Dear Professor Hawks,
I enjoy reading your webpage and musing about the data. I have long thought our family were part Neanderthal. Recent vindication is sweet.
The estimate of 1-4% Neanderthal SNP's in non African DNA begs the question: What part of the Neanderthal contribution resides within the 2% of the genome that codes for proteins? Alternately phrased, what part of the Neanderthal contribution is neutral, and what part is under selection pressure?
I expect you would say I have no clue. Up to 100% of non African DNA protein coding regions could contain Neanderthal SNP's somewhere in the population.
We're working on this problem very actively now. The initial answer is that the 1-4% is largely different in everybody. As more and more people are examined, I think it very likely that most of the protein-coding complement of the Neandertal genome is preserved in somebody living today at low frequency.
We cannot yet say whether the proportion surviving in protein-coding regions is larger than the proportion in gene deserts, which is an interesting question...
