Ainu men and Ainu woman, 18th century painting by Kodama Sadayoshi (source)
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:
Omoto (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.
This point is sometimes hard to grasp. Real evolutionary change—the kind that shapes physical appearance—involves only a tiny fraction of the genome. The rest of the genome will change little in a new environment with a new set of selection pressures, either because it has little or no adaptive value (i.e., junk DNA) or because it has the same adaptive value in a wide range of environments.
So the evolutionary changes that made other East Asians look different from the Ainu involve relatively few genes. At other genes, the two groups are genetically indistinguishable. We likewise see genetic overlap between many sibling species that are nonetheless anatomically distinct. The same disconnect exists between genetic and anatomical data when we look at dog breeds … or human populations.
But why have the Ainu been so evolutionarily conservative? Why has time stood still for them? They probably didn’t undergo the severe selection pressures that shaped the appearance of other East Asians, notably selection for Arctic adaptations like the epicanthic eye-fold. Keep in mind that the Japanese archipelago enjoyed a relatively mild climate during the last ice age. As a “refugium” it did not impose the harsh selection pressures that mainland Asia imposed on its human populations.
Jinam, T., N. Nishida, M. Hirai, S. Kawamura, H. Oota, K. Umetsu, R. Kimura, J. Ohashi, A. Tajima, T. Yamamoto, H. Tanabe, S. Mano, Y. Suto, T. Kaname, K. Naritomi, K. Yanagi, N. Niikawa, K. Omoto, K. Tokunaga, & N. Saitou. (2012). The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations, Journal of Human Genetics advance online publication 8 November 2012; doi: 10.1038/jhg.2012.114
Omoto, K. (1972). Polymorphisms and genetic affinities of the Ainu of Hokkaido. Hum. Biol. Oceania, 1, 278–288.
Omoto, K. (1973). The Ainu: a racial isolate? Israel J. Med. Sci., 9, 1195–1215.
Rogers, R.A. (1986). Language, human subspeciation, and Ice Age barriers in Northern Siberia. Canadian Journal of Anthropology, 5, 11‑22.