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How a Weed, Once a Prehistoric Cavity Fighter
By RANJODH SINGH, The New York Times, August 18, 2014

Cyperus rotundus, commonly known as purple nutsedge or nutgrass, is considered one of the world’s worst invasive weeds. But new research suggests that prehistoric humans in what is now central Sudan may have gotten an unusual benefit from it.

Stephen Buckley, an archaeological chemist from the University of York in England, analyzed dental calculus — a form of hardened plaque — in fossilized teeth from people who lived thousands of years ago, in the pre-Mesolithic, Neolithic, and Meroitic periods.

In a paper published in the journal PLOS One, Dr. Buckley and his colleagues report that the teeth had remarkably few cavities and high levels of the chemical compounds found in purple nutsedge, suggesting that the plant may have protected against tooth decay.



How might these early humans have used the plant?

“They were eating the tubers, that is, the underground storage organ,” said the senior author of the study, Karen Hardy, of the Autonomous University of Barcelona in Spain. “The purple nutsedge stores its energy and carbohydrates in these underground organs. The main usage by the prehistoric people most surely would have been food.”

Other uses of the plant may have drawn on its medicinal or aromatic qualities, she said, adding, “This study provides direct evidence not only of the fact that they ate plants, but also has identified a specific plant that was collected and eaten, before agriculture developed.”







Tuberculosis Is Newer Than Thought, Study Says
By CARL ZIMMER, The New York Times, August 20, 2014

New research indicates that some seal species carried tuberculosis across the Atlantic Ocean.

After a remarkable analysis of bacterial DNA from 1,000-year-old mummies, scientists have proposed a new hypothesis for how tuberculosis arose and spread around the world.

The disease originated less than 6,000 years ago in Africa, they say, and took a surprising route to reach the New World: It was carried across the Atlantic by seals.

The new study, published Wednesday in the journal Nature, has already provoked strong reactions from other scientists.

“This is a landmark paper that challenges our previous ideas about the origins of tuberculosis,” said Terry Brown, a professor of biomolecular archaeology at the University of Manchester. “At the moment, I’m still in the astonished stage over this.”

But Helen Donoghue, an expert on ancient DNA at the University College London, rejected the idea that tuberculosis could have emerged so recently. “It just cannot be right,” she said, citing earlier fossil evidence of the disease.



Tuberculosis has long been one of the deadliest diseases. In 2012, 8.6 million people became ill with this infection, and it caused 1.3 million deaths, according to the World Health Organization. The invading bacterium, Mycobacterium tuberculosis, attacks the lungs, where it causes widespread scarring.

To better understand the disease, a number of scientists have worked for decades to reconstruct its history.

In some people who get tuberculosis, the bacteria attack the skeleton, and archaeologists have found signs of tuberculosis damage in bones dating back centuries. Other scientists have examined DNA from different strains of the bacteria, using the mutations in different lineages to draw its family tree.

But archaeological studies and genetic research have often reached different conclusions about the disease’s origins.

Some scientists have argued that tuberculosis spread from cows to humans when the animals were first domesticated 10,000 years ago. Others have argued that the disease is far older, having evolved about 70,000 years ago, and spread from humans to cows and other animals.

The geographical distribution of the disease has also puzzled scientists. Tuberculosis strains found today in the New World are closely related to strains from Europe. That genetic link suggests that colonists brought the bacteria with them.

But archaeologists have found human bones with telltale signs of tuberculosis that date back centuries before Columbus’s arrival.

In 2012, a group of archaeologists and geneticists joined forces, searching for tuberculosis DNA in samples of bones from 68 sets of New World remains.

The scientists failed to find tuberculosis DNA in most of the specimens, but they succeeded in finding genetic material in three 1,000-year-old mummies from the Chiribaya culture of southern Peru.

The scientists retrieved many fragments of DNA from each mummy — so many, in fact, that they could recreate the entire genome of the bacteria in each victim. Before this new study, the oldest tuberculosis genome was reconstructed from a woman who died in Hungary in 1797.

The Peruvian genomes held two surprises.

The scientists expected that the tuberculosis DNA would be most closely related to some particular human strain of the disease. Instead, they found that it was most closely related to animal strains.

When they expanded their search, they found that the most closely related DNA belonged to tuberculosis strains found only in seals.

“We had not thought about seals at all,” said Kirsten I. Bos, a postdoctoral researcher at the University of Tubingen and lead author of the new paper.

The second surprise came when Dr. Bos and her colleagues used the genomes to estimate when tuberculosis first evolved.

Over many generations, bacteria accumulate mutations at a clocklike rate. Understanding that the Chiribaya bacteria were 1,000 years old, the scientists were able to estimate how many mutations the bacteria accumulate in a year, establishing its “molecular clock.”

They used this clock to determine the age of the common ancestor of all the tuberculosis strains in their study.

Dr. Bos and her colleagues ultimately estimated that tuberculosis was less than 6,000 years old — much younger than most scientists had thought.

In the new paper, the team proposes that humans acquired tuberculosis in Africa around 5,000 years ago. The disease spread to people across the Old World along trade routes. Meanwhile, Africans also spread the disease to animals such as cows and goats.

Seals that hauled out onto African beaches to raise their pups became infected. The bacteria then spread through seal populations until reaching South America. Ancient hunters there became infected when they handled contaminated meat.

There is some circumstantial evidence in support of the idea. Seals have given tuberculosis to cows grazing on beaches, and even to zookeepers. And archaeological remains from South America show that pre-Columbian hunters got tapeworms and other pathogens from seals.

Dr. Bos and her colleagues can’t say whether the tuberculosis in the Chiribaya mummies came directly from seals, or even if the bacteria spread from person to person. Nor can the scientists yet say whether the strain spread into North America through human contact.

Dr. Donoghue found the idea of hunters picking up tuberculosis from seals “quite feasible,” but she pointed to fossil evidence suggesting that tuberculosis is far older than 6,000 years.

In Israel, for example, archaeologists have found 9,000-year-old human remains that contain molecules produced by the bacteria. In a Wyoming cave, they have found 17,000-year-old bison bones with similar markers.

“I think they should be rapped over the knuckles for ignoring work that contradicts their conclusions a bit,” Dr. Donoghue said of the new study.





Neanderthals in Europe Died Out Thousands of Years Sooner Than Some Thought, Study Says
By KENNETH CHANG, The New York Times, August 20, 2014

Neanderthals, our heavy-browed relatives, spread out across Europe and Asia about 200,000 years ago. But when did they die out, giving way to modern humans?

A new analysis of Neanderthal sites from Spain to Russia provides the most definitive answer yet: about 40,000 years ago, at least in Europe. That is thousands of years earlier than some scientists have suggested, and it narrows the period that Neanderthals and modern humans overlapped in Europe.

“After that, we don’t think there are any Neanderthals on the continent anymore,” said Thomas Higham, the deputy director of the radiocarbon accelerator unit at the University of Oxford in England.

On the other hand, the dating also argues against the view that modern humans overwhelmed the Neanderthals as soon they arrived in Europe. While modern humans and Neanderthals do not appear to have intermingled in the same locales, the findings suggest they co-existed in neighboring regions for up to several thousand years.

The findings, reported Wednesday in the journal Nature, run counter to claims that pockets of Neanderthals persisted in Portugal, Spain and Gibraltar until just 30,000 years ago, even as modern humans spread outward.



“This is a very strong compilation,” said Chris Stringer, who leads research in human origins at the Natural History Museum in London and who was not involved in the research. “I think it kind of replaces the picture we had before.”

In 1995, researchers including Jean-Jacques Hublin, now at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announced fossil evidence of Neanderthals living 30,000 years ago in a cave near the southern Spanish city of Málaga.

Dr. Hublin said he had changed his mind as better radiocarbon dates became available. “To me, I’m ready to buy the new date,” he said. Modern humans migrated out of Africa at least 60,000 years ago, and anthropologists have been trying to figure out what happened when the two groups encountered each other.

One of the reasons some researchers think Neanderthals survived longer on the Iberian peninsula is that there are no signs of modern humans living there at that time.

A recent analysis of Neanderthal DNA shows that Neanderthals and modern humans not only crossed paths, but interbred. For non-African people living today, 1 to 4 percent of their genome has Neanderthal origins.

The genetics suggest that interbreeding occurred about 50,000 to 60,000 years ago, somewhere in western Asia.

“You’ve kind of got two parts of the story,” Dr. Stringer said. “There must have been a western Asia coexistence, which included interbreeding. Then there was a later coexistence in Europe, for which we have no evidence of interbreeding but possible evidence of some cultural contact between the groups.”

Dr. Higham, the lead author of the Nature paper, and his colleagues took advantage of advances in radiocarbon dating in testing samples of bone, charcoal and shell from 40 sites, mostly in Western Europe. The dating method takes advantage of unstable, radioactive carbon 14 atoms produced from the bombardment of the atmosphere by cosmic rays from outer space. The radioactive carbon combines with oxygen atoms to form carbon dioxide, and plants and animals take up some of it as long as they are alive.

But when they die, they absorb no additional radioactive carbon, and the carbon 14 disappears over time. The ratio of carbon 14 to carbon 12, which is stable, thus tells the age and can be used to date bones and artifacts up to about 50,000 years ago.

Contaminants containing younger organic molecules can distort the dating. Dr. Higham said just 1 percent of modern carbon infiltrating a 50,000-year-old fossil would make it look 7,000 to 8,000 years younger. The researchers prepared samples that would extract collagen in the bone and remove the contaminants.

“What we find is often the dates get older,” Dr. Higham said. “We’ve managed to chip away at these erroneous younger Neanderthal dates to come up with a more refined, and we think accurate, estimate for when Neanderthals disappeared.”

Dr. Higham said his team would like to expand the research to Neanderthal sites in Eastern Europe and across Russia to Siberia. It is possible that Neanderthals survived later in those areas.

Some of the conclusions are tentative because many of the sites do not have bones of the actual inhabitants, and paleontologists are still debating whether it was Neanderthals or modern humans who made the tools found at some sites.

“This gives us a framework, basically, which allows us to ask more interesting questions,” said William Davies of the University of Southampton in England, who wrote an accompanying commentary in Nature. “About what the tools might mean, how they were used, what they tell us about Neanderthal interactions.”

The findings so far indicate that Neanderthals did not disappear all at once.

“I think we’ll see patchy disappearance prior to extinction,” Dr. Higham said.

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