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Photo of a skeleton of a Homo heidelbergensis from Sima de los Huesos, a unique cave site in Northern Spain.

The bones were first thought to belong to European Neanderthals, but analysis showed they are genetically closer to the Siberian Denisovans.

PHOTOGRAPH BY JAVIER TRUEBA, MADRID SCIENTIFIC FILMS

Karl Gruber

for National Geographic

Published December 4, 2013

New tests on human bones hidden in a Spanish cave for some 400,000 years set a new record for the oldest human DNA sequence ever decoded—and may scramble the scientific picture of our early relatives.

Analysis of the bones challenges conventional thinking about the geographical spread of our ancient cousins, the early human species called Neanderthals and Denisovans. Until now, these sister families of early humans were thought to have resided in prehistoric Europe and Siberia, respectively. (See also: "The New Age of Exploration.")

But paleontologists write in a new study that the bones of what they thought were European Neanderthals appear genetically closer to the Siberian Denisovans, as shown by maternally inherited "mitochondrial" DNA found in a fossil thighbone uncovered at Spain's Sima de los Huesos cave.

"The fact that they show a mitochondrial genome sequence similar to that of Denisovans is irritating," says Matthias Meyer of Germany's Max Planck Institute for Evolutionary Anthropology in Leipzig, lead author of the study, published Wednesday in Nature.

"Our results suggest that the evolutionary history of Neanderthals and Denisovans may be very complicated and possibly involved mixing between different archaic human groups," he said.

Neanderthals and Denisovans arose hundreds of thousands of years before modern-looking humans spread worldwide from Africa more than 60,000 years ago. The small traces of their genes now found in modern humans are signs of interbreeding among ancient human groups.

Previously, the oldest human DNA sequenced came from bones that were less than 120,000 years old.

Meyer said stable temperatures in the cave helped preserve the mitochondrial DNA, and credited recent advances in gene-sequencing technology for establishing the basis for the new milestone.

Mixed Up or Mixing It Up?

For humanity's tangled past, the new mitochondrial DNA results raise an unexpected question: How does a Spanish early human species end up with Siberian DNA?

The authors propose several possible scenarios. For instance, Sima hominins could simply be close relatives of the Denisovans. But that would mean they lived right alongside Neanderthals without having close genetic ties to them.

The Sima hominins could also be a completely independent group that mingled with Denisovans, passing on their mitochondrial DNA, but it would be hard to explain why they also have Neanderthal features.

Another possibility, suggested by anthropologist Chris Stringer of the Natural History Museum in London, is that mitochondrial DNA from the Sima people reached the Denisovans thanks to interspecies sexual adventures among early humans, which introduced the DNA to both the Sima and Denisovans.

In the end, the identity of these ancient people remains a mystery, and further work is needed to clarify their identity. "The current genetic data [mitochondrial DNA] is too limited to conclude much about their population history," Meyer says.

As with the Denisovans, only the decoding of the full genetic map or genome, and not just the mitochondrial DNA, will provide convincing evidence of Sima family history, Meyer says.

Gif of the oldest human DNA

New Piece of the Puzzle

In recent years, paleogeneticists have released surprising reports about such early human species, notably the interspecies breeding that likely occurred among Neanderthals, Denisovans, and modern humans.

Uncovered only in 2010, Denisovans are known solely from a pinkie and a tooth found in 30,000- to 50,000-year-old rock layers in Siberia's Denisova cave. DNA from those Siberian bones first established their owners as genetically distinct from Neanderthals and modern people.

(Read "The Case of the Missing Ancestor" in National Geographic magazine.)

"The fact that the Sima de los Huesos [mitochondrial DNA] shares a common ancestor with Denisovan rather than Neanderthal [mitochondrial DNA] is unexpected in light of the fact that the Sima de los Huesos fossils carry Neanderthal-derived features," says the study.

But paleoanthropologist John Hawks of the University of Wisconsin, Madison, who was not part of the study, says "there's not really anything very surprising" about the Spanish bones' bearing mitochondrial DNA that is not an earlier version of Neanderthal genes.

Ancient mitochondrial DNA from many other species—"bison, mammoths, cave bears, and others"—doesn't resemble that of more recent species, he notes.

Hawks is more cautious than the study authors about regarding the Spanish genes and younger Denisovan ones as being closely related: "The difference between Sima and Denisova [gene] sequences is about as large as the difference between Neanderthal and living human sequences.

"It would not be fair to say that Denisova and Sima represent a single population, any more than that Neandertals and living people do."

One reason for caution is that mitochondrial DNA results in the past have pointed scholars in errant directions; for example, some early studies suggested that humans and Neanderthals did not share any common ancestry.

Mitochondrial DNA is a small part of the human genome that is generally transmitted only through the female line, from mothers to offspring. This has important implications for the study of past events.

For instance, ancient interspecies breeding events might not be picked up by mitochondrial DNA.

But mitochondrial DNA can be transferred between species when interspecies mingling events occur. Such scenarios have been observed for other groups, such as polar and brown bears, where it has been found that interspecies breeding led to mixed-up mitochondrial genomes.

The Mountain of Bones

The Atapuerca Mountains, where the human bones were found, is a world-famous archaeological site located in northern Spain; a group of caves there contain some of Western Europe's oldest known human remains.

The most famous of these caves, Sima de los Huesos, has been studied since 1997 and hosts more than 6,000 ancient bone samples belonging to 28 ancient humans that lived roughly 400,000 years ago. The exact origin of the bone pile is unclear.

"Could a natural catastrophe or carnivore activities explain the accumulation of so many bodies?" asks anthropologist Juan-Luis Arsuaga, a co-author of the study and lead excavator at the cave for the past 30 years. "Or were there hominins that accumulated the corpses of their relatives and friends in such a dark and remote place: a pit in a cave?

"I would like to live to know the answer."

The bones of the Sima people share the features of Neanderthals, notably their thick-browed skulls, as well as the features of a much older group of human ancestors called Homo heidelbergensis, which lived about 600,000 years ago.

That species is also considered an ancestor of modern humans, Denisovans, and Neanderthals.

72 comments
Yolande Maarsen
Yolande Maarsen

Sima bones may contain Denisovan mitochondrial DNA while still exhibiting Neanderthal features.  If the mothers were deliberately taken by Neanderthals for mating or slavery the evidence of paternity would be revealed in the Y-DNA carried only by males.  Conceivably, interspecies mixing could have been one-sided with the dominant species taking the weaker species' females captive in an early form of dissemination or slavery. 

Vanda Burns
Vanda Burns

At 400,000 yrs old it probably is still Homo Heidelburgensis. Also article suggests Denisovan's were only found in Siberia. It was one bone and the person could've migrated there from the west. Also, Homo Erectus migrated all the way to southeast China. Who knows, maybe the Sima homo and the Denisovian homo were both late Erectus. We have Denisova's genetics but no skull/skeleton to compare to Erectus and we have no Erectus to compare genetics to. Heidelburgensis is around the 5-400,000 yr mark. Just sayin!

Jerry Tausch
Jerry Tausch

Understanding things is always a challenge.

Andrew Klein
Andrew Klein

Note: Mitochondrial Eve, our common African mother according to theory, is dated only 100,000-200,000 years ago. Chromosomal Adam from Africa: oldest date is 338,000 years ago. Neanderthal origins: 350,000-600,000 years ago (few DNA  correlations with the modern humans that remained  in Africa).  Denisovan origins: over 400,000 years ago. So we have some older uncles and aunts, it appears, who are assumed also to have came from Africa, starting out there 650,000-1.3 million years ago.

Andrew Klein
Andrew Klein

Seems these guys were around for a whole lot longer than the accepted historical development of so-called "modern humans" in Africa 200,000 years ago and their supposed exit from that continent about 50,000 years ago .  What did we get from these earlier peoples through interbreeding in Europe/Asia?  What does it mean for the "out of Africa"  theory? Looks better and better for the fertile modern human hybrid model, with one-way gene transmittal, generated after leaving Africa and replacing these older types.

Sarah C.
Sarah C.

Wow!  I absolutely loved reading everyone's educated views from such diverse point of views.  I just learned a ton and will have to research some of the this (personal DNA, Brain Grain, female captives/movement of people, brain size debates, agricultural debates, ...love it.  -Middle School Social Studies Teacher

Sharon Magnin
Sharon Magnin

I have 2.5% Denisovan DNA and 2.0% Neanderthal DNA.  I'm interested in hearing from others who have Denisovan DNA

Al Barrs
Al Barrs

They are overlooking the possibility that female captives were at the top of the want list for male members of other tribes out on raiding forays, a practice that prevailed right into the Native American population only a couple of hundred years ago...

Roger Sinden
Roger Sinden

Is it possible that the specimens which have been used for DNA sequencing are just too far apart both geographically and chronologically to really pin down specifics of speciation?  Our species is highly prone to exploration, and it would seem likely that Desnovians and Neanderthals would be similar.  Assuming that finding one strain of genetic specimen anchors the species in that geographic location seems a bit off base to me.  Considering the extent of time passage between the dated fossil bones would it not be possible that peoples would have explored and moved and settled many areas over hundreds of thousands of years?  Thus inter-species breeding would not be uncommon, but maybe how we humans were derived?

james visentine
james visentine

This article really  makes you wonder what humans will look like and be like another 400,000 years from now. There have been catastrophic events in the distant past where entire species who roamed our planet millions of years ago have been eradicated from existence. Will the same fate happen to our species, homo sapiens?  Today, the world's population is about 7 billion people. The world's population is expected to increase to  10-11 billion people by 2050. How on earth will we feed, clothe, educate and provide energy and health care for that many people?

Vincent Zee
Vincent Zee

There will come a day when researchers just take our DNA string and strip stuff away to find the origin of humans. Evolution is the most wonderful thing, ever in progress.

Richard Veloso
Richard Veloso

This also may indicate the Denisovan might have looked like Neanderthals. Since we don't have Denisovan skull or full skeleton and the fact that Sima was mistaken for Neanderthal for many years, it stands to reason they might have looked the same. They may have thought that all were the same people, not knowing there own origins.

J. Kidd
J. Kidd

Science is so wonderful, but one day we will know for sure what we came from...I hope! 

Richard Veloso
Richard Veloso

As I have inherited Neanderthal DNA from my mother and Denisovan DNA from my father.

I am quite interested in seeing where this all leads. Might their be an "Alpha"  ancestor like Homo heidelbergensis that gave rise to both separate protohumans? Then thousands of year later they inbred. And might modern humans be some kind latter group out of Africa that mingled with those two? In any case the time lines that are based on artifact only seem to all off, DNA seems tell a more complete story. 

Stewart Mitchell
Stewart Mitchell

the   bones in a caves point to a serious famine in the past. A solar storm may have destroyed all the food on the surface. The survivors ate the Homo My guess is the Reptilians did the eating. There are rumors that they like humans.  A solar storm is predicted to occur soon . Cannibalism will make a come back. Perhaps comet Ison?

There are rumors of underground cities as well as martian colonies. This would explain why the government is psychotic.

Maddy Perrien
Maddy Perrien

I also don't understand why we're calling them Sima because it translates to pit in Spanish

Maddy Perrien
Maddy Perrien

How could the Sima live alongside the Neanderthals if the Sima are 400,000 years old and Neanderthals are less than 120,000 years old???

Art Fournier
Art Fournier

Why should this be construed as curious? Intraspecies mixing surely did occur. I am unsurprised. This patently reinforces evolutionary accretion and selective gnome modulation.

Cooper Gaskins
Cooper Gaskins

I wonder, do scientists try and run a genetic test on everything they find that looks reasonably close to being human? Because if they don't, they definitely should. Most curious. 

WILLIAM HALEY
WILLIAM HALEY

The bones were originally identified as Neanderthal because of their appearance. Of the Denisovan we have only a finger bone and a couple of theeth, along with the entire genome. These 400KYO remains share a Mt DNA relationship with the Denisovans. Perhaps the denisovans were anatomically simalar to the Neanderthals?

C. York
C. York

I think I would post My credentials if I was going to be talking about what the professionals should be doing, or was you there for the dig? I guess I expected to much from this blog too.

Juan Rivera
Juan Rivera

I can't wait until they sequence the entire genome.  I have a feeling there's going to be a few more surprises.  What if they do find Denisovan DNA made into the modern Homo sapien gene pool and Spanish people are found to be carriers.

El Gabilon
El Gabilon

Will this bit of news put food on our table? Will it help end war? Perhaps improve the economic decline in America? What was believed yesterday, won't be true tomorrow. What is true tomorrow won't be true years from now.  It is all very interesting to some but boring to the majority! The simple fact is that we moderns are here today and the question is what are we going to do about our situation worldwide.

Sean King
Sean King

Wow, the article mentioned that mtDNA is "thought" to be transmitted only through the female line. What? Isn't that certainty a known fact? Yes, mtDNA is only passed on from the mother, but it's passed on to females AND males. This article states that it's passed down only to females. Seems like such an amateur mistake. Am I missing something?

Tom Carberry
Tom Carberry

@james visentine  


I think HG Wells did an excellent job of describing this in The Time Machine with his Eloi race of frail degenerate humans.


I say this because since the dawn of agriculture about 10,000 years ago, humans have shrunk drastically in physical size and more importantly, in brain size.  The average modern human has a brain more than 10% smaller than the average pre-agricultural human.


For example, modern European women have an average brain volume of 1200 cc, which pre-agricultural European women had an average brain size of 1500 cc.  


This happened because of malnutrition and will continue because the foods I call the "starvation foods," foods humans had to eat to survive, namely grasses that became our modern day wheat, rice, corn, and other grasses, have become the main staples of our diets.


Humans should not eat grains.  Grains shrink your brain.  Many new studies have linked eating grains to dementia diseases such as Alzheimers.


But humans love grains.  They eat sandwiches, and croissants, and cookies, and almost everything seems to have one grain or another in it.  Billions eat wheat and rice every day of their lives, and causing harm to their brain with every bite.


The book Grain Brain talks about the effects of grains on the brain.  It doesn't mention the evolutionary aspect.


http://www.amazon.com/Grain-Brain-Surprising-Sugar--Your-Killers/dp/031623480X/ref=sr_1_1?ie=UTF8&qid=1389643001&sr=8-1&keywords=grain+brain


This blog discusses the evolutionary aspects of smaller brains:


http://johnhawks.net/research/hawks-2011-brain-size-selection-holocene/


And of course industrial farming focuses on the "staple" foods, which means that most people have no choice but to eat them.



Jean Lamb
Jean Lamb

@Maddy Perrien The human bones were found from the Sima de los Huesos (Pit of Bones) in Northern Spain's Sierra de Atapuerca.

kim brooks
kim brooks

@Maddy Perrien , i didn't understand the time line either....(article wasn't written very clearly?)  i thought they said there was also human dna in the 400,00 year old denisovan bones!  

Sean King
Sean King

@Juan Rivera It is! My DNA is 0.8% Denisovan, and 1.6% Neanderthal (sequenced by the NatGeo Human Genographic Project 2.0). It's just not a part of the Neanderthal I believe. 

Tim Morris
Tim Morris

@El Gabilon Oh god, not this tired old argument again. People study things because knowledge is power, to leave anything unstudied is against human nature, and besides that is negligent and anti-intellectual.

Sean King
Sean King

@El Gabilon Such a flippant comment. Yeah you're right, let's retard our knowledge of the world, history, and prehistory, with respect to anthropology - the study of human evolution. If that view had predominated, we'd still think biology is fixed and would have no real idea where humans came from. Let alone the revolutionary fundamental ideas of evolution and natural selection.  You think that's a good thing? For one, genetics has essentially proven that the idea of 'race' doesn't exist, that there is no biological basis for it. You don't think that if everyone understood this and adapted this proven idea from a young age that there would be less racism in the world? That understanding through various scientific fields (e.g. genetics/paleoanthropology) the justification for racism is absolutely impossible? This means nothing to you?

Genetics has already made headway in understanding disease, and how certain diseases affect certain ethnic groups (those who evolved in different areas, for a certain amount of time). But apparently this is useless, and instead we should buy food and place it on the table. Yep, that'll move the species forward. 

Eric Paul
Eric Paul

@El Gabilon What an idiotic and pointless post - ironic considering that's exactly what you were complaining about.  Studying our past is important because, unlike you, MOST people actually care to one day answer the question - Where did we come from?

John Sumner
John Sumner

@Tom Carberry @james visentine  I'm sorry but to me a lot of what you said is just silly. Brain size is not necessarily indicative of intelligence. Sperm whales, elephants, and other large mammals have larger brains than humans. Conversely a crow's brain is smaller than a walnut and common crows are among the most clever creatures on Earth. Human male brains on average are bigger than female's, and I don't think anyone would argue that men are smarter than women. I know that you did not say or imply that, but you seem to be drawing a connection between brain size and our "downfall" and there really is no evidence to support that. 


I'm not going to argue that grain is good or bad for us. I have no knowledge on the subject and you're probably right on certain aspects of that argument. It is also certainly true the introduction of red meat into our diet as our ancestors became more proficient in hunting was an enormous contributing factor to our larger brain sizes and the evolutionary advancement of our species.

 However to say agriculture was a bad thing for humans is just not true. The invention of agriculture and the shift from hunting/gathering to husbandry is the sole reason humans were able to create food surpluses that allowed us to establish permanent settlements and eventually create civilizations and empires. Before that, humans rarely lived to 30 years old, and were unable to stay in one place as we had to move in sync with animal migrations and other food resources. Agriculture is indeed the only reason I'm even able to turn on my laptop, connect to the internet, and write out this message. 

John Sumner
John Sumner

@Tom Carberry @james visentine  I'm sorry but to me a lot of what you said is just silly. Brain size is not necessarily indicative of intelligence. Sperm whales, elephants, and other large mammals have larger brains than humans. Conversely a crow's brain is smaller than a walnut and common crows are among the most clever creatures on Earth. Human male brains on average are bigger than female's, and I don't think anyone would argue that men are smarter than women. I know that you did not say or imply that, but you seem to be drawing a connection between brain size and our "downfall" and there really is no evidence to support that. 

I'm not going to argue that grain is good or bad for us. I have no knowledge on the subject and you're probably right on certain aspects of that argument. It is also certainly true the introduction of red meat into our diet as our ancestors became more proficient in hunting was an enormous contributing factor to our larger brain sizes and the evolutionary advancement of our species.

 However to say agriculture was a bad thing for humans is just not true. The invention of agriculture and the shift from hunting/gathering to husbandry is the sole reason humans were able to create food surpluses that allowed us to establish permanent settlements and eventually create civilizations and empires. Before that, humans rarely lived to 30 years old, and were unable to stay in one place as we had to move in sync with animal migrations and other food resources. Agriculture is indeed the only reason I'm even able to turn on my laptop, connect to the internet, and write out this message. 

Terra L.
Terra L.

I agree with you, Tom! My Anthropology prof in college always said that agriculture was the downfall of human civilization. Yes, it allows us to feed the masses but it is not what our bodies were meant to eat. Once grains and bread were introduced into cultures, we see a big uptik in people dying from malnutrition, more birth defects, smaller bodies and bad teeth! We have been a hunter gatherer species for so long and only just recently in the big scheme of things did we turn to grains. It is not what we were meant to have!

Sharon Magnin
Sharon Magnin

@Sean King @Juan Rivera I also had my DNA analysis by the NatGeo Human Genographic Project 2.0.  I found out my DNA is 2.5% Denisovan and 2% Neanderthal.  We are awaiting results of my husband's analysis.

Juan Rivera
Juan Rivera

@Sean King @Juan Rivera Wow, that sounds like a cool story.  Why did you decide to get your genome sequenced, how did you contact NatGeo for it, did you have to pay, what kinds of info did you find out about yourself?  You really could write a book about that experience.

Rick Moore
Rick Moore

@Sean King @El Gabilon Right, we all look the same... eg. a Polar Bear and Brown Bear/ and a Tiger and a Lion are the same animal! Give me a break!

Sean King
Sean King

@El Gabilon We should probably stop exploring space as well. What a waste of money!

N. D
N. D

@Eric Paul @El Gabilon studying evolutionary genetics is a big part of getting people medical care; understanding genetic background of disease and evolution of viruses and bacteria alongside human evolution. 


some parts of it does help put food on the table because we get to see how our diet has evolved, for example, the gene for lactose digestion evolved independently in multiple prehistoric groups around the world. 

Marvin Dookharan
Marvin Dookharan

@John Sumner @Tom Carberry @james visentine Whales and elephants have larger brains than humans do, but they have less neurons in their brains than humans do.


No known species has as many neurons in their brains as humans do.


Also those animals you mentioned with larger brains don't have arms, hands, and fingers like humans do, so they can't use their intelligence in the same way that humans can.


If humans didn't have anything like arms we'd probably appear a lot less intelligent.

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