Old DNA, New Tricks

Over the past decade, researchers have learned to reconstruct ancient DNA from fossils.  In December 2013, we were stunned to learn that refinements in techniques made it possible to restore human DNA from as far back as 400,000 years ago. 

Quickly on the heels of that advance, another new development has been announced in the 27-31 January online edition of PNAS.  Scientists at the University of Uppsala, in cooperation with the pioneering team in Leipzig, have developed a way to separate the old DNA sequences from contamination.

Photo Credit: Creative Commons, posted by Archaeogenetics, no restrictions.

Why is that important?  Because contamintion is a leading problem when it comes to reconstructing ancient DNA.  Literally thousands of fossils fill draws and shelves in museums around the world.  They contain DNA, too much of it, in fact, to be of any use.  Bits of ancient DNA are surrounded by more modern DNA from humans and from other organisms.  Now, researchers have learned to separate the old from the new. 
 
What makes the new breakthrough exciting is that now, at least some DNA information from many of these old fossils might be retreivable. 

"Many extremely interesting DNA data sets from ancient humans never see the light of day because of contamination. The idea behind this method was to change that," says Pontus Skoglund, a lead author at Uppsala University.
 
To test the new technique, the researchers used it to reconstruct the mitochondrial DNA from a previously unusuable Neandertal bone from the Altai Mountain region of Siberia.  The sample compared well with other known Neandertal DNA sequences in contrast to more modern humans.
 
It is hard to predict just where this new technology will lead.  At the very least, it seems to unlock the file boxes of museums throughout the world.  Previously discovered fossils, some of them very well dated, might be analyzed for the DNA.  Who knows what we will learn.

"There are many really interesting ancient human remains that we can rescue from severe contamination with this method. And the method is not limited to Neanderthals, even remains of anatomically modern humans that are contaminated by modern-day humans can be rescued," says co-investiagor Mattias Jakobsson in a press release from the University of Uppsala.
 
The new technique is described in a paper entitled "Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal." Skoglund, P.; Jakobsson, M.; Northoff, B.H.; Pääbo, S.; Krause, J.; Shunkov, M.V.; Derevianko, A.P; PNAS Online Early Edition the week of Jan 27-Jan31, 2014.

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.

Denisovan DNA in Focus

Using new techniques to study ancient DNA, scientists have unraveled the genetic details of a young girl who lived in central Asia around 50,000 years ago. She is the only individual of her kind, a unique branch of the human family called the Denisovans, named for the cave where her remains were found in 2008.

What makes the research all the more startling is that only two teeth and one pea-size bone fragment has been found. But from those tiny fragments of humanity, the story of the Denisovans is being pieced together.

The new techniques were developed by Matthias Meyer, working at the Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology in Leipzig, a research program led by Svante Pääbo. DNA extracted from the bone fragment was separated into two strands that were amplified and analyzed separately, many times over, until a highly reliable sequence was determined.

Laboratory for the extraction of ancient DNA. [Image courtesy of Max Planck Institute for Evolutionary Anthropology].

Researchers claim that the result is as complete and accurate as the sequence of living human beings. Already, the new technique is being used to study other ancient remains, including samples of Neandertal DNA. Denisovans and Neandertals, distinct but closely related forms of humanity, overlapped with anatomically modern humans (AMH) and interbred with them.

New methods in genetics, including the technical breakthrough described in this paper, are opening new windows on the human family tree, which resembles an inter-grown vine more than a straight line of branches.

So accurate is the genetic analysis that researchers can reach some conclusions about other Denisovans, even though no samples exist for them. For one thing, despite their wide geographic spread, they apparently never reached high numbers. Their DNA lives on today in the faint echo of ancient interbreeding found in the uniquely-Denisovan sequences carried by those who live in the islands of southeast Asia.

No one knows what Denisovans looked like, but they probably resembled us in many ways. The Denisovan girl whose DNA was studied carried genes that are associated today with brown hair, brown eyes, and dark skin. Like us they had 23 pairs of chromosomes (compared to chimps with 24), making interbreeding more readily possible.

Denisova molar, distal. [Image courtesy of Max Planck Institute for Evolutionary Anthropology].

One of the more tantalizing aspects of the report is the light it sheds not on the Denisovans or the Neandertals but on us anatomically modern human beings who live today. Why did we survive and flourish culturally when they did not?

One explanation may lie in the genetic differences between us and them, which can be studied for the first time in detail. In this paper, researchers identify specific changes in genes that are associated with brain complexity, synaptic connections, and speech development. According to the paper, “it is thus tempting to speculate that crucial aspects of synaptic transmission may have changed in modern humans.” In other words, tiny differences in DNA led to still relatively small differences in brain function that led to huge differences in culture.

Future technical advances will continue to shed new light on the complex story of recent human ancestry. By gaining ever-higher clarity on the genetic differences between Neandertals, Denisovans, and modern humans, we will come to know the story of our humanity in greater detail.

The paper ends with this reflection: “This [work] should ultimately aid in determining how it was that modern humans came to expand dramatically in population size as well as culturally complexity which archaic humans eventually dwindled in numbers and became physically extinct.” The paper, “A High-Coverage Genome Sequence from an Archaic Denisovan Individual,” is published in the 30 August 2012 issue of Science, published by the American Association for the Advancement 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.

How Old Is Art?

Confirmed dates for the world’s oldest art just got older, according to the report of an international research team published in the May 14 issue of the Proceedings of the National Academy of Sciences.

Dating back about 37,000 years, the art consists of engravings made in stone that has since fallen from the ceiling of a cave at Abri Castanet in southwestern France. While not as visually arresting as the more famous cave art found at Chauvet, the Castanet engravings are both older and represent what is very likely an earlier stage in the history of the Aurignacian culture, which spanned 40,000 to about 28,000 years ago. Some of the Chauvet paintings are now confirmed at between 30,000 and 32,000 years ago.

Credit: HTO. A replica of a painting, now in the public domain.

The Castanet engravings are both simpler artistically and were located in the general living area of the cave. The Aurignacian culture that created both the paintings and the engravings is known for is many forms of art. According to New York University anthropology professor Randall White, one of the study's co-authors, the Aurignacians "had relatively complex social identities communicated through personal ornamentation, and they practiced sculpture and graphic arts."

"But unlike the Chauvet paintings and engravings, which are deep underground and away from living areas, the engravings and paintings at Castanet are directly associated with everyday life, given their proximity to tools, fireplaces, bone and antler tool production, and ornament workshops," White said in press release issued by NYU.

With more refined archeological techniques, the story of the rise of human symbolic culture is likely to become more complex and more ancient. While there may well have been bursts of cultural creativity in which symbolic advance occurred rapidly, additional findings may also suggest a more steady rise in the story of human art. The study, entitled “Context and dating of Aurignacian vulvar representations from Abri Castanet, France,” appears in the May 14, 2012 edition of PNAS.

A Million Years of Fire

One of our newest technologies has just shed new light on one of our oldest.

When did our human ancestors learn to control and use fire? Armed with the latest high tech tools, an international team of researchers has pushed the date back to 1 million years. That’s 300,000 years earlier than previous unambiguous dates.

The massive Wonderwerk Cave is in northern South Africa on the edge of the Kalahari. Previous excavations have shown extensive human occupation. Using the new techniques of micromorphological analysis and Fourier transform infrared microspectroscopy (mFTIR), researchers analyzed cave sediments at a far more detailed level than possible before.

Caption: This is a panoramic view of the entrance to Wonderwerk Cave, South Africa. Credit: H. Ruther. Usage Restrictions: None

In the cave sediments researchers found bits of ash from plants along with fragments of burned bone. Did the wind blow burning debris into the cave? The evidence—collected about 100 feet from the current opening of the cave—supports the conclusion that the fire burned in the cave. Also part of the proof: the surrounding surfaces are discolored.

”The analysis pushes the timing for the human use of fire back by 300,000 years, suggesting that human ancestors as early as Homo erectus may have begun using fire as part of their way of life," anthropologist Michael Chazan said in a press release from the University of Toronto.

According to the paper, "Through the application of micromorphological analysis and Fourier transform infrared microspectroscopy (mFTIR) of intact sediments and examination of associated archaeological finds— fauna, lithics, and macrobotanical remains—we provide unambiguous evidence in the form of burned bone and ashed plant remains that burning events took place in Wonderwerk Cave during the early Acheulean occupation, approximately 1.0 Ma. To date, to the best of our knowledge, this is the earliest secure evidence for burning in an archaeological context."

Caption: Interior of Wonderwerk Cave. Images courtesy of M. Chazan.

"The control of fire would have been a major turning point in human evolution," says Chazan. "The impact of cooking food is well documented, but the impact of control over fire would have touched all elements of human society. Socializing around a camp fire might actually be an essential aspect of what makes us human."

How important are fire and cooking for human evolution. A recent book, Catching Fire: How Cooking Made Us Human by Richard Wrangham, argues that cooking is essential to our humanity. Now in the paper published on April 2, the team concludes that its study “is the most compelling evidence to date offering some support for the cooking hypothesis of Wrangham.”

Their work is published as “Microstratigraphic evidence of in situ fire in the Acheulean strata of Wonderwerk Cave, Northern Cape Province, South Africa,” in the April 2, 2012 issue of the Proceedings of the National Academy of Sciences.

Red Deer People? Really?

Did our human family tree just grow a new branch? That seems to be the tentative conclusion reported today in the online journal, PLoS ONE.

A first analysis of human remains from two caves in southwest China has prompted researchers to make some astounding claims: These "Red Deer People" are not anatomically modern humans (AMH). Their remains date from 14,500 to 11,500 years ago, far more recent than anything similar ever found on the mainland of Asia. They shared their territory with modern humans just at the time when early agriculture was being developed. And—even more puzzling—they shared anatomical features with modern and archaic humans.

Caption: An artist's reconstruction of fossils from two caves in southwest China have revealed a previously unknown Stone Age people and give a rare glimpse of a recent stage of human evolution with startling implications for the early peopling of Asia. The fossils are of a people with a highly unusual mix of archaic and modern anatomical features and are the youngest of their kind ever found in mainland East Asia. Dated to just 14,500 to 11,500 years old.

Credit: Art copyright by Peter Schouten Usage Restrictions: Image may be used in association with initial news media reports - otherwise seek permission from Peter Schouten: info@studioschouten.com.au

Who were they? The international team of researchers speak of these early humans as the “Red-Deer People,” named for extinct species of deer they hunted and for the Maludong or “Red Deer Cave” where some of the remains were discovered. The team was led by Professor Darren Curnoe of the University of New South Wales and Professor Ji Xueping of the Yunnan Institute of Cultural Relics and Archeology.

But researchers hesitate to draw any conclusions about species. "These new fossils might be of a previously unknown species, one that survived until the very end of the Ice Age around 11,000 years ago," says Professor Curnoe in a press release issued by UNSW. "Alternatively, they might represent a very early and previously unknown migration of modern humans out of Africa, a population who may not have contributed genetically to living people."

Although the remains were first discovered in 1979, they remained encased in rock until 2009. While the researchers have been able to compare anatomical features with modern and archaic human remains, they have not been able to extract DNA from the samples. According to the paper, “our ongoing attempts to extract DNA from a specimen from Maludong have so far proven unsuccessful owing to a lack of recoverable genetic material.”

"The discovery of the red-deer people opens the next chapter in the human evolutionary story – the Asian chapter – and it's a story that's just beginning to be told," says Professor Curnoe.

The paper is entitled "Human Remains from the Pleistocene-Holocene Transition of Southwest China Suggest a Complex Evolutionary History for East Asians" and appears in the March 14, 2012 issue of PLoS ONE.