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Comparison of Neanderthal anatomy to modern human anatomy.

A comparison of Neanderthal anatomy to modern human anatomy.

Photograph Joe McNally, National Geographic

Ed Yong

for National Geographic

Published January 29, 2014

When modern humans migrated out of Africa some 60,000 years ago, they found the Eurasian continent already inhabited by brawny, big-browed Neanderthals. We know that at least some encounters between the two kinds of human produced offspring, because the genomes of people living outside Africa today are composed of some 1 to 4 percent Neanderthal DNA.

Two studies published concurrently in Nature and Science on Wednesday suggest that while the Neanderthal contribution to our genomes was modest, it may have proved vitally important.

Some parts of non-African genomes are totally devoid of Neanderthal DNA, but other regions abound with it, including those containing genes that affect our skin and hair. This hints that the Neanderthal gene versions conferred some benefit, and were kept during evolution.

"It seems quite compelling that as modern humans left Africa, met Neanderthals, and exchanged genes, we picked up adaptive variants in some genes that conferred an advantage in local climatic conditions," says Joshua Akey, who led the study in Science.

"The adaptive things from Neanderthals are very interesting because they are not obvious," says John Hawks of the University of Wisconsin-Madison, who was not involved in either study. Based on fossil bones alone, anthropologists would never have predicted that Neanderthals contributed to the keratin filaments and immune systems of modern people.

The fact that Neanderthal DNA is totally absent from other stretches of the modern non-African genome suggests that their versions of the genes in these regions would have caused problems in modern humans, and were weeded out by natural selection.

In the Nature study, Sriram Sankararaman and David Reich of Harvard Medical School used the previously sequenced Neanderthal genome to screen 1,004 modern genomes for sequences with distinctive Neanderthal features.

For example, if a fragment of DNA is shared by Neanderthals and non-Africans, but not Africans or other primates, it is likely to be a Neanderthal heirloom. Also, Neanderthal sequences are typically inherited in large batches, since they were imported into the modern human genome relatively recently and have not had time to break apart.

In the Science study, Akey and Benjamin Vernot, both of the University of Washington in Seattle, used similar statistical features to search for Neanderthal DNA in the genomes of 665 living people—but they initially did so without the Neanderthal genome as a reference. They still managed to identify fragments that collectively amount to 20 percent of the full Neanderthal genome.

Neanderthal Influence on Skin, Hair, Common Diseases

Despite their different approaches, both teams converged on similar results. They both found that genes involved in making keratin—the protein found in our skin, hair, and nails—are especially rich in Neanderthal DNA.

For example, the Neanderthal version of the skin gene POU2F3 is found in around 66 percent of East Asians, while the Neanderthal version of BNC2, which affects skin color, among other traits, is found in 70 percent of Europeans.

The Neanderthal version of these genes may have helped our ancestors thrive in parts of the world that they were not familiar with but that Neanderthals had already adapted to. "Neanderthals had been in these environments for hundreds or thousands of years," says Sankararaman. "As modern human ancestors moved into these areas, one way to quickly adapt would be to get genes from the Neanderthals."

"Unfortunately, skin and hair do so many things that it's hard to speculate on what specifically that adaptive trait was," says Akey.

Sankararaman also found Neanderthal variants in genes that affect the risk of several diseases, including lupus, biliary cirrhosis, Crohn's disease, and type 2 diabetes. The significance of these sequences is "even less clear."

Both teams found that non-African genomes have large continuous "deserts" that are totally devoid of Neanderthal DNA. These regions include genes such as FOXP2, which is involved in motor coordination and could play an important role in human language and speech.

The Neanderthal-poor deserts are especially big in the X chromosome, and include genes that are specifically activated in testes. This hints that some Neanderthal genes may have reduced the fertility of male modern humans and were eventually lost. However, Hawks cautions that this probably happened over hundreds of generations—it was very unlikely that the sons of Neanderthals and modern humans were obviously infertile.

DNA Hints at Other Mystery Humans

Both teams are now planning to apply their methods to other hominids like the Denisovans—an enigmatic group whose presence in Asia some 40,000 years ago is known just from DNA from a finger bone and some teeth found in a single cave in Russia.

And Akey's work shows that it may even be possible to partially reconstruct the genomes of unknown groups of ancient humans without any prehistoric DNA samples.

"That's one of the things that I'm most excited about," he says. "Paleogenomics is a difficult field because it often requires finding suitable fossils with well-preserved DNA. "Maybe we're not always beholden to bones. We can look at the genomes of present-day individuals."

It is becoming increasingly clear that the Pleistocene was awash with many different groups of early humans, hooking up with each other to various degrees. Recent studies, for instance, have found tantalizing hints of unknown groups from Asia and Africa that left genes in Denisovans and modern humans, respectively. Akey's method could give us our first glimpse at these mystery humans.

"If there is no fossil evidence and potentially never will be, this will be the only way of finding out about groups that were important in human history," he added.

35 comments
Peter Hendriks
Peter Hendriks

Does this all mean Africans are the true homo sapiens race and Europeans and Asian some kind of hybrids. Malcolm X must be laughing in his grave. 

matthew warren
matthew warren

ok what you missed is that modern man popped out into existence 60,000 years ago and evolved from no other species. The only reason some of modern man has any Neanderthal genes in the is because they breed with some after they left africa. sorry to break the news to ya but modern man was clearly made. Its not what something is made out of that makes it special, its how its made that does.

Victor Bailey
Victor Bailey

I think I missed something here. Where did Neanderthals come from?

john thomas
john thomas

On the one hand we are being told that human and Neanderthal DNA is about 99% the same -- so that about 1% is different. On the other hand we are being told that about 1- 2% of our DNA came from the Neanderthals.  What am I misunderstanding

Doug  L.
Doug L.

It is possible that the researchers from Cambridge and UNED were correct and Svante Paabo's team here is, again, wrong in assuming that the presents of Neanderthal DNA in non-African populations means the European & Eurasia migrants mated with this separate species when we arrived.  Neanderthal are very different in many ways and it is important we continue to look at those differences instead of just end exploration because of a baseless assumption that were all the same species anyway because of a proven-wrong theory that we mated with this amazing, but radically different species. UNED researches re-dated Neandethal fossils in August of last year and showed they were gone before we got to Europe.


Dr Andrea Manica of Cambridge led a study published in Aug 2013 in PNAS, after the interbreeding bombshell, that proved there was no basis to Paabo's theory because there was a more likely model showing that many groups of modern humans were spread out in Africa, some more closely related to our common ancestor with Neanderthal than others and some of those groups left Africa.  You see this same diversity of ancestry in modern primate groups but you can't assume something mated with giraffe every time you see a long neck, so to speak. This is some great science structured around wrong information as often great science is.


Important info here if you can look past the mistake.  Dr Manica's model also fits the diverse haploid types of modern humans in Africa and fits the Pleistocene situation in Africa that possibly caused the situation of many closely related groups of hominids and modern humans seemingly living side by side.  This Pleistocene circumstance may have been  many cycles of geographic isolation and reconnection during each individual glacial where cycles swinging from large to small lakes and rivers pulsed as glacier blocked lakes gave way around Ethiopia and elsewhere.  Whatever the cause, diversity of closely related, or same species, hominids , including modern humans, seems to be the tune we are hearing in Africa from almost the last 2 million years.  It seems to have accelerated evolution or diversity. You have Homo Heidelberg; Rhodesiensis & Erectus all over Africa at the same 500 to 750 thousand years ago, while they were outside of Africa, too.  There may have been transitional species between Neanderthal Ancestor & modern Human from just before that time or something like Erectus and Rhodensiensis giving rise to Neanderthal and Humans, respectively while some groups completing speciation more completely than others. Mating between species just seems like fantastic melodrama that some want to be true despite the science that says otherwise.

Kathleen Cleary
Kathleen Cleary

The thing about breeding is that the mating pair have to be of the same species to produce offspring which are fertile. Therefore, Neanderthals and "modern humans" are both human. If they are both equally human the distinction between us and them is like the distinction between races of people, nothing more. Neanderthals have just been abosorbed into a collective gene pool. 

Susan Sona
Susan Sona

Still wonder if these ancients were hairer than moderns of today.

Susan Sona
Susan Sona

Seriously doubt it was Neanderthal that contribute disorders like Lupus since there were cases of lupus in Africa as well.

Tom Carberry
Tom Carberry

I think modern humans, neanderthals, and other variants, all came from one common ancestor and that some worldwide disaster caused a massive die out, and inbreeding among the few who survived in various pockets around the world.


Geneticists now have shown signs of inbreeding in humans, neanderthals, and denisovans.  This new research shows tons of neanderthal DNA in modern humans.


Unfortunately, I think the ice sheets that covered much of the world for many thousands of years have destroyed what evidence we might have found.

Jamie Shreeve
Jamie Shreeve

On Denise's point - there are indeed some key fossils in the Levant around 100,000 years ago, notably at Qafzeh and Skhul, and the latter in particular was often thought of as a possible Neanderthal-modern human hybrid. More recently, the very modern-looking Qafzeh material has been viewed as evidence of an earlier "failed" excursion of AMH's out of Africa. And the genetic analysis recently (2012?) done by David Reich et. al.  puts the date of interbreeding between Neanderthals and AMH's between 37,000 and 86,000 years ago, suggesting that those 100,000-year old guys were not involved. But it's hardly the last word. It would indeed be sensational to get some DNA out of any of those Middle Pleistocene Levantine hominids... but seems unlikely given the hot climate.

Wayne T.
Wayne T.

Hey, what an early Human and a Neanderthal want to do in their cave is their business.

Gabriele Menefee
Gabriele Menefee

Yes, I concur with what Denise is saying.  I would be interested also in some sort of study for those other areas.  All you have to do is look at some people and you can see for yourself the genetic codes have been passed down from many generations.  Peoples have absorbed the DNA from Neanderthals and Denisovans a long time ago.  The dominate genes take over and many of the Neanderthal traits have disappeared but they are still there ( hidden ).  They come out every now and again.


Denise Ryan
Denise Ryan

 It's a stretch limiting this interaction to only 60,000 years.  Neanderthals and modern humans were coexisting and likely interbreeding over 100,000 years ago in the Levant.  Mount Carmel has Neanderthal remains dating back 120,000 years.  There could well have been a long history of interbreeding in that entire region even before homo sapiens started moving into the southern Europe and along the Mediterranean.  Neanderthal and modern human burials have been found in close proximity in several area in the Levant -- it would be very interesting to see the results of genetic studies from these remains.  There is also the possibility that the 'deserts' in the modern human genome which don't show any Neanderthal genetic heritage could mean that both groups shared  in common large vestiges of genetic material from earlier hominid populations.  But what I find the most interesting is that 10 years ago, everyone was saying that the Neanderthals were a dead end and had nothing to do with modern human genetics.  Big surprise!  

Jonathan Williams
Jonathan Williams

I am 1.8%  Neanderthal and 1.4% Denisovan which is the perfect mix in my book.

Didier Newman
Didier Newman

After all, what is the difference between the life that is in a cell, a chimp, a neanderthal or a modern homo sapiens? Do not come and vanishes in the same way, in one breath alone? Isn’t life a single indivisible movement, an information flow that stores and changes from a common ancestor? Or is there a unique quality in some place of the tree of life, a qualitative leap detached from all evolutionary processes and unrelated to the rest of life? If so, is it the same leap that the human language makes when differentiating between life itself and the rest of the universe? Also between human beings and the rest of animals, between food and eaters, health and disease, between life and death? Along these lines, there is a peculiar book, if you want there is a preview in http://goo.gl/rfVqw6 Just another suggestion, in order to free-think for a while.

Jon Normandin
Jon Normandin

If you translate d'Capatian you get "of the big head" and I believe that to be Neanderthal and or Denisovan.  The d'Capatians were the royal families of Europe and the royal families had to protect the blood ..... they were also sire.   They understood the importance of protecting the blood line and bringing it into the general human population.  Just my opinion, I am 3.5% Neanderthal and 3.4 % Denisovan. 

Angela Dallemagne
Angela Dallemagne

It's so awesome to learn about this stuff. Thanks science :D

Brandt Hardin
Brandt Hardin

Don’t expect this “science” to sneak its way into the classrooms here in the South.  Our Lord and Savior made it very clear there is no way we evolved from these savages.  Tennessee has passed the Monkey Law legislation which ensures teachers can challenge these so-called scientists and their twisted research funded by the liberals in Washington.  Read about how we’re keep Christ in the Classroom at http://dregstudiosart.blogspot.com/2012/04/pulpit-in-classroom-biblical-agenda-in.html

Matthew Fero
Matthew Fero

@john thomas  We also share 90% of our DNA with chimpanzees.  The reason  is that we share a common ancestor if you go back even further in time.  But that doesn't mean that we inherited anything from chimps recently. 


When they say we got 2% of our DNA from Neanderthal's, they mean more recently from Neanderthal's, not just from a common ancestor at earlier times.  (So yes, they are only referring to 2% of the 1% of the genome that was different between the two groups to begin with).  This means that there was interbreeding of the groups along the way, and the ancestral map is more complicated than a simple branch point at the time of earlier ancestors.  What we ended up with was mostly from the "modern human" coming out of Africa, not Neanterthal. 

Richmond Acosta
Richmond Acosta

@Kathleen Cleary Not true all the time. One species of dolphin was found to have risen from interbreeding of two separate species. 

For fertlity of the offspring of two separate species, the offspring can only be infertile if the number of chromosomes do not match. But if they did, it is possible to have an offspring who is fertile. The fertile offsprings can be only males or only the females or both sex.

Doug  L.
Doug L.

@Kathleen Cleary  This is true, if interbreeding happened we would be the same species and the uniqueness of each wouldn't matter that much. 


The above article provides some great science but, fortunately, two other important studies show it may be incorrect about the theory of hybridization being the cause of shared DNA.

One study that indicates we could not have interbred was published on Feb 4 of last year in the Journal 'Proceedings of the National Academy of Science' (PNAS).  Here, the Department of Prehistory and Archaeology at the Spanish National Distance Education University (UNED) used "ultrafilterration" to clean carbon contaminants that interfered with proper radio carbon dating and  found that the extinction of Neanderthal likely happened 50,000 years ago while modern humans didn't leave Africa to settle in the Iberian Peninsula region until 42,000 years ago. In the same journal in August 13 of the same year, Dr Andrea Manica, who led a Cambridge study on this subject said, "Our work shows clearly that the patterns currently seen in the Neanderthal genome are not exceptional, and are in line with our expectations of what we would see without hybridization."  Hard to say which researchers are right but the science article in Nature that the above article is based upon, provides as references, some work done by the same authors where the same claims are made. That's like quoting yourself to validate what you are saying.  Obviously, I could never dare deny the sensational proof that Neanderthals & Modern Humans did it, because my comment wouldn't be published, but I can say there are some crazy radicals out there that have other, completely unfounded ideas.

Richmond Acosta
Richmond Acosta

@S S It was the genes that increase the risk to having that disease that the article was talking aboutl. We are separate species from dogs and rats, but they do get cancer too. It just that certain gebes make people more at risk to these diseases.

Mark Moore
Mark Moore

@Brandt Hardin Science is how we learn about the wonder of God's creations. If your theology is in conflict with science, it's your theology that is the problem. If God is capable of creating the entire universe 6,000 or 10,000 years ago, he is fully capable of creating the entire universe with billions of years of history built-in.

If you cut down a tree in the Garden of Eden two days after creation, it would have tree rings indicating that it was much older than 48 hours. There's no reason the entire universe couldn't have been created the same way.


Creationism and evolution are not incompatible. Any religion that forces you to abandon your logic and reason and to ignore the truth in order to believe in God isn't much of a religion.

Angi Gray
Angi Gray

Lupus affects more people of African descent than any other; therefore the implication is that this genetic contribution effects risk to the benefit of those inheriting it, lowering the chance of Lupus in those populations with the gene in question. They never said any or all of the contributions were negative.

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