I was thinking again about that Denisovan allele of EPAS1 that plays a big role in Tibetan altitude adaptation. Considering modern humans, it has only been found in Tibetans (high frequency) and in the Chinese (couple of percent). The preferred model in the paper is that it entered the common ancestors of Tibetans and Han, rising to high frequency among the Tibetans because of its advantage. I doubt this: the authors are clinging to a claim of a recent split in a previous publication of theirs – but the idea that the modern Tibetans are a fusion of a Han-like population with a long-established group of Tibetan hunter-gatherers seems more likely to me. So the few copies of the high-altitude EPAS1 allele among the Chinese are probably a result of recent gene flow, possibly from the Tibetan empire (618-841) that controlled parts of China, or from ethnic Tibetans identifying as Chinese.
This allele has some pretty powerful effects on the hypoxia response, which is there for a reason. The usual evolutionary rule is that change is bad: even though the Denisovan allele confers a big advantage at high altitude, the odds are that it is disadvantageous at low altitude. This would explain why it is rare in China and apparently unknown in Japan. This would also explain why it never made it to the Andes – even though there might have been a copy or two in the long-ago East Asian ancestors of the Amerindians, who have a bit of Denisovan admixture admixture (at least, I think they do – interesting if that isn’t the case) , it would most likely have been lost in Beringia. Along the same lines, altitude adaptations probably never managed to travel from Ethiopia to Tibet, which is why they have different approaches to altitude adaptation today.
It is therefore no surprise that this EPAS1 allele does not exist in Melanesians, even though they have 25 times as much Denisovan ancestry as mainland East Asians.
At low altitude, it was likely disadvantageous in Denisovans as well. Probably it was only found in Denisovans who lived at fairly high altitude, or that had recently migrated from a high-altitude area. Which suggests that Denisovans in Denisova Cave had recent ancestors living at high altitude.
The introgression was most likely to be successful in an area where it conferred advantage, which suggest that admixture probably occurred in or near the Tibetan plateau. When you think about it, anatomically modern humans would have more trouble than average displacing archaics from areas for which they had special adaptations not possessed by AMH – so Denisovans may have lingered longer in Tibet and neighboring high-altitude areas, affording greater opportunities for gene flow. This was especially the case when the local environmental challenge could not be solved by ancient technology – you can deal with cold through better clothes, but people weren’t quite up to oxygen masks 40,000 years ago.
As I have said before, Denisovans might have persisted longer in Sundaland because of resistance to local infectious disease – same principle.
West Hunter 
Powerful stuff indeed.
How high does land have to be before the trade-offs favour genetic mutation? Switzerland? Colorado? The Caucasus? Or are Ethiopia, the Andes and Tibet the only contenders?
I think there’s some evidence for altitude adaptation in the Caucasus. But Ethiopia, the Andes and Tibet are the main examples.
Human height is amazingly dependent on nutritional factors in early life, which really complicates population studies of height. ‘Stockiness’ is even more difficult to get a handle on. On the other hand, height and build are phenotypically simple variables that must be constantly and readily selected for throughout human history and I have long suspected that, counter-examples like the Yugoslavs notwithstanding, all else equal every 1,000 meters above sea level costs a population a cm. or two or so, and gains them some corresponding stockiness. It may be that respiratory factors don’t drive the stockiness until you get to Andean altitudes and the barrel-chests, but I suspect there are other factors driving change in height and build at considerably lower altitudes, especially crop results for farming populations. Of course, that’s just where the environmental, nutritional aspect of height become very difficult to tease out.
Interesting. I think that’s what Jaakko was getting at with his pink flamingo example; that environment can act on precisely that portion of a trait that is heritable, rather than it being an either/or situation. Of course, diet is exceptional in that it is both nature and nurture. Whereas, ‘books in the home’, say, would be more wholly nurture and seems to impact less, if at all.
[btw Jayman, thanks for your reply and I hope the teething is going well, or perhaps you are through that stage now.]
Interesting that the Central Asian half-human half-ape cryptids are often described as high altitude dwellers. I’m thinking of the Yeti and of the Almas. Here’s a thought: maybe these stories and legends have the same grain of truth that (maybe) the Ebu Gogo and Orang Pendek have, in the case of Sundaland with its Homo floresiensis?
Wierdly the Minatogawa postcrania are being compared to Liang Bua. Add to that the small braincase and something needs explaining.
I can only think of the Mongoloid type as evolving up there TBH. MA1 shows the cold adaptations couldn’t have been in Siberia so the Himalaya seem most likely, with the dolichocranial Khams Tibetans being plesiomorphic enough to represent fairly closely the first Mongoloids.
Muscle type might also disadvantage high altitude adapted people at low altitudes.
Slow twitch muscles are also much more efficient (energy and oxygen wise) than fast twitch muscles, so the proportion of slow twitch muscle should be higher in populations adapted to high altitudes. East Africans (Ethiopians, Kenyans, etc.) generally have a lot of slow twitch muscle, which partially explains marathon dominance. I would guess than Tibetans have way more slow twitch on average than, say, Japanese.
Slow twitch is also much less powerful than fast twitch and if you’re doing something requiring power/speed like sprinting, non-mechanized combat, basketball, football, soccer, etc… slow twitchers would be at a huge disadvantage and would appear weak and slow compared to the fast twitchers. So, I can imagine that people adapted to high altitudes would generally be at a disadvantage at lower altitudes for at least that other reason.
Maybe that’s why the Falasha prove to be such a disappointment in the Israeli military, whereas the Oromo runners keep coming down from the hills and knocking ’em all dead in the distance running races, as long as they scoot back up to their hill villages with their gold medals.
The real irritation for me is that weight training just adds more slow twitch muscle, it won’t grow you any more quick twitch muscle than you already have. Or so I have read. Please tell me that is wrong, if it is.
Okay, if the paleoindians had Denisovan genes and Denisovans had high altitude adaption wouldn’t that get expressed in the Andes? Unless not all Denisovans had the adaption and there were different denisovan/human hook-ups at different times and places or those useful adaptions were lost between Tibet and Peru.
“Which suggests that Denisovans in Denisova Cave had recent ancestors living at high altitude.”
I am pretty sure that the sequenced Denisovan genome did NOT have this allele. It only had the most similar surrounding mutations.
Have been any hominid finds in the Tibetan Plateau? Are the Chinese doing any field work? There must be many interesting sites there.
*Probably it was only found in Denisovans who lived at fairly high altitude, or that had recently migrated from a high-altitude area. Which suggests that Denisovans in Denisova Cave had recent ancestors living at high altitude.* – – there might be an alternative explanation. The “high altitude allele” allows Tibetan to live with 40% less oxygen intake than the rest of H.S. This might have played different role in denisovans – to provide them with the ability to survive a low-oxygen environment in *low altitude* , which would let them spend harsh siberian winters in a state of relative hibernation, without going in hipoxia. The low oxigent requirement -low hemoglobin-low adrenalin would have helped brain maintenance during months long winter hibernation. The anecdotal evidence is, some Tibetians can still go in the same state as well. Call it meditation. Om.
Along the lines you describe: in some parts of France the peasantry would quasi-hibernate in the Middle Ages – which in rural France ended quite recently.
http://en.wikipedia.org/wiki/The_Discovery_of_France
What do you make of Eckhardt’s claim that there is no unique Flores taxon?
I think he’s probably wrong, but it’s hard to be sure with such a limited sample. But in a larger sense, I would say that the people who just know that evolution couldn’t possibly have gone in this direction in humans are completely, definitely, 100% wrong.
I was thinking about island isolate species of Homo in Indonesia before we ever found these skeletons.
Interesting point about the lack of the EPAS1 gene in modern human populations in the Andes. While it would have likely been advantageous at their final destination high up in the Andes mountains, it would have been very disadvantageous during their ancestor’s trip across Berengia and down through North and Central America.