Novel collagen fingerprinting identifies a Neanderthal bone among 2,000 fragments

Scientists from the universities of Oxford and Manchester have used a new molecular fingerprinting technique to identify one Neanderthal bone from around 2,000 tiny bone fragments. 

All the tiny pieces of bone were recovered from a key archaeological site, Denisova Cave in Russia, with the remaining fragments found to be from animal species like mammoths, woolly rhino, wolf and reindeer. It is the first time that researchers have identified traces of an extinct human from an archaeological site using a technique called 'Zooarchaeology by Mass Spectrometry' or ZooMS. From just a microscopic sample of bone, their analysis revealed the collagen peptide sequences in the bone that mark out one species from another. Their paper, which appears in the journal Scientific Reports, suggests that ZooMS has huge potential to increase our understanding of human evolution, including the amount of interbreeding that went on between our closely related cousins and modern humans.

The international research team was led by Professor Thomas Higham and his student Sam Brown of the University of Oxford, with the developer of the ZooMS method, Dr Michael Buckley from the University of Manchester; the Max Planck Institute in Leipzig; Cranfield University; and the Institute of Archaeology and Ethnography, Russia. The sequences of collagen peptides in bone differ in tiny ways between different animal species. The team profiled the sequences using microscopic samples from 2,300 unidentified bone fragments from the site. They then compared the sequences obtained against a reference library of peptides from known animal species.

On discovering that one 2.5 cm-long piece of bone had a clear human fingerprint, Sam Brown said: 'When the ZooMS results showed that there was a human fingerprint among the bones I was extremely excited. After a lot of hard work, finding this tiny bone which yields so much information about our human past was just fantastic. The bone itself is not exceptional in any way and would otherwise be missed by anyone looking for possible human bones amongst the dozens of fragments that we have from the site.'

Study co-author Professor Svante Pääbo and his group from the Max Planck Institute in Leipzig found that the bone belonged to a Neanderthal on the basis of its mitochrondrial genome. The results suggest that this Neanderthal was most closely related to other Neanderthals in the Altai region and more distantly related to those further to the west. The Neanderthal bone was also radiocarbon dated and shown to be more than 50,000 years old, as expected based on its deep position in the site. Acid etching on the surface of the bone also shows that it probably passed through the stomach of a hyaena for a short time before it was deposited in the cave sediments, says the paper.

Denisova Cave in the Russian Altai region is a key site for archaeologists wanting to understand the nature of evolution over the last 100,000 years. Its cold climate means that bones from the cave are often exceptionally well-preserved in their DNA and collagen, which is ideal for genetics and radiocarbon dating. In 2010, Pääbo and his team discovered a new species of human, the so-called 'Denisovans' at the site, using state-of-the-art genetic methods. His team have also found that Denisovans, Neanderthals and modern humans interbred periodically with one another in Eurasia and Europe.

During the Ice Age, there were periods when the cave was also occupied by carnivores such as hyaenas and wolves that crunched the bones into tiny pieces. This is why more than 95% of the bone fragments excavated were difficult to identify.

Professor Thomas Higham said: 'This is a real breakthrough, showing that we can now use bioarchaeological methods like ZooMS to search the archaeological record and find even tiny fossil remains, where there are proteins that survive. In the Palaeolithic period, where we have Neanderthals, Denisovans and modern humans, this is potentially very important because if the fragments that we recover are big enough then we can date and analyse the DNA from the same bone. One of the big challenges is in understanding what happened when modern humans and Neanderthals met. We want to know over what period of time and where this happened. Fossils are the key, but for modern humans they are extremely rare in archaeological sites. We hope that more work like this will yield more human bone remains.'
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Reference:

Phys.org. 2016. “Novel collagen fingerprinting identifies a Neanderthal bone among 2,000 fragments”. Phys.org. Posted: March 29, 2016. Available online: http://phys.org/news/2016-03-collagen-fingerprinting-neanderthal-bone-fragments.html

Bones with names: Long-dead bodies archaeologists have identified

Historians record biographies of the rich and famous: kings, queens, emperors and knights. Archaeologists, more often than not, dig up common people, who remain stubbornly anonymous in death.

Occasionally, however, the written record and the archaeological record collide. In rare situations, researchers are actually able to identify a collection of bones as a person in the historical record. Many of these identifiable, or "individualized," remains belonged to royalty or other high-profile people, the sort who tend to be buried in lavish graves stamped with their names.

The bodies of royalty are not necessarily more important to archaeologists, who can learn much about diet and lifestyle by examining the bones of commoners. But there's something thrilling about uncovering this concrete evidence of the past. Read on for seven skeletons that have regained their rightful names, and three more that are tantalizingly close.

1. Richard III

The last Plantagenet king of England set off an international fervor in 2013, when archaeologists announced the discovery of his bones under a parking lot in Leicester. The king, who died in 1485 at the Battle of Bosworth Field, had been scrunched into a hastily dug grave. Researchers identified him by his battle wounds, which matched those the king was reported to have sustained during and after his death, and by his DNA, thanks to a pair of living descendants via his sister's line. 

After the analysis of his remains, Richard III finally got a royal burial at Leicester Cathedral on March 26, 2015 — 530 years after his death.

2. King Tut

The older a skeleton, the less likely historical records survive to identify it. Fortunately, the ancient Egyptians and their carefully prepared mummies provide an exception to this rule. Although the boy king Tutankhamun died in approximately 1323 B.C., his identification was in no doubt after Howard Carter and George Herbert discovered his gold-laden tomb in 1922.

Tut's mummy revealed him to be a slight young man with a clubfoot. Having a positive ID on the young king is enabling researchers to tie together the dynastic family tree using DNA. In 2010, researchers announced they'd identified mummies belonging to Tutankhamun's father, mother and grandmother. 

3. Queen Eadgyth

In 2008, German archaeologists opened a tomb in the Magdeburg Cathedral, expecting it to be empty. To their surprise, they found a lead sarcophagus inscribed with the words "EDIT REGINE CINERES HIC SARCOPHGVS HABET." This translates to: "The remains of Queen Eadgyth are in this sarcophagus."

Slam dunk identification, right? Not so fast. Archaeologists knew that the bones of the Saxon queen Eadgyth, who died in 946 A.D., had been moved at least three times. They could have easily been lost and replaced. 

So scientists set to analyzing the bones. They extracted isotopes, variations of certain molecules, from the skeleton's teeth. Isotopes are integrated into the body through the diet, so they can pinpoint what an individual ate during their lives. 

The tooth isotopes pointed to a childhood in Wessex, England, matching the historical record of Queen Eadgyth. She also ate a high-protein diet and her skeleton bore signs of horseback riding, the archaeologists discovered, befitting her royal status.

4. Xin Zhui

One of the best-preserved bodies ever discovered by archaeologists belonged to Xin Zhui, also known as Lady Dai. Xin Zhui was the wife of the Marquis of Dai during the third century B.C., and when she died around the age of 50 in what is now Hunan, China, she was buried in style. Her tomb was full of her belongings, including cosmetic boxes, musical instruments, painted silk and tablets about health and medicine.

Tucked away in four nested pine boxes, Xin Zhui was so well-preserved upon her discovery in the 1970s that her skin was still moist and her limbs pliable. Her body is now kept in a preserved state at the Hunan Provincial Museum. 

5. Ramesses I

The tomb of the first ruler of Egypt's 19th dynasty, Ramesses I, was discovered in 1817. Unfortunately, Ramesses I wasn't in it.

Years later, in 1881, a family of Egyptian goat-herders-turned-tomb-robbers revealed to archaeologists where they'd been getting the items they'd been selling on the black market for years: a cliff-side tomb above Deir el-Bahri, a mortuary complex across the Nile from the city of Luxor.

The tomb acted as a cache for royal mummiesremoved during the looting of tombs elsewhere, according to the Michael C. Carlos Museum at Emory University. Inside was a coffin inscribed with the name of Ramesses I — but inside that was nothing but loose bandages. So where was Ramesses?

Canada, as it turned out. Yes, the founder of Egypt's 19th dynasty and grandfather of the famed Ramesses the Great was acting as a sideshow exhibit for tourists at the Niagara Falls Museum and Daredevil Hall of Fame. At the time, purchasing mummies from Egypt was as easy as walking down the right alley to find a street merchant selling looted tomb goods. The body of Ramesses I ended up in this trade. When the Niagara Falls Museum sold off its collections in 1999, Emory raised the money to purchase the suspected Ramesses I mummy in less than two weeks. Researchers there used computed tomography (CT) scans, facial reconstructions and detailed study of the mummification techniques to confirm that the roaming mummy was indeed the lost pharaoh. (The mummy was returned to Egypt in 2003.) 

6. Ramesses III

Talk about a cold case: Ramesses III, the second pharaoh of Egypt's 20th dynasty, died in 1155 B.C. In 2012, researchers solved his murder.

Historical records, penned on papyrus, told of a palace plot to murder Ramesses III, but no one knew if that plot had succeeded. A CT scan of the pharaoh's mummy suggested that it did: Ramesses III's throat had been slit. The cut would have severed the trachea, esophagus and major blood vessels to the head, killing him quickly, the researchers reported in the British Medical Journal.

During his mummification, priests placed a healing amulet in the neck wound and bound it tightly with bandages. 

7. Copernicus

The first astronomer to realize that the Earth revolves around the sun, not the other way around, was buried in an unmarked grave in a Polish cathedral in 1543. But in 2009, Swedish and Polish researchers announced in the journal Proceedings of the National Academy of Sciences that they'd positively identified the remains of Nicolaus Copernicus.

The identification took some doing. First, researchers created a facial reconstruction of a skull of a man of the proper age found under the church floor in 2005. The results were promising — a mug that looked quite similar to contemporary paintings of Copernicus.

Next, the researchers turned to a few shed hairs found stuck in the bindings of a calendar owned by Copernicus. DNA testing revealed that two of the hairs matched the suspected Copernicus bones. 

8. A Viking king?

Not everyone in history is considerate enough to leave DNA-bearing hair behind. In most cases, researchers have to take their best guess at an identification.

One such case is the discovery of a young man's skeleton buried near Auldhame in Scotland. The skeleton, which dated back to the 10th century, was found surrounded by expensive goods, including a Viking belt. This suggests that he was a high-status individual — perhaps even the Viking King Olaf Guthfrithsson himself.

King Olaf died in A.D. 941. Shortly before his death, the king attacked Auldhame and the nearby hamlet of Tyninghame. The location of the grave, combined with the goods inside it, suggests that skeleton could be Olaf himself. Unfortunately, archaeologists said, the evidence is only circumstantial, and with no living relatives for DNA comparison, the identification will remain speculative. 

9. An unknown soldier?

After the Battle of Waterloo in 1815, the mass graves of fallen soldiers were raided for bones, which were ground up and used to fertilize fields in what is now Belgium. As a result, few full skeletons from the battle have been found.

But in 2012, a construction crew discovered the complete skeleton of a Waterloo casualty. The musket ball that killed the man was still lodged in his ribcage. Nearby were 20 coins, a spoon and a piece of wood engraved "CB," according to The Independent.

It wasn't enough to identify the man. That is, until archaeologists noticed the traces of an "F" before the "CB" and a military historian named Gareth Glover took up the case. By cross-referencing records of German soldiers who fought in the battle, Glover was able to determine that only one German with those initials had died: a 23 year-old named Friedrich Brandt.  

As of June 2015, the body identified as Brandt was on display at the Lion's Mound Museum & Visitor Centre in Belgium. 

10. Which Philip?

When archaeologists cracked open an ancient Macedonian tomb near Vergina, Greece, in 1977, they also cracked open a mystery that rages to this day. The date of the tomb, and its lavish contents, strongly suggest the male and female skeletons inside were relatives of Alexander the Great. But which relatives? The debate boils down to two camps: those who believe the male tomb occupant to be Philip II, the father of Alexander who set the stage for his son's unprecedented conquests, and those who believe the skeleton belongs to Philip III Arrhidaios, Alexander's less-illustrious half-brother who ruled as a figurehead briefly after Alexander's death. (The female skeleton is presumed to be the wife, or one of the wives, of these men.)

Examinations of the bones have yet to yield any firm proof either way. Archaeologists argue over whether the bodies were cremated right after death, or later — Philip III was buried for more than a year before being exhumed for a royal cremation and funeral. They also bicker over whether the bones show signs of Philip II's known battle wounds. Ultimately, the bodies may not even provide the final clues, said Maria Liston, an anthropologist at the University of Waterloo who studies cremated remains.

"It's going to have to be, in the end, based a little bit at looking at the bones, but honestly on the dates of the pottery [in the tomb] and things like that," Liston told Live Science.
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Reference:

Pappas, Stephanie. 2015. “Bones with names: Long-dead bodies archaeologists have identified”. Live Science. Posted: Available online: http://www.livescience.com/51140-skeletons-with-names.html

Identifying malaria in the bone marrow of ancient human remains

A Yale University scientist has developed a promising new method to identify malaria in the bone marrow of ancient human remains. It is the first time researchers have been able to establish a diagnostic, human skeletal profile for the disease, which is transmitted by mosquitoes and continues to infect millions of people a year.

The new process may allow scientists to track the spread of malaria back to its first appearance in human populations. The method, which works effectively on bones resistant to previous forms of testing, also may be applicable to other diseases.

“The data set we build with this will be revolutionary for establishing the epidemiological curve for malaria in ancient societies,” said Jamie Inwood, a Yale graduate student in archaeology who led the research team. “By understanding how this parasite reacted to societal shifts in the past, we can aid in predicting its future behaviour. We can understand the way it has evolved.”

Inwood and her colleagues spent several years identifying chemical and spectral indicators for malaria in archaeological bones. Specifically, they looked for the polymer hemozoin, which is produced by the parasite that causes malaria.

The technique is more effective than other methods of analysis, such as pathogen aDNA extraction, which often produce inconclusive results and are difficult to conduct when poor preservation conditions are a factor.

An epidemic

However, the aDNA method did help Inwood find an archaeological site to test her new technique. A previous research team led by University of Arizona archaeologist David Soren had arranged for aDNA testing of human remains from 550 A.D. at Lugnano in Teverina, Italy. Soren provided Inwood with bone samples from the site – representing roughly 100 infants and toddlers in a cemetery within a destroyed Roman villa. These had been interred with heavy roof tiles to weigh them down.

“Researchers from the University of Arizona had found burial practices that were throwbacks to pagan rituals,” Inwood said. “It was suspected there must have been an epidemic in the community that caused fever or fits.”

Using femur and humerus bone samples from the site, Inwood confirmed the presence of black, crystalline hemozoin clumps in the bone marrow. She and her team worked at Yale’s archaeohistology laboratory, where they scraped the hemozoin from bone marrow and used X-ray defraction to identify it.

Hemozoin “dances” under the microscope, she said.

Ceremony to honour the deceased

Later this spring, Inwood will return to Lugnano in Teverina for a ceremony with Soren and local officials, to honour the memory of the deceased and acknowledge the new information about what happened long ago. She and her colleagues said understanding the past is essential to the continuing human struggle against malaria around the world.

“There is a constant evolution of this disease, because of changes in human populations and changes in the medicines we use to treat it,” said Roderick McIntosh, a professor of anthropology at Yale. “Knowing the history of the mechanisms by which malaria evolves is a very good thing. We want to put together enough data for a timeline of malaria in humans.”

In order to do so, Inwood expects to do some travelling. In particular, she said, she has begun to amass data from archaeological sites in West Africa. She also will refine a set of methodology guidelines that can be adopted by other researchers using diagnostic techniques to look for disease markers in ancient bones.

Despite the age of the remains, she said, the need for such information is contemporary and quite urgent. “That is the reason this work has been initiated,” Inwood said. “In the case of malaria, it is a battle.”
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Reference:

Past Horizons. 2015. “Identifying malaria in the bone marrow of ancient human remains”. Past Horizons. Posted: March 17, 2015. Available online: http://www.pasthorizonspr.com/index.php/archives/03/2015/identifying-malaria-in-the-bone-marrow-of-ancient-human-remains

Ancient bone hand ax identified in China

People may have dug up roots with shovellike tool

Researchers say they have identified the first example of a bone, not stone, hand ax crafted by ancient humans in East Asia. Makers of the curved, pear-shaped implement probably used it to dig up edible roots in a densely vegetated part of South China around 170,000 years ago, say paleontologist Guangbiao Wei of China Three Gorges Museum in Chongqing and his colleagues.

Part of a lower jaw from a stegodon, a now-extinct, elephant-like creature, provided raw material for the tool, the researchers report January 8 in Quaternary International. The jaw includes a wide, thick piece of curved bone with a grip-ready indentation on its inner surface, the scientists say.

Excavation of a Chinese cave in 2002 yielded the hand ax, along with bones of stegodons and other large animals. Until now, though, the artifact’s age was unknown. Wei’s team dated the find by measuring the decay rate of forms of uranium and thorium in the fossilized bone.

Bone hand axes are rare, even outside East Asia. A handful of such tools previously unearthed in Africa, Europe and West Asia were made from limb bones, ribs and tusks of creatures such as mammoths. Stone hand axes, which preserve far better than bone artifacts, are more numerous and date to 800,000 years ago in South China (SN: 3/4/00, p. 148).

Editor's note: This article was updated on January 16, 2015, to correct that the researchers measured the decay rates of uranium and thorium, not just two forms of uranium. 
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Bower, Bruce. 2015. “Ancient bone hand ax identified in China”. Science News. Posted: January 14, 2015. Available online: https://www.sciencenews.org/article/ancient-bone-hand-ax-identified-china

Issue: Magazine issue: Vol. 187 No. 3, February 7, 2015

The ancient American bones at centre of two lawsuits

They may have been dead for more than 9000 years, but the future looks uncertain for two early Americans unearthed in 1976 below the University of California in San Diego.

Members of a local Native American tribe – the Kumeyaay – want to rebury the remains, which they believe are their ancestors. In December, UCSD agreed to hand over the skeletons, but in April three palaeoanthropologists filed a lawsuit against UCSD to keep the remains for research. The Kumeyaay had anticipated the move and filed their own lawsuit days earlier. Last week, the university agreed to a judge's order to keep the remains in a safe place until a final ruling.

Since 1990, US law has mandated universities to return Native American artefacts and remains to their respective tribes. But UCSD's scientific advisory board determined that there is no evidence that these two skeletons are related to the Kumeyaay, even though they were discovered on that tribe's ancestral lands. Isotopic evidence taken from the skeletons suggests they ate seafood – unlike the Kumeyaay's traditional diet – and the Kumeyaay traditionally cremate their deceased rather than bury them.

James McManis, an attorney in San Jose who represents the three palaeoanthropologists, is confident that scientific evidence outweighs the tribe's claim. Lawyers for the tribe nevertheless insist that research on the bones would be disrespectful.

"Nowhere in the world is this sensitivity so acute as in the US," says anthropologist Bryan Sykes at the University of Oxford. He believes that tensions were escalated by a recent case where researchers in Arizona performed DNA analysis on the Havasupai tribe's ancestry without their consent. The results indicated that the people hadn't always lived in North America, contrary to tribal beliefs.
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References:

Reardon, Sara. 2012. "The ancient American bones at centre of two lawsuits". New Scientist. Posted: May 16, 2012. Available online: http://www.newscientist.com/article/dn21817-the-ancient-american-bones-at-centre-of-two-lawsuits.html

Prehistoric bones a cottage industry in Siberia

One of Zimov's prized mammoth tusks. Source: Dmitry Solovyov/NBC News

It’s hard to imagine, looking out at the frozen expanses of Yakutia, in North Eastern Siberia, that 30,000 or so years ago, so many animal species, now extinct, roamed the Pleistocene grasslands. From 12-foot tall, five-ton wooly mammoth bulls to tiny rodents, an Ice Age hunter would have found as many as 100 animals in each square mile he tracked, at least according to Sergei Zimov, our Ice Age expert, geo-physicist and guide during our recent visit.

Today, Siberia’s thick icy crust, or permafrost, which has held the remains of predators and herbivores alike in an epochal deep freeze, is beginning to melt. And the bones of prehistoric rhinos, bison, reindeer, horses – and yes, mammoths – are rising to Yakutia’s surface at an amazing rate. One literally trips over bones on a short stroll along the banks of the Kolyma River. The downside, of course, is the attendant release of so much CO2 – a greenhouse gas - as this melting permafrost exposes a 150-foot thick layer of plant and animal remains. But there is an upside: a burgeoning cottage industry in the finding and selling of prehistoric bones.

Zimov says that 30 years ago, only a handful of Russian "bone" men – serious businessmen - were attracted to the adventurous lifestyle, spending their summers combing Pleistocene beaches and valleys. Today, at least 1,000 bone hunters work throughout Russia, with several dozen focusing on Siberia’s permafrost zone, where the best prizes are to be found.

Professional hunters like Feodor Shidlovsky and Alexander Votagin are at the top of the bone chain. Shidlovsky has arguably the biggest mammoth bone collection in Russia, displaying them in his own natural history museum in Moscow. The money he makes from the sale of mammoth bones goes into his exhibitions, the funding of artists who fashion jewelry from the ancient bone, and scientific expeditions.

Every summer, Votagin leads his team to Dvarii Yar – or Windy Cliffs – a remote stretch of Kolyma riverbank that has given up the richest finds of prehistoric bones over the past decade. Located about 400 miles north of Zimov’s isolated science station in Cherskiy - Yakutia’s main airport and hub - the so-called New Siberian Islands (all underwater in Pleistocene times) are now a treasure trove of bones. Local hunters collect more than 20 tons of mammoth, rhino and bison bones a year, selling most of them to local dealers in Cherskiy – presumably to sell them to tourists like us, though the Russian government bans the export abroad.

And here’s why: prehistoric bones can be a very lucrative catch. While fishermen and hunters now augment their meager incomes with up to $10 per mammoth tooth or ivory shard, the more professional - and lucky – hunters can fetch more than $80,000 for a pair of mammoth tusks in good condition. Zimov keeps such a pair in the living room of his science station cum abode – but isn’t tempted to sell them.

"These are like my family," he told us. "Would you sell your brothers for $80,000?" In fact, Zimov has never sold any bones he’s collected over his decades of combing Yakutia for clues to global warming. On one such outing, he and his son Nikita collected some 1,200 bones – which he thinks is a world record - all which remained of a pack of mammoths and all within a few hundred yards of beach. For amusement, they arranged their bone hoard into the shapes of mammoths, horses and bison.

Until the mass, mysterious extinction of so many Ice Age animals took place - triggered, probably, by extreme change of climate and habitat - the so-called "Mammoth Steppe Eco-system" chugged along like a glacier, both efficient and self-sustaining. Mammoths knocked over heat-absorbing trees, grasses grew, and dozens of herbivore species not only grazed on those grasses, but fertilized them too.

Though that eco-system died some 15,000 years ago, mammoths and other Pleistocene throwbacks are helping to maintain today’s human population, with a $5 prehistoric bison jaw here, a $10 wooly rhino knee bone there or $1,000 piece of wooly mammoth tusk, buried right under your feet.
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References:

Maceda, Jim. 2012. "Prehistoric bones a cottage industry in Siberia". MSNBC: The Daily Nightly. Posted: Available online: http://dailynightly.msnbc.msn.com/_news/2011/12/30/9834873-prehistoric-bones-a-cottage-industry-in-siberia