome in 2010, that Neanderthals [illustrated with a museum model] and humans must have interbred,' quantitative biologist Professor Adam Siepel of Cold Spring Harbor Laboratory (CSHL) explained

THE 'OUT OF AFRICA' THEORY AND THE ROUTE TAKEN

The first modern humans to arrive in Europe and Asia migrated north out of Egypt around 55,000 years ago, according to a study published in May last year.

It answers a long-standing question about the route early Homo sapiens took when spreading from the African continent.

It also shows most Europeans and Asians living today are more closely related genetically to people living in Egypt than in Ethiopia.

This suggests Egypt was the last stop for people migrating out of Africa 55,000 years ago rather than taking a more southerly route through Ethiopia.

Some scientists believed that humans may have travelled from Ethiopia across the Bab el Mandeb strait to the Arabian Peninsula.

However, the new research suggests a northern route from Egypt, through the Sinai Peninsula and then out into Asia and Europe was the most likely route.

The findings also support evidence that these first humans to leave Africa came into contact with Neanderthals in the Levant at the time.

Dr Toomas Kivisild, an anthropologist at the University of Cambridge who lead the study, said the results ‘paint a clear picture in which the main migration out of Africa followed a Northern, rather than a Southern route'

But the team's evidence of 'gene flow' from descendants of modern humans into the Neanderthal genome applies to one specific Neanderthal, whose remains were found some years ago in a cave in south western Siberia, in the Altai Mountains, near the Russia-Mongolia border.

The modern human ancestor who contributed genes to this particular Neanderthal individual – known as the Altai Neanderthal from a tiny toe bone fragment - must have migrated out of Africa long before the main migration that led Homo sapiens into Europe and Asia 60,000 years ago, the scientists claimed.

In contrast, two Neanderthals from European caves that were sequenced for this study - one from Croatia, another from Spain - both lack DNA derived from ancestors of modern humans, indicating there was no early interbreeding event.

In contrast, two Neanderthals from European caves that were sequenced for this study - one from Croatia, another from Spain - both lack DNA derived from ancestors of modern humans, indicating there was no early interbreeding event. A stock image of a Neanderthal skull is shown above

ARE NEANDERTHALS TO BLAME FOR MODERN DISEASES?

Neanderthals and modern humans are thought to have co-existed for thousands of years and interbred, meaning Europeans now have roughly two per cent Neanderthal DNA.

These 'legacy' genes have been linked to an increased risk from cancer and diabetes by new studies looking at our evolutionary history.

However, some genes we inherited could have also improved our immunity to other diseases.

Scientists have found that part of our HLA system, which helps white blood cells to identify and destroy foreign material in the body, could have come from Neanderthals.

Other researchers suggest humans outside Africa are more vulnerable to Type 2 Diabetes because they interbred with Neanderthals.

Researchers from Oxford and Plymouth universities have also found that genes thought to be risk factors in cancer were present in the Neanderthal genome.

A gene that can cause diabetes in Latin Americans is believed to have come from Neanderthals, long before their ancestors colonised the New World.

Another recent genetic study by scientists at the University at Buffalo has suggested that Neanderthals may have suffered from psoriasis and Crohn's disease, a condition that affects the digestive system.

The team also analysed the DNA of another archaic human relative - a Denisovan individual - whose remains were found in the same cave in the Altai Mountains as the Altai Neanderthal.

Denisovans, like Neanderthals, are members of the human line that eventually became extinct.

The Denisovan's genome showed no traces of modern human DNA unlike, Neanderthal found in the same cave.

These findings do not mean modern human ancestors never mated with Denisovans or European Neanderthals, but Professor Siepel said 'the signal we're seeing in the Altai Neanderthal probably comes from an interbreeding event that occurred after this Neanderthal lineage diverged from its archaic cousins, a little more than 100,000 years ago.'

It is possible a group of modern human ancestors from Africa separated early from other humans, at a time when present-day African populations diverged from one another, around 200,000 years ago.

The researchers suggest there must therefore have been a long lag between the time when this group branched off the modern human family tree, roughly 200,000 years ago, and the time they left their genetic mark in the Altai Neandertal, about 100,000 years ago.

The group were then lost to extinction.

Martin Kuhlwilm of the Max Plank Institute for Evolutionary Anthropology said the team focused on the genomes of contemporary individuals from five populations across Africa to identify mutations which most of them have in common.

This was the data that provided evidence of 'regions in the Altai Neanderthal genome that carry mutations observed in the Africans - but not in the Denisovan' or in Neanderthals found in European caves.

Professor Sipel added: 'This is consistent with the scenario of gene flow from a population closely related to modern humans into the Altai Neanderthal.

'After ruling out contamination of DNA samples and other possible sources of error, we are not able to explain these observations in any other way.'

WHO WERE THE DENISOVANS?

A finger bone from the Denisova 3 find

The Denisovans are an extinct species of human that appear to have lived in Siberia and even down as far as southeast Asia.

Although remains of these mysterious early humans have only been discovered at one site - the Denisova Cave in the Altai Mountains in Siberia, DNA analysis has shown they were widespread.

DNA from these early humans has been found in the genomes of modern humans over a wide area of Asia, suggesting they once covered a vast range.

They are thought to have been a sister species of the Neanderthals, who lived in western Asia and Europe at around the same time.

The two species appear to have separated from a common ancestor around 200,000 years ago, while they split from the modern human Homo sapien lineage around 600,000 years ago.

Bone and ivory beads found in the Denisova Cave were discovered in the same sediment layers as the Denisovan fossils, leading to suggestions they had sophisticated tools and jewellery.

Professor Chris Stringer, an anthropologist at the Natural History Museum in London, said: 'Layer 11 in the cave contained a Denisovan girl's fingerbone near the bottom but worked bone and ivory artefacts higher up, suggesting that the Denisovans could have made the kind of tools normally associated with modern humans.

'However, direct dating work by the Oxford Radiocarbon Unit reported at the ESHE meeting suggests the Denisovan fossil is more than 50,000 years old, while the oldest 'advanced' artefacts are about 45,000 years old, a date which matches the appearance of modern humans elsewhere in Siberia.'


Sleeping with the Enemy

Svante Pääbo’s genome-sequencing project hopes to point up the differences that enabled humans, unlike the Neanderthals, with whom they interbred, to build complex societies. Art by ATELIER DAYNÈS PHOTOGRAPH: S. ENTRESSANGLE

The Max Planck Institute for Evolutionary Anthropology, in Leipzig, is a large, mostly glass building shaped a bit like a banana. The institute sits at the southern edge of the city, in a neighborhood that still very much bears the stamp of its East German past. If you walk down the street in one direction, you come to a block of Soviet-style apartment buildings in the other, to a huge hall with a golden steeple, which used to be known as the Soviet Pavilion. (The pavilion is now empty.) In the lobby of the institute there’s a cafeteria and an exhibit on great apes. A TV in the cafeteria plays a live feed of the orangutans at the Leipzig Zoo.

Svante Pääbo heads the institute’s department of evolutionary genetics. He is tall and lanky, with a long face, a narrow chin, and bushy eyebrows, which he often raises to emphasize some sort of irony. Pääbo’s office is dominated by a life-size model of a Neanderthal skeleton, propped up so that its feet dangle over the floor, and by a larger-than-life-size portrait that his graduate students presented to him on his fiftieth birthday. Each of the students painted a piece of the portrait, the over-all effect of which is a surprisingly good likeness of Pääbo, but in mismatched colors that make it look as if he had a skin disease.

At any given moment, Pääbo has at least half a dozen research efforts in progress. When I visited him in May, he had one team analyzing DNA that had been obtained from a forty- or fifty-thousand-year-old finger bone found in Siberia, and another trying to extract DNA from a cache of equally ancient bones from China. A third team was slicing open the brains of mice that had been genetically engineered to produce a human protein.

In Pääbo’s mind, at least, these research efforts all hang together. They are attempts to solve a single problem in evolutionary genetics, which might, rather dizzyingly, be posed as: What made us the sort of animal that could create a transgenic mouse?

The question of what defines the human has, of course, been kicking around since Socrates, and probably a lot longer. If it has yet to be satisfactorily resolved, then this, Pääbo suspects, is because it has never been properly framed. “The challenge is to address the questions that are answerable,” he told me.

Pääbo’s most ambitious project to date, which he has assembled an international consortium to assist him with, is an attempt to sequence the entire genome of the Neanderthal. The project is about halfway complete and has already yielded some unsettling results, including the news, announced by Pääbo last year, that modern humans, before doing in the Neanderthals, must have interbred with them.

Once the Neanderthal genome is complete, scientists will be able to lay it gene by gene—indeed, base by base—against the human, and see where they diverge. At that point, Pääbo believes, an answer to the age-old question will finally be at hand. Neanderthals were very closely related to modern humans—so closely that we shared our prehistoric beds with them—and yet clearly they were not humans. Somewhere among the genetic disparities must lie the mutation or, more probably, mutations that define us. Pääbo already has a team scanning the two genomes, drawing up lists of likely candidates.

“I want to know what changed in fully modern humans, compared with Neanderthals, that made a difference,” he said. “What made it possible for us to build up these enormous societies, and spread around the globe, and develop the technology that I think no one can doubt is unique to humans. There has to be a genetic basis for that, and it is hiding somewhere in these lists.”

Pääbo, who is now fifty-six, grew up in Stockholm. His mother, a chemist, was an Estonian refugee. For a time, she worked in the laboratory of a biochemist named Sune Bergström, who later won a Nobel Prize. Pääbo was the product of a lab affair between the two, and, although he knew who his father was, he wasn’t supposed to discuss it. Bergström had a wife and another son Pääbo’s mother, meanwhile, never married. Every Saturday, Bergström would visit Pääbo and take him for a walk in the woods, or somewhere else where he didn’t think he’d be recognized.

“Officially, at home, he worked on Saturday,” Pääbo told me. “It was really crazy. His wife knew. But they never talked about it. She never tried to call him at work on Saturdays.” As a child, Pääbo wasn’t particularly bothered by the whole arrangement later, he occasionally threatened to knock on Bergström’s door. “I would say, ‘You have to tell your son—your other son—because he will find out sometime,’ ” he recalled. Bergström would promise to do this, but never followed through. (As a result, Bergström’s other son did not learn that Pääbo existed until shortly before Bergström’s death, in 2004.)

From an early age, Pääbo was interested in old things. He discovered that around fallen trees it was sometimes possible to find bits of pottery made by prehistoric Swedes, and he filled his room with potsherds. When he was a teen-ager, his mother took him to visit the Pyramids, and he was entranced. He enrolled at Uppsala University, planning to become an Egyptologist.

“I really wanted to discover mummies, like Indiana Jones,” he said. Mostly, though, the coursework turned out to involve parsing hieroglyphics, and instead of finding it swashbuckling Pääbo thought it was boring. Inspired by his father, he switched first to medicine, then to cell biology.

In the early nineteen-eighties, Pääbo was doing doctoral research on viruses when he once again began fantasizing about mummies. At least as far as he could tell, no one had ever tried to obtain DNA from an ancient corpse. It occurred to him that if this was possible, then a whole new way of studying history would open up.

Suspecting that his dissertation adviser would find the idea silly (or worse), Pääbo conducted his mummy research in secret, at night. With the help of one of his former Egyptology professors, he managed to obtain some samples from the Egyptian Museum in what was then East Berlin. In 1984, he published his results in an obscure East German journal. He had, he wrote, been able to detect DNA in the cells of a mummified child who’d been dead for more than two thousand years. Among the questions that Pääbo thought mummy DNA could answer were what caused pharaonic dynasties to change and who Tutankhamun’s mom was.

While Pääbo was preparing a version of his mummy paper for publication in English, a group of scientists from the University of California at Berkeley announced that they had succeeded in sequencing a snippet of DNA from a zebralike animal known as a quagga, which had been hunted to extinction in the eighteen-eighties. (The DNA came from a hundred-and-forty-year-old quagga hide preserved at the National History Museum in Mainz.) The leader of the team, Allan Wilson, was an eminent biochemist who had, among other things, come up with a way to study evolution using the concept of a “molecular clock.” Pääbo sent Wilson the galleys of his mummy paper. Impressed, Wilson replied asking if there was any space in Pääbo’s lab he might like to spend a sabbatical there. Pääbo had to write back that he could not offer Wilson space in his lab, because, regrettably, he didn’t have a lab—or even, at that point, a Ph.D.

Pääbo’s mummy paper became the cover article in Nature. It was also written up in the Times, which called his achievement “the most dramatic of a series of recent accomplishments using molecular biology.” Pääbo’s colleagues in Sweden, though, remained skeptical. They urged him to forget about shrivelled corpses and stick to viruses.

“Everybody told me that it was really stupid to leave that important area for something which looked like a hobby of some sort,” he said. Ignoring them, Pääbo moved to Berkeley, to work for Wilson.

“He just kind of glided in,” Mary-Claire King, who had also been a student of Wilson’s, and who is now a professor of genome sciences at the University of Washington, recalled. According to King, Pääbo and Wilson, who died in 1991, turned out to share much more than an interest in ancient DNA.

“Each of them thought of very big ideas,” she told me. “And each of them was very good at translating those ideas into testable hypotheses. And then each of them was very good at developing the technology that’s necessary to test the hypotheses. And to have all three of those capacities is really remarkable.” Also, although “they were both very data-driven, neither was afraid to say outrageous things about their data, and neither was afraid to be wrong.”

DNA is often compared to a text, a comparison that’s apt as long as the definition of “text” encompasses writing that doesn’t make sense. DNA consists of molecules known as nucleotides knit together in the shape of a ladder—the famous double helix. Each nucleotide contains one of four bases: adenine, thymine, guanine, and cytosine, which are designated by the letters A, T, G, and C, so that a stretch of the human genome might be represented as ACCTCCTCTAATGTCA. (This is an actual sequence, from chromosome 10 the comparable sequence in an elephant is ACCTCCCCTAATGTCA.) The human genome is three billion bases—or, really, base pairs—long. As far as can be determined, most of it is junk.

“Your mother and I are separating because I want what’s best for the country and your mother doesn’t.”

With the exception of red blood cells, every cell in an organism contains a complete copy of its DNA. It also contains many copies—hundreds to thousands—of an abridged form of DNA known as mitochondrial DNA, or mtDNA. But as soon as the organism dies the long chains of nucleotides begin to break down. Much of the damage is done in the first few hours, by enzymes inside the creature’s own body. After a while, all that remains is snippets, and after a longer while—how long seems to depend on the conditions of decomposition—these snippets, too, disintegrate. “Maybe in the permafrost you could go back five hundred thousand years,” Pääbo told me. “But it’s certainly on this side of a million.” Five hundred thousand years ago, the dinosaurs had been dead for more than sixty-four million years, so the whole “Jurassic Park” fantasy is, sadly, just that. On the other hand, five hundred thousand years ago modern humans did not yet exist.

When Pääbo arrived in California, he was still interested in finding a way to use genetics to study human history. He’d discovered, however, a big problem with trying to locate fragments of ancient Egyptian DNA: they look an awful lot like—indeed, identical to—fragments of contemporary human DNA. Thus a single microscopic particle of his own skin, or of someone else’s, even some long-dead museum curator’s, could nullify months of work.

“It became clear that human contamination was a huge problem,” he explained. (Eventually, Pääbo concluded that the sequences he had obtained for his original mummy paper had probably been corrupted in this way.) As a sort of warmup exercise, he began working on extinct animals. He analyzed scraps of mtDNA from giant ground sloths, which disappeared about twelve thousand years ago, and from mammoths, which vanished around the same time, and from Tasmanian tigers, which were hunted to extinction by the nineteen-thirties. He extracted mtDNA from moas, the giant flightless birds that populated New Zealand before the arrival of the Maori, and found that moas were more closely related to birds from Australia than to kiwis, the flightless birds that inhabit New Zealand today. “That was a blow to New Zealand self-esteem,” he recalled. He also probed plenty of remains that yielded no usable DNA, including bones from the La Brea tar pits and fossilized insects preserved in amber. In the process of this work, Pääbo more or less invented the field of paleogenetics.

“Frankly, it was a problem that I wouldn’t have tackled myself, because I thought it was too difficult,” Maynard Olson, an emeritus professor at the University of Washington and one of the founders of the Human Genome Project, told me. “Pääbo brought very high standards to this area, and took the field of ancient DNA study from its ‘Jurassic Park’ origins to a real science, which is a major accomplishment.”

“There’s nothing unique about most of science,” Ed Green, a professor of biomolecular engineering at the University of California at Santa Cruz who works on the Neanderthal Genome Project, said. “If you don’t do it, somebody else is going to do it a few months later. Svante is one of the rare people in science for whom that is not true. There wouldn’t even be a field of ancient DNA as we know it without him.”

“It’s a nice rarity in science when people take not only unique but also productive paths,” Craig Venter, who led a rival effort to the Human Genome Project, told me. “And Svante has clearly done both. I have immense respect for him and what he’s done.”

While Pääbo was living in California, he sometimes went to Germany to visit a woman who was attending graduate school at the University of Munich. “I had many relationships with men, but I also had girlfriends now and again,” he told me. The relationship ended shortly afterward, the University of Munich offered Pääbo an assistant professorship. With no pressing reason to move to Germany, he demurred. The offer was increased to a full professorship: “So then I said, ‘Germany isn’t that bad after all. I’ll go there for a few years.’ ”

Pääbo was still in Munich several years later when he got a call from the Rhenish State Museum, in Bonn. The museum houses the bones of the first Neanderthal to be identified as such, which was discovered in the summer of 1856. What did Pääbo think the odds were that he could extract usable DNA? He had no way of determining what kind of shape the bones were in until he dissolved them.

“I didn’t know what to tell them, so I said, ‘There’s a five-per-cent chance that it works,’ ” he recalled. A few months later, he received a small chunk of the Neanderthal’s right humerus.

The first Neanderthal was found in a limestone cave about forty-five miles north of Bonn, in an area known as the Neander Valley, or, in German, das Neandertal. Although the cave is gone—the limestone was long ago quarried into building blocks—the area is now a sort of Neanderthal theme park, with its own museum, hiking trails, and a garden planted with the kinds of shrubs that would have been encountered during an ice age. In the museum, Neanderthals are portrayed as kindly, if not particularly telegenic, humans. By the entrance to the building, there’s a model of an elderly Neanderthal leaning on a stick. He is smiling benignantly and resembles an unkempt Yogi Berra. Next to him is one of the museum’s most popular attractions—a booth called the Morphing-Station. For three euros, visitors to the station can get a normal profile shot of themselves and, facing that, a second shot that has been doctored. In the second, the chin recedes, the forehead slopes, and the back of the head bulges out. Kids love to see themselves—or, better yet, their siblings—morphed into Neanderthals. They find it screamingly funny.

When the first Neanderthal bones showed up in the Neander Valley, they were treated as rubbish (and almost certainly damaged in the process). The fragments—a skullcap, four arm bones, two thighbones, and part of a pelvis—were later salvaged by a local businessman, who, thinking they belonged to a cave bear, passed them on to a fossil collector. The fossil collector realized that he was dealing with something much stranger than a bear. He declared the remains to be traces of a “primitive member of our race.”

As it happened, this was right around the time that Darwin published “On the Origin of Species,” and the fragments soon got caught up in the debate over the origin of humans. Opponents of evolution insisted that they belonged to an ordinary person. One theory held that it was a Cossack who had wandered into the region in the tumult following the Napoleonic Wars. The reason the bones looked odd—Neanderthal femurs are distinctly bowed—was that the Cossack had spent too long on his horse. Another attributed the remains to a man with rickets: the man had been in so much pain from his disease that he’d kept his forehead perpetually tensed—hence the protruding brow ridge. (What a man with rickets and in constant pain was doing climbing into a cave was never really explained.)

Over the next decades, bones resembling those from the Neander Valley—thicker than those of modern humans, with strangely shaped skulls—were discovered at several more sites, including two in Belgium and one in France. Meanwhile, a skull that had been unearthed years earlier in Gibraltar was shown to look much like the one from Germany. Clearly, all these remains could not be explained by stories of disoriented Cossacks or rachitic spelunkers. But evolutionists, too, were perplexed by them. Neanderthals had very large skulls—larger, on average, than people today. This made it hard to fit them into an account of evolution that started with small-brained apes and led, through progressively bigger brains, up to humans. In “The Descent of Man,” which appeared in 1871, Darwin mentioned Neanderthals only in passing. “It must be admitted that some skulls of very high antiquity, such as the famous one of Neanderthal, are well developed and capacious,” he noted.

In 1908, a nearly complete Neanderthal skeleton was discovered in a cave near La Chapelle-aux-Saints, in southern France. The skeleton was sent to a paleontologist named Marcellin Boule, at Paris’s National Museum of Natural History. In a series of monographs, Boule invented what might be called the cartoon version of the Neanderthals—bent-kneed, hunched over, and brutish. Neanderthal bones, Boule wrote, displayed a “distinctly simian arrangement,” while the shape of their skulls indicated “the predominance of functions of a purely vegetative or bestial kind.” Boule’s conclusions were studied and then echoed by many of his contemporaries the British anthropologist Sir Grafton Elliot Smith, for instance, described Neanderthals as walking with “a half-stooping slouch” upon “legs of a peculiarly ungraceful form.” (Smith also claimed that Neanderthals’ “unattractiveness” was “further emphasized by a shaggy covering of hair over most of the body,” although there was—and still is—no clear evidence that they were hairy.)

In the nineteen-fifties, a pair of anatomists, Williams Straus and Alexander Cave, decided to reëxamine the skeleton from La Chapelle. What Boule had taken for the Neanderthal’s natural posture, Straus and Cave determined, was probably a function of arthritis. Neanderthals did not walk with a slouch, or with bent knees. Indeed, given a shave and a new suit, the pair wrote, a Neanderthal probably would attract no more attention on a New York City subway “than some of its other denizens.” More recent scholarship has tended to support the idea that Neanderthals, if not quite up to negotiating the I.R.T., certainly walked upright, with a gait we would recognize more or less as our own. The version of Neanderthals offered by the Neanderthal Museum—another cartoon—is imbued with cheerful dignity. Neanderthals are presented as living in tepees, wearing what look like leather yoga pants, and gazing contemplatively over the frozen landscape. “Neanderthal man was not some prehistoric Rambo,” one of the display tags admonishes. “He was an intelligent individual.”

Pääbo announced his plan to sequence the entire Neanderthal genome in July, 2006, just in time for the hundred-and-fiftieth anniversary of the Neanderthal’s discovery. The announcement was made together with an American company, 454 Life Sciences, which had developed a so-called “high throughput” sequencing machine that, with the help of tiny resin spheres, could replicate tens of thousands of DNA snippets at a time. Both inside and outside the genetics profession, the plan was viewed as wildly ambitious, and the project made international news. “A STUDY WITH A LOT OF BALLS,” the headline in The Economist declared.

By this point, a complete version of the human genome had been published. So, too, had versions of the chimpanzee, mouse, and rat genomes. But humans, chimps, mice, and rats are all living organisms, while Neanderthals have been extinct for thirty thousand years. The first hurdle was simply finding enough Neanderthal DNA to sequence. The chunk of the original Neanderthal that Pääbo had received had yielded shreds of genetic information, but nowhere near the quantities needed to assemble—or reassemble—an entire genome. So Pääbo was placing his hopes on another set of bones, from Croatia. (The Croatian bones turned out to have belonged to three individuals, all of them women the original Neanderthal was probably a man.)

“I wish I had that kind of energy.”

Toward the end of 2006, Pääbo and his team reported that, using a piece of Croatian bone, they had succeeded in sequencing a million base pairs of the Neanderthal genome. (Just like the human genome, the full Neanderthal genome consists of roughly three billion base pairs.) Extrapolating from this, they estimated that to complete the project would take roughly two years and six thousand “runs” on a 454 Life Sciences machine. But later analysis revealed that the million base pairs had probably been contaminated by human DNA, a finding that led some geneticists to question whether Pääbo had rushed to publish results that he should have known were wrong. Meanwhile, subsequent bones yielded a much lower proportion of Neanderthal DNA and a much higher percentage of microbial DNA. (Something like eighty per cent of the DNA that has been sequenced for the Neanderthal Genome Project belongs to microorganisms and, as far as the project is concerned, is useless.) This meant the initial estimates of the labor involved in finishing the genome were probably far too low. “There were times when one despaired,” Pääbo told me. No sooner would one problem be resolved than another materialized. “It was an emotional roller coaster,” Ed Green, the biomolecular engineer from Santa Cruz, recalled.

About two years into the project, a new puzzle arose. Pääbo had assembled an international team to help analyze the data the sequencing machines were generating—essentially, long lists of A’s, T’s, G’s, and C’s. Sifting through the data, one of the members of this team, David Reich, a geneticist at Harvard Medical School, noticed something odd. The Neanderthal sequences, as expected, were very similar to human sequences. But they were more similar to some humans than to others. Specifically, Europeans and Asians shared more DNA with Neanderthals than did Africans. “We tried to make this result go away,” Reich told me. “We thought, This must be wrong.”

For the past twenty-five years or so, the study of human evolution has been dominated by the theory known in the popular press as “Out of Africa” and in academic circles as the “recent single-origin” or “replacement” hypothesis. This theory holds that all modern humans are descended from a small population that lived in Africa roughly two hundred thousand years ago. (Not long before he died, Pääbo’s adviser Allan Wilson developed one of the key lines of evidence for the theory, based on a comparison of mitochondrial DNA from contemporary humans.) Around a hundred and twenty thousand years ago, a subset of the population migrated into the Middle East, and by fifty thousand years ago a further subset pushed into Eurasia. As they moved north and east, modern humans encountered Neanderthals and other so-called “archaic humans,” who already inhabited those regions. The modern humans “replaced” the archaic humans, which is a nice way of saying they drove them into extinction. This model of migration and “replacement” implies that the relationship between Neanderthals and humans should be the same for all people alive today, regardless of where they come from.

Many members of Pääbo’s team suspected another case of contamination. At various points, the samples had been handled by Europeans perhaps they had got their DNA mixed in with the Neanderthals’. Several tests were run to assess this possibility. The results were all negative. “We kept seeing this pattern, and the more data we got, the more statistically overwhelming it became,” Reich told me. Gradually, the other team members started to come around. In a paper published in Science, in May, 2010, they introduced what Pääbo has come to refer to as the “leaky replacement” hypothesis. (The paper was later voted the journal’s outstanding article of the year, and the team received a twenty-five-thousand-dollar prize.) Before modern humans “replaced” the Neanderthals, they had sex with them. The liaisons produced children, who helped to people Europe, Asia, and the New World.

The leaky-replacement hypothesis—assuming for the moment that it is correct—provides further evidence of the closeness of Neanderthals to modern humans. Not only did the two interbreed the resulting hybrid offspring were functional enough to be integrated into human society. Some of these hybrids survived to have kids of their own, who, in turn, had kids, and so on to the present day. Even now, at least thirty thousand years after the fact, the signal is discernible: all non-Africans, from the New Guineans to the French to the Han Chinese, carry somewhere between one and four per cent Neanderthal DNA.

One of Pääbo’s favorite words in English is “cool.” When he finally came around to the idea that Neanderthals bequeathed some of their genes to modern humans, he told me, “I thought it was very cool. It means that they are not totally extinct—that they live on a little bit in us.”

The Leipzig Zoo lies on the opposite side of the city from the Institute for Evolutionary Anthropology, but the institute has its own lab building on the grounds, as well as specially designed testing rooms inside the ape house, which is known as Pongoland. Since none of our very closest relatives survive (except as little bits in us), researchers have to rely on our next closest kin, chimpanzees and bonobos, and our somewhat more distant cousins—gorillas and orangutans—to perform live experiments. (The same or, at least, analogous experiments are usually also performed on small children, to see how they compare.) One morning, I went to the zoo, hoping to watch an experiment in progress. That day, a BBC crew was also visiting Pongoland, to film a program on animal intelligence, and when I arrived at the ape house I found it strewn with camera cases marked “Animal Einsteins.”

For the benefit of the cameras, a researcher named Héctor Marín Manrique was preparing to reënact a series of experiments he’d performed earlier in a more purely scientific spirit. A female orangutan named Dokana was led into one of the testing rooms. Like most orangutans, she had copper-colored fur and a world-weary expression. In the first experiment, which involved red juice and skinny tubes of plastic, Dokana showed that she could distinguish a functional drinking straw from a non-functional one. In the second, which involved more red juice and more plastic, she showed that she understood the idea of a straw by extracting a rod from a length of piping and using the pipe to drink through. Finally, in a Mensa-level show of pongid ingenuity, Dokana managed to get at a peanut that Manrique had placed at the bottom of a long plastic cylinder. (The cylinder was fixed to the wall, so it couldn’t be knocked over.) She fist-walked over to her drinking water, took some water in her mouth, fist-walked back, and spit into the cylinder. She repeated the process until the peanut floated within reach. Later, I saw this experiment re-staged with some five-year-old children, using little plastic containers of candy in place of peanuts. Even though a full watering can had been left conspicuously nearby, only one of the kids—a girl—managed to work her way to the floating option, and this was after a great deal of prompting. (“How would water help me?” one of the boys asked, just before giving up.)

One way to try to answer the question “What makes us human?” is to ask “What makes us different from apes?,” or, to be more precise, from nonhuman apes, since, of course, humans are apes. As just about every human by now knows—and as the experiments with Dokana once again confirm—nonhuman apes are extremely clever. They’re capable of making inferences, of solving complex puzzles, and of understanding what others are (and are not) likely to know. When researchers from Leipzig performed a battery of tests on chimpanzees, orangutans, and two-and-a-half-year-old children, they found that the chimps, the orangutans, and the kids performed comparably on a wide range of tasks that involved understanding of the physical world. For example, if an experimenter placed a reward inside one of three cups, and then moved the cups around, the apes found the goody just as often as the kids—indeed, in the case of chimps, more often. The apes seemed to grasp quantity as well as the kids did—they consistently chose the dish containing more treats, even when the choice involved using what might loosely be called math—and also seemed to have just as good a grasp of causality. (The apes, for instance, understood that a cup that rattled when shaken was more likely to contain food than one that did not.) And they were equally skillful at manipulating simple tools.

Where the kids routinely outscored the apes was in tasks that involved reading social cues. When the children were given a hint about where to find a reward—someone pointing to or looking at the right container—they took it. The apes either didn’t understand that they were being offered help or couldn’t follow the cue. Similarly, when the children were shown how to obtain a reward, by, say, ripping open a box, they had no trouble grasping the point and imitating the behavior. The apes, once again, were flummoxed. Admittedly, the kids had a big advantage in the social realm, since the experimenters belonged to their own species. But, in general, apes seem to lack the impulse toward collective problem-solving that’s so central to human society.

“Chimps do a lot of incredibly smart things,” Michael Tomasello, who heads up the institute’s department of developmental and comparative psychology, told me. “But the main difference we’ve seen is ‘putting our heads together.’ If you were at the zoo today, you would never have seen two chimps carry something heavy together. They don’t have this kind of collaborative project.”

Pääbo usually works late, and most nights he has dinner at the institute, where the cafeteria stays open until 7 P.M. One evening, though, he offered to knock off early and show me around downtown Leipzig. We visited the church where Bach is buried, and ended up at Auerbachs Keller, the bar to which Mephistopheles brings Faust in the fifth scene of Goethe’s play. (The bar was supposedly Goethe’s favorite hangout when he was a university student.) Pääbo’s wife, Linda Vigilant, an American primatologist who also works at the institute, joined us. Pääbo and Vigilant first met in the nineteen-eighties, in Berkeley, but they didn’t get together until both moved to Leipzig, in the late nineties. (Vigilant was then married to another geneticist, who works at the institute, too.) Pääbo and Vigilant have a six-year-old son, and Vigilant has two older sons from her previous marriage.

I had been to the zoo, and I asked Pääbo about a hypothetical experiment. If he had the opportunity to subject Neanderthals to the sorts of tests I’d seen in Pongoland, what would he do? Did he think he’d be able to talk to them? He sat back in his chair and folded his arms across his chest.

“One is so tempted to speculate,” he said. “So I try to resist it by refusing questions such as ‘Do I think they would have spoken?’ Because, honestly, I don’t know, and in some sense you can speculate with just as much justification as I can.”

By now, scores of Neanderthal sites have been excavated, from western Spain to central Russia and from Israel to Wales. They give lots of hints about what Neanderthals were like, at least for those inclined to speculate. Neanderthals were extremely tough—this is attested to by the thickness of their bones—and probably capable of beating modern humans to a pulp. They were adept at making stone tools, though they seem to have spent tens of thousands of years making the same tools over and over, with only marginal variation. At least on some occasions, they buried their dead. Also on some occasions, they appear to have killed and eaten each other. Wear on their incisors suggests that they spent a lot of time grasping animal skins with their teeth, which in turn suggests that they processed hides into some sort of leather. Neanderthal skeletons very often show evidence of disease or disfigurement. The original Neanderthal, from Mettmann, for example, seems to have suffered and recovered from two serious injuries, one to his head and the other to his left arm. The Neanderthal whose nearly complete skeleton was found in La Chapelle endured, in addition to arthritis, a broken rib and kneecap. Both individuals survived into their fifties, which indicates that Neanderthals had the capacity for collective action, or, if you prefer, empathy. They must—at least sometimes—have cared for their wounded.

From the archeological record, it’s inferred that Neanderthals evolved in Europe or western Asia and spread out from there, stopping when they reached water or some other significant obstacle. (During the ice ages, sea levels were a lot lower than they are now, so there was no English Channel to cross.) This is one of the most basic ways modern humans differ from Neanderthals and, in Pääbo’s view, also one of the most intriguing. By about forty-five thousand years ago, modern humans had already reached Australia, a journey that, even mid-ice age, meant crossing open water. Archaic humans like Homo erectus “spread like many other mammals in the Old World,” Pääbo told me. “They never came to Madagascar, never to Australia. Neither did Neanderthals. It’s only fully modern humans who start this thing of venturing out on the ocean where you don’t see land. Part of that is technology, of course you have to have ships to do it. But there is also, I like to think or say, some madness there. You know? How many people must have sailed out and vanished on the Pacific before you found Easter Island? I mean, it’s ridiculous. And why do you do that? Is it for the glory? For immortality? For curiosity? And now we go to Mars. We never stop.” If the defining characteristic of modern humans is this sort of Faustian restlessness, then, by Pääbo’s account, there must be some sort of Faustian gene. Several times, he told me that he thought it should be possible to identify the basis for this “madness” by comparing Neanderthal and human DNA.

“If we one day will know that some freak mutation made the human insanity and exploration thing possible, it will be amazing to think that it was this little inversion on this chromosome that made all this happen and changed the whole ecosystem of the planet and made us dominate everything,” he said at one point. At another, he said, “We are crazy in some way. What drives it? That I would really like to understand. That would be really, really cool to know.”

According to the most recent estimates, Neanderthals and modern humans share a common ancestor who lived about four hundred thousand years ago. (It is unclear who that ancestor was, though one possibility is the somewhat shadowy hominid known, after a jawbone found near Heidelberg, as Homo heidelbergensis.) The common ancestor of chimps and humans, by contrast, lived some five million to seven million years ago. This means that Neanderthals and humans had less than one-tenth the time to accumulate genetic differences.

Mapping these differences is, in principle, pretty straightforward—no harder, say, than comparing rival editions of “Hamlet.” In practice, it’s quite a bit more complicated. To begin with, there’s really no such thing as the human genome everyone has his or her own genome, and they vary substantially—between you and the person sitting next to you on the subway, the differences are likely to amount to some three million base pairs. Some of these variations correspond to observable physiological differences—the color of your eyes, say, or your likelihood of developing heart disease—and some have no known significance. To a first approximation, a human and a Neanderthal chosen at random would also vary by three million base pairs. The trick is ascertaining which of these millions of variations divide us from them. Pääbo estimates that when the Neanderthal Genome Project is completed, the list of base-pair changes that are at once unique to humans and shared by all humans will number around a hundred thousand. Somewhere in this long list will lie the change—or changes—that made us human to begin with. Identifying these key mutations is where the transgenic mice come in.

From an experimental viewpoint, the best way to test whether any particular change is significant would be to produce a human with the Neanderthal version of the sequence. This would involve manipulating a human stem cell, implanting the genetically modified embryo into a surrogate mother, and then watching the resulting child grow up. For obvious reasons, such Island of Dr. Moreau-like research on humans is not permitted, nor is it necessarily even possible. For similar reasons, such experimentation isn’t allowed on chimpanzees. But it is allowed on mice. Dozens of strains of mice have been altered to carry humanized DNA sequences, and new ones are being created all the time, more or less to order.

Several years ago, Pääbo and a colleague, Wolfgang Enard, became interested in a gene known as FOXP2, which in humans is associated with language. (People who have a faulty copy of the gene—an extremely rare occurrence—are capable of speech, but what they say is, to strangers, mostly incomprehensible.) Pääbo and Enard had some mice bred with a humanized version of the gene, and then studied them from just about every possible angle. The altered mice, it turned out, squeaked at a lower pitch than their un-humanized peers. They also exhibited measurable differences in neural development. (While I was in Leipzig, I watched a graduate student cut the heads off some of the altered mice and then slice up their brains, like radishes.) The Neanderthals’ FOXP2 gene, it turns out, is in almost all ways identical to humans’, but there is one suggestive base-pair difference. When this difference was discovered, it prompted Pääbo to order up a new round of transgenic mice, which, at the time of my visit, had just been born and were being raised under sterile conditions in the basement.

Genes that seem to play a role in speech are obvious places to look for human-specific changes. But one of the main points of sequencing the Neanderthal genome is that the most obvious places to look may not be the right ones.

“The great advantage with genomics in this form is that it’s unbiased,” Pääbo told me. “If you go after candidate genes, you’re inherently saying what you think the most important thing is. Language, many people would say. But perhaps we will be surprised—perhaps it’s something else that was really crucial.” Recently, Pääbo has become interested in a gene known as RUNX2, which is involved in bone formation. When members of his team analyzed the human and Neanderthal genomes mathematically, RUNX2 emerged as a place where significant changes in the human lineage seem to have occurred. People who have faulty copies of the RUNX2 gene often develop a condition, known as cleidocranial dysplasia, whose symptoms include such Neanderthal-like features as a flared rib cage. Two genes that have been implicated in autism, CADPS2 and AUTS2, also appear to have changed substantially between Neanderthals and humans. This is interesting because one of the symptoms of autism is an inability to read social cues.

One afternoon, when I wandered into his office, Pääbo showed me a photograph of a skullcap that had recently been discovered by an amateur collector about half an hour from Leipzig. From the photograph, which had been e-mailed to him, Pääbo had decided that the skullcap could be quite ancient—from an early Neanderthal, or even a Homo heidelbergensis. He’d also decided that he had to have it. The skullcap had been found at a quarry in a pool of water—perhaps, he theorized, these conditions had preserved it, so that if he got to it soon, he’d be able to extract some DNA. But the skull had already been promised to a professor of anthropology in Mainz. How could he persuade the professor to give him enough bone to test?

Pääbo called everyone he knew who he thought might know the professor. He had his secretary contact the professor’s secretary to get the professor’s private cell-phone number, and joked—or maybe only half joked—that he’d be willing to sleep with the professor if that would help. The frenzy of phoning back and forth across Germany lasted for more than an hour and a half, until Pääbo finally talked to one of the researchers in his own lab. The researcher had seen the actual skullcap and concluded that it probably wasn’t very old at all. Pääbo immediately lost interest in it.

With old bones, you never really know what you’re going to get. A few years ago, Pääbo managed to get hold of a bit of tooth from one of the so-called “hobbit” skeletons found on the island of Flores, in Indonesia. (The “hobbits,” who were discovered in 2004, are generally believed to have been diminutive archaic humans—Homo floresiensis—though some scientists have argued that they were just modern humans who suffered from microcephaly.) The tooth, which was about seventeen thousand years old, yielded no DNA.

Then, about a year and a half ago, Pääbo obtained a fragment of finger bone that had been unearthed in a cave in southern Siberia along with a weird, vaguely human-looking molar. The finger bone—about the size of a pencil eraser—was believed to be more than forty thousand years old. Pääbo assumed that it came either from a modern human or from a Neanderthal. If it proved to be the latter, then the site would be the farthest east that Neanderthal remains had been found.

In contrast to the hobbit tooth, the finger fragment yielded astonishingly large amounts of DNA. When the analysis of the first bits was completed, Pääbo happened to be in the United States. He called his office, and one of his colleagues said to him, “Are you sitting down?” The DNA showed that the digit could not have belonged to a Neanderthal or to a modern human. Instead, its owner must have been part of some entirely different and previously unsuspected type of hominid. In a paper published in December, 2010, in Nature, Pääbo and his team dubbed this group the Denisovans, after the Denisova Cave, where the bone had been found. “GIVING ACCEPTED PREHISTORIC HISTORY THE FINGER,” ran the headline on the story in the Sydney Morning Herald. Amazingly—or perhaps, by now, predictably—modern humans must have interbred with Denisovans, too, because contemporary New Guineans carry up to six per cent Denisovan DNA. (Why this is true of New Guineans but not native Siberians or Asians is unclear, but presumably has to do with patterns of human migration.)

It has been understood for a long time that modern humans and Neanderthals were contemporaries. The discovery of the hobbits and now the Denisovans shows that humans shared the planet with at least two additional creatures like ourselves. And it seems likely that as DNA from more ancient remains is analyzed still other human relatives will be found as Chris Stringer, a prominent British paleoanthropologist, told me, “I’m sure we’ve got more surprises to come.”

“If these other forms of humans had survived two thousand generations more, which is not so much, then how would that have influenced our view of the living world?” Pääbo said, once the excitement over the skullcap had passed and we were sitting over coffee. “We now make this very clear distinction between humans and animals. But it might not be as clear. That is sort of an interesting thing to philosophize about.” It’s also interesting to think about why we’re the ones who survived.


Study scepticism

Simple stone tools of a similar age have been found in only one place: Homo floresiensis, the “hobbit”, left a record of relatively simple stone tools on the Indonesian island of Flores.

But even these tools show a level of complexity not seen at the mastodon site, says Adam Brumm at Griffith University in Queensland, Australia, who works on the Flores archaeological record. “If these are indeed humanly modified artefacts they make the typical hobbit tool look like an iPhone,” he says.

Brumm’s general reaction to the new study is scepticism. “Most archaeologists will simply never believe it – the dates are too old, the ‘tools’ too untool-like and the implications too mind-boggling.”

Fullagar isn’t disheartened by such scepticism, though. “I’ve spent about four years looking at these artefacts and the team has been looking at the evidence for about 24 years,” he says. “It’s understandable that it might be difficult to get your head around the nature of this evidence in a couple of days.”

And the reaction to the new evidence isn’t universally sceptical. Gerrit van den Bergh was already aware of the research because he works at the University of Wollongong alongside Fullagar. “I think the team has very strong arguments and good evidence,” he says.

Stringer is also prepared to be open-minded. “The paper has come through thorough peer review,” he says. “[But] many of us will want to see supporting evidence of this ancient occupation from other sites before we abandon the conventional model.”