May 17, 2006
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01:11:09 pm, Categories: Life Sciences, 652 words
Neanderthal Nuclear DNA Sequenced Rex Dalton at Nature is reporting that ancient DNA guru Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and his team have managed to obtain nuclear DNA sequences from a Neanderthal. The new sequences--which comprise about a million base pairs, or about 0.03 percent of genome--come from a 45,000-year-old male Neanderthal from Vindija Cave, located in northwestern Croatia. Paabo's team discussed the work last week at a meeting at New York's Cold Spring Harbor Laboratory.
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You may recall that Paabo was the first to recover mitochondrial DNA (mtDNA) from a Neanderthal, back in 1997. It was a big deal, because it brought a new type of evidence to the longstanding debate among paleoanthropologists over whether these beetle-browed hominids, which lived throughout Europe and western Asia from roughly 300,000 years ago to 30,000 years ago, were a species separate from our own that did not contribute to the modern human gene pool, or whether they are among our ancestors.
The ancient mtDNA sequences--which were judged by Paabo's team to differ significantly from those of living humans--were held up as confirmation of the increasingly popular view that the Neanderthals were an entirely separate species that did not mix with Homo sapiens. And subsequent studies of mtDNA recovered from other specimens produced similar results. But critics countered that the case was far from closed. Nuclear DNA might tell a totally different story, they argued.
Problem is, ancient nuclear DNA has been much harder to obtain than is ancient mtDNA because there is rather less of it to start with. The secret of the team's success this time appears to have been the use of a novel sequencing technique. Dalton describes it thusly:
Typically, DNA to be sequenced must be cloned in bacteria to produce large enough amounts for study. But because the Neanderthal DNA had broken down into tiny fragments, Paabo and his colleagues used a new sequencing technique, developed by 454 Life Sciences in Branford, Connecticut, that allows genetic fragments in an emulsion to be sequenced directly in tiny wells. They are now analysing the results to work out how the different fragments fit together so that they can be compared with the modern human genome sequence.
Time will tell which side of the divide the new sequences fall on, though Dalton reports that
...the Neanderthal Y chromosome is substantially more different from human and chimp Y chromosomes than are other chromosomes. This suggests that little interbreeding occurred, at least among the more recent Neanderthal species.
Dalton further notes that the DNA is also being sequenced using the traditional method, and that analysis of the 75,000 base pairs sequenced thus far indicates that Neanderthals branched off from the lineage that led to modern humans around 315,000 years ago, which is consistent with previous estimates.
Even if the results of these analyses, once completed, turn out to support the hypothesis that Neanderthals belong on their own branch on the family tree, I wonder whether skeptics will remain. Over the years several researchers have remarked to me that contamination is a real problem in ancient mtDNA analyses. I summarized it this way in a news story I wrote in our August 2003 issue:
...some anthropologists complain that to ensure that the sequences truly come from Neandertals and not modern contaminants, molecular biologists typically accept as valid only those sequences that lie outside of the modern human range. This requirement thereby stacks the deck against Neandertals that might have DNA like ours....
Could the same complaint be made regarding ancient nuclear DNA analyses? I guess we'll have to wait and see. Regardless, this is an exciting development--the species question aside, there is much to be learned from whatever genetic differences they do find. Certainly it bodes well for Paabo's Neanderthal Genome Project, which apparently is aiming to sequence 10 Neanderthal genomes in the next 10 years.
Update: Anthropologist and blogger John Hawks has his own take on the Neanderthal DNA news here.
http://blog.sciam.com/index.php?title=neandertal_nuclear_dna_sequenced&more=1&c=1&tb=1&pb=1