Category Archives: Transhuman News

An analysis of the oldest known DNA from a human reveals a mysterious group that roamed northern Asia

The Ust-Ishim femur. Credit:Bence Viola, MPI EVA

A 45,000-year-old leg bone from Siberia has yielded the oldest genome sequence forHomo sapienson record revealing a mysterious population that may once have spanned northern Asia. The DNA sequence from a male hunter-gatherer also offers tantalizing clues about modern humans journey from Africa to Europe, Asia and beyond, as well as their sexual encounters with Neanderthals.

His kind might have remained unknown were it not for Nikolai Peristov, a Russian artist who carves jewellery from ancient mammoth tusks. In 2008, Peristov was looking for ivory along Siberias Irtysh River when he noticed a bone jutting from the riverbank. He dug it out and showed it to a police forensic scientist, who identified it as probably human.

The bone turned out to be a human left femur, and eventually made it to the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, where researchers carbon-dated it. It was quite fossilized, and the hope was that it might turn out old. We hit the jackpot, says Bence Viola, a palaeoanthropologist who co-led the study of the remains. It was older than any other modern human yet dated. The luck continued when Violas colleagues found that the bone contained well-preserved DNA, and they sequenced its genome to the same accuracy as that achieved for contemporary human genomes (Q.Fuetal.Nature514,445449; 2014).

The researchers named their find Ust-Ishim, after the district where Peristov found the remains. They dated him to between 43,000 and 47,000 years old, nearly twice the age of the next-oldest known complete modern-human genome, although older, archaic-human genomes exist.

DNA may be the only chance to connect the remains to other humans. This guy came out of nowhere theres no archaeology site we could connect it to, says Viola, suggesting that his group roamed far and wide.

The Ust-Ishim man was probably descended from an extinct group that is closely related to humans who left Africa more than 50,000years ago to populate the rest of the world, but later went extinct, Viola says.

The most intriguing clue about his origin is that about 2% of his genome comes from Neanderthals. This is roughly the same level that lurks in the genomes of all of todays non-Africans, owing to ancient trysts between their ancestors and Neanderthals. The Ust-Ishim man probably got his Neanderthal DNA from these same matings, which, past studies suggest, happened after the common ancestor of Europeans and Asians left Africa and encountered Neanderthals in the Middle East.

Until now, the timing of this interbreeding was uncertain dated to between 37,000 and 86,000 years ago. But Neanderthal DNA in the Ust-Ishim genome pinpoints it to between 50,000 and 60,000 years ago on the basis of the long Neanderthal DNA segments in the Ust-Ishim mans genome. Paternal and maternal chromosomes are shuffled together in each generation, so that over time the DNA segments from any individual become shorter.

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45,000-Year-Old Man's Genome Sequenced

Bence Viola, MPI EVA

The Ust-Ishim femur.

A 45,000-year-old leg bone from Siberia has yielded the oldest genome sequence for Homo sapiens on record revealing a mysterious population that may once have spanned northern Asia. The DNA sequence from a male hunter-gatherer also offers tantalizing clues about modern humans journey from Africa to Europe, Asia and beyond, as well as their sexual encounters with Neanderthals.

His kind might have remained unknown were it not for Nikolai Peristov, a Russian artist who carves jewellery from ancient mammoth tusks. In 2008, Peristov was looking for ivory along Siberias Irtysh River when he noticed a bone jutting from the riverbank. He dug it out and showed it to a police forensic scientist, who identified it as probably human.

The bone turned out to be a human left femur, and eventually made it to the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, where researchers carbon-dated it. It was quite fossilized, and the hope was that it might turn out old. We hit the jackpot, says Bence Viola, a palaeoanthropologist who co-led the study of the remains. It was older than any other modern human yet dated. The luck continued when Violas colleagues found that the bone contained well-preserved DNA, and they sequenced its genome to the same accuracy as that achieved for contemporary human genomes (Q.Fu etal.Nature 514, 445449; 2014).

The researchers named their find Ust-Ishim, after the district where Peristov found the remains. They dated him to between 43,000 and 47,000 years old, nearly twice the age of the next-oldest known complete modern-human genome, although older, archaic-human genomes exist.

DNA may be the only chance to connect the remains to other humans. This guy came out of nowhere theres no archaeology site we could connect it to, says Viola, suggesting that his group roamed far and wide.

The Ust-Ishim man was probably descended from an extinct group that is closely related to humans who left Africa more than 50,000years ago to populate the rest of the world, but later went extinct, Viola says.

The most intriguing clue about his origin is that about 2% of his genome comes from Neanderthals. This is roughly the same level that lurks in the genomes of all of todays non-Africans, owing to ancient trysts between their ancestors and Neanderthals. The Ust-Ishim man probably got his Neanderthal DNA from these same matings, which, past studies suggest, happened after the common ancestor of Europeans and Asians left Africa and encountered Neanderthals in the Middle East.

Until now, the timing of this interbreeding was uncertain dated to between 37,000 and 86,000 years ago. But Neanderthal DNA in the Ust-Ishim genome pinpoints it to between 50,000 and 60,000 years ago on the basis of the long Neanderthal DNA segments in the Ust-Ishim mans genome. Paternal and maternal chromosomes are shuffled together in each generation, so that over time the DNA segments from any individual become shorter.

Excerpt from:
Oldest-known human genome sequenced

Edico Genomes Dragen genome processor, mounted on a standard computer board.

A super-fast genome processor called the Dragen Bio-IT Processor is now on sale by San Diego's Edico Genome. The processor, which is sold on a standard PCIe computer board, is meant to relieve the bottleneck in analyzing the flood of genomic data.

The Dragen processor is a special-purpose microprocessor adapted to analyzing the human genome, said Pieter van Rooyen, Edico's chief executive. That enables the accelerator card to outperform general-purpose computer chips, such as those used in servers now used to characterize genomic data.

Gene sequencing technology cuts genetic material into fragments, determines the sequence of each fragment, then reassembles these fragments like an immensely complicated jigsaw puzzle.

Software algorithms and high-powered clusters of computers are now used to do that reassembling, but it takes many hours, van Rooyen said. A human genome has 3 billion base pairs, or DNA letters.

To produce a medical-grade genome, each genome is read and reassembled more than 30 times, and the results compared to reduce errors. Each genome is compared to a reference genome.

"What we've done is take that processing that needs to be done to reassemble that giant jigsaw puzzle, and put it in a chip," van Rooyen said.

"The chip does secondary processing. It does all the processing to map those reads, figure out where they came from, stack them up, compensate for the errors, and then identify how are you different from the reference (genome). Do you have a mutation in one of your genes that might cause cancer? Or if you have cancer, what type do you have?"

My teams use of the Dragen processor has enabled us to analyze our RNA-seq data more than 60 fold faster than a 16-core CPU," said Gene Yeo, of the Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California San Diego, in an Edico statement.

A video of Scripps Health geneticist/cardiologist Eric Topol discussing the Dragen processor can be viewed at http://www.youtube.com/watch?v=TXcrErjf3x8.

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Edico starts selling high-powered genome processor

Genome providesexperts with a more accurate window into exactly when modern humans mated with their Neanderthal cousins Itoccurredwhen they moved from Africa into Europe, between 50,000 and 60,000years ago - a more accurate date than previously known DNA was collected from a bone found near Ust-Ishim in western Siberia

By Sarah Griffiths for MailOnline

Published: 12:00 EST, 22 October 2014 | Updated: 02:16 EST, 23 October 2014

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Scientists have sequenced the oldest complete human genome.

The DNA comes from an anatomically modern man who roamed Western Siberia 45,000 years ago.

It provides experts with a more accurate timeline of when modern humans mated with their Neanderthal cousins as they moved from Africa into Europe, between 50,000 and 60,000 years ago.

Scientists have sequenced the oldest complete human genome. The DNA comes from an anatomically modern man who roamed Western Siberia 45,000 years ago. His remains were fund near thesettlement of Ust-Ishim in western Siberia in 2008. A view of the river Irtysh and the village is pictured

Excerpt from:
Oldest complete human genome sequenced: DNA of 45,000-year-old man who roamed Siberia unravelled - and it sheds light ...

The femur from which the DNA samples originated.

Bence Viola, MPI EVA

Svante Pbo's lab at the Max Planck Institute for Evolutionary Anthropology in Germany has mastered the process of obtaining DNA from ancient bones. With the techniques in hand, the research group has set about obtaining samples from just about any bones they can find that come from the ancestors and relatives of modern humans. In their latest feat, they've obtained a genome from a human femur found in Siberia that dates from roughly the time of our species' earliest arrival there. The genome indicates that the individual it came from lived at a time where our interbreeding with Neanderthals was relatively recent, and Europeans and Asians hadn't yet split into distinct populations.

The femur comes from near the town of Ust-Ishim in western Siberia. It eroded out of a riverbank that contains a mixture of bones, some from the time where the sediments were deposited (roughly 30 to 50,000 years ago), and some likely older that had been washed into the sediments from other sites. The femur shows features that are a mixture of those of paleolithic and modern humans and lacks features that are typical of Neanderthal skeletons.

Two separate samples gave identical carbon radioisotope dates; after calibration to the 14C record, this places the bone at 45,000 years old, give or take a thousand years. That's roughly when modern humans first arrived in the region. That also turned out to be consistent with dates estimated by looking at the DNA sequence, which placed it at 49,000 years old (the 95 percent confidence interval was 30 to 65,000 years).

Even though the majority of the DNA obtained from similar bones is typically bacterial, Pbo's group managed to obtain collections of short DNA molecules that were between two and 10 percent human. Contamination with current human sequences, which was often a problem in earlier work, appears to be less than half a percent of the total sequences.

The short DNA fragments that persist in these ancient samples limit the areas of the human genome that you can match the fragments tolots of the human genome is repetitive, and you can't tell which repeat a fragment comes from. Of the 1.9 billion bases that can be matched uniquely, the genome the researchers obtained covered the typical base over 40 times (in the lingo of the field, it provided 42-fold coverage). That's more than enough to do some comparisons with other humans, current and past.

Because the human population is genetically diverse, the two copies of each chromosome we possess differ at known rates. In Africans, the oldest and thus most genetically diverse populations, there are about 10 differences for every 10,000 DNA bases. Non-Africans, by contrast, typically only have six or seven differences in the same amount of DNA. The Ust-Ishim genome clearly groups with non-Africans, at 7.7 differences every 10,000 bases. This is consistent with the idea that the migration out of Africa created a bottleneck, with only a fraction of our genetic diversity getting exported to populations that left the continent.

So, who was this individual related to? Based on Y chromosome and mitochondrial genome, the Ust-Ishim DNA appears to reside at the base of a broad group of populations that exist in current Eurasia. The rest of the genome indicates that it lacks many of the individual DNA changes that have appeared in current populations. All of which suggests that the population it belongs to is ancestral to Europeans and Asians.

But if you look at overall relatedness, the genome is slightly closer to current Asian populations than it is to Europeans. The authors note that other data has led researchers to hypothesize that Europeans have had an influx of DNA from a population that did not participate in the initial migration out of Africaperhaps a second wave out of Africa.

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45,000-year-old modern human bone yields a genome

LEIPZIG, Germany, Oct. 23 (UPI) -- Scientists have reconstructed the oldest known human genome after finding the bones of a 45,000-year-old man in Siberia.

The findings allowed scientists to further confirm that early humans and Neanderthals mixed and had children, said the researchers of the study published in Nature.

"What's exciting about this paper is that it's looking at a very ancient modern human who would have lived around the same time as Neanderthals," said Sarah Tishkoff, a geneticist at the University of Pennsylvania, who was not on the research team.

The bone and genetic sequence showed the man had both human and Neanderthal genes.

The one mystery that remains is what happened after the two interbred. Humans survived and Neanderthals died out but scientists still don't understand why.

The study also alludes to humans leaving Africa 60,000 years ago, much later than previously thought.

"We have caught evolution red handed!" said Svante Pbo, a director at the Max Planck Institute for Evolutionary Anthropology and lead on the study.

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45,000-year-old man reveals earliest human genome