NARRATOR: They were the brutes of Ice Age Europe.

Although a branch of our human family tree, they were seen as a dead end, deep in our prehistoric past.

They were called Neanderthals.

Neanderthals have the mother of all image problems.

NARRATOR: They eked out a marginal existence, hunting by brute force, with only simple stone tools.

They were considered primitive, with no language, art or the higher-level thinking of advanced species like us.

They lacked the same intelligence as modern humans.

NARRATOR: They began to disappear 40,000 years ago as modern humans, our species, came on the scene.

But this primitive picture is being replaced by a different image of Neanderthals.

It's bringing them much closer to us, as genetic evidence revises our human family tree and reveals their mysterious presence right within our genes.

We started to look at the problem from different angles.

They answer would come back, "It's Neanderthal."

That was quite shaking to me, and I thought, "This must be a statistical fluke."

NARRATOR: Now archaeologists are finding new evidence to help resolve bitter debates.

This is the smoking gun.

We have the case to settle the controversy.

NARRATOR: In toolmaking, they're seeing signs of language.

There is some sort of advanced talking going on.

NARRATOR: A new Neanderthal mind emerges.

We're not talking about idiots.

NARRATOR: And if scientists are finally finding the real legacy of the Neanderthals buried deep in our history and our genes, what does it say about all of us?

"Decoding Neanderthals," right now on NOVA.

Major funding for NOVA is provided by the following: NARRATOR: 40,000 years ago, Europe is in the grip of an ice age.

In harsh, unforgiving terrain live members of an ancient human species.

The Neanderthals.

It is a brutal time to be alive.

Only the toughest survive.

They were very muscular, short, wide, very stocky, very powerfully built.

THOMAS WYNN: They were hunter-gatherers.

They had scarce game to find.

Most Neanderthals were probably dead by 30 years old.

So it was a brief, brutal life.

NARRATOR: Hunting was extremely dangerous.

STRINGER: They were confrontational hunters, so they had to get close in to their prey with stabbing spears.

This required not only a lot of bravery but a lot of sheer physical strength.

FREDERICK L. COOLIDGE: These Neanderthals could bench-press 300 to 500 pounds.

They had big thrusting spears that they thrust into the side of 2,000- and 3,000-pound animals.

NARRATOR: The Neanderthals survived the harsh conditions in Europe for at least 300,000 years.

Then, around 40,000 years ago, a different human species arrives on the scene... our species, Homo sapiens.

They migrated from Africa, spreading across Neanderthal territory, outnumbering them ten to one.

Suddenly you've got two species competing for the same resources, hunting the same animals, collecting the same plant resources, wanting to live in the best territories and the best caves.

NARRATOR: After another 10,000 years, the Neanderthals disappear.

ED GREEN: The story of the Neanderthals is a murder mystery.

They were there and now they're gone, and they go away at about the same time as we are showing up on the scene.

NARRATOR: So why did they vanish while we survived?

For years, many scientists believed we wiped them out, a simple case of our brain outclassing their brawn.

This theory emerged when archaeologists unearthed the very first Neanderthal skulls over 150 years ago.

To scientists at the time, skulls like these looked primitive compared to ours.

Chris Stringer is one of the world's preeminent Neanderthal experts.

STRINGER: We can tell a Neanderthal skull 100% of the time.

We've got a very broad skull, this double-arched brow ridge, and perhaps their most distinctive feature, the middle of the face is pulled forwards, the cheekbones are swept back.

NARRATOR: One influential discovery featured a skeleton crippled by acute arthritis, incorrectly reconstructed with a hunched posture and a shuffling walk.

This early find helped shape popular perceptions of Neanderthals for decades, launching a wave of images of the Neanderthal as a brutish caveman.

Neanderthals have the mother of all image problems.

They're brooding, they're stupid-looking... they have no personality.

STRINGER: They were reconstructed as being much more apelike, stooped, grasping big toes, very hairy, head hung forward, shambling in their gait.

NARRATOR: Critically, scientists believed the Neanderthals lacked the one thing that defines us... our brainpower.

They lacked the same intelligence as modern humans.

NARRATOR: With only limited stone tools and no art or personal ornaments, Neanderthals seemed less advanced than modern humans.

But was that really the whole story?

Now, new discoveries in genetics and archaeology are challenging this traditional view of the Neanderthals.

(stones tapping) Metin Eren has spent six years studying Neanderthal technology.

These Levallois flakes, named after the place in France where they were first found, were the Neanderthals' tool of choice.

At first glance, they look rudimentary, the product more of luck than judgment.

But when Eren tried to reproduce one, he got a surprise.

I find the Levallois technology much more difficult to make than any of the modern Homo sapien technologies.

It took me about 18 months to master Levallois technology, and this was after I'd been flint-knapping for a number of years.

The fact that there seems to be a goal involved.

They're not simply just striking flakes to get a sharp cutting edge.

NARRATOR: Eren began to realize this was no hit-or-miss process.

He wanted to discover just how they did it.

So he turned to morphometrics, a technique which analyzes the exact shapes and angles of objects.

It revealed Neanderthals must have used a precise set of strikes to turn a raw flint block into a carefully shaped object known as the core.

The final crucial step involved striking the core with a single precision blow.

Only if aimed just right would this create the perfect flake and a remarkably versatile tool.

EREN: I shape this in such a way that the core has a gentle convexity such that the large flake that comes off has a sharp edge all around its perimeter, and that enhances the utility of this particular piece in a number of ways.

Because it's uniformly thick, you can resharpen it more times than you can other types of stone flakes.

We also found that the Levallois flake is statistically more symmetrical.

That means when you use it, you basically reduce torque, so it actually has ergonomic properties.

I can actually get a lot more force with each cut and each slice.

I'll just put a little more pressure and the Levallois flake goes right through it and we got one big piece of gammon.

That took about a minute and a half.

No problem.

This is an amazing tool.

They were engineering their rocks to get particular products that have specific properties.

They were able to discover a technique that is incredibly difficult to do.

It is just a testament to how intelligent they must have been to actually invent it in the first place.

NARRATOR: Metin Eren's work reveals the complexity of Neanderthal toolmaking.

But there's even more surprising evidence of sophisticated Neanderthal technologies.

Dutch archaeologist Wil Roebroeks is studying new finds, one of them dating back a quarter of a million years.

This is a flint spearhead, at its base, a large sticky black mass most likely used as a glue.

Evidence from many sites had already shown how Neanderthals attached stone flakes to wooden shafts, first binding them with sinew or leather, then securing the binding with a gluelike substance.

This turned the flake and its shaft into a robust weapon.

ROEBROEKS: What you see there is a nice flint flake, at least for an archaeologist, a nice, sharp, razor-sharp flint flake, which is covered at the base in this pitch material.

It is a material that they used probably in many aspects of everyday life.

NARRATOR: At first, it was thought this Neanderthal glue was nothing more than sap from a pine tree, easy for them to find and use.

But detailed analysis revealed something different.

It was a type of manmade pitch from birch trees.

Chemical studies have shown that that material was produced from heating birch bark.

Neanderthals were producing these pitches.

So it is not something like the stuff that you can retrieve from a pine when you hit a tree, the natural stuff that comes out.

NARRATOR: This is the world's oldest known synthetic material.

It makes Neanderthals, and not us, the inventors of perhaps the first industrial process.

But how could an allegedly primitive species have done this?

To find out more, Wil Roebroeks decides to mount an experiment with a colleague, Friedrich Palmer.

They will try to replicate the Neanderthal technique of pitch extraction, a complex process called "dry distillation."

Crucially, they'll use only materials available to Neanderthals 250,000 years ago: an upturned animal skull to catch the pitch... a small stone on which the pitch would condense... some rolls of birch bark, the source of the pitch... and a layer of ash to exclude oxygen and prevent the bark from burning.

Roebroeks and Palmer need to heat the bark to 400 degrees centigrade.

Any less and it won't produce pitch.

Any more and it will simply burn.

After eight hours, any pitch should have condensed on the stone within the skull.

Yeah.

Oh, look at that.

Yeah, that's a bit dry.

NARRATOR: Today, Roebroeks and Palmer manage to extract only a tiny smear of pitch.

That's not much.

NARRATOR: They are on the right track, but it isn't nearly enough to glue a spearhead to a shaft, as the Neanderthals did.

It seems this experiment is on too small a scale to produce enough pitch.

Neanderthals must have figured out how to scale up the technique in a way we haven't yet reproduced.

However they managed it, the Neanderthals had evidently mastered a complex thermal process.

The Neanderthals' extraction of pitch and their distinctive toolmaking suggest their technology was more advanced than previously thought.

What's more, artifacts like these have been found across a wide area of Europe.

And this raises a question.

How did Neanderthals communicate these complex ideas?

Could it be they shared that one ability we usually think of as unique to us?

Language.

One could infer that there was some communication maybe between generations or between peers in a group.

But language, of course, is very difficult to excavate.

NARRATOR: Now, fresh evidence is emerging from a completely different branch of science, applied to Neanderthal research for the first time.

Svante Paabo is one of a new breed of detectives examining our deepest past.

He's not an archaeologist.

He does his digging in the lab.

Paabo is interested in humans and what sets us apart from our closest relatives.

As a geneticist, his work involves comparing our genetic material with that of the rest of our family tree.

It's really about finding out what makes us special in the world... ...what made things such as modern humans spreading across the entire globe, developing all the technology, all the culture that's typical in modern humans.

DAVID SCOTT: There's a fundamental truth to our nature.

Man must explore.

NARRATOR: Paabo and his colleagues want to look at specific genes, where you'd expect humans and our closest relatives to differ-- like a gene fundamental for language named FoxP2.

FoxP2 is a very interesting gene in that it's one of a few genes that's directly related to this uniquely human characteristic, speech and language.

Four violets, a fiver!

Four violets, a fiver!

(chanting) (phone rings) Nine hundred, nine hundred.

NARRATOR: FoxP2 is found in many species, although the human version is distinctive.

By comparing it with a potential Neanderthal version, Paabo was hoping to shed light on what makes human language special.

But before he could even begin, Paabo needed to have the genetic blueprint for both Neanderthals and humans-- their genomes.

A genome is the distinctive genetic recipe for a species, made up of a specific set of chromosomes.

These are responsible for the characteristics that make every species different.

Within the chromosomes, genes determine whether we have two legs or four, grow feathers or fur, and every part of this unique recipe is encoded within just one molecule... DNA.

When Svante Paabo started his work, the human genome had already been decoded.

No one had attempted to map the Neanderthal genome.

Paabo faced a seemingly impossible task in attempting to map the DNA in the nucleus of a 30,000-year-old cell.

Ed Green is a geneticist on Paabo's team.

As soon as it was obvious that this was possible in theory, we started to think about how do we do this in practice, if we can get nuclear data, if we can get some amount.

And we did some back-of-the-envelope calculations and it looked like, yes, this is feasible.

PAABO: So we spent a lot of time looking at many archaeological sites and many different bones... ...and eventually identified this site in Croatia.

NARRATOR: The Vindija cave in northern Croatia contained genetic gold dust-- the 30,000-year-old leg bone fragments of three female Neanderthals.

The exceptionally well-preserved bones offered Paabo's team the best chance of extracting Neanderthal DNA.

In sterile conditions, the team took samples of bone, carefully dissolving them in solution before spinning them at high speed in a centrifuge to retrieve the strands of DNA.

But then the real difficulties began.

The bone samples carried billions of unwanted passengers.

PAABO: Most bones we look at might contain a few molecules of Neanderthal DNA, but the vast, vast majority come from bacteria and fungi that colonized the bone when it was in the ground in the cave for tens of thousands of years.

NARRATOR: Before the team could go any further, they'd have to destroy the rogue DNA.

So they invented a cleanup technique using enzymes that target and eliminate bacterial DNA from the sample.

The resulting clean sample contained five times the concentration of Neanderthal DNA compared to the original, which made the analysis easier.

Still, reconstructing the genome remained a formidable challenge.

The DNA molecule's intertwining strands are held together by four key chemicals, represented by letters.

These bond together as pairs-- always C to G and A to T. These letters are like building blocks, repeating units which spell out the genome's unique recipe.

Their order is critical.

Just one letter out of place within three billion pairs and the genome would be inaccurate.

But the DNA was in tiny fragments, like a colossal jigsaw puzzle.

The team would have to place each piece in precisely the right order.

Svante and others were very skeptical.

It was in the realm of the impossible that a genome would ever be sequenced.

During the course of this project there were actually many times when we despaired about being able to make it.

NARRATOR: It would take them four years.

But finally, the last piece of the puzzle fell into place.

Human evolution is something that everyone cares about and it's such an incredible thing, technically, to be able to do.

Add to that that it's our closest extinct ancestor and all that it can tell us about human evolution and human biology.

It's the most exciting thing I've ever worked on.

NARRATOR: This is the result of all their work-- the Neanderthal genome.

Here is one tiny part of the actual sequence of over three billion letters corresponding to each DNA building block, the genetic blueprint of a species of human that became extinct 30,000 years ago.

Now, at last, Paabo's team could begin comparing Neanderthal to modern human genes.

One of the first areas they looked at was FoxP2, the gene associated with language.

Would an identical gene be shared between human and Neanderthal?

Would the gene be there at all?

To my surprise, I must say, it turned out that it's shared.

NARRATOR: Neanderthals had exactly the same version of the FoxP2 gene as humans-- the same chemical letters in exactly the same order.

PAABO: I'm very sure that the Neanderthals had communication.

If it was a language exactly as we would understand language, that's another question.

STRINGER: I think they had language.

That doesn't mean it was the same as our language, as complex as our language.

I think, again, that modern humans probably had another level of complexity.

But I think they had language.

Yes, I absolutely think they couldn't have survived the way they did without it.

NARRATOR: Paabo's work adds weight to the growing argument that Neanderthals and modern humans shared more abilities than previously thought.

But it begged a billion-dollar question.

Did we have enough in common that we could have interbred?

If Neanderthals and modern humans had interbred successfully, traces of their DNA would be found in ours.

Most scientists, Paabo included, thought this highly unlikely.

When different species mate, their offspring are usually infertile.

PAABO: I was biased against interbreeding.

There is no evidence for it so I don't think it really happened.

NARRATOR: But with the Neanderthal genome now sequenced, Paabo and his team could examine this question.

The first step was to map the individual genomes of five people from different ethnic groups.

Then they compared this modern DNA with Neanderthal.

They focused only on small specific regions, called "variable areas," where the order of the DNA letters often differs from one individual to the next.

Here, if interbreeding had taken place, letter sequences typical of Neanderthal DNA would show up in the human DNA strand.

But with no interbreeding, there would be no trace of Neanderthal DNA in the variable areas.

Paabo expected to see the same negative result in the genomes of all five modern humans, regardless of ethnic group.

Well, if Neanderthals are equally distantly related to everybody, then Neanderthal should match the French guy and the West African guy equally often.

NARRATOR: But that is not what they found.

When we compared one African to a European individual, the Neanderthal matched the European individual more often than the African one.

NARRATOR: The result indicated that Neanderthals were genetically closer to Europeans and Asians than they were to Africans.

It meant that somewhere along the line, European and Asian humans had picked up Neanderthal DNA.

So that was sort of quite shaking to me.

I thought this must be a statistical fluke.

It was not quite significant.

This would surely go away when we had more data.

NARRATOR: So Paabo told his team to do the work again... and again... and again.

We really needed to make it absolutely sure that we were right.

We started to look at the problem from different angles.

And every time we would ask the question in a little bit different way.

The answer would come back, it's Neanderthal.

We were able to convince one another and eventually the world that we have a little bit of Neanderthal ancestry in modern human genomes.

NARRATOR: The amount of Neanderthal DNA in these modern genomes is small, between just one and four percent, but the implications are staggering.

After migrating out of Africa, early humans must have mated with Neanderthals and produced fertile offspring, who inherited segments of Neanderthal DNA.

What we have shown clearly is that we could interbreed with them, we could have fertile children and at least some of these children became incorporated in the human community and reproduced and contributed to present-day humans.

NARRATOR: Paabo's groundbreaking research forces a radical shift in perspective regarding Neanderthals.

They were genetically close enough to have children with our species.

They probably also had language.

And there are yet more revelations as archaeologists reexamine previously discounted evidence in favor of Neanderthal skills and abilities.

A hallmark of our species is our age-old affinity for art, ritual and adornment.

STRINGER: We see the astonishing cave art.

We see statuettes over the whole range of modern humans from Western Europe right across to Siberia.

And I think that's part of the fact that modern humans are entering new territories, they're covering wider distances and they're having to signal and network with each other.

NARRATOR: Communicating with others through art and ritual has long been considered a uniquely human trait.

JOAO ZILHAO: There has been the notion that Neanderthals were less intelligent, and one way archaeologists have to deal with this question is by assessing the extent to which people used symbols.

NARRATOR: Evidence of Neanderthal symbolism has been elusive until recently.

This is one of many fragments of manganese dioxide, a black mineral found in a Neanderthal cave in France, its tip worn down as if used as a crayon.

In Neanderthal sites in Gibraltar, archaeologists have discovered cut marks on the wing bones of crows and birds of prey, bones with little value as food.

The marks suggest Neanderthals were cutting off the feathers and using them to decorate their hair or bodies.

And in Spain, seashells have revealed faint traces of hematite, or iron ore, a red mineral often used as pigment.

Neatly pierced holes allow the decorated shells to be worn as ornaments.

Anthropologist Joao Zilhao believes the evidence offers a glimpse into the Neanderthal mind.

Now, he is reexamining finds from a Neanderthal site in Spain, excavated in the '80s.

ZILHAO: This is a fragment of a naturally pointed horse bone, and when we looked at the tip of the bone under the microscope we found that there was lots of reddish dots.

NARRATOR: Although so faded they are hard to see, the chemical analysis proves the spots are the red pigment hematite.

And there is more.

ZILHAO: This shell is from the Mediterranean oyster, and you can see adhering to the inner side of the shell a remnant of a pigment which is black and reflective.

NARRATOR: Zilhao has found a pencil-like sliver of bone with a red mineral at its tip, and a shell stained with a shiny pigment, alongside other fragments of colored minerals.

It adds up to a significant collection, or so Zilhao believes.

You know, they look like just shells collected off the beach, but the amount of information they contain is tremendous.

NARRATOR: Putting all the pieces of the puzzle together, Zilhao is convinced he is looking at the remains of a Neanderthal body-painting kit.

ZILHAO: This suggests that what was being prepared in this shell was a cosmetic preparation used as a tool to prepare something like glitter makeup.

This is the smoking gun.

We have here the case to settle the controversy concerning Neanderthal symbolism.

NARRATOR: Zilhao believes Neanderthals used body paint as a symbolic way of distinguishing friend from foe, just as we do today.

(chanting) ZILHAO: When you go to a football stadium and there are two teams playing, how do you know whether you're safe to sit next to someone who may be supporting the team that hates yours?

You use an artifact that identifies you as a supporter.

And it's this kind of information about yourself that these kinds of objects transmit.

NARRATOR: But even if the Neanderthals were painting themselves and engaging in symbolic behavior, does it mean they thought the same way as modern humans?

Our modern human ancestors practiced ritual and religion.

Similar evidence for Neanderthals has been elusive.

Then a team of archaeologists made an intriguing discovery in southern Spain.

Their finds hint at the existence of a Neanderthal ritual.

Inside this cave, a team led by Michael Walker excavated a deep shaft in which they found more than 300 bones from around ten Neanderthals buried by rockfalls from the unstable ceiling.

Three of the Neanderthals stood out.

Walker thinks they weren't necessarily the victims of a rockfall.

If there are rocks falling on you from a natural rockfall, it would be very strange to find nobody trying to escape and one of them with the hands close to the head in almost sleeping position.

NARRATOR: Although the bones of this young female are fused to the limestone rock and are hard to see, Michael Walker thinks her body may have been carefully arranged in a fetal position.

If he's right, this was no rockfall.

Around 50,000 years ago, someone had intentionally buried her, piling stones to protect her body.

And this cave had yet more to reveal.

Near the girl's body, Walker's team uncovered the fossilized bones of a pair of panther paws.

WALKER: This articulated paw of a panther was found close by.

And since the panther hadn't eaten and disturbed the bones here, it's more likely that the Neanderthals disturbed the panther and cut its paw off.

I just wonder whether in the way that today hunters in America cut off bear paws, I'm wondering if the Neanderthals occasionally didn't cut off a panther paw and keep it as a trophy.

NARRATOR: Walker's idea-- that the severed panther paws were a trophy or funeral offering-- is an intriguing speculation.

I think that there are enough examples of Neanderthal burials, well articulated individuals, to suggest that they are intentionally burying their dead.

Perhaps when you come to the issue of grave goods and whether they're putting material in those graves and whether they're, if you like, sending messages beyond the grave through these materials, that's more controversial.

You see in humans elaborate ritual burials, maybe about 27,000 years ago, the clearest evidence in this place in Russia.

These two children are buried with, like, 10,000 beads.

There's nothing like that in Neanderthal burials.

NARRATOR: Whether Neanderthal burials are evidence of complex rituals and beliefs is hotly debated.

But many clues now point to the idea that Neanderthals were more accomplished and advanced than previously thought.

And this opens up perhaps the biggest question of all: Why are we still here and Neanderthals are not?

The Neanderthal story seems simple.

Their forerunners reached Europe around 800,000 years ago.

When Homo sapiens joined them around 40,000 years ago, it marks the beginning of the end.

Some 10,000 years after modern humans arrive, virtually all traces of Neanderthals are gone.

Some scientists believe we drove them into extinction by outcompeting them for scarce resources, maybe even by killing them.

But the latest evidence points to another possibility.

Soon after Svante Paabo's team revealed that Neanderthals and modern humans outside Africa had interbred, anthropologist John Hawks reopened the case files.

He wanted to know if this interbreeding had happened a little or a lot.

Hawks needed more than just the five modern human genomes that Paabo had analyzed.

And he got a lucky break.

A team of scientists published a huge new database of individual human genomes from around the world.

The 1000 Genomes Project data began to become available.

And so we were able to expand the comparison to literally more than a thousand individuals from different populations.

NARRATOR: If interbreeding had been a relatively rare event, then all non-African humans across the world would have inherited the same small dosage of Neanderthal DNA.

But that's not what Hawks found.

HAWKS: Now, my lab, we were able to look at more people in China, more people in Tuscany, in the UK.

And as we're doing this, we're discovering that there are some differences among these populations.

NARRATOR: Hawks uses the jelly beans to illustrate the relative percentages of Neanderthal DNA he found in different groups of modern humans across the world.

We see that in China there is a little less.

In Europe it's a little more.

And when we compare Europeans, in southern Europe, in Tuscany, it's a little more than it is in other parts of Europe.

NARRATOR: Outside Africa, Hawks' data showed the Chinese have the smallest dose of Neanderthal DNA, some individuals having as little as two percent.

But in Tuscany, northern Italy, this rises to around four percent.

So Hawks' data shows that Tuscans have more Neanderthal genes than any other people living today.

If Hawks is right, Ice Age Southern Europe was a hotbed of Neanderthal-human interbreeding.

HAWKS: This was Neanderthal habitat.

Modern humans were interbreeding with them, for a longer time and over a larger geographic space.

And subsequently, Europeans got a little bit more Neanderthal DNA.

NARRATOR: Today, a simple blood test can estimate how much of our genetic identity is Neanderthal.

HAWKS: Do you guys want to find out?

STUDENTS: Yes.

Are you sure you're ready?

Yes, yes, get over it, okay, all right.

At 1.3 percent, the least is Arial.

That's very characteristic, actually, of African Americans in our sample.

Next, 2.5 percent, is Vang.

And the most... you're left.

How much do you think it is?

No more than three percent.

Not five?

I hope not.

(everyone laughing) All right, you're the most with three percent, yes.

NARRATOR: This field of research is in its infancy and evolving rapidly.

Other experts report different percentages of Neanderthal DNA.

But most agree on one key finding.

There wasn't just a handful of sexual encounters between humans and Neanderthals, but many.

That presents a dramatically different picture of how humans and Neanderthals interacted in Ice Age Europe and leads to a new outlook on the Neanderthals' disappearance.

HAWKS: When we think about the process of extinction in other kinds of animals, we think of it usually as a really sudden event, like an asteroid hits the earth and they're gone.

With the Neanderthals, what you're looking at is a much more gradual process, a process that unfolded over thousands of years.

NARRATOR: Hawks believes the Neanderthals' DNA was absorbed by the dominant population.

Outnumbered ten to one by modern humans, Neanderthals weren't hunted to extinction by a supposedly superior species.

They were bred out, genetically swamped.

HAWKS: So a million, you know, compared to three billion base pairs in your whole genome...

I would frame the end of the Neanderthals as a process of interaction and absorption.

Neanderthals were sort of on the losing end of that.

And their only route toward success was probably interbreeding with our population.

NARRATOR: But is our dosage of Neanderthal DNA just a quirk of genetic history?

Or is there a serious side to this inheritance?

What, if anything, have Neanderthals done for us?

Ed Green and his team are looking closer at the sections of Neanderthal DNA that we inherited.

One obvious follow-up question is, what is the impact of Neanderthal genetic contribution into people today?

NARRATOR: Most of the genes they examine don't have any known function.

But then the team finds something intriguing: Neanderthal DNA in locations fundamental to our immune system, involving genes that are vital to our ability to fight off disease.

These areas are called human leukocyte antigens, or HLAs.

They make the cells that attack viruses and bacteria.

Since Neanderthals lived in Ice Age Europe for hundreds of thousands of years, their immune systems must have been specially adapted to fight off the diseases there.

This was something that modern humans, arriving from Africa, didn't have.

Our ancestors, when they came into the Neanderthal range, were, for the first time, encountering this environment.

Our immune systems would not be adept at recognizing and fighting pathogens new to us.

HAWKS: Oh, it's absolutely a survival toolkit.

HLA types are important because they help our body resist disease.

So it's very clear that one product of this interaction was the inheritance of immune system versions of genes.

Maybe they conferred some selective advantage.

Maybe the Neanderthals have a version of these immune system genes that were beneficial for the Neanderthal and they were beneficial to human people who got these genes by interbreeding.

NARRATOR: This is the Epstein-Barr virus, linked to both mononucleosis and a type of blood cancer.

Green's team found that an HLA we inherited from Neanderthals could reduce the risk of contracting this deadly virus.

But this may be just the tip of the iceberg.

As we look more and more at the Neanderthal genome and characterize what things are where, I think we're going to find more of these.

NARRATOR: It seems the Neanderthals who mated with our human ancestors may have given their offspring a lifesaving legacy, a legacy that is potentially saving lives even to this day.

The genetic and archaeological evidence is still unfolding.

But already it is telling us something profound.

The Neanderthal story goes to the heart of who we are today.

We're finding out we owe a debt to a mysterious, long-vanished branch of the human family in ways we are only just beginning to discover.

The exploration continues on NOVA's website, where you can watch this and other NOVA programs, see expert interviews, interactives, video extras and more.

Follow NOVA on Facebook and Twitter, and find us online at pbs.org/nova.

This NOVA program is available on DVD.

To order, visit shopPBS.org, or call 1-800-play-PBS.

NOVA is also available for download on iTunes.

Captioned by Media Access Group at WGBH access.wgbh.org