By using the high coverage Denisova genome, we are able to show that the admixture rate into East Asians is 40% higher than into Europeans.Of course, the interesting question is why East Asians have this excess of Neandertal ancestry, given that Neandertals were a west Eurasian-distributed species (for the most part). Similarly, we would not have expected Australo-Melanesians to possess higher Denisovan admixture, and yet they do. Some models of multiregional evolution assumed regional continuity with pre-existing archaic populations in different parts of the world (e.g., Europeans with Neandertals), but clearly much more interesting things were taking place in deep prehistory.
Of particular interest is this conclusion:
In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.The publication of Tianyuan has shown that by ~40kya, differentiation of Asians from Europeans was already on its way, and this is a date close to the disappearance of the Neandertals, the date of which is contested, but one can imagine that already-differentiated Eurasians may have encountered some lingering Neandertal groups.
Genetics doi: 10.1534/genetics.112.148213
Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans
Jeffrey D. Wall et al.
Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from roughly 30-300 thousand years ago (Kya). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 Kya. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.