Neandertal genome halfway done

Ewen Callaway, writing in New Scientist, reports on developments in the Neandertal Genome Project:

Half the Neanderthal genome has been decoded and the rest should be sequenced by year's end, a scientist involved in the project told a human evolution conference last week.
Researchers will roll out a rough draft of the Neanderthal nuclear genome after their sequencers have read every letter in the genome on average once - "1x coverage" in genomics speak.

The principals have been giving talks about their results here and there. This story does a good job of putting together some of the ongoing conclusions. First, have they found evidence of interbreeding?

On that question, the answer seems to be probably not. Although the two species seemed to have lived together, if the first European humans regularly interbred with Neanderthals, researchers would expect the genome of modern Europeans to share more similarities with Neanderthals than those of modern Africans.
This is not the case, Briggs says. Europeans and Africans appear to have equal numbers of genetic differences with Neanderthals, suggesting that the first anatomically modern humans to arrive in Europe replaced their close relatives Homo neanderthalensis.

Not the right test of that hypothesis. These observations are more relevant:

Neanderthals also seem to lack a mutation associated with increased fertility, identified in Icelanders. A 2005 paper suggested that this mutation had entered humans through inbreeding with Neanderthals.
Nor do Neanderthals boast mutations in a gene called microcephalin, linked to bulging brains in humans. This might shoot down another controversial hypothesis contending that this version of microcephalin also evolved in Neanderthals then spread to humans through inbreeding.

Better to be cautious, considering we're talking about a single individual at half coverage. We can't say the genes weren't there, but we can say that they were not fixed. Also, microcephalin isn't "linked to bulging brains" -- after all, our brains have been shrinking over the time since Neandertals, but in any event the gene doesn't explain variation in brain size.

Nevertheless, those were good candidates for introgression from Neandertals, and the findings aren't confirming their presence in Croatian Neandertals. Microcephalin in particular really looks like it came in from somewhere; Neandertals were a plausible source, but not the only one. The other gene candidate, MAPT, might have stuck around because of a selective balance instead of population structure.

Next, what are they finding in terms of possible functional genetic differences?

Preliminary results suggest that Neanderthals were lactose intolerant, hardly surprising since the ability to digest dairy products in adulthood only became common in humans after the domestication of cows, 10,000 years ago.

Hmm.... Now you begin to see the problem with working with the sequence. The things that confirm what you thought should be there become so much easier to accept. Nearly half the lactase haplotypes in Croatia today are the non-persistent version. Find enough things that look the way they ought to look, and you start having more and more confidence. But then, you'll likely be biased against finding things that are surprising!

Twenty thousand genes is a lot of work. We have some projects in mind here, so we're eagerly waiting for results.