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Archive for August, 2008

Sequencing Neanderthals

Just out now in Cell is a wonderful article on the full sequence of mitochondria DNA from the Neanderthal. The paper is already receiving much interest in the media, and Nature has a news story somewhat misleadingly entitled “First complete Neanderthal genome sequenced“.

Using very rigorous methods for extracting DNA material from the Vindija Cave in Croatia and keeping it clean from (human) contamination, the researchers were able to analyze 35 samples. The paper abstract basically tells the main findings:

A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.

But even more interesting is that a month ago, I unexpectedly met one of the co-authors on this paper. Michael Egholm had entered my wife’s gallery for a brief visit to check out her famous microscopy paintings. While it took me some time to understand who he was, and who he worked with (such as Svante Pääbo), our conversation continued after he’d left for the US. Luckily to you English-only readers, Egholm has spent too many years to feel comfortable writing science in his native Danish. He sent me the submitted manuscript with the following comment:

The somewhat simplistic grand purpose of the Neanderthal project is to figure out what makes us human – presumably our unique brain function.  By comparing the Neanderthal sequence with Chimpanzee and Human we can ideally pin point areas on the genome that has undergone rapid evolution the last 660K years (the new split time determined in the paper). It is generally accepted that something dramatic happened within the last 100K years or so which eventually let to the exodus from Africa and population of the rest of the world along with the extinction of other hominoids.  So with the Neanderthal genome we’re on the safe side but a lot closer than our divergence from Chimpanzee (est. at 6M years).  Obviously, we will be blind in areas of the Neanderthal genome that have undergone evolution since the split from modern humans.

The mitochondrial genome is an obvious first milestone in the project because of its overrepresentation and because it does not undergo recombination the analysis is a lot simpler with respect to split time etc.  Anyways, there is one big surprise and/or coincidence in the 13 proteins that are coded for by the mtDNA in that we find one gene with 4 ns changes – this is exactly what we had hoped for and while highly statistically significant within the context of the 13 proteins of the mtDNA it is not within the context of 20K+ genes.

How’s that for an explanation?

-Thomas

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