quote:New Machine Sheds Light on DNA of Neanderthals
Published: November 15, 2006 The archaic human species that dominated Europe until 30,000 years ago is about to emerge from the shadows. With the help of a new DNA sequencing machine that operates with firefly light, the bones of the Neanderthals have begun to tell their story to geneticists. One million units of Neanderthal DNA have already been analyzed, and a draft version of the entire genome, 3.2 billion units in length, should be ready in two years, said Dr. Svante Paabo, the leader of the research project at the Max-Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Biologists expect knowledge of the Neanderthal genome to reveal, by its differences with the human genome, many distinctive qualities of what it means to be human. Researchers also hope to resolve such questions as whether the Neanderthals spoke, their hair and skin color, and whether they interbred at all with the modern humans who first arrived on their doorstep 45,000 years ago, or were driven to extinction without leaving any genetic legacy. Dr. Paabo has shared some of his precious source of Neanderthal DNA with Edward M. Rubin of the Joint Genome Institute in Walnut Creek, Calif., whose team has identified 62,250 units of Neanderthal DNA by a different method. The two teams report their results in the journals Nature and Science respectively, saying they have independent proof of the principle that recovery of the Neanderthal genome now seems possible. “I think these results are monumental,” said Richard Klein, a paleoanthropologist at Stanford University. The full Neanderthal genome will resolve many longstanding issues about Neanderthals and their relationship to modern humans, including their physical and perhaps behavioral differences, he said. The Neanderthals, who flourished for 400,000 years, physically resembled modern humans, but the middle of their face jutted forward and their large brain cases had a distinctive bulge or bun at the back. They were heavily muscled and presumably well adapted to the cold conditions of the last ice age. They would probably have been terrifying to the lighter-boned modern humans who first encountered them, except that their weapons were considerably less advanced. The Neanderthals still used a million-year-old stone tool kit that modern humans had abandoned. Archaeologists have shown that as sites of the first modern humans, known as the Aurignacian culture, moved westward across Europe, those of the Neanderthals receded in parallel. By 30,000 years ago or even earlier, the Aurignacian conquest of Europe was complete, and the Neanderthals had disappeared from their last refuges in what are now Spain and Portugal. Dr. Paabo began his quest for Neanderthal DNA more than a decade ago, and has had to overcome a daunting array of obstacles. Many extravagant claims were then being made about DNA in old bones, with some scientists claiming to have recovered DNA from dinosaur bones that were millions of years old. But such bones were often contaminated by the DNA of the people who handled them, and Dr. Paabo saved the field from sliding into disrepute by demonstrating the extreme precautions necessary to avoid analyzing human DNA by mistake. In 1997 he succeeded in analyzing part of the Neanderthal mitochondrial DNA, showing that it differed profoundly from modern human DNA. Mitochondria, the small organelles that provide the cell’s energy, are separate from the main genome in the cell’s nucleus. Since the nuclear DNA in old bones is degraded into millions of short fragments, 50 or so units in length, it seemed beyond hope of retrieval. Enter a new kind of DNA sequencing machine, made by 454 Life Sciences of Branford, Conn. The machine prompts each DNA unit to generate a flash of light by stimulating luciferase, the enzyme found in fireflies. The flashes are captured by a charge-coupled device, the image-sensing plate used in telescopes to capture the light of distant stars. From the timing and position of the flashes, a computer reconstructs the sequence of the DNA units. As it happens, the kind of DNA the 454 machine works best with are tiny fragments the size of those found in old bones. Dr. Paabo then scoured the museums of Europe for Neanderthal bones that might still retain DNA. Most of the 70 he tested had none, since DNA quickly degrades after the death of the organism. Many others were heavily contaminated with DNA from the curators and scientists who had handled them. Since human DNA is 99.9 percent identical to Neanderthal DNA, the contamination posed serious problems. Just one bone, retrieved from the Vindija cave in Croatia, turned out to retain DNA and be fairly free of human contamination. Asked what made it so special, Dr. Paabo said that because it was small and uninteresting it had been “thrown in a big box of uninformative bones in the museum in Zagreb and wasn’t handled very much.” The original owner of the Vindija bone was a male Neanderthal who died about 38,000 years ago. As with other ancient bones, most of the surviving DNA on this one belongs to the bacteria that consumed it when it was fresh. Less than 6 percent is Neanderthal DNA, and what there is of it has suffered a chemical degradation of the four DNA bases, referred to as A, T, G and C: some of the C’s have converted to T’s and some G’s to A’s. Dr. Paabo has developed methods for distinguishing the real Neanderthal DNA and addressing the chemical conversion problem. Dr. Paabo hopes to find other Neanderthal bones with retrievable DNA. But even if no more turn up, he believes there is enough DNA in the Vindija bone alone to complete a draft of the full Neanderthal genome. He and his team still have many more problems to overcome, but other researchers are impressed with the progress so far. “He’s superbright and superthoughtful, and if anyone’s ever going to do it, it’s him,” Dr. Klein said. If the full Neanderthal genome is retrieved, biologists may be able to ask if the Neanderthals had language by looking at their version of the human gene known as FoxP2, thought to be one of the last components to evolve in mediating the modern human language faculty. FoxP2 has changed significantly since the human lineage split apart from that of chimps some six million years ago. If the Neanderthal version resembles the chimp version, that would make it less likely they had modern, syntactical language. The Neanderthal genome should also enable biologists to calculate which aspects of human evolution took place between 6 million and 500,000 years ago, and which are more recent. The latter is the approximate date at which the Neanderthal and human lineages split apart. Dr. Paabo also believes the Neanderthal genome will help geneticists identify which human genes have been subject to the pressures of natural selection in the last 500,000 years. This would be of great interest in understanding which are the distinctive genetic attributes of modern humans. From the data already obtained, Dr. Paabo and his colleagues estimate that the ancestral Neanderthal population was very small, perhaps less than 10,000 individuals. Since the ancestral population of modern humans was much the same size, it seems that all populations of early humans were tiny, expanding only after the ice age ended.
posted
I'm beginning to wonder now, why are geneticists so obsessed with trying connect modern Europeans to prehistoric non-homo sapien sapien cavemen? Is the desire to deny the African origins of modern humans that bad?
Posts: 2601 | From: Vicksburg | Registered: Feb 2006
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posted
^ I have been having the same questions, exactly. And I'm afraid that it indeed may be the case that these Europeans want to dissociate themselves from Africans that badly...
Even though not only is their ancestry African, but it is the very reason for their intellectual prowess and advanced culture!
Before Homo sapiens sapiens entered the scene, there was no complex culture in Europe. LOL In fact, in the TV program of Spencer Well's Journey of Man, it was remarked about how tall the early Modern men were for them to make those famous cave paintings in France at such a height in the cave walls. And as Jablonsky explained, it was because they still possessed African body builds unlike their distant short Neanderthal cousins!
To me, these European geneticists and other experts make themselves look more ridiculous, the more they try to make their ancestors more 'European' or somehow 'special' from their Eurasian brethren, let alone their brethren who never left Africa.
Posts: 26356 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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quote: I'm beginning to wonder now, why are geneticists so obsessed with trying connect modern Europeans to prehistoric non-homo sapien sapien cavemen? Is the desire to deny the African origins of modern humans that bad?
This is because Europeans are closely related to Africans. If they can find a relationship with the Neanderthals they can develop an alternative view of their origin.
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-------------------- C. A. Winters Posts: 13012 | From: Chicago | Registered: Jan 2006
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posted
I don't see where the latest report on Neanderthal genes suggests their connection to modern Europeans.
What I did see in Wade's NY TIMES article is the attributing of culture to European Aurignacians but that can't be blamed on the geneticists on whose work Wade is only reporting. Wade is just a journalist.
quote:... the first modern humans, known as the Aurignacian culture, moved westward across Europe ...
by Wade, a journalist
quote:The full Neanderthal genome will resolve many longstanding issues about Neanderthals and their relationship to modern humans, including their physical and perhaps behavioral differences.
by Richard Klein, a paleoanthropologist not on the reporting team
Note Klein's focus is on differences not similarities.
Statements by Paabo and Rubin in other news sources (the BBC) clearly comment on the distinction and disruption between Neanderthal and HSS emphatic about the former not being ancestral to the latter but that if anything HSS contributed to Neanderthal!
Posts: 8014 | From: the Tekrur in the Western Sahel | Registered: Feb 2006
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-------------------------------- Neanderthal DNA secrets unlocked
By Paul Rincon Science reporter, BBC News
A genetic breakthrough could help clear up some long-standing mysteries surrounding our closest evolutionary relatives: the Neanderthals.
Scientists have reconstructed a chunk of DNA from the genome of a Neanderthal man who lived 38,000 years ago.
The genetic information they extracted from a thigh bone has allowed them to identify more than a million building blocks of Neanderthal DNA so far.
Details of the efforts appear in the journals Nature and Science.
"The sequence data will serve as a DNA time machine," said co-author Edward Rubin, from the Joint Genome Institute in Walnut Creek, California, US.
quote: Research will now extend to complete the whole genome of a Neanderthal Prof Chris Stringer, Natural History Museum
"[It] will tell us about aspects of Neanderthal biology that we can never get from their bones and associated artefacts."
Studying the Neanderthal genome will shed light on the genetic changes that made our species what it is, after the evolutionary lineages of Neanderthals and modern humans diverged from one another.
It could also reveal what colour hair, eyes and skin Neanderthals had, whether they were capable of modern speech, shed light on aspects of their brain function and determine whether they contributed to the modern human gene pool.
'Technical triumph'
Researchers have already sequenced mitochondrial DNA (mtDNA) from 12 Neanderthals. This is DNA from the cell's powerhouses, and which is passed down from mother to child.
While mtDNA has confirmed that Neanderthals were indeed different from us, the information gleaned from it is limited.
quote: THE DNA MOLECULE The double-stranded DNA molecule is held together by chemical components called bases Adenine (A) bonds with thymine (T); cytosine(C) bonds with guanine (G) These "letters" form the "code of life"; there are 3.2 billion base-pairs in the Neanderthal genome Written in the DNA are genes, which cells use as starting templates to make proteins; these sophisticated molecules build and maintain the body
To answer more detailed questions about our evolutionary cousins, scientists had to extract DNA that came from the cell's nucleus. This nuclear DNA encodes most of an organism's genetic blueprint.
Researchers used cutting-edge DNA sequencing techniques to retrieve genetic material from the Neanderthal femur found in the Vindija Cave, Croatia.
Writing in Nature journal, Professor Svante Paabo and colleagues describe how they recovered more than one million base-pairs - the building blocks of DNA - by directly reading the genetic sequence.
In another paper published in Science magazine, Professor Rubin's team used a different approach called metagenomics, in which the fragments of genetic material were incorporated into bacteria. These then copied themselves, generating a living "library" of DNA sequences.
This method resulted in the recovery of 65,250 base-pairs of Neanderthal DNA.
While direct sequencing allows scientists to recover more genetic material, it is a random process. The metagenomic approach should allow scientists to call up specific genetic sequences of interest from the DNA library in a targeted manner.
Language question
Professor Paabo told BBC science correspondent Pallab Ghosh that he planned to look at the form of the gene FOXP2 in Neanderthals; this gene is implicated in the development of language skills and has undergone evolution in modern humans since our divergence from chimpanzees.
"We have two little snippets of genes involved in skin and hair colour, but they don't give any hint of a special variant that would be of interest," Paabo told the BBC News website.
The two teams basically agree, within their margins of error, that the evolutionary lineages of Neanderthals and modern humans split somewhere around 500,000 years ago. This fits with previous estimates from mtDNA and archaeological data.
Professor Paabo, from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and his team also show that Neanderthals came from a very small ancestral population of about 3,000 individuals.
At their peak, Neanderthals dominated a wide range - stretching from Britain and Iberia in the west, to Israel in the south and Uzbekistan in the east. This stocky, muscular human species was our closest evolutionary relative.
Modern humans entered Europe about 40,000 years ago; and within 10,000 years, the Neanderthals had largely disappeared from the continent. By 24,000 years ago, the last survivors had vanished from their refuge in the Iberian Peninsula.
Extinct relative
The question of whether modern humans and Neanderthals mated when they encountered each other 40,000 years ago is highly controversial.
The researchers say more extensive sequencing is needed to address this possibility.
Professor Chris Stringer, from London's Natural History Museum, said the results "confirm the distinctiveness of the Neanderthals, and support previous estimates of the divergence time.
"Research will now extend to complete the whole genome of a Neanderthal and to examine Neanderthal variation through time and space to compare with ours."
The researchers aim to produce a rough draft of the full Neanderthal genome sequence over the next two years.
quote:Originally posted by Clyde Winters: This is because Europeans are closely related to Africans. If they can find a relationship with the Neanderthals they can develop an alternative view of their origin.
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Yes, that is because Europeans have recent admixture from Africans...
Unlike black Dravidian Indians who are only distantly related to Africans about as much as fair-skinned Japanese.
"Alternative views of origin" seems to be something that you yourself are caught in with regards to Indians and even Meso-Americans.
Posts: 26356 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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I have been having the same questions, exactly. And I'm afraid that it indeed may be the case that these Europeans want to dissociate themselves from Africans that badly...
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