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Physorg.com, and nhm.ac.uk: The genetic code of the Neanderthals has been revealed for the first time, giving surprising clues to their intimate relations with modern humans, scientists report in the journal Science.
An international team analysed DNA from the remains of 3 Neanderthal individuals. After extracting ancient DNA from the 40,000 year old bones of Neanderthals, the scientists obtained a draft sequence of the whole Neanderthal genetic code, or genome, the first time this has been done. They also compared the Neanderthal genome to modern humans, Homo sapiens, from different parts of the world. Neanderthals are usually regarded as a separate species, Homo neanderthalensis. They were our closest relatives and they died out about 30,000 years ago.
The Neanderthal Genome Project
Richard E Green, an assistant professor of biomolecular engineering, University of California, Santa Cruz, began working on the Neanderthal genome as a postdoctoral researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Svante Pääbo, director of the institute’s genetics department, leads the Neanderthal Genome Project, which involves an international consortium of researchers. David Reich, a population geneticist at the Broad Institute of MIT and Harvard, also played a leading role in the new study and the ongoing investigation of the Neanderthal genome.
The Neanderthal genome sequence allows us to begin to define all those features in our genome where we differ from all other organisms on the planet, including our closest evolutionary relative, the Neanderthals.
Svante Pääbo
The sequence was derived from DNA extracted from three Neanderthal bones found in the Vindiga Cave in Croatia. Smaller amounts of sequence data were also obtained from three bones from other sites. Two of the Vindiga bones could be dated by carbon dating of collagen and were found to be about 38,000 and 44,000 years old.
Deriving a genome sequence—representing the genetic code on all of an organism’s chromosomes—from such ancient DNA is a remarkable technological feat. The Neanderthal bones were not well preserved, and more than 95 percent of the DNA extracted from them came from bacteria and other organisms that had colonized the bone. The DNA itself was degraded into small fragments and had been chemically modified in many places.
The researchers identified a catalog of genetic features unique to modern humans by comparing the Neanderthal, human, and chimpanzee genomes. Genes involved in cognitive development, skull structure, energy metabolism, and skin morphology and physiology are among those highlighted in the study as likely to have undergone important changes in recent human evolution.
The researchers had to develop special methods to extract the Neanderthal DNA and ensure that it was not contaminated with human DNA. They used new sequencing technology to obtain sequence data directly from the extracted DNA without amplifying it first. Although genome scientists like to sequence a genome at least four or five times to ensure accuracy, most of the Neanderthal genome has been covered only one to two times so far.
Interbreeding
Neanderthals lived in much of Europe and western Asia, coexisting with humans for thousands of years before dying out 30,000 years ago. Until now, scientists could only speculate whether Neanderthals ever interbred with modern humans—fossil evidence led some scientists to speculate that interbreeding may have occurred—but the team’s results revealed some surprises. Modern humans outside of Africa share genetic information with Neanderthals, so they probably interbred with Neanderthals soon after they left Africa around 60,000 years ago, leaving Neanderthal DNA sequences in the genomes of present day non Africans.
In all probability, there was gene flow from Neanderthals to modern humans.
Richard E Green
The Neanderthal DNA signal shows up not only in the genomes of Europeans, but also in people from East Asia and Papua New Guinea, where Neanderthals never lived. Green said:
The scenario is not what most people had envisioned. We found the genetic signal of Neanderthals in all the non African genomes, meaning that the admixture occurred early on, probably in the Middle East, and is shared with all descendants of the early humans who migrated out of Africa. We are just scratching the surface. The Neanderthal genome is a goldmine of information about recent human evolution, and it will be put to use for years to come.
The study did not address the functional significance of the finding that between 1 and 4 percent of the genomes of non Africans is derived from Neanderthals. But Green said that there is no evidence that anything genetically important came over from Neanderthals. The signal was sparsely distributed across the genome. If there was something that conferred a fitness advantage, we probably would have found it already by comparing human genomes.
Professor Chris Stringer, the Natural History Museum’s human origins expert, is one of the architects of the “Out of Africa” theory, which explains how all humans living today share an African origin, and that those outside Africa migrated out in small groups during the last 60,000 years. His book The Origin of Our Species will be published early next year. He explains:
This research suggests that the genomes of people from Europe, China and New Guinea lie slightly closer to the Neanderthal sequence than do those of Africans. The most likely explanation for this finding is that the ancestors of people in Europe, China and New Guinea interbred with Neanderthals—or at least with populations that had a component of Neanderthal genes—in North Africa, Arabia or the Middle East, as they were exiting Africa, but before they spread out across the rest of the world.
Previous genetic studies
There have been genetic studies on Neanderthals before, Prof Stringer points out:
The first tiny piece of DNA from a Neanderthal fossil was published in 1997, and since then, with improvements in recovery techniques and computing power, 20 Neanderthals have yielded up increasing amounts of ancient DNA.
These DNA studies support evidence from the fossil record, showing that Neanderthals split from modern humans around 400,000 years ago. And similarly, studies on DNA from living people support fossil records showing that modern humans share an African origin within the last 200,000 years.
As one of the architects of “Out of Africa”, I have regarded the Neanderthals as representing a separate lineage, and most likely a separate species from Homo sapiens. Although I have never ruled out the possibility of interbreeding, I have considered this to have been small and insignificant in the bigger picture of our evolution – for example, the results of isolated interbreeding events could easily have been lost in the intervening millennia. Now, the Neanderthal genome strongly suggests those genes were not lost, and that many of us outside of Africa have some Neanderthal inheritance. Any functional significance of these shared genes remains to be determined, but that will certainly be a focus for the next stages of this fascinating area of research.
Prof Stringer
Comparison with Chimps
As well as comparing the Neanderthal genome with modern humans, the team also compared it with chimps. They found that genetic changes linked to skin and bone, metabolism, and brain functions, were unique to Homo sapiens.
The draft Neanderthal sequence is probably riddled with errors, Green said, but having the human and chimpanzee genomes for comparison makes it extremely useful despite its limitations. Places where humans differ from chimps, while Neanderthals still have the ancestral chimp sequence, may represent uniquely human genetic traits. Such comparisons enabled the researchers to catalog the genetic changes that have become fixed or have risen to high frequency in modern humans during the past few hundred thousand years.
It sheds light on a critical time in human evolution since we diverged from Neanderthals. What adaptive changes occurred in the past 300,000 years as we were becoming fully modern humans? That’s what I find most exciting. Right now we are still in the realm of identifying candidates for further study.
R E green
The ancestral lineages of humans and chimpanzees are thought to have diverged about 5 or 6 million years ago.
Recent Gene Flow
By analyzing the Neanderthal genome and genomes of present-day humans, Green and his colleagues estimated that the ancestral populations of Neanderthals and modern humans separated between 270,000 and 440,000 years ago.The evidence for more recent gene flow between Neanderthals and humans came from an analysis showing that Neanderthals are more closely related to some present day humans than to others. The researchers looked at places where the DNA sequence is known to vary among individuals by a single “letter”. Comparing different individuals with Neanderthals, they asked how frequently the Neanderthal sequence matches that of different humans.
The frequency of Neanderthal matches would be the same for all human populations if gene flow between Neanderthals and humans stopped before human populations began to develop genetic differences. But that’s not what the study found. Looking at a diverse set of modern humans—including individuals from Southern Africa, West Africa, Papua New Guinea, China, and Western Europe—the researchers found that the frequency of Neanderthal matches is higher for non Africans than for Africans.
Even a little interbreeding could account for these results. The researchers estimated that the gene flow from Neanderthals to humans occurred between 50,000 and 80,000 years ago. The best explanation is that the admixture occurred when early humans left Africa and encountered Neanderthals for the first time. Green said:
How these peoples would have interacted culturally is not something we can speculate on in any meaningful way. But knowing there was gene flow is important, and it is fascinating to think about how that may have happened.
The researchers were not able to rule out one possible alternative explanation for their findings. In that scenario, the signal they detected could represent an ancient genetic substructure that existed within Africa, such that the ancestral population of present day non Africans was more closely related to Neanderthals than was the ancestral population of present day Africans. Green said:
We think that’s not the case, but we can’t rule it out.
The researchers expect many new findings to emerge from ongoing investigations of the Neanderthal genome and other ancient genetic sequences. Pääbo’s group recently found evidence of a previously unknown type of hominid after analyzing DNA extracted from what they had thought was a Neanderthal finger bone found in Siberia. Green is also taking part in that continuing investigation.
Timing of human protein evolution as revealed by massively parallel capture of Neanderthal nuclear DNA sequences, Science on Thursday, May 6, 2010. The paper is available online at
http://www.sciencemag.org/sciencexpress/recent.dtl
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