The paper on the Denisovan origin of one of the key altitude-adaptation genes (EPAS1) in Tibetans is now out (lead author Emilia Huerta-Sanchez, senior author Rasmus Nielsen).
It’s on a Denisovan haplotype. Likely Denisovans occupied a lot of East Asia, and quite a bit of that area is fairly high altitude, not just Tibet. We have evidence that East Asians have a bit of Denisovan ancestry, and a small amount of admixture is all it takes to pick up a highly advantageous variant.
Denisovans were probably in Asia for at least a couple of hundred thousand years, much longer than anatomically modern humans. Homo erectus and descendants were there a good deal earlier, and this variant might have originated that far back, although it may not be divergent enough for that to be plausible.
Here’s what Rasmus Nielsen said about this discovery:
“It was a complete surprise,” says Nielsen. “It took years after the Denisovan genome was published for us to even try this, because we thought it was so far-fetched.
Which is strange, because it was quite obvious. Not just in the sense that I told y’all about it over and over, wrote an article with Hawks on it in 2006, and mentioned it in our book – clearly I should have gone ahead with the fiery-letters-in-the-sky approach. Let me tell you about a conversation I once had with Jim Crow, maybe ten years ago. I was saying that adaptive introgession from Neanderthals was likely, and he mentioned once hearing someone say that although there might have been a bit of admixture with Neanderthals, it would have been biologically insignificant. He heard that and thought “No!”; he knew that even a few copies of an adaptive variant would likely rise to high frequency. He never wrote it up for the Neanderthal case, but he knew.
Of course it was also likely because the Tibetan adaptations are too damn good – different from the Andean ones, more like those seen in mammalian species that have lived at high altitude for a long time. Which Nielsen should have noted. Which is why the Ethiopian adaptations, some of them anyhow, surely have pre-modern-human origins – unless anatomically modern humans originated up on that plateau. Which I doubt.
This may sound as if I think Nielsen is dumb, but I don’t. He was wrong, but not dumb: I don’t pretend to know what screwed up his thinking on this issue. One could always blame Ernst Mayr.
On the other hand, I can think of a couple of fairly well-known players in this business who really don’t seem to understand much of anything. I’ll let you guess who they are.