Warning: highly speculative post ahead.
As I mentioned the other day:
(Please note that Africans do not have chimpanzee admixture, despite the labeling on the graph–no human group has chimp admixture, because chimps and humans have different #s of chromosomes, so even if you could get a successful cross, the resulting child would be infertile, like a mule. I assume the point of the chimp node is just to represent that which has neither Neanderthal nor Denisovan admixture, though of course there is the possibility of some other form of archaic hominin admixture in Africans.)
So, Native Americans appear to have a ton of Neanderthal DNA. (Relatively speaking.)
Possibilities:
- It’s all measurement error/convergent evolution/something else other than archaic admixture.
As much as I hate to say it, I still consider this very likely. There is just a ton of stuff that we don’t about the Americas–like how and when people first got here. I’m sticking here with what I think are the most scientifically-supported theories, but a lot of this is still quite disputed. In particular, all of this genetic admixture business is still kind of speculative, and when people start talking about finding admixture in the admixture, either life is totally awesome, or we’re trying too hard.
2. Survival at the Fringes theory
A lot of people seem to look at this data and respond with something like, “But Neanderthals are from Europe, not America!” But this is not a big issue; the Indians are descended from people who passed through Neanderthal-inhabited regions (the Middle East), just like everyone else with Neanderthal DNA. The migration to the Americas took place long after they acquired Neanderthal admixture.
But this doesn’t explain why they have so much of it.
My “concentration on the edge” theory states that when one population is displaced by another population, you end up with a “fringe” of the original population’s traits. Sometimes this fringe results in isolated groups, as the invading population completely surrounds or cuts off a remnant population from their former range.
The Ainu, for example, resemble certain other Oceanin groups, but not their neighbors, the Japanese. I’m speculating here, so don’t take my word for it.
But I have a much better case with the distribution of red hair: 
(So far I have found nothing explaining that dot over in Russia.)
Red hair is highly associated with the so-called Celtic fringe. It looks like it’s highly concentrated in Wales, Scotland, and parts of Ireland, but since I know a little history, and I know these aren’t areas of concentration, but just the areas that managed to escape being displaced by Anglo-Saxon invaders, just by virtue of being further away from the south-east coast of Britain.
One can imagine that the isolated dot in the middle of Russia might, at one time, have been connected with the other red-haired regions before other peoples invaded the lands between them and cut them off.
Compare to the map of blond hair:
Blond hair looks like it has been spreading steadily outward from a central source.
So what does this have to do with Neanderthal admixture in Native Americans?
It means that I think the Native Americans may have closer to original levels of Neanderthal admixture, while people in Europe and Asia have lower admixture because they mixed with later waves of people who came from Africa and had no Neanderthal admixture.
3. The Bering Strait selected for Neanderthal admixture
Alternatively, the harsh conditions of life in the Bering Strait–where some scientists think the ancestors of today’s Indians hung out (or “paused”) for thousands of years before the ice sheets opened up to let them through–may have selected for winter adaptations that came from ice-age Neanderthals. I have speculated previously that Type-2 Diabetes may actually be a winter adaptation picked up from Neanderthal DNA; now scientists think this DNA may be responsible for high rates of Type-2 Diabetes in Native Americans.
4. Western diseases selected for Western immune responses
One of the interesting things about the Neanderthal DNA hanging around in people is that it appears to code for certain immune responses. West Hunter recently had a great post (TLRs, PAMPs, and Alley Oop) detailing how they work, but for our purposes, “provide immunity” is sufficient. Austin Whittall suggests that back when smallpox, influenza, measles, and all of the other Western diseases tore through the Native Americans, killing about 90% of them, the guys who had more Neanderthal DNA were more likely to survive because they were more likely to be immune to the same stuff as Europeans. By contrast, those Indians with less Neanderthal DNA may have had less immunity to the European diseases, and so been more likely to die, leaving behind a population of high-Neanderthal DNA people.
5. One thing we can say for sure: if the data’s correct, the peopling of the Americas was more complex than previously thought.
There are four areas of particular interest:
A. The highly Neanderthal area in the Pacific Northwest
B. The highly Denisovan area in Brazil
C. The low-Neanderthal area on the South American coast
D. The low-Neanderthal and low-Denisovan area along the Baja gulf in Mexico.
I’ve got nothing on A and C; supply your own theories.
6. Speculations on the origins of high-Denisovan people in Brazil:
A couple of papers in Science and Nature recently proposed that Melanesian-related people somehow made it to the rain forest long after the other Indians got to the area. West Hunter helpfully summarizes them.
West Hunter suggests that the Melanesian-related people with their high-Denisovan DNA got to the Americas first, and were then replaced throughout the continents by later invaders, the ancestors of current Indians. The one place the Melanesian-related people managed to survive was in the depths of the rainforest, a very difficult place to conquer. Even today, there are “uncontacted tribes” living in the Amazon rainforest; if anywhere were a good spot for a group of humans to avoid getting conquered, the depths of the rainforest is a good one.
7. The low-Neanderthal and low-Denisovan area along the Baja gulf in Mexico.
So what’s up with that? As far as I know, the only people who don’t have any Neanderthal or Denisovan are Africans. (And even there, there’s a little, just due to back-migration from the rest of the world.)
Are these people descended from a totally different group that came directly from Africa?
There’s a tiny ethnic group in the area, called the Seri:
According to the Wikipedia, the Seri speak a language isolate–that is, their language, like Basque, doesn’t appear to be related to any other language on Earth–and they are not culturally connected with any of their neighbors. They’ve also held out significantly against Spanish and Mexican assimilation. In other words, they might very well be a totally isolated population that is not related at all to any of their neighbors.
Some more information on the Seris.
Then I found this interesting map:
I found these maps over on Austin Whittall’s post on Denisovans and America.
Looks like the same spot, doesn’t it?
The two different “real” maps how different things because they come from different scientists who came up with different data, but the overall picture is similar–if you look closely, both maps show a hotspot in Israel, for example. The second map looks less detailed, (hence their miss of several Middle Eastern hotspots,) but has a wider global range, which is obviously useful for our purposes. They also help show the importance of not putting too much stock in any single study about the distribution of a particular gene or allele or whathaveyou; different scientists come up with different numbers.
At any rate, while this could be just a totally random coincidence, if it isn’t, it’s awfully interesting, isn’t it? I know the Egyptians circumnavigated Africa; the Carthaginians and Phoenicians were also noted sea-farers. Or perhaps some other group I know nothing about from the region, before folks started keeping good records. Who knows?
8. Other people’s theories: Neanderthals, Denisovans, and H erectus made it to America before we did, and H Sapiens intermixed with them after they arrived; humans evolved in American, and then migrated to the rest of the world from there.
