Synopsis:
Europe has a touch more Neandertal than East Asia; Tuscans have more than any other European sampleThe Tuscans have the highest level of Neandertal similarity of any of the 1000 Genomes Project samples. They have around a half-percent more Neandertal similarity than Brits or Finns in these samples. The CEU sample is slightly elevated compared to Brits and Finns as well.
It is tempting to interpret these differences as a north-south cline in Neandertal ancestry. I wouldn’t jump too quickly on this idea, because Holocene population movements in Europe are now known to have covered up or erased a substantial fraction of the Upper Paleolithic gene pool. If we have a bonus of extra Neandertal ancestry in southern Europe, we need to explain how that cline persisted across subsequent history. Still, the difference is statistically very strong and deserves some explanation. Likewise, the populations within East Asia have some differences in Neandertal similarity.
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