I want to elaborate on my earlier post, Deep Denisovan Population Structure. Though I don’t put much stock in any particular result, including the most recent ones reported at a conference, I think that biogeography tells us a lot about what we should expect in the future.
First, notice that Neanderthals, Denisovans, and European hunter-gatherers have all exhibited evidence of being subject to massive bottlenecks and very low effective population sizes. Things changed in Europe with the arrival of Neolithic farmers, whose higher genetic diversity is in the range of modern people. I think this is indicative of the fact that abiotic factors, climatic shocks, drove down population sizes periodically consistently with all these northern hominins. I’m not saying that population sizes couldn’t get large periodically, but the fact that later Altai Neanderthals are genetically closer to Neanderthals from Croatia than earlier Altai Neanderthals indicate lots of local population extinction. It applied to Neanderthals, it applied to northern Denisovans, and, it applied to northern modern humans. Only with a change in the mode of production were higher long-term population sizes feasible.
But, I do think there was a difference between Neanderthals and Denisovans. As can be seen in the above map: the eastern Eurasian hominins likely had a tropical reservoir. Neanderthals did not. Part of this is due to geography, with the barrier of the Mediterranean, and marginally habitable zones in the Near East. And this factor is probably related to why there is a genetic difference between the Neanderthal meta-population, and the African meta-population, the latter of which may have prevented southward migration of Neanderthals during difficult climatic periods because their niches were too similar.
In contrast, I think the southern range of Denisovans in southeast Asia probably meant they overlapped with other hominins. I don’t think this should be that surprising. Consider that primates are just more speciose in the tropics, and there are apes in Southeast Asia, as well as Africa. One of the reasons that these forest apes survived down to the present is that they are forest apes, who occupy a different niche than modern humans. In the deep past, one can imagine that Homo floresiensis and various late “erectus” populations could have coexisted with Denisovans, who descended from a migration out of Africa ~750,000 years ago (the common Denisovan-Neanderthal model). It was the expansion of modern humans around ~50,000 years ago that was the real game changer in driving all other hominins toward extinction.
Another reason that I believe Denisovans had a southern range is that like African populations, there is evidence in them of very deeply diverged admixture. It doesn’t look like a multi-hominin situation really persisted in northern Eurasia for long. Though Denisova cave was a point of contact between Neanderthals and Denisovans, obviously with Denny, for most of the high latitude range there was one hominin species. If Denisovans have deep diverged admixture, I think that is probably from southern populations which were in contact with small remnant clusters of other hominins.
Finally, I think Browning et al. is pretty persuasive that there were two pulses of Denisovan admixture in eastern Eurasia. The most parsimonious explanation for these results is that Denisovans occupied the Pacific facade, and as humans moved north they interacted with different Denisovan groups from those of the south. The very fact that Denisovan admixture can be ascertained to have been from different deeply structured in modern humans, while the Neanderthal admixture seems very similar to Vindija population from Croatia, points to the reality that these two Eurasian hominin groups had different long-term meta-population dynamics due to their geographic constraints.