There is a new article out on the genome of the Altai Neanderthal, found in the same cave as the Denisovan. The authors find clear signs that this population of Neanderthals had some admixture with modern humans, roughly 100k years ago, or perhaps a bit more. That’s a twist, especially considering that the main migration of modern humans out of Africa is thought to have occurred roughly 65-70k years ago.
There was an earlier expansion of anatomically modern human out of Africa: the Qafzef-Shkul skeletons, around 125-90 k years ago, in Israel – probably this occurred during the last interglacial. As the climate cooled, Neanderthals returned to the area. Humans didn’t yet have the moxie required to beat out archaic humans on their own territory, and the Qafzeh-Shkul population is usually thought to be a dead end.
Maybe it’s not as simple as that. Those Altai Neanderthals had to pick up those genes from someone – maybe it was from the lost colony, Qafzeh-Shkul. Apparently there is another paper coming out suggesting that there’s a touch of ancestry from a separate human expansion, roughly that old, in New Guinea
Another point: in that Altai Neanderthal genome, there seems to be some adaptive introgression of modern human variants (FOXP2, for example), while at the same time, you see a lower amount of human introgression in regions of the genome under strong purifying selection – much the same pattern as we see with Neanderthal introgression in modern humans. This is strong evidence that this purging effect is mostly due to incompatibility between very different groups (dawning species), rather than genetic load in the smaller populations. Which we knew couldn’t have had the nasty effects suggested in those earlier papers, since archaic humans like Neanderthals and Denisovans didn’t lose rapidly when they first encountered modern humans.
Meta: a high-quality ancient genome contains an enormous amount of information (billions and billions !): it’s not like any other kind of fossil. You can figure out interesting properties of a population, including a lot about its history, from the genome of a single individual. Although there have to be limits: the Chinese have more Neanderthal admixture than Europeans (about 1.2 times as much) – and maybe they picked up the extra from a different Neanderthal population – maybe those Altai Neanderthals. So they might carry a tiny amount of genetic material from those Qafzef-Shkul types: but this way lies madness.