A comment below that captures my thoughts well:
The deeper I dig into the Tianyuan discussions posted online, the less I seem to understand… seriously, we NEED more samples from east Asia, specifically China to piece together the east Eurasian developments and to understand where Tianyuan fits in all of this. Is it even more divergent than Papuans and Onge? Is it somewhere between them and east Asians in a very broad term (this includes east, southeast Asians and native Americans) or is it in the broad east Asian ‘protomongoloid’ nest…. I have no clue at this point.
The reality is it is only in Europe do we have a really robust and well-supported graph of human population history over the last 40,000 years. Even in West Asia, there is some fuzziness (at least until the Reich group comes out with their West Asia paper, which has new samples according to Iosif Lazaridis), and what we know about South Asia is ancillary to what we know about West Asia and Europe (ergo, non-West Eurasian ancestry in South Asians gets thrown into a big bucket).
If you read papers about the Jomon one thing that seems clear is that there are lots of “basal” lineages in the past. It’s hard to place them robustly on a modern graph. What this really reflects is that rapid demographic expansion in the Holocene of farming groups seems to have obscured a lot of the deep structure that had existed in the Pleistocene. The erratic results on the Jomon, the “Australo-Melanesian” ancestry in Amazonians, and the distribution of Y haplogroup D is all part of this bigger puzzle.
D is found at high frequency among Japanese, some Siberians, Tibetans, and Andamanese natives. To me, this isn’t due to close relationships, but the fact that these groups relate somehow to the near polytomic diversification of “East Eurasian” lineages ~45,000 years ago. Oceanian people are clearly part of this, and some ancient Southeast Asian people seem to be closer to Oceanian people than Northeast Asians. This is not surprising seeing as Oceanians almost certainly derive from ancient Southeast Asians (or, that that was the last bifurcation).
Finally, there’s the issue with “Denisovans.” The most likely hypothesis to me is that this was a highly divergent group of human populations, which occupied a much more ecologically diverse territory than Neanderthals. And, unlike Neanderthals, they were not genetically homogeneous, as southern “Denisovans” had larger population sizes and did not suffer periodic extinctions in the meta-population.