I read with interest your post on: http://johnhawks.net/weblog/reviews/neandertals/pigmentation/neandertal-introgression-1000-genomes-style-2011.html in particular: "People of Han Chinese ethnicity sampled in Beijing appear to have on average a half percent more Neandertal ancestry than people of the same ethnicity sampled in southern China." Apologies if you know this already but Han Chinese civilization started in the Yellow River area and only later expanded south. The original people in the south of China are Viet people and have more in common with modern Vietnamese. They all became "Han" people after their kingdoms were conquered by the north and are really Han in name only. Northern and Southern Chinese people look different and their spoken dialects (languages) are mutually incomprehensible to each other. Chinese people from the province of Shantung have the reputation of being the biggest in size, always attributed to their diet of wheat, but they are probably the last purest reservoir of Neandertal genes in the East. Shantung people generally have big noses, fair skin and big bones.
Yes indeed, these are very deep differences, at least as great as between northern and southern Europe genetically, and maybe more. That’s why we find the contrast so useful in comparison with the archaic human genomes. The current samples are not ideal because the “South Chinese” were sampled in Beijing based on ancestry, and so are a diverse set. We are hoping soon to have data from many more Southeast and Northeast Asian populations, which will give us some resolution on when things changed.