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The Mysterious Ainu
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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.

(Republished from Evo and Proud by permission of author or representative)
• Category: Science • Tags: Ainu, East Asians, Genetics, Japan 
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  1. Anonymous • Disclaimer says:

    selection for Arctic adaptations like the epicanthic eye-fold


    What about these comments from this post:

    Anon: "Could the epicanthic fold just be due to pleiotropy?

    They say all babies or fetuses have epicanthic folds that most of them shed, except for Asians, Amerindians, etc. Perhaps other genes end up inactivating or suppressing this shedding process.

    Also, the epicanthic fold is just an excess skin fold. Asians have less muscle tone and more fatty tissue, so perhaps it is related to that."

    n/a: "Epicanthal folds are caused by a flat/underdeveloped nose. They are "shed" when the nose develops normally (which it does not in Down's syndrome, for example).

    So, yes, whether or not epicanthi were a target of selection in Mongoloids and Bushmen, they'd occur incidental to facial flattening, regardless."

    Anon: "Yes, maybe that is all there is to epicanthic folds.

    The nasal bridge – the bony part of the nose between the eyes – projects outward from the face and naturally tugs on the skin around it, including presumably the skin of the eyelid.

    If there is no nasal bridge, or if it's very flat, there is not going to be this tugging action that stretches the skin of the eyelid, resulting in epicanthic folds.

    Perhaps that is the explanation."

  2. Anonymous • Disclaimer says:

    What you say is basically plausible (pleisomorphy in Ainu and West Eurasians as a cause for similarities wrt facial flatness).

    Caveats –

    1) Rasmussen et al have convincingly shown pan Asian mixture between a population akin to West Eurasians and a population akin to Negritos and Papuans as important in the formation of the East Asian gene pool.

    2) The Skhul-Qafzeh skulls ( are similarly flat faced to modern East Asians. I do not regard it as convincing that the East Asian facial configuration (wrt flatness and great facial height – the breadth element is more convincing) is due to cold adaptation.

    Nor is it clear that the proto-Eurasian people had transversely projecting mid-faces and that transversely projecting faces are pleisomorphic.

  3. Anonymous • Disclaimer says:

    The Skhul-Qafzeh skulls ( are similarly flat faced to modern East Asians.

    It says here that the skulls possess a "projecting facial profile":

  4. Anonymous • Disclaimer says:

    Peter, I've always wondered about this. Are South East Asians, particularly Malays also descended from these Proto-Europeans or do they come from another branch?

  5. Anonymous • Disclaimer says:

    It says here that the skulls possess a "projecting facial profile":

    No citation, no worries.

  6. Anonymous • Disclaimer says:

    To expand, the paper I gave stated:

    "Stringer (1989) provides naso-frontal and zygomaxillary angles de?ned by Howells (1973) for a series of cranial samples from the late Pleistocene. Figure 8 illustrates the fronto-orbital and zygomaxillary indices of the samples used in the present study, together with several late Pleistocene fossil remains reported by Stringer (1989).

    The late Pleistocene anatomically modern samples show generally ?at faces, comparable to present eastern Asian samples in at least fronto-orbital ?atness . Moreover, the variation of facial ?atness in anatomically modern humans in the late Pleistocene falls within the range of facial ?atness in current human groups from around the world"

    The Wikipedia section is not really clear whether it refers to alveolar or facial prognathism (I think more present in the flat mid-faced Skhul Qafzeh samples than most present populations) or what…

  7. Sean says:

    "So the evolutionary changes that made other East Asians look different from the Ainu involve relatively few genes"

    Is it settled that those kind of morphological traits in humans are by relatively few genes of big effect? Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping says:- ""This type of evolution [soft sweeps] is likely when variation in a trait of interest is controlled by a large number of loci with small effect, which is now known to be the case with a number of highly heritable quantitative metabolic and morphological traits in humans. A long-term selection experiment in Drosophila melanogaster also uncovers evidence for this kind of adaptation.[Michael R. Rose's Drosophila melanogaster experiment] Artificial selection in dogs appears to have caused genetic variants with much larger phenotypic effects to segregate at high frequencies, resulting in the simplification of the genetic architecture of phenotypic variation. In some cases, breed-defining characteristics such as chondrodysplasia, skin wrinkling and brachycephaly are likely to result from hard sweeps at breed creation. However, many variants with large phenotypic effects appear to show continuous variation between breeds that correlates with particular traits, including genetic variants that associate with body size in the IGF1 locus on chromosome 15 and with drop ear on chromosome 10, suggesting that selection by attenuation of allele frequencies is also common. Hence, although hard sweeps are likely to be a more common form of selection in domestic compared with wild species, it is likely that more minor changes in allele frequencies across many loci also contribute to phenotypic evolution."

  8. Anonymous • Disclaimer says:


    You can look up the detail on this, but I think what is the case is that the genome just has so many neutral locii and allelic variation that even soft sweeps involving large numbers of small frequency shifts (soft sweeps) will largely leave the autosome massively unchanged.

    "Relatively few" is the term in question – it's relatively few relative to the massive size of the neutral variation in the autosome, not necessarily a few genes of large effect.

  9. Anonymous • Disclaimer says:

    How pure are the sampled Ainu? Haven't the Ainu mixed with the Japanese?

  10. Sean says:

    Going into it in more detail (not difficult as I barely understand the subject), it seems Peter is right about the nature of genetic adaptation in a new environment:- Human population structure and the adaptive response to pathogen-induced selection pressures.
    "A similar pattern is observed in one of the most canonical examples of adaptive evolution in humans, selection for lactase persistence. [an older comment of mine] Evidence of a partial selective sweep in European populations has been detected at the loci that control lactase persistence [48]. The partial nature of the sweep is probably the result of the recent age of onset of the selective pressure, here believed to be due to the advent of dairy culture and the digestion of dairy products throughout an individual's lifetime. Recent work on lactase persistence in Africa and the Middle East has shown how a different set of mutations contributes to lactase persistence in these populations [49]. This is another example of how multiple, geographically localized mutations have been involved in human adaptation to recent selective pressures.

    While these examples do not prove a rule, they are suggestive that a model of parallel mutation, in which there are hard sweeps locally and soft sweeps globally, may be typical for recent human adaptive evolution."

  11. Off topic. FYI, Mr. Frost have you heard about the findings at the Yale Baby Lab. Are Babies born with an inherent justice system. It was portrayed on CBS's 60 Minutes: Are Babies born Good

    The interesting part is that the babies show bias.

    I would like to tie that in with Johann Herder's premises of group dynamics of sense of belonging and racial prejudice. The findings of the Yale Baby Lab are very interesting and exciting. This proves the Natural Law.

  12. Juoni says:

    Nothing to do with this particular post, but what is your opinion on the effect of agriculture to intelligence?

    As far as I'm concidered the mean intelligence of arctic pastoral peoples (the Sami for example) is around 90. Hence it seems plausable to me that despite of the shrinkening of the brain during the last 10 000 years or so agriculture has somehow increased intelligence.

    What else could explain the IQ difference of almost-arctic agricultural peoples like Finns and Swedes and arctic pastoral peoples like Sami?

    Greetings from Finland

  13. Anon,

    We're talking about two levels of causation: proximal and distal. Yes, the epicanthic eyefold could be a fetal trait that is retained into adulthood by certain populations. That's the proximal cause. The distal cause is the selective advantage, which may be to protect the eyes from reflected glare.


    The consensus today is that the Skhul-Qafzeh hominins were a dead-end, although a significant portion of the sub-Saharan gene pool seems to come from them or from a related population.


    As recently as historic times (perhaps 3,000-4,000 years ago), South-East Asia was inhabited by hunter-gatherers who were similar in appearance to Papuan-New-Guineans. There are still a few relic groups here and there who descend from this earlier population.

    The South-East Asian gene pool still has a significant substrate from this earlier population. Most of it, however, is from successive waves of migrants who moved in from East Asia. Malays in particular originated from somewhere in southern China about three thousand years ago. There still is an indigenous Malay minority on Taiwan.


    When I say "relatively few genes" I mean in relation to the size of the entire genome. Of course, there are many genes involved.


    Most Ainu are intermixed with Japanese to some extent. The study's database could be used to approximate the original Ainu genome, see posts by Dienekes and Ahnenkult on this study.

    W.Lindsay Wheeler,

    Yes, I'm still looking over that study. I'd rather not comment until I've checked its findings with those of other studies.


    The Saami have an IQ of only 90? Could you provide a reference?

    Yes, cranial capacity has decreased with the replacement of hunting/gathering by agriculture. This decrease is probably due to a decreased need to store large amounts of spatiotemporal information for hunting (e.g., simulation of movements of game animals over space and time, memorization of landmarks for routes to and from hunting grounds, etc.)

  14. Anonymous • Disclaimer says:

    Yes, cranial capacity has decreased with the replacement of hunting/gathering by agriculture. This decrease is probably due to a decreased need to store large amounts of spatiotemporal information for hunting (e.g., simulation of movements of game animals over space and time, memorization of landmarks for routes to and from hunting grounds, etc.)

    Is brain size reduction in Southern African and Australian hgs a symptom of a shift towards vegetation based subsistence then, in your view?

  15. Anyone know the IQ of the Ainu?

  16. B and B says:

    The Ainu are not pure epi-Jomon. Genetically and culturally they were swamped by the Okhotsk people and there is reason to assume that the Ainu language was imported at this time. The Ainu are about 1/3 genetically Neomongoloid. The Okhotsk race were themselves between mainland Neomongoloids and the living Ainu suggesting the Okhotsk proto-Ainu were themselves dilited significintly by admixture with the pre-Ainu epi-Jomonese.

    The Ryukyus deserve a special mention because even in the Jomon period they score unusually on facial flatness by standard measures, indeed they deceptively score as though they were super-Mongoloid. But are quite visibly not flat faced, it is that they have an unusual profile of the face which is only sporadic in Asia and is present among the Red Deer Cave people.

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