Three's a crowd

[neufer]

http://www.washingtonpost.com/wp-dyn/co ... 01926.html

DNA from bone shows new human forerunner, and raises array of questions
By David Brown, Washington Post, Thursday, March 25, 2010

<<A team of European researchers has identified a new lineage of proto-human that left Africa about a million years ago, traveling as far as Siberia and then dying out -- a discovery that raises new questions about early human history.

The existence of the new lineage was discovered by analyzing DNA extracted from a single bone fragment, according to a study published Wednesday in the journal Nature. What the beings looked like, how they lived and what happened to them are a mystery. All that's known is that they existed as recently as 40,000 years ago, which is the approximate age of the bone.

"Whoever carried this DNA out of Africa is some new creature that hasn't been on our radar screen so far," said Johannes Krause, a researcher at the Max Planck Institute for Evolutionary Anthropology in Germany, who helped lead the research team.

The new lineage, which has not yet been declared a separate species, occupied Russia's Altai Mountains during a long period when early modern humans and Neanderthals were also there. Whether its members had contact with those other early people -- or might have interbred with them -- isn't known.

Nevertheless, the possible cohabitation of the three groups gives rise to at least two narratives of the first chapter of Eurasian history.

That landmass might have been a peaceable kingdom of competing "hominin" species. Or it could have been the site of genocide, with the Neanderthals and the just-discovered group of beings dying out to the last man and woman.

"People are going to be what we call 'gobsmacked' by this news," said Terry Brown, a molecular paleontologist at the University of Manchester, who wrote a commentary accompanying the paper in Nature. "There is going to be open-mouth amazement."
ad_icon

Apart from adding an unknown prehistoric cousin and a new "out-of-Africa" migration to the story of our origins, the finding marks a first in the way anthropological discoveries are made. The new lineage was determined to be distinct from other early humans not by the shape and size of its skeleton, but exclusively by differences in its genetic material.

That material was extracted from a fragment of a child's pinkie in the form of mitochondrial DNA. The bone, found in 2008 in a cave during a routine archeological excavation, is the only physical remains of the group. As a consequence, the researchers have no idea what its members looked like compared with the more ancient Homo erectus, the beetle-browed Neanderthals or the recently discovered "Hobbit people" of Indonesia.

The discovery raises the possibility that there might have been many waves of migration out of Africa by evolving proto-humans, each group genetically distinguishable from the others. It is likely to spur the search for other prehistoric bone fragments in places cool and dry enough to have surviving remnants of DNA.

"Maybe it is overly simplistic to think of particular migrations out of Africa," said Svante Paabo, the other leader of the German team. "There might have been a more or less continuous flow of migration. The picture that may emerge in the next few years is likely to be much more complicated."

The vast majority of the DNA in human cells resides in the nucleus, in long strands called chromosomes. The chromosomes encode about 20,000 genes, which one inherits from both mother and father.

A tiny amount of DNA, however, is in satellite structures outside the nucleus called mitochondria. They are inherited exclusively from the mother. Mitochondrial DNA, or mtDNA, which encodes fewer than 40 genes, defines an unbroken line of mother-to-child descent.

The linear order (called the "sequence") of the DNA "letters" in mtDNA is extremely stable over time. Nevertheless, mutations do creep in, and the rate at which they do is known, at least approximately. For that reason, differences in mtDNA function as a "molecular clock." They can be used to estimate how long ago the two populations had an ancestor in common.

Modern humans differ from Neanderthals by an average of 202 "letters" out of about 16,500 in the complete mtDNA strand. The Siberian bone's mtDNA differs by 385 letters. Chimpanzees and modern humans differ by 1,462 mtDNA letters, on average. Analysis of those differences led the researchers to conclude that the new lineage shared a common ancestor with Neanderthals and modern humans about 1 million years ago.

A more ancient proto-human, Homo erectus, left Africa about 1.9 million years ago. Neanderthals' ancestors left 500,000 to 300,000 years ago. Modern humans left 50,000 years ago.

The researchers think the ancestors of the "Denisova hominin" -- named after the cave where the finger bone was found -- almost certainly left Africa in a migration separate from those of the other species. Paabo believes it probably occurred 800,000 to 900,000 years ago.

The bone fragment has also yielded remnants of nuclear DNA, which may be enough to sketch a few details of its owner, believed to be a 6- or 7-year-old child.

If the nuclear DNA's genetic fingerprint is similar to that of modern humans or Neanderthals, it will imply that some of the child's ancestors were the product of interbreeding with those species. On the other hand, if it is as different from those species' as the mitochondrial DNA is, the researchers can conclude the child was a "purebred" member of the newly discovered lineage.

So far, there's no firm evidence of interbreeding between early modern humans and Neanderthals. To discover that the Denisova hominin was a hybrid -- the answer should be known in a few months -- would change the view of man's prehistory considerably.

Neanderthal remains have been found less than 100 miles from Denisova Cave. Artifacts in nearby caves and in Denisova itself suggest the presence of Upper Palaeolithic-age people, which might include modern humans. The time when the three groups occupied the same region spanned at least 10,000 years; whether they were exact contemporaries is unknown.

If they were, Paabo said, that "raises the potential of all sorts of interactions" between them. One is a fight to the death -- although there's no evidence for that so far.

"Something happened that only we survived," Paabo said. He added that he shares the view that "we were somehow responsible" for the disappearance of the other lineages. "But whether it was in a direct way, or some kind of ecological competition, we don't know.">>

[bystander]

Discover Blogs / The Loom / The X-Woman’s Fingerbone

[wonderboy]

If it was a fight to the death situation then it just goes to show that its bred into humans to fight each other which is a shame really. I remember watching a progamme on tv about neanderthals vs relatives of the modern day humans. We won because our brains were bigger which allowed us to create weapons. Our issues were created at a very early stage eh?

[neufer]

At 400,000 Years, Oldest Human DNA Yet Found Raises New Mysteries
by Carl Zimmer, NY Times, Dec. 4, 2013

<<In a paper in the journal Nature, scientists reported Wednesday that they had retrieved ancient human DNA from a fossil dating back about 400,000 years, shattering the previous record of 100,000 years. The fossil, a thigh bone found in Spain, had previously seemed to many experts to belong to a forerunner of Neanderthals. But its DNA tells a very different story. It most closely resembles DNA from an enigmatic lineage of humans known as Denisovans. Until now, Denisovans were known only from DNA retrieved from 80,000-year-old remains in Siberia, 4,000 miles east of where the new DNA was found.

The mismatch between the anatomical and genetic evidence surprised the scientists, who are now rethinking human evolution over the past few hundred thousand years. It is possible, for example, that there are many extinct human populations that scientists have yet to discover. They might have interbred, swapping DNA. Scientists hope that further studies of extremely ancient human DNA will clarify the mystery. “Right now, we’ve basically generated a big question mark,” said Matthias Meyer, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and a co-author of the new study.

Hints at new hidden complexities in the human story came from a 400,000-year-old femur found in a cave in Spain called Sima de los Huesos (“the pit of bones” in Spanish). The scientific team used new methods to extract the ancient DNA from the fossil. “This would not have been possible even a year ago,” said Juan Luis Arsuaga, a paleoanthropologist at Universidad Complutense de Madrid and a co-author of the paper. Finding such ancient human DNA was a major advance, said David Reich, a geneticist at Harvard Medical School who was not involved in the research. “That’s an amazing, game-changing thing,” he said.

Since the 1970s, Spanish scientists have brought out a wealth of fossils from the cave dating back hundreds of thousands of years. “The place is very special,” said Dr. Arsuaga, who has found 28 nearly complete skeletons of humans during three decades of excavations. Based on the anatomy of the fossils, Dr. Arsuaga has argued that they belonged to ancestors of Neanderthals, which lived in western Asia and Europe from about 200,000 to 30,000 years ago.

When Dr. Meyer and his colleagues drilled into the femur, they found ancient human DNA inside, just as they had hoped. “Our expectation was that it would be a very early Neanderthal,” Dr. Meyer said. But the DNA did not match that of Neanderthals. Dr. Meyer then compared it to the DNA of the Denisovans, the ancient human lineage that he and his colleagues had discovered in Siberia in 2010. He was shocked to find that it was similar. “Everybody had a hard time believing it at first,” Dr. Meyer said. “So we generated more and more data to nail it down.”

The extra research confirmed that the DNA belonged on the Denisovan branch of the human family tree. The new finding is hard to reconcile with the picture of human evolution that has been emerging in recent years based on fossils and ancient DNA. Denisovans were believed to be limited to East Asia, and they were not thought to look so Neanderthal-like.

Based on previously discovered ancient DNA and fossil evidence, scientists generally agreed that humans’ direct ancestors shared a common ancestor with Neanderthals and Denisovans that lived about half a million years ago in Africa. Their shared ancestors split off from humans’ lineage and left Africa, then split further into the Denisovans and Neanderthals about 300,000 years ago. The evidence suggested that Neanderthals headed west, toward Europe, and that the Denisovans moved east. Humans’ ancestors, meanwhile, stayed in Africa, giving rise to Homo sapiens about 200,000 years ago. Humans then expanded from Africa into Asia and Europe about 60,000 years ago. They then interbred not only with Neanderthals, but with Denisovans, too. Later, both the Denisovans and Neanderthals became extinct. “Now we have to rethink the whole story,” Dr. Arsuaga said.

Dr. Arsuaga doubts that Denisovans were spread out across so much of the Old World, from Spain to Siberia, masquerading as Neanderthals. One alternative explanation is that the humans of Sima de los Huesos were not true Neanderthals, but belonged to the ancestors of both Denisovans and Neanderthals. It is also possible that the newly discovered DNA was passed to both Neanderthals and Denisovans, but eventually disappeared from Neanderthals, replaced by other variants. “It got lost in one lineage but made its way in the other,” suggested Jean-Jacques Hublin, a Max Planck paleoanthropologist who was not involved in the research.

Beth Shapiro, an expert on ancient DNA at the University of California, Santa Cruz, favors an even more radical possibility: that the humans of Sima de los Huesos belong to yet another branch of humans. They might have been a species called Homo erectus, which originated about 1.8 million years ago and became extinct within the last few hundred thousand years. “The more we learn from the DNA extracted from these fossils, the more complicated the story becomes,” Dr. Shapiro said.

This complicated story has come to light only because of advances over the past 20 years in retrieving ancient DNA. When an organism dies, its DNA breaks down into smaller and smaller fragments, while also becoming contaminated with the DNA of other species like soil bacteria. So piecing the fossil DNA together is a bit like putting together a jigsaw puzzle created by a sadist.

In 1997, Svante Paabo of the Max Planck Institute and his colleagues, who had pioneered the techniques for retrieving DNA fragments, published a snippet of DNA from a Neanderthal fossil dating back about 40,000 years. They and other scientists then built on this success by searching for bits of DNA from other Neanderthals. In 2006, a team of French and Belgian researchers obtained a fragment of Neanderthal DNA dating back 100,000 years, which until now held the record for the oldest human DNA ever found.

Meanwhile, using improved methods, Dr. Paabo, Dr. Meyer and their colleagues assembled a rough draft of the entire Neanderthal genome in 2010. That discovery shed light on how Neanderthals and humans’ ancestors split from a common ancestor hundreds of thousands of years ago. It also revealed that Neanderthals and humans interbred about 50,000 years ago.

At about the same time as that discovery, Russian collaborators sent the Max Planck team 80,000-year-old fossils they had found in a cave in Siberia called Denisova. When the German scientists sequenced the entire genome from the finger bone of a girl, it turned out to be neither human nor Neanderthal, but from a separate lineage, which Dr. Paabo and his colleagues named Denisovans.

Dr. Meyer is hopeful that he and his colleagues will be able to get more DNA from the Spanish fossil, as well as other fossils from the site, to help solve the puzzle they have now stumbled across. “It’s extremely hard to make sense of,” Dr. Meyer said. “We still are a bit lost here.”>>