Stone bracelet is oldest ever found in the world

Dating back 40,000 years to the Denisovan species of early humans, new pictures show beauty and craftsmanship of prehistoric jewellery.

It is intricately made with polished green stone and is thought to have adorned a very important woman or child on only special occasions. Yet this is no modern-day fashion accessory and is instead believed to be the oldest stone bracelet in the world, dating to as long ago as 40,000 years.

Unearthed in the Altai region of Siberia in 2008, after detailed analysis Russian experts now accept its remarkable age as correct. 

New pictures show this ancient piece of jewellery in its full glory with scientists concluding it was made by our prehistoric human ancestors, the Denisovans, and shows them to have been far more advanced than ever realised.

'The bracelet is stunning - in bright sunlight it reflects the sun rays, at night by the fire it casts a deep shade of green,' said Anatoly Derevyanko, Director of the Institute of Archaeology and Ethnography in Novosibirsk, part of the Siberian Branch of the Russian Academy of Sciences.

'It is unlikely it was used as an everyday jewellery piece. I believe this beautiful and very fragile bracelet was worn only for some exceptional moments.'

The bracelet was found inside the famous Denisova Cave, in the Altai Mountains, which is renowned for its palaeontological finds dating back to the Denisovans, who were known as homo altaiensis, an extinct species of humans genetically distinct from Neanderthals and modern humans.

Made of chlorite, the bracelet was found in the same layer as the remains of some of the prehistoric people and is thought to belong to them.

What made the discovery especially striking was that the manufacturing technology is more common to a much later period, such as the Neolithic era. Indeed, it is not clear yet how the Denisovans could have made the bracelet with such skill. Writing in the Novosibirsk magazine, Science First Hand, Dr Derevyanko said: 'There were found two fragments of the bracelet of a width of 2.7cm and a thickness of 0.9 cm. The estimated diameter of the find was 7cm. Near one of the cracks was a drilled hole with a diameter of about 0.8 cm. Studying them, scientists found out that the speed of rotation of the drill was rather high, fluctuations minimal, and that was there was applied drilling with an implement - technology that is common for more recent times.

'The ancient master was skilled in techniques previously considered not characteristic for the Palaeolithic era, such as drilling with an implement, boring tool type rasp, grinding and polishing with a leather and skins of varying degrees of tanning.'

Chlorite was not found in the vicinity of the cave and is thought to have come from a distance of at least 200km, showing how valued the material was at the time.

Dr Derevyanko said the bracelet had suffered damage, including visible scratches and bumps although it looked as if some of the scratches had been sanded down. Experts also believe that the piece of jewellery had other adornments to make it more beautiful.

'Next to the hole on the outer surface of the bracelet can be seen clearly a limited polished zone of intensive contact with some soft organic material,' said Dr Derevyanko. 'Scientists have suggested that it was a leather strap with some charm, and this charm was rather heavy. The location of the polished section made it possible to identify the 'top' and 'bottom' of the bracelet and to establish that it was worn on the right hand.'

Located next to the Anuy River, about 150 km south of Barnaul, the Denisova Cave is a popular tourist attraction, such is its paleontological importance. Over the years a number of remains have been found there, including some of extinct animals such as the woolly mammoth. In total evidence of 66 different types of mammals have been discovered inside, and 50 bird species.

The most exciting discovery was the remains of the Denisovans, a species of early humans that dated back as early as 600,000 years ago and were different to both Neanderthals and modern man.

In 2000 a tooth from a young adult was found in the cave and in 2008, when the bracelet was found, archaeologists discovered the finger bone of a juvenile Denisovan hominin, whom they dubbed the 'X woman'. Further examination of the site found other artifacts dating as far back as 125,000 years.

The institute's deputy director Mikhail Shunkov suggested that the find indicates the Denisovans - though now extinct - were more advanced than Homo sapiens and Neanderthals.

'In the same layer, where we found a Denisovan bone, were found interesting things; until then it was believed these the hallmark of the emergence of Homo sapiens,' he said. 'First of all, there were symbolic items, such as jewellery - including the stone bracelet as well as a ring, carved out of marble.'

The full details of the ring are yet to be revealed. 

'These finds were made using technological methods - boring stone, drilling with an implement, grinding - that are traditionally considered typical for a later time, and nowhere in the world they were used so early, in the Paleolithic era. At first, we connected the finds with a progressive form of modern human, and now it turned out that this was fundamentally wrong. Obviously it was  Denisovans, who left these things.'

This indicated that 'the most progressive of the triad' (Homo sapiens, Homo Neanderthals and Denisovans) were Denisovans, who according to their genetic and morphological characters were much more archaic than Neanderthals and modern human.' 

But could this modern-looking bracelet have been buried with older remains?

The experts considered this possibility but rejected it, saying they believe the layers were uncontaminated by human interference from a later period. The soil around the bracelet was also dated using oxygen isotopic analysis.

The unique bracelet is now held in the Museum of History and Culture of the Peoples of Siberia and the Far East in Novosibirsk. Irina Salnikova, head the museum, said of the bracelet: 'I love this find. The skills of its creator were perfect. Initially we thought that it was made by Neanderthals or modern humans, but it turned out that the master was Denisovan, at least in our opinion.

'All jewellery had a magical meaning for ancient people and even for us, though we do not always notice this. Bracelets and neck adornments were to protect people from evil spirits, for instance. This item, given the complicated technology and 'imported' material, obviously belonged to some high ranked person of that society.'

While bracelets have been found pre-dating this discovery, Russian experts say this is the oldest known jewellery of its kind made of stone.
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Reference:

Liesowska, Anna. 2015. “Stone bracelet is oldest ever found in the world”. Siberian Times. Posted: May 7, 2015. Available online: http://siberiantimes.com/science/casestudy/features/f0100-stone-bracelet-is-oldest-ever-found-in-the-world/

Extinct human cousin gave Tibetans advantage at high elevation

Denisovan gene helped Tibetans adapt to low oxygen at high altitudes

Tibetans were able to adapt to high altitudes thanks to a gene picked up when their ancestors mated with a species of human they helped push to extinction, according to a new report by University of California, Berkeley, scientists.

An unusual variant of a gene involved in regulating the body's production of hemoglobin – the molecule that carries oxygen in the blood – became widespread in Tibetans after they moved onto the high-altitude plateau several thousand years ago. This variant allowed them to survive despite low oxygen levels at elevations of 15,000 feet or more, whereas most people develop thick blood at high altitudes, leading to cardiovascular problems.

"We have very clear evidence that this version of the gene came from Denisovans," a mysterious human relative that went extinct 40,000-50,000 years ago, around the same time as the more well-known Neanderthals, under pressure from modern humans, said principal author Rasmus Nielsen, UC Berkeley professor of integrative biology. "This shows very clearly and directly that humans evolved and adapted to new environments by getting their genes from another species."

This is the first time a gene from another species of human has been shown unequivocally to have helped modern humans adapt to their environment, he said.

Nielsen and his colleagues at BGI-Shenzhen in China will report their findings online July 2 in advance of publication in the journal Nature.

The gene, called EPAS1, is activated when oxygen levels in the blood drop, triggering production of more hemoglobin. The gene has been referred to as the superathlete gene because at low elevations, some variants of it help athletes quickly boost hemoglobin and thus the oxygen-carrying capacity of their blood, upping endurance. At high altitude, however, the common variants of the gene boost hemoglobin and its carrier, red blood cells, too much, increasing the thickness of the blood and leading to hypertension and heart attacks as well as low-birth-weight babies and increased infant mortality. The variant or allele found in Tibetans raises hemoglobin and red blood cell levels only slightly at high elevation, avoiding the side-effects seen in most people who relocate to elevations above 13,000 feet.

"We found part of the EPAS1 gene in Tibetans is almost identical to the gene in Denisovans and very different from all other humans," Nielsen said. "We can do a statistical analysis to show that this must have come from Denisovans. There is no other way of explaining the data."

Harsh conditions on Tibetan plateau

The researchers first reported the prevalence of a high-altitude version of EPAS1 in Tibetans in 2010, based on sequencing of the genomes of numerous Han Chinese and Tibetans. Nielsen and his colleagues argued that this was the result of natural selection to adapt to about 40 percent lower oxygen levels on the Tibetan plateau. That is, people without the variant died before reproducing at a much higher rate than those with it. About 87 percent of Tibetans now have the high-altitude version, compared to only 9 percent of Han Chinese, who have the same common ancestor as Tibetans.

Nielsen and his colleagues subsequently sequenced the EPAS1 gene in an additional 40 Tibetans and 40 Han Chinese. The data revealed that the high-altitude variant of EPAS1 is so unusual that it could only have come from Denisovans. Aside from its low frequency in Han Chinese, it occurs in no other known humans, not even Melanesians, whose genomes are nearly 5 percent Denisovan. A high quality sequence of the Denisovan genome was published in 2012.

Nielsen sketched out a possible scenario leading to this result: modern humans coming out of Africa interbred with Denisovan populations in Eurasia as they passed through that area into China, and their descendants still retain a small percentage – perhaps 0.1 percent – Denisovan DNA. The group that invaded China eventually split, with one population moving into Tibet and the other, now known as Han Chinese, dominating the lower elevations.

He and his colleagues are analyzing other genomes to pin down the time of Denisovan interbreeding, which probably happened over a rather short period of time.

"There might be many other species from which we also got DNA, but we don't know because we don't have the genomes," Nielsen said. "The only reason we can say that this bit of DNA is Denisovan is because of this lucky accident of sequencing DNA from a little bone found in a cave in Siberia. We found the Denisovan species at the DNA level, but how many other species are out there that we haven't sequenced?"
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References:

EurekAlert. 2014. “Extinct human cousin gave Tibetans advantage at high elevation”. EurekAlert. Posted: July 2, 2014. Available online: http://www.eurekalert.org/pub_releases/2014-07/uoc--ehc062714.php

Ancient Humans Had Sex with Mystery Relatives, Study Suggests

A new, improved sequencing of ancient human relative genomes reveals that Homo sapiens didn't only have sex with Neanderthals and a little-understood line of humans called Denisovans. A fourth, mystery lineage of humans was in the mix, too.

As reported by the news arm of the journal Nature, new genetic evidence suggests that several hominids — human relatives closer than humans' current living cousin, the chimpanzee — interbred more than 30,000 years ago. This group of kissing cousins included an unknown human ancestor not yet revealed by the ancient DNA record.

"It's implied it could be something like Homo erectus or similar," said Carles Lalueza-Fox, a paleogenomics researcher at Pompeu Fabra University in Spain, who was not involved in the research, but who was present at a talk on the findings given by lead author David Reich of Harvard Medical School at a meeting on ancient DNA sponsored by the Royal Society in London on Nov. 18. Homo erectus is an extinct species of human that originated in Africa and spread into Asia.

Ancient human lineages

Neanderthals are an extinct group of humans who lived between about 30,000 and 130,000 years ago. Despite their reputation as bone-headed dummies, Neanderthals were likely as advanced as modern humans in areas such as tool-making, though they were probably less socially adept.

Denisovans are a far more mysterious group. These early humans lived in Siberia and probably split off from the branch of the human family tree that would eventually give rise to Neanderthals about 300,000 years ago. Little is known about how Denisovans lived and what they looked like.

But genetic analyses of Neanderthals, Denisovans and modern humans suggest the three groups occasionally had sex and produced offspring. Denisovan genes show up in modern Pacific Islanders and in people from Southeast Asia and southern China. Neanderthal genes appear in 1 to 4 percent of modern Eurasian people, suggesting that Homo sapiens and Neanderthals interbred after modern humans trekked out of Africa.

For unknown reasons, Homo sapiens are the only human survivors, as all others in the Homo genus eventually went extinct.

New genomes, new discoveries

The new research has been submitted to a scientific journal for publication. Under the journal's rules, lead author Reich cannot speak to the news media about the study until the paper comes out.

A Nature News reporter who attended the Nov. 18 talk, however, reports that Reich and his colleagues have created much more complete sequences of the Denisovan and Neanderthal genomes than those used in previous research.

The sequences confirmed previous findings that Denisovans mated with the ancestors of Pacific Islanders and East Asians, but also revealed a surprise: Genetic traces of an unknown population of human ancestors were found in the Denisovan gene, suggesting even more interbreeding than previously expected. Mark Thomas, an evolutionary geneticist at University College London, described the ancient environment to Nature as a "'Lord of the Rings'-type world" with many human populations living side-by-side.

Lalueza-Fox said the question of the mystery fourth ancestor is a "paleontological debate," but that the genetic work done by Reich and his colleagues opens the door to a deeper understanding of the individual diversity of ancient human ancestors. New techniques will enable researchers to tease out original DNA from later contaminants, he said.

"Some samples that were considered not suitable for genomic approaches are now going to be good samples," Lalueza-Fox said.

In the past, Lalueza-Fox said, geneticists were stuck trying to extrapolate details about human evolution from modern human DNA. Now, he said, they can go directly to the ancient DNA.

"We have been trying to understand human evolution from the study of modern human genomes, but clearly we missed part of the picture, which is now emerging from ancient hominin genomes," Lalueza-Fox said.
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References:

Pappas, Stephanie. 2014. “Ancient Humans Had Sex with Mystery Relatives, Study Suggests”. Live Science. Posted: December 2, 2013. Available online: http://www.livescience.com/41610-ancient-human-sex.html

Mysterious ancient human crossed Wallace's Line

Scientists have proposed that the most recently discovered ancient human relatives -- the Denisovans -- somehow managed to cross one of the world's most prominent marine barriers in Indonesia, and later interbred with modern humans moving through the area on the way to Australia and New Guinea.

Three years ago the genetic analysis of a little finger bone from Denisova cave in the Altai Mountains in northern Asia led to a complete genome sequence of a new line of the human family tree -- the Denisovans. Since then, genetic evidence pointing to their hybridisation with modern human populations has been detected, but only in Indigenous populations in Australia, New Guinea and surrounding areas. In contrast, Denisovan DNA appears to be absent or at very low levels in current populations on mainland Asia, even though this is where the fossil was found.

Published today in a Science opinion article, scientists Professor Alan Cooper of the University of Adelaide in Australia and Professor Chris Stringer of the Natural History Museum in the UK say that this pattern can be explained if the Denisovans had succeeded in crossing the famous Wallace's Line, one of the world's biggest biogeographic barriers which is formed by a powerful marine current along the east coast of Borneo. Wallace's Line marks the division between European and Asian mammals to the west from marsupial-dominated Australasia to the east.

"In mainland Asia, neither ancient human specimens, nor geographically isolated modern Indigenous populations have Denisovan DNA of any note, indicating that there has never been a genetic signal of Denisovan interbreeding in the area," says Professor Cooper, Director of the University of Adelaide's Australian Centre for Ancient DNA. "The only place where such a genetic signal exists appears to be in areas east of Wallace's Line and that is where we think interbreeding took place -- even though it means that the Denisovans must have somehow made that marine crossing."

"The recent discovery of another enigmatic ancient human species Homo floresiensis, the so-called Hobbits, in Flores, Indonesia, confirms that the diversity of archaic human relatives in this area was much higher than we'd thought," says Professor Stringer, Research Leader in Human Origins, Natural History Museum, in London. "The morphology of the Hobbits shows they are different from the Denisovans, meaning we now have at least two, and potentially more, unexpected groups in the area.

"The conclusions we've drawn are very important for our knowledge of early human evolution and culture. Knowing that the Denisovans spread beyond this significant sea barrier opens up all sorts of questions about the behaviours and capabilities of this group, and how far they could have spread."

"The key questions now are where and when the ancestors of current humans, who were on their way to colonise New Guinea and Australia around 50,000 years ago, met and interacted with the Denisovans," says Professor Cooper.

"Intriguingly, the genetic data suggest that male Denisovans interbred with modern human females, indicating the potential nature of the interactions as small numbers of modern humans first crossed Wallace's Line and entered Denisovan territory."
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References:

EurekAlert. 2013. “Mysterious ancient human crossed Wallace's Line”. EurekAlert. Posted: October 17, 2013. Available online: http://www.eurekalert.org/pub_releases/2013-10/uoa-mah101513.php

Extinct Human Genome Reveals Brown-Eyed Girl

Genetic analysis of a fossil up to 80,000 years old reveals it belonged to a little girl with dark skin, brown hair and brown eyes.

The genome of a recently discovered branch of extinct humans known as the Denisovans that once interbred with us has been sequenced, scientists said today.

Genetic analysis of the fossil revealed it apparently belonged to a little girl with dark skin, brown hair and brown eyes, researchers said. All in all, the scientists discovered about 100,000 recent changes in our genome that occurred after the split from the Denisovans. A number of these changes influence genes linked with brain function and nervous system development, leading to speculation that we may think differently from the Denisovans. Other changes are linked with the skin, eyes and teeth.

"This research will help [in] determining how it was that modern human populations came to expand dramatically in size as well as cultural complexity, while archaic humans eventually dwindled in numbers and became physically extinct," said researcher Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Future research may turn up other groups of extinct humans in Asia "in addition to Neanderthals and Denisovans," Pääbo told LiveScience.

Although our species comprises the only humans left alive, our planet was once home to a variety of other human species. The Neanderthals were apparently our closest relatives, and the last of the other human lineages to vanish.

However, scientists recently revealed another group of extinct humans once lived at the same time as ours. DNA from fossils unearthed in Denisova Cave in southern Siberia in 2008 revealed a lineage unlike us and closely related to Neanderthals. The precise age of the Denisovan material remains uncertain — anywhere from 30,000 to 80,000 years of age.

"The Denisovan genome is particularly close to my heart, because it was the first time that a new group of extinct humans was discovered and defined just from DNA sequence evidence and not from the morphology of bones," Pääbo said.

Denisovan genes unzipped

Now, based on only a tiny sample of genetic material from a finger bone, scientists have sequenced the complete genome of the Denisovans (pronounced deh-NEESE-so-vans), as they are now called.

To make the most of what little genetic material they had, the researchers developed a technique that unzipped the double strands of DNA in the bone, doubling the amount of DNA they could analyze. This enabled them to sequence each position in the genome about 30 times over, generating an extremely thorough genome sequence.

"We have very few errors in the sequences, even less errors than we often have when you sequence a person today," Pääbo said. "With just a few technical reservations, there is actually today then no difference in what we can learn genetically about a person that lived 50,000 years ago and from a person today, provided that we have well-enough preserved bones."

Comparing the Denisovan genome with ours confirmed past research suggesting the extinct lineage once interbred with ours and lived in a vast range from Siberia to Southeast Asia. The Denisovans share more genes with people from Papua New Guinea than any other modern population studied.

In addition, more Denisovan genetic variants were found in Asia and South America than in European populations. However, this likely reflects interbreeding between modern humans and the Denisovans' close relatives, the Neanderthals, rather than direct interbreeding with the Denisovans, researchers said.

Denisovans began to diverge from modern humans in terms of DNA sequences about 800,000 years ago. Among the genetic differences between Denisovans and modern humans are likely changes that "are essential for what made modern human history possible, the very rapid development of human technology and culture that allowed our species to become so numerous, spread around the whole world, and actually dominate large parts of the biosphere," Pääbo said.

Eight of these genetic changes have to do with brain function and brain development, "the connectivity in the brain of synapses between nerve cells function, and some of them have to do with genes that, for example, can cause autism when these genes are mutated," Pääbo added.

What makes humans special?

It makes a lot of sense to speculate that what makes us special in the world relative to the Denisovans and Neanderthals "is about connectivity in the brain," Pääbo said. "Neanderthals had just as large brains as modern humans had — relative to body size, they even had a bit larger brains. Yet there is, of course, something special in my mind that happens with modern humans. It's sort of this extremely rapid technological cultural development that comes, large societal systems, and so on. So it makes sense that, well, what pops up is sort of connectivity in the brain."

The fact that differences are seen between modern humans and Denisovans in terms of autism-linked genes is especially interesting, because whole books have been written "suggesting that autism may affect sort of a trait in human cognition that is also crucial for modern humans, for how we put ourselves in the shoes of others, manipulate others, lie, develop politics and big societies and so on," Pääbo said.

The genetic diversity suggested by this Denisovan sample was apparently quite low. This was probably not due to inbreeding, the researchers say — rather, their vast range suggests their population was initially quite small but grew quickly, without time for genetic diversity to increase as well.

"If future research of the Neanderthal genome shows that their population size changed over time in similar ways, it may well be that a single population expanding out of Africa gave rise to both the Denisovans and the Neanderthals," Pääbo said.

Intriguingly, comparing the X chromosome, which is passed down by females, to the rest of the genome, which is passed down equally in males and females, revealed "there is substantially less Denisovan genetic material in New Guinea on the X chromosome than there is on the rest of the genome,"researcher David Reich at Harvard Medical School in Boston told LiveScience.

One possible explanation "is that the Denisovan gene flow into modern humans was mediated primarily by male Denisovans mixing with female modern humans," Reich said. "Another possible explanation is that actually there was natural selection to remove genetic material on the X chromosome that came from Denisovans once that entered the modern human population, perhaps because it caused problems for the people who carried it."

These current Denisovan findings have allowed the researchers to re-evaluate past analysis of the Neanderthal genome. They discovered modern humans in the eastern parts of Eurasia and Native Americans actually carry more Neanderthal genetic material than people in Europe, "even though the Neanderthals mostly lived in Europe, which is really, really interesting," Reich said.

The researchers would now like to upgrade the Neanderthal genome to the quality seen with the Denisovan genome. The genetic techniques they used could also be employed in forensic investigations, and in analyzing other fossil DNA, said researcher Matthias Meyer, also at the Max Planck Institute for Evolutionary Anthropology.
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References:

Choi, Charles. 2012. “Extinct Human Genome Reveals Brown-Eyed Girl”. Discovery News. Posted: August 30, 2012. Available online: http://news.discovery.com/human/mysterious-extinct-human-fossil-120830.html

Entire genome of extinct human decoded from fossil

The Max Planck Institute for Evolutionary Anthropology, in Leipzig, Germany, has completed the genome sequence of a Denisovan, a representative of an Asian group of extinct humans related to Neanderthals

In 2010, Dr. Svante Pääbo and his colleagues presented a draft version of the genome from a small fragment of a human finger bone discovered in Denisova Cave in southern Siberia. The DNA sequences showed that this individual came from a previously unknown group of extinct humans that have become known as Denisovans. Together with their sister group the Neandertals, Denisovans are the closest extinct relatives of currently living humans.

The Leipzig team has now developed sensitive novel techniques which have allowed them to sequence every position in the Denisovan genome about 30 times over, using DNA extracted from less than 10 milligrams of the finger bone. In the previous draft version published in 2010, each position in the genome was determined, on average, only twice. This level of resolution was sufficient to establish the relationship of Denisovans to Neandertals and present-day humans, but often made it impossible for researchers to study the evolution of specific parts of the genome. The now-completed version of the genome allows even the small differences between the copies of genes that this individual inherited from its mother and father to be distinguished. This Wednesday the Leipzig group makes the entire Denisovan genome sequence available for the scientific community over the internet.

"The genome is of very high quality", says Dr. Matthias Meyer, who developed the techniques that made this technical feat possible. "We cover all non-repetitive DNA sequences in the Denisovan genome so many times that it has fewer errors than most genomes from present-day humans that have been determined to date".

The genome represents the first high-coverage, complete genome sequence of an archaic human group - a leap in the study of extinct forms of humans. "We hope that biologists will be able to use this genome to discover genetic changes that were important for the development of modern human culture and technology, and enabled modern humans to leave Africa and rapidly spread around the world, starting around 100,000 years ago" says Pääbo. The genome is also expected to reveal new aspects of the history of Denisovans and Neandertals.

The group plans to present a paper describing the genome later this year. "But we want to make it freely available to everybody already now" says Pääbo. "We believe that many scientists will find it useful in their research".

The project is made possible by financing from the Max Planck Society and is part of efforts since almost 30 years by Dr. Pääbo's group to study ancient DNA. The finger bone was discovered by Professor Anatoly Derevianko and Professor Michail Shunkov from the Russian Academy of Sciences in 2008 during their excavations at Denisova Cave, a unique archaeological site which contains cultural layers indicating that human occupation at the site started up to 280,000 years ago. The finger bone was found in a layer which has been dated to between 50,000 and 30,000 years ago.

The genome is available at www.eva.mpg.de/denisova/.
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References:

EurekAlert. 2012. "Entire genome of extinct human decoded from fossil".EurekAlert. Posted: February 7, 2012. Available online: http://www.eurekalert.org/pub_releases/2012-02/m-ego020712.php

Humans on many roads to Asia

The discovery by Russian archaeologists of the remains of an extinct prehistoric human during the excavation of Denisova Cave in Southern Siberia in 2008 was nothing short of a scientific sensation. The sequencing of the nuclear genome taken from a circa. 30,000-year-old finger bone revealed that Denisova man was neither a Neanderthal nor modern human, but a new form of hominin. Minute traces of the Denisova genome are still found in some individuals living today. The comparisons of the DNA of modern humans and prehistoric human species provide new indications of how human populations settled in Asia over 44,000 years ago.

Tracking Denisovan DNA

As scientists from Harvard Medical School in Boston (USA) and the Max Planck Institute for Evolutionary Anthropology in Leipzig have discovered, the Denisova hominin passed on genetic material not only to populations that live in New Guinea today, but also to Australian aborigines and population groups in the Philippines. David Reich, professor of Genetics at Harvard Medical School, says: “The Denisovan DNA is comparable to a medical contrast agent that can be used to make a person’s blood vessels visible. It has such a high recognition value that even small volumes can be detected in individuals. Therefore, we were able to track down Denisovan DNA in human dispersals. The sequencing of prehistoric DNA is an important tool for researching human evolution.”

The scientists have discovered that, contrary to the information available up to now, modern humans possibly populated Asia in at least two migration waves. According to David Reich, the original inhabitants who still populate Southeast Asia and Oceania today came from the first migration wave. Later migrations formed populations in East Asia that are related to the population found in Southeast Asia today.

Accordingly, Denisova hominins were spread across an extraordinarily large ecological and geographical area extending from Siberia to tropical Southeast Asia. “The fact that Denisovan DNA can be detected in some but not other original inhabitant populations living in Southeast Asia today shows that numerous populations with and without Denisovan DNA existed over 44,000 years ago,” says Mark Stoneking, professor at the Department of Evolutionary Genetics at the Max Planck Institute for Evolutionary Anthropology and leading author of the study. “The simplest explanation for the presence of Denisovan genetic material in some but not all groups is that Denisova people themselves lived in Southeast Asia.”

In December 2010, Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology reported in the journal Nature that Denisova hominins contributed genes to human populations living in New Guinea today.

Genetic footprint

The new study, which was initiated by Mark Stoneking – an expert in the field of human genetic variation in Southeast Asia and Oceania – is now researching the genetic footprint that the Denisova hominin has left behind in us modern humans. The scientists analysed the genomes of 33 populations living in Southeast Asia and Oceania today, including people from Borneo, Fiji, Indonesia, Malaysia, Australia, the Philippines, Papua New Guinea and Polynesia. Some of this data were already available and others were recorded in the context of the current study.

The analysis carried out by the researchers shows that the Denisova hominin contributed genetic material not only to the people living in New Guinea today but also to Australian aborigines, the Mamanwa, a Philippine “Negrito” group, and some other populations in eastern Southeast Asia and Oceania. In contrast, western and northwestern groups, including other “Negrito” groups, such as the Onge people who inhabit the Andaman Islands and the Jehai of Malaysia, and the mainland East Asians did not mix with the Denisova people.

The researchers conclude from this that Denisova hominins interbred with modern humans at least 44,000 years ago, before the Australians and inhabitants of New Guinea separated from each other. As opposed to this, Southeast Asia was first colonised by modern humans who were not related to today’s Chinese and Indonesian populations. The latter arrived in the course of subsequent migratory movements. This hypothesis on the settlement of Southeast Asia and Oceania, which is referred to as the “South Route” has already been substantiated by archaeological finds. However, strong support in the form of genetic evidence has yet to be found.
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References:

Past Horizons. 2012. "Humans on many roads to Asia". Past Horizons. Posted: December 22, 2011. Available online: http://www.pasthorizonspr.com/index.php/archives/12/2011/humans-on-many-roads-to-asia

Shared Genes With Neanderthal Relatives: Modern East Asians Share Genetic Material With Prehistoric Denisovans

During human evolution our ancestors mated with Neanderthals, but also with other related hominids. In this week's online edition of Proceedings of the National Academy of Sciences, researchers from Uppsala University are publishing findings showing that people in East Asia share genetic material with Denisovans, who got the name from the cave in Siberia where they were first found.

"Our study covers a larger part of the world than earlier studies, and it is clear that it is not as simple as we previously thought. Hybridization took place at several points in evolution, and the genetic traces of this can be found in several places in the world. We'll probably be uncovering more events like these," says Mattias Jakobsson, who conducted the study together with Pontus Skoglund.

Previous studies have found two separate hybridization events between so-called archaic humans (different from modern humans in both genetics and morphology) and the ancestors of modern humans after their emergence from Africa: hybridization between Neanderthals and the ancestors of modern humans outside of Africa and hybridization between Denisovans and the ancestors of indigenous Oceanians. The genetic difference between Neandertals and Denisovans is roughly as great as the maximal level of variation among us modern humans.

The Uppsala scientists' study demonstrates that hybridization also occurred on the East Asian mainland. The connection was discovered by using genotype data in order to obtain a larger data set. Complete genomes of modern humans are only available from some dozen individuals today, whereas genotype data is available from thousands of individuals. These genetic data can be compared with genome sequences from Neandertals and a Denisovan which have been determined from archeological material. Only a pinky finger and a tooth have been described from the latter.

Genotype data stems from genetic research where hundreds of thousands of genetic variants from test panels are gathered on a chip. However, this process leads to unusual variants not being included, which can lead to biases if the material is treated as if it consisted of complete genomes. Skoglund and Jakobsson used advanced computer simulations to determine what this source of error means for comparisons with archaic genes and have thereby been able to use genetic data from more than 1,500 modern humans from all over the world.

"We found that individuals from mainly Southeast Asia have a higher proportion of Denisova-related genetic variants than people from other parts of the world, such as Europe, America, West and Central Asia, and Africa. The findings show that gene flow from archaic human groups also occurred on the Asian mainland," says Mattias Jakobsson.

"While we can see that genetic material of archaic humans lives on to a greater extent than what was previously thought, we still know very little about the history of these groups and when their contacts with modern humans occurred," says Pontus Skoglund.

Because they find Denisova-related gene variants in Southeast Asia and Oceania, but not in Europe and America, the researchers suggest that hybridization with Denisova man took place about 20,000-40,000 years ago, but could also have occurred earlier. This is long after the branch that became modern humans split off from the branch that led to Neandertals and Denisovans some 300,000-500,000 years ago.

"With more complete genomes from modern humans and more analyses of fossil material, it will be possible to describe our prehistory with considerably greater accuracy and richer detail," says Mattias Jakobsson.
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References:

Science Daily. 2011. "Shared Genes With Neanderthal Relatives: Modern East Asians Share Genetic Material With Prehistoric Denisovans". Science Daily. Posted: October 31, 2011. Available online: http://www.sciencedaily.com/releases/2011/10/111031154119.htm

Journal Reference:

1. Pontus Skoglunda and Mattias Jakobssona. Archaic human ancestry in East Asia. Proceedings of the National Academy of Sciences, 2011 DOI: 10.1073/pnas.1108181108

DNA study suggests Asia was settled in multiple waves of migration

Analysis reveals archaic Denisovans lived from Siberia to Southeast Asia

An international team of researchers studying DNA patterns from modern and archaic humans has uncovered new clues about the movement and intermixing of populations more than 40,000 years ago in Asia.

Using state-of-the-art genome analysis methods, scientists from Harvard Medical School and the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have found that Denisovans—a recently identified group of archaic humans whose DNA was extracted last year from a finger bone excavated in Siberia—contributed DNA not just to present-day New Guineans, but also to aboriginal Australian and Philippine populations.

The study demonstrates that contrary to the findings of the largest previous genetic studies, modern humans settled Asia in more than one migration. According to David Reich, a professor of genetics at Harvard Medical School, "Denisova DNA is like a medical imaging dye that traces a person's blood vessels. It is so recognizable that you can detect even a little bit of it in one individual. In a similar way, we were able to trace Denisova DNA in the migrations of people. This shows the power of sequencing ancient DNA as a tool for understanding human history."

The patterns the researchers found can only be explained by at least two waves of human migration: the first giving rise to the aboriginal populations that currently live in Southeast Asia and Oceania, and later migrations giving rise to relatives of East Asians who now are the primary population of Southeast Asia.

The study also provides new insights about where the ancient Denisovans lived. According to Mark Stoneking, a professor at the Max Planck Institute who is senior author of the paper, Denisovans must have inhabited an extraordinarily large ecological and geographic range, from Siberia to tropical Southeast Asia. "The fact that Denisovan DNA is present in some aboriginal populations of Southeast Asia but not in others shows that there was a checkerboard of populations with and without Denisova material more than 44,000 years ago," he said. "The presence of Denisovan genetic material in some but not all the groups there can most easily be explained if Denisovans lived in Southeast Asia itself."

The findings appear on September 22 in the American Journal of Human Genetics.

This research builds on previous work by Reich and colleagues at the Max Planck Institute, in which they analyzed an ancient pinky bone uncovered by Russian archaeologists in the Siberian Denisova Cave in 2008. The Max Planck Institute team led by Svante Pääbo sequenced the bone's nuclear genome, and Reich led the population genetic analysis using algorithms that he and colleagues developed.

Reporting December 2010 in Nature, the team identified Denisovans as a distinct group of archaic humans (hominins) that lived more than 30,000 years ago and contributed genes to present-day New Guineans. They concluded that Denisovans were neither Neandertals nor early modern humans, though they shared a common ancestry.

This paper helped fill in some empty pieces in the evolutionary puzzle that began after early humans left Africa and reinforces the view that humans have intermixed throughout history.

Genetic footprints

The new study was initiated by Stoneking, an expert on genetic variation in Southeast Asia and Oceania who has assembled diverse samples from that region. The study takes a closer look at the Denisovans' genetic footprint. The researchers analyzed DNA from dozens of present-day populations in Southeast Asia and Oceania, including Borneo, Fiji, Indonesia, Malaysia, Australia, the Philippines, Papua New Guinea and Polynesia. Some of the data already existed, and some were newly collected for the study.

Their analysis shows that, in addition to New Guineans, Denisovans contributed genetic material to Australian aborigines, a Philippine "Negrito" group called Mamanwa, and several other populations in eastern Southeast Asia and Oceania. However, groups in the west or northwest, including other Negrito groups such as the Onge in the Andaman Islands and the Jehai in Malaysia, as well as mainland East Asians, did not interbreed with Denisovans.

The researchers concluded that:

* Denisovans interbred with modern humans in Southeast Asia at least 44,000 years ago before the time of the separation of the Australians and New Guineans.
* Southeast Asia was first colonized by modern humans unrelated to present-day Chinese and Indonesians, and that these and other East Asians arrived in later migrations. This "southern route" hypothesis has previously been supported by archaeological evidence, but has never had strong genetic support.
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References:

EurekAlert. 2011. "DNA study suggests Asia was settled in multiple waves of migration
". EurekAlert. Posted: September 22, 2011. Available online: http://www.eurekalert.org/pub_releases/2011-09/hms-dk091611.php

Fossil Finger Bone Yields Genome of a Previously Unknown Human Relative

A 30,000-year-old finger bone found in a cave in southern Siberia came from a young girl who was neither an early modern human nor a Neanderthal, but belonged to a previously unknown group of human relatives who may have lived throughout much of Asia during the late Pleistocene epoch. Although the fossil evidence consists of just a bone fragment and one tooth, DNA extracted from the bone has yielded a draft genome sequence, enabling scientists to reach some startling conclusions about this extinct branch of the human family tree, called "Denisovans" after the cave where the fossils were found.

The findings are reported in the Dec. 23 issue of Nature by an international team of scientists, including many of the same researchers who earlier this year published the Neanderthal genome. Coauthor Richard Green of the University of California, Santa Cruz, played a lead role in the analysis of the genome sequence data, for which a special portal was designed on the UCSC Genome Browser. The team was led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

By comparing the Denisovan genome sequence with the genomes of Neanderthals and modern humans, the researchers determined that the Denisovans were a sister group to the Neanderthals, descended from the same ancestral population that had separated earlier from the ancestors of present-day humans. The study also found surprising evidence of Denisovan gene sequences in modern-day Melanesians, suggesting that there was interbreeding between Denisovans and the ancestors of Melanesians, just as Neanderthals appear to have interbred with the ancestors of all modern-day non-Africans.

"The story now gets a bit more complicated," said Green, an assistant professor of biomolecular engineering in the Baskin School of Engineering at UC Santa Cruz. "Instead of the clean story we used to have of modern humans migrating out of Africa and replacing Neanderthals, we now see these very intertwined story lines with more players and more interactions than we knew of before."

The Denisovans appear to have been quite different both genetically and morphologically from Neanderthals and modern humans. The tooth found in the same cave as the finger bone shows a morphology that is distinct from Neanderthals and modern humans and resembles much older human ancestors, such as Homo habilis and Homo erectus. DNA analysis showed that the tooth and the finger bone came from different individuals in the same population.

The finger bone was found in 2008 by Russian scientists in Denisova Cave, an archaeological site in southern Siberia. Pääbo, who had worked with the Russian scientists before, obtained the bone for his research on ancient DNA. In Leipzig, researchers extracted DNA from the bone and sequenced the mitochondrial genome, a smaller DNA sequence separate from the chromosomal DNA and easier to obtain from ancient samples. The results, published earlier this year, showed a surprising divergence from the mitochondrial genomes of Neanderthals and modern humans, and the team quickly began working to sequence the nuclear genome.

"It was fortuitous that this discovery came quickly on the heels of the Neanderthal genome, because we already had the team assembled and ready to do another similar analysis," Green said. "This is an incredibly well-preserved sample, so it was a joy to work with data this nice. We don't know all the reasons why, but it is almost miraculous how well-preserved the DNA is."

The relationship between Denisovans and present-day Melanesians was a completely unexpected finding, he said. The comparative analysis, which included genome sequences of individuals from New Guinea and Bougainville Island, indicates that genetic material derived from Denisovans makes up about 4 to 6 percent of the genomes of at least some Melanesian populations. The fact that Denisovans were discovered in southern Siberia but contributed genetic material to modern human populations in Southeast Asia suggests that their population may have been widespread in Asia during the late Pleistocene, said David Reich of Harvard Medical School, who led the population genetic analysis.

It is not clear why fossil evidence had not already revealed the existence of this group of ancient human relatives. But Green noted that the finger bone was originally thought to be from an early modern human, and the tooth resembles those of other ancient human ancestors. "It could be that other samples are misclassified," he said. "But now, by analyzing DNA, we can say more definitively what they are. It's getting easier technically to do this, and it's a great new way to extract information from fossil remains."

In the light of the Neanderthal and Denisovan genomes, a new, more complex picture is emerging of the evolutionary history of modern humans and our extinct relatives. According to Green, there was probably an ancestral group that left Africa between 300,000 and 400,000 years ago and quickly diverged, with one branch becoming the Neanderthals who spread into Europe and the other branch moving east and becoming Denisovans. When modern humans left Africa about 70,000 to 80,000 years ago, they first encountered the Neanderthals, an interaction that left traces of Neanderthal DNA scattered through the genomes of all non-Africans. One group of humans later came in contact with Denisovans, leaving traces of Denisovan DNA in the genomes of humans who settled in Melanesia.

"This study fills in some of the details, but we would like to know much more about the Denisovans and their interactions with human populations," Green said. "And you have to wonder if there were other populations that remain to be discovered. Is there a fourth player in this story?"

The paper's 28 coauthors include scientists from Germany, Spain, China, Russia, Canada, and the United States. Reich and Green are among seven coauthors credited with contributing equally to this work. This research was supported by the Max Planck Society, the Krekeler Foundation, the U.S. National Institutes of Health, and the U.S. National Science Foundation.
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References:
Science Daily. 2010. "Fossil Finger Bone Yields Genome of a Previously Unknown Human Relative". Science Daily. Posted: December 22, 2010. Available online: http://www.sciencedaily.com/releases/2010/12/101222131119.htm