Still chewing on the Neanderthal genome draft (Green 2010). Only today I have got some time to dwell on some of its details.
Alleles specific to all Homo sapiens (and not to Neanderthals)
It's interesting not just that some of us carry a small apportion of Neanderthal alleles but also the list of alleles that are exclusive of our species. Green et al. dwell on this matter in the section titled A catalog of features unique to the human genome.
There is a list of 78 alleles (table 2) that are fixated in the derived (non-Chimpanzee) form in the species Homo sapiens exclusively and found in their ancestral state among Neanderthals. Many are not really known their role but others seem to accumulate in certain processes such as skin (sweat...), melanin, smell, vision, sperm motility, hormonal and cellular division regulatory processes. This suggests me that there were some marked biological and appearence differences among the two species in spite of the proximity.
Therefore the inter-species barrier was possibly rather high even if still not total.
The authors emphasize specially five alleles in which more than one SNP is different, suggesting greater differences. These are specially related to skin morphology and regulatory substitutions (specificity).
Also the studied certain regions in clear rapid evolutionary change in the line leading to humans called HARs. The vast majority of these HARs had already evolved before the Neanderthal-Sapiens transition but a few (c. 1.7%) had not yet and belong specifically to Homo sapiens.
These human-specific HARs include genes related to mental functions (associated with mental disorders such as Dow syndrome, schizophrenia and autism) as well as a the RUNX2 (CBFA1) gene that would be related to changes in skull, clavicle and ribcage morphology.
Are Chinese slightly 'more Neanderthal' than other Eurasians?
Less definitely, when working with the comparative data at table 4, I find that the Han Chinese sample (n=2) appears very slightly but maybe significantly "more Neanderthal" than the other Eurasians, including the only Japanese. The Chinese individuals differ from the African sample in Neanderthal alleles by an average factor of 5.05 (4.95 and 5.15), while the non-Han Eurasian average is 4.21 (3.93-4.65), that is: almost a point more. Only one European individual (4.65) really approaches the Han Chinese figures, which differ by almost a whole point (0.92) from the rest.
This, of course, can only be a very preliminary indication but it does seem intriguing and potentially meaningful. The fact that the greatest difference is with the, otherwise very close, Japanese could even point to some greater diversity patterns in East Eurasia in regard to Neanderthal genes in us, and, considering the tiny sample sizes, even in much of the rest of Eurasia.