Vindija nuclear DNA report

Nature News is reporting that a million base pairs of a Neandertal specimen from Vindija cave have been sequenced. There's no paper; it's just a press report from a conference talk. So few details to examine.

Svante Pääbo, a palaeogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, began his Neanderthal Genome Project about two years ago. He and his team have probed 60 Neanderthal specimens from museums for hints that the DNA might have survived millennia of degradation. The species lived across Europe and western Asia from 300,000 to around 30,000 years ago, with the first specimen found in 1856 near Dusseldorf, Germany.
Two of the specimens showed promise, and on 12 May Pääbo's team reported at the Biology of Genomes meeting at New York's Cold Spring Harbor Laboratory that they had managed to sequence around a million base pairs of nuclear DNA -- around 0.03% of the genome -- from one of them. This is a 45,000-year-old male specimen found in Vindija Cave outside Zagreb, Croatia.

This has been an open rumor for awhile (since the cave bear sequencing of last year, and it is the same group of people involved with this one.

Edward Rubin, director of the Joint Genome Institute in Walnut Creek, California, works with Pääbo. The two are also working to sequence Neanderthal DNA by the traditional method. James Noonan, a postdoc in Rubin's lab, reported at the Cold Spring Harbor meeting that preliminary analysis of the 75,000 base pairs sequenced so far shows that Neanderthals diverged from the lineage that led to modern humans about 315,000 years ago - around the time that had been thought.

Of course, one of the issues with this kind of sequencing is that you can't necessarily pick and choose what parts of the genome you will get. They appear to have focused on the Y chromosome for phylogenetic reasons:

One finding so far is 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.

I assume this is a misquote or misunderstanding of some sort, because it doesn't make much sense on the surface. Since living human Y chromosomes apparently have a very recent derivation from a single common ancestor (possibly within the last 70,000 -- 100,000 years), it is almost inevitable that an archaic human might not have a haplotype carried by living people. That won't be true for other chromosomes, because most of the sequences taken from those chromosomes have much longer coalescence times in humans than the Y chromosome does. For example the coalescence time of beta-globin is on the order of 800,000 years ago -- separating living people with maximally different alleles.

So sequences taken from human autosomes look more different from each other than human Y chromosomes do. Neandertal Y chromosomes are almost certain to be more similar to human Y chromosomes than human autosomal sequences are to each other. From this standpoint, it doesn't make sense to compare the Y and autosomes at all -- they are different in their evolutionary dynamics to an extent that makes the comparison meaningless.

Bringing in the chimpanzee here doesn't make much sense either, unless they are saying that the divergence time of human and Neandertal Y chromosomes is surprisingly high. Of course, in that case we should be hearing about a much higher date than 315,000 years ago, which is on the low end of the mitochondrial estimates.

In any event, I would look for natural selection on the Y -- something has to explain that low human coalescence time.

Clearly the actual research will make all this more clear. And the article suggests that they hope to have as many as 10 Neandertal genomes (presumably sections of genomes) in the next 10 years. There will be a lot of digging to be done into gene function in living and archaic humans.

UPDATE (5/17/2006): The DOI link to Nature didn't work, so I've replaced it with the subscription link to Nature.