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Maybe they have more Neanderthal DNA, but their physical features underwent more noticeable changes ...It has indeed been hypothesized and supported with evidence that common East Asian characteristics developed more recently and that the Ainu just changed less:
The Ainu of northern Japan have long been a puzzle. With their bushy beards, profuse body hair, large sunken eyes, and robust facial features, they look more European than East Asian. Yet genetic studies have shown no particular link to Europeans, at least no more than for East Asians in general:QuoteOmoto (1972, 1972) computed genetic distances among various populations of the world, and by constructing a phylogenetic tree he concluded that the Ainu population may have originated in East Asia, in spite of their unique morphological characters somewhat resembling West Eurasians. (Jinam et al., 2012)
This conclusion has been confirmed by a new study using close to a million single nucleotide polymorphisms. Genetically, the Ainu are closest to the Ryukyans, the inhabitants of Japan’s southernmost islands, and then to the Japanese themselves (Jinam et al., 2012).
So is the physical similarity to Europeans just a matter of chance? Convergent evolution? No, it may be that the Ainu have just not changed as much physically as other East Asians. They may thus preserve more of the original appearance that ancestral Eurasians once had before the last ice age split them into East and West Eurasians some 20,000 years ago (Rogers, 1986). This may also be why Kennewick Man (an ancient skeleton found in Kennewick, Washington and dated to 8410 BP) looks more like a European than a present-day Amerindian. Kennewick Man might have been closer to that proto-Eurasian population.
http://evoandproud.blogspot.com/2012/11/the-mysterious-ainu.html (http://evoandproud.blogspot.com/2012/11/the-mysterious-ainu.html)
And what if there were different types of Neanderthals, like there are different looking types of Homo Sapiens? Perhaps a more East-Asian looking Neanderthal.There were also the Denisovans, though they are considered a separate species or subspecies.