The Surprising Story of 400,000 Year Old Human DNA

Researchers have just announced a major advance in their quest to recover DNA from ancient humans.  400,000 year old bones contain badly damaged DNA sequences, but experts in Leipzig, Germany, have developed new techniques to extract and piece together tiny fragments until they can read at least a small portion of the genes carried by ancient humans who once lived in northern Spain.

Caption: The Sima de los Huesos hominins lived approximately 400,000 years ago during the Middle Pleistocene. Credit: Javier Trueba, Madrid Scientific Films.Usage Restrictions: None

A team led by Matthias Meyer at the Max Planck Institute for Evolutionary Anthropology in Leipzig worked together with a Spanish team of paleontologists led by Juan-Luis Arsuaga to extract tiny amounts of bone from fossil remains found at Sima de los Huesos, northern Spain’s famous “bone pit.”  This site has been excavated for more than two decades.  It has yielded at least 28 skeletons, usually classified as Homo heidelbergensis, a form of humans seen as the ancestors of the Neandertals.

 

But here is where this study broke new ground.  It turns out that the Sima de los Huesos humans were more closely related to the recently discovered Denisovans than to the Neandertals.  "The fact that the mtDNA of the Sima de los Huesos hominin shares a common ancestor with Denisovan rather than Neandertal mtDNAs is unexpected since its skeletal remains carry Neandertal-derived features," Meyer said in a press release provided by the journal Nature, which carries the report in its 4 December 2013 issue. 

What makes this finding all the more intriguing is that the Denisovans were completely unknown to us until 2010, when the Leipzig team “discovered” them by reconstructing their DNA and comparing it to Neandertals and today’s humans.  Through a spectacular technological achievement, Leipzig researchers discovered that these Denisovans lived as a distinct population some tens of thousands of years ago, when they interbred with other humans. 

"This unexpected result points to a complex pattern of evolution in the origin of Neandertals and modern humans. I hope that more research will help clarify the genetic relationships of the hominins from Sima de los Huesos to Neandertals and Denisovans" says Arsuaga. 

Caption: This is a skeleton of a Homo heidelbergensis from Sima de los Huesos, a unique cave site in Northern Spain.  Credit: Javier Trueba, Madrid Scientific Films.  Usage Restrictions: None

 

According to the most recent discovery, the Sima de los Huesos hominins seem to have shared a common ancestor with the Denisovans some 700,000 years ago.  The idea that they are more closely related to Denisovans than to Neandertals suggests that these mysterious Denisovans, totally unknown just four years ago, may have played a far bigger role in the story of human origins than ever imagined. 

It is important to point out that so far, researchers have only reconstructed the DNA of the mitochondrial.  And even there, the work is not complete.  Whether they succeed in reconstructing the DNA of the far more daunting heidelbergensis genome remains to be seen.  But if past experience is any predictor, we might look for advances not just here but in other human remains from hundreds of thousands of years ago.  Each technical achievement may fill in a page in our past, maybe even re-writing whole chapters.  When it comes to human origins, we should expect more surprises. 

Putting this most recent news in a larger context, Svante Pääbo, the director of the Leipzig research, said this in the Nature press release: "Our results show that we can now study DNA from human ancestors that are hundreds of thousands of years old. This opens prospects to study the genes of the ancestors of Neandertals and Denisovans. It is tremendously exciting."

The article, “A mitochondrial genome sequence of a hominin from Sima de los Huesos,” appears in the 4 December 2013 issue of the journal Nature. 

 

 

 

Is Neandertal Technology Still in Use Today?

Those primitive Neandertals may not have been so primitive after all.  Some 50,000 years ago, they were using a highly crafted bone tool virtually identical to a tool in use by human leather-workers today.

The tool is called a lissoir, was made by Neandertals living in southwestern France long before the arrival of the people we like to call “anatomically modern humans.”  The discovery, reported in the August 16, 2013 online issue of PNAS, is sure to fuel the debate over the cultural sophistication of the Neandertals.

Caption: Four views of the most complete lissoir found during excavations at the Neandertal site of Abri Peyrony.  Credit: Image courtesy of the Abri Peyrony and Pech-de-l’Azé I Projects.

Ever since their discovery over 150 years ago, Neandertals have been seen as “cavemen,” primitive in every respect compared to us “modern” humans who replaced them.


But in recent decades, the cultural achievements of Neandertals have been recognized.  Even so, the debate continues.  Did they learn more advanced technology from the modern human invaders of Europe and Asia, or did they develop it on their own?  The new findings lends support to the view that Neandertals were able to create and invent on their own. 

Neandertals were very likely the first to use sophisticated bone tools in Europe.  The tool found in France was made from the rib bone of red deer or possibly reindeer.  Making it required breaking, grinding, and polishing.  It shows evidence of being used to work leather, much like similar tools today.  When rubbed against an animal hide, it makes the leather soft, shiny, and more water resistant.

"For now the bone tools from these two sites are one of the better pieces of evidence we have for Neandertals developing on their own a technology previously associated only with modern humans", explains Shannon McPherron of the Max Planck Institute for Evolutionary Anthropology in Leipzig according to a press release from the Institute. 

Tools like this first appear in Africa much earlier.  But this new finding raising intriguing questions.  Did “modern” humans bring this technology from Africa and pass it to Neandertals prior to 50,000 years ago? Is there a technology transfer around the same time as modern/Neandertal interbreeding?  Or did Neandertals invent this technology on their own and transfer it to the modern humans who began to arrive in Europe around 40,000 years ago? 

"If Neandertals developed this type of bone tool on their own, it is possible that modern humans then acquired this technology from Neandertals. Modern humans seem to have entered Europe with pointed bone tools only, and soon after started to make lissoirs. This is the first possible evidence for transmission from Neandertals to our direct ancestors," says Marie Soressi of Leiden University in The Netherlands, part of the team of researchers who made this discovery.

"Lissoirs like these are a great tool for working leather, so much so that 50 thousand years after Neandertals made these, I was able to purchase a new one on the Internet from a site selling tools for traditional crafts," says Soressi. "It shows that this tool was so efficient that it had been maintained through time with almost no change. It might be one or perhaps even the only heritage from Neandertal times that our society is still using today."

Neandertals at this time were making sophisticated stone tools.  But these tools were made of bone because bone can is more adaptable for certain uses.  According to McPherron, "here we have an example of Neandertals taking advantage of the pliability and flexibility of bone to shape it in new ways to do things stone could not do."

The deeper question that lies behind this research is whether “modern humans” burst on the scene suddenly as a unique phenomenon of evolution, or whether the process of becoming human is more gradual and more widely distributed than we once thought.  

The research reported here was conducted by teams from Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and the University of Leiden in the Netherlands.  The article, entitled “Neandertals made the first specialized bone tools in Europe,” appears in the August 16, 2013 online edition of the Proceedings of the National Academy of Sciences.
 

Did Neandertals Wear Ornaments?

A small but tantalizing find provides further evidence for Neandertal culture.  Working in the foothills of the Alps just north of Venice, Italy, researchers have discovered and analyzed a small marine shell that originally came from about 60 miles away.  It was thinly coated with a dark red substance that turns out to be pure hematite and was most likely used as a pigment.  One possibility is that the shell was used as an ornament.

The paper, freely available online in the journal PLoS One, dates the shell’s pigmentation to a period just before 45,000 years ago, right before the arrival of so-called “modern” humans in Europe. 

Photo Caption: A shell possibly "painted" by Neandertals about 45,000 years ago.  Photo available from PLoS One.

According to the paper, “deliberate transport and coloring of an exotic object, and perhaps its use as pendant, was a component of Neandertal symbolic culture, well before the earliest appearance of the anatomically modern humans in Europe.”

Quoting more of the paper, “this discovery adds to the ever-increasing evidence that Neandertals had symbolic items as part of their culture.”

Debates about Neandertal culture have intensified recently, in part because of genetic evidence of interbreeding between Neandertals and the modern humans coming into Asia and Europe.  While these modern humans began their migration out of Africa about 80,000 years ago and probably interbred around 55,000 years ago, they did not reach Europe until more like 40,000 years ago.  If all these dates hold up in future research, this shell does provide a small but intriguing hint about the culture of Neandertals at just about the time of their encounter with “modern” humans. 

So who exactly is modern?  The differences between ourselves (the humans we like to call “modern”) and the Neandertals are not as great than we once imagined.  The paper ends with these words: “Future discoveries will only add to our appreciation of Neandertals shared capacities with us.”

The paper, entitled "An Ochered Fossil Marine Shell From the Mousterian of FumaneCave, Italy," appears in the current issue of PLoS One and is freely available online.

Asians, Europeans, and Neandertals

New research suggests that Europeans and Asians diverged at least 40,000 years ago, starting a process leading to the subtle differences that distinguish people to this day.

Working with bones discovered in 2003, researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig were able to reconstruct portions of DNA from an individual who lived in China about 40,000 years ago. Earlier analysis of the bones suggested that this individual showed “archaic” features, somewhat like Neandertal bones.

Credit: A Photograph of China's Empress Dowager, taken in the 1890s by Xunling, the Imperial Court Photographer. In the public domain.

The Max Planck team, led by Svante Pääbo, is well-known for work in producing the virtually complete Neandertal genome. In addition, using just a tiny fragment of a finger bone, this team produced the genome of a previously unknown form of humanity, called the Denisovans.

In their earlier work, they discovered that Europeans and Asians are descended in part from Neandertals, who disappeared about 30,000 years ago. In addition, some Asians, especially those living on the islands south of Asia, are partly descended from the Denisovans.

One of the reasons why the team was interested in this new sample was to look more deeply into the relationship between Europeans and Asians and to ask what role Neandertal and Denisovan interbreeding might have played.

Comparing the newly-reconstructed DNA sequence from the 40,000 year old bones, they found they were looking at an individual who also was descended from Neandertals, pretty much the way Europeans and Asians are today. And they also learned that this individual showed no evidence of Denisovan interbreeding.

What this means, they suggest, is that 40,000 years ago, an early version of anatomically modern Eurasians lived in China, near Beijing. While this human community was very much like the humans moving into Europe at about the same time, these two lineages were beginning a process of divergence.

On the basis of additional comparisons, the team concluded that the early-modern human community in China 40,000 about years ago was closely related to today’s Native Americans.

The report is also significant because it shows the power of new approaches to DNA extraction and sequencing. In their raw form, the samples extracted from the bones contained mostly DNA from microorganisms. In fact the human DNA was less than one-tenth of one percent of the total DNA. Even so, researchers were able to establish reliable human sequences, suitable for comparison with other human genomes.

What does that mean? At the very least, it means that many more discoveries like this lie ahead. The new technology means that old findings take on new significance.

The research appears online January 22, 2013, in the Proceedings of National Academy of Sciences, as "DNA analysis of an early modern human from Tianyuan Cave, China."

Stone-Tipped Weapons: Older than We Thought

Stone-tipped spears have been around for at least 500,000 years, according to new research. That is about 200,000 years earlier than previously thought.

Why is that important? In part because it suggests that modern humans did not invent this technology. They did not get it from the Neandertals, nor did Neandertals get it from modern humans. Instead, it now seems that Neandertals and modern humans both used stone-tipped spears because both inherited this technology from an earlier form of human life.

It is generally believed that Neandertals and modern humans diverged about 500,000 years ago. The current view is that both came from earlier humans known as Homo heidelbergensis.

"Rather than being invented twice, or by one group learning from the other, stone-tipped spear technology was in place much earlier," according to Benjamin Schoville, who coauthored the study and is affiliated with the Institute of Human Origins at Arizona State University. "Although both Neandertals and humans used stone-tipped spears, this is the first evidence that this technology originated prior to or near the divergence of these two species," Schoville said according to a press release from his university.

Caption: A ~500,000-year-old point from Kathu Pan 1. Multiple lines of evidence indicate that points from Kathu Pan 1 were used as hafted spear tips. Scale bar = 1 cm. Credit: Jayne Wilkins. Usage Restrictions: Image may be used to illustrate coverage of this research only.

"This changes the way we think about early human adaptations and capacities before the origin of our own species," said Jayne Wilkins, a lead author from the University of Toronto. Technological advance—in this case stone-tipped spears—is now seen as more widely shared among the various forms of humanity and not so confined to anatomically modern humans like us. Creating stone-tipped spears requires more forethought and care than simpler stone tools, especially in preparing the tips for mounting to the wooden shaft of the spear. This process is called “hafting,” and the result is that a more efficient hunting weapon is created.

In this study, researchers re-examined stone points discovered more than thirty years ago. By comparing the damage to the spear tips with simulated damage re-created under laboratory conditions, researchers found evidence that strongly supports the view that the original tips were used for spears.

"When points are used as spear tips, there is a lot of damage that forms at the tip of the point, and large distinctive fractures form. The damage on these ancient stone spear points is remarkably similar to those produced with our calibrated crossbow experiment, and we demonstrate they are not easily created from other processes," said coauthor Kyle Brown, a skilled stone tool replicator from the University of Cape Town.

Brown, along with others who worked on the current paper, also collaborated on a study just released describing further stone weapons refinements that occurred about 70,000 years ago and probably gave modern humans an advantage over Neadertals. For more on that, see Better Technology, Better Weapons.

The most recent findings that push the date of stone-tipped spears back to 500,000 years ago are published as "Evidence for Early Hafted Hunting Technology" in the November 16, 2012 issue of Science.

Art in an Age of Neandertals

The oldest confirmed date for cave art has just been pushed back again. New research re-dates paintings in caves in northern Spain to a staggering 40,800 years ago, right at the time when anatomical modern humans (AMHs) like us were just arriving in the region and encountering Neandertals.

In fact, this art is so ancient that it raises the haunting possibility that Neandertals were the painters. If so, then modern humans are not the only form of humanity to create cave art. For now, however, the question of who painted this art is a matter of speculation, something that might be settled by further research.

In work published in the June 15, 2012 issue of Science, researchers studied 50 paintings in eleven caves in the northernmost part of Spain, including the UNESCO World Heritage sites of Altamira, El Castillo and Tito Bustillo. The work was conducted by an international team led by Alistair Pike of the University of Bristol.

The Corredor de los Puntos, El Castillo Cave, Spain. Red disks here have been dated to 34,000-36,000 years ago, and elsewhere in the cave to 40,600 years, making them examples of Europe's earliest cave art. Image courtesy of Pedro Saura.

This research comes on the heels of a re-dating of cave painting in France, recently pushed back to 37,000 years. The latest study adds almost another 4,000 years to the confirmed date of the oldest art. What’s the combined effect of the two studies? In just the past month, our view of the antiquity of art has jumped by nearly 10,000 years, prompting us to wonder how much further back it might go. After all, it is known that AMHs mixed pigments as far back as 100,000 years ago.

Using a new method called uranium-thorium dating, Pike’s research team took a closer look at an old find. They extracted tiny samples of naturally forming deposits that covered the paintings. By dating the deposits, scientists are able to discover the date before which the paint was applied. The date of more than forty thousand years ago, therefore, is a minimum date, suggesting that some of the paintings—here or elsewhere—may be even older.

The specific painting that exceeds 40,800 years is a simple red disk, seemingly primitive when compared to paintings made later in the same caves. More striking are the handprint paintings on the wall of El Castillo cave, made by blowing paint and common in early cave art but now dated to 37,300 years ago.

Commenting on the age of the oldest painting, Pike pointed out the tight fit between the painting and the arrival of AMHs in northern Spain: “Evidence for modern humans in Northern Spain dates back to 41,500 years ago, and before them were Neanderthals. Our results show that either modern humans arrived with painting already part of their cultural activity or it developed very shortly after, perhaps in response to competition with Neanderthals – or perhaps the art is Neanderthal art,” Pike said in a press release issued by the University of Bristol.

The Panel of Hands, El Castillo Cave, Spain. A hand stencil has been dated to earlier than 37,300 years ago and a red disk to earlier than 40,600 years ago, making them the oldest cave paintings in Europe. Image courtesy of Pedro Saura.

Pike also speculated further on the possibility that researchers may someday identify some European cave art as Neandertal. He suggested that perhaps, “cave painting started before the arrival of modern humans, and was done by Neanderthals. That would be a fantastic find as it would mean the hand stencils on the walls of the caves are outlines of Neanderthals' hands, but we will need to date more examples to see if this is the case."

The article in entitled “U-series dating of Palaeolithic Art in 11 Caves in Spain” and appears in the June 15, 2012 issue of the journal Science.

Complicating the Family Tree

Our view of our past keeps getting more complicated. Our family tree, it turns out, is more of a twisted vine than a neatly linear branch.

Evidence keeps building by the day that our anatomically modern human (AMH) ancestors interbred with earlier forms of “archaic” humans. In the 31 Oct 2011 early online issue of PNAS, Pontus Skoglund and Mattias Jakobsson present evidence for the view that the genetic legacy of the Denisovans is wider than ever thought before.

First is was the Neandertals. This branch of the human family diverged from our own somewhere around 500,000 years ago. Somewhere between 100,000 and just 50,000 years ago, however, AMHs and Neandertals interbred successfully. The result lives on today in our genes. For many of us, our DNA is 2-3% from our Neanderthal ancestors. The Neandertals may be extinct, but their DNA lives on in every cell in the human body.

Then it was the Denisovans, a recently discovered branch of the human family more closely related to Neandertals than to us. What about AMH-Denisovan iInterbreeding? An international team of researchers led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig was able to extract Denisovan DNA from tiny fragments of remains. From the extracts, they reconstructed the Denisovan genome and compared it with the human genome. What they found was clear evidence of interbreeding. Some living human beings—those identified as Melanesians—carry Denisovan genes. That was reported in December 2010.

In September, however, Pääbo was joined by David Reich and Mark Stoneking and other colleagues in reporting that the legacy of Denisovan DNA extends beyond the Melanesians. It’s all over the islands that extend below Southeast Asia, including Australia. Not just Aboriginal Australians but Near Oceanians, Polynesians, Fijians, east Indonesians, and other groups as far as the Philippines are carriers of the Denisovan legacy.

According to this study, the genetic legacy of AMH-Denisovan admixture does not include East Asians. This led the authors to conjecture that there are at least two main waves of AMH migration into southeast Asia. The first wave interbred with Denisovans while the second, apparently, did not.

Their work appeared in the 7 Oct 2011 issue of the American Journal of Human Genetics. Reich discusses these findings in a video. Hint: start at minute 22:30.

But now a study published in the online early edition of the Proceedings of the National Academy of Sciences for the week of 31 Oct 2011 presents evidence that East Asians are also descended in part from the Denisovans. In the paper, the authors (Pontus Skoglund and Mattias Jakobsson) write that “we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome.”

Experts in the field will no doubt debate these findings. Just how widespread is the effect of AMH-Denisovan interbreeding? How widely did AMHs and archaic humans interbreed? To what extent does admixture provide any benefit? Does it shed any light on observable differences between different groups within the human family today?

According to Skoglund and Jakobsson, the “history of anatomically modern and archaic humans might be more complex than previously proposed.”

If our past is more complex than we thought, so is our present. What does it mean to be human? It no longer seems to mean that we are all part of a biological species. Whether we like to call ourselves "anatomically modern humans" (AMHs) or Homo sapiens, we are learning that the very concept of species is becoming unfocused by research. Should we speak of AMH-Denisovan "interbreeding" or "hybridization"? Does it matter? Are we separate species or one slightly-tangled humanity?