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Population Differences in Intellectual Capacity: a New Polygenic Analysis

PISA test documents at a German school (source: Theo Müller). PISA and IQ tests are informing us about differences in intellectual capacity by country. Meanwhile, genetic studies are informing us about genomic differences by country. Davide Piffer has been tapping into these two pools of data to explore the links between genes and intellectual capacity.

Between individuals and populations, intellectual capacity seems to differ through small differences at many genes. This is hardly surprising. Intelligence is a complex trait that involves many different genes interacting with each other and with the environment. If one gene changes, the immediate effect may be beneficial, but there will be side effects at other genes, and most of those side effects will likely be harmful. The bigger the effect at any one gene, the greater the likelihood of negative side effects elsewhere.

So evolution has proceeded through tinkering. A small effect here, a small effect there, but nothing that will rock the boat.

We must therefore pool data from many genes to understand the evolution of complex traits like intelligence. This is what Davide Piffer (2013) has done in a recent study. He began with seven genes (SNPs) whose different alleles are associated with differences in intellectual capacity, as measured by PISA or IQ tests. Then, for fifty human populations, he looked up the prevalences of the alleles that seem to increase intellectual capacity. Finally, for each population, he calculated their average prevalence at all seven genes.

The average prevalence was 39% among East Asians, 36% among Europeans, 32% among Amerindians, 24% among Melanesians and Papuan-New Guineans, and 16% among sub-Saharan Africans. The lowest scores were among San Bushmen (6%) and Mbuti Pygmies (5%). A related finding is that all but one of the alleles seem to be derived. In other words, they are specific to humans and not shared with ancestral primates.

Since these alleles have only small effects on intellectual capacity, there might be other causes for the above geographic pattern. For instance, as modern humans spread out of Africa, older alleles would have gradually given way to newer ones simply through founder effects and other random events. On the other hand, these derived alleles do not reach their highest prevalence in populations that are farthest removed from Africa, like the native inhabitants of the Americas and Oceania. The highest prevalences are actually reached less far away, in Europe and East Asia. Furthermore, the African/non-African difference is much greater for these alleles than for derived alleles in general. Derived alleles typically have a prevalence of 42% among sub-Saharan Africans and 56-57% among East Asians and Europeans (Watkins et al., 2001). This difference is tiny in comparison to the one for alleles that seem to increase intellectual capacity.

Principal component analysis

In this study and in a subsequent one (Piffer, 2014), principal component analysis has shown that a single factor explains much of the variability in the data (45%). Moreover, this one factor correlates highly with average IQ scores (r=0.9) and PISA scores (r=0.8) for each population. A common neural property thus seems to be the target of the various derived alleles. Could it be the elusive g factor?

The existence of such a large factor is further proof that we are dealing with some kind of selection pressure, and not random genetic changes like founder effects. It doesn’t follow, however, that the “unexplained variability” is without significance. Selection for intellectual capacity, like selection for any complex trait, may follow different paths in different cultural contexts. Moreover, there may be tradeoffs between different kinds of mental ability, and these tradeoffs may likewise vary according to the cultural context.

A final caveat

These seven genes are a small subset of the many genes that affect intellectual capacity. They thus provide only a rough picture of how this trait varies within the human species. Nonetheless, this picture is probably not far from reality.


Piffer, D. (2013). Factor analysis of population allele frequencies as a simple, novel method of detecting signals of recent polygenic selection: The example of educational attainment and IQ, Interdisciplinary Bio Central, provisional manuscript

Piffer, D. (2014). Simple statistical tools to detect signals of recent polygenic selection, Interdisciplinary Bio Central, 6, article 1

Watkins, W.S., C.E. Ricker, M.J. Bamshad, M.L. Carroll, S.V. Nguyen, M. A. Batzer, H.C. Harpending, A.R. Rogers, and L.B. Jorde. (2001). Patterns of ancestral human diversity: An analysis of Alu-insertion and restriction-site polymorphisms, American Journal of Human Genetics, 68, 738-752.

(Reprinted from Evo and Proud by permission of author or representative)
• Category: Science • Tags: Amerindians, Davide Piffer, East Asians, Europeans, IQ, PISA 
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  1. "The average prevalence was 39% among East Asians, 36% among Europeans, 32% among Amerindians, 24% among Melanesians and Papuan-New Guineans, and 16% among sub-Saharan Africans. The lowest scores were among San Bushmen (6%) and Mbuti Pygmies (5%)."

    Hahahaha! My goodness, why do we observe such a clear rank-ordering for these derived alleles when Stephen Jay Gould, or Jared Diamond, or Martin Luther King Jr., or, gosh, *somebody* must have proven that all population differences in ability boil down to stereotype threat, or poverty, or the differential effects of the Earth's magnetic fields on people who do or do not wear amulets secretly distributed by the CIA? Let's all think really hard about this one, now!

    Thank you very much for drawing my attention this, Peter.

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  2. hmm, similar to the rank ordering of neandertal genes: asia > europe > sub-saharan africa…

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  3. BTW, re Lewontin's fallacy, did anyone tried his reasoning (greater variabilirt between individuals than between groups) with respect to sexes or even species? I suspect than genetic variability between any two males may be greater than between males and females. Any links? I can't get a question specific enough for google to give me definite answer, and I am too poor at genetics to work the answer myself.

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  4. Anon,

    Two of those three people are now dead, and their presuppositions reflected a world that differed a lot from the one we now live in. It's time for all of us to move on and accept that things are not what we had thought them to be.

    I might also add that Jared Diamond is not the sort of radical blank-slatist that some make him out to be.


    None of the alleles in question are of Neanderthal origin.


    If you're referring to the Y chromosome, there is very little genetic overlap between men and women, unless you're including trannies as women.

    Yes, there are many species where we see more genetic variability within than between. This is often the case with sibling species that have diverged from each other recently and/or have maintained some ongoing gene flow.

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  5. Peter Frost: Thanks for the answer.
    But really about the genetic differences between the sexes? I would think that since the only reliable indicator of sex if Y chromosome, and I constantly hear that it is very small and has few genes compared to others, then differences between sexes in terms of variability should not be large (46 chromosomes, one of them X vs Y, 1/46 is a bit more than 2%). I didn't know genes were sex-sorted also on other chromosomes..

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  6. His ranking basically sounds like JP Rushton’s. Interesting that Papuans rank above sub-saharan Africans.

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  7. Anonymous says:     Show CommentNext New Comment

    His ranking basically sounds like JP Rushton’s. Interesting that Papuans rank above sub-saharan Africans.

    One of the issues with this kind of thing though is

    See –

    Africans theoretically seem to tend to experience a lot of sweeps on variants of smaller effect, as they have more genetic variation.

    These are called "soft sweeps". Small frequency changes but very wide, hard to detect.

    And it's easier for studies to detect "hard sweeps" with big frequency changes in a few alleles of large effect.

    This is most extreme when very low diversity populations like Amerinds and Oceanians are compared against the most diverse Africans, like Bushmen.

    This might not remove the effect Peter is describing here entirely, but it might cause some noise in the prediction here when comparing Europeans (more diverse) against South East Asians (less diverse).

    And it would probably smooth the picture whereby Amerinds and Oceanians (e.g. Aborigines) seem to have higher frequency on these loci compared to West Africans despite being about the same in intelligence.

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  8. How was the relationship between g and the seven genes detected? Presumably a strong correlation was observed?

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  9. "Two of those three people are now dead, and their presuppositions reflected a world that differed a lot from the one we now live in."

    In a sense, no, it didn't. There was enough information even in the early 20th century to draw the correct conclusions on these issues, and reasonable discussions were offered by thinkers like William McDougall in "Is America Safe for Democracy." The basic implications of evolutionary theory, combined with evidence from breeds of horses, dogs, cats, and other domesticated animals, together with IQ data and ethnographic data which became available early on, were enough to present a clear picture even then. Of course, this doesn't mean that there was no room for reasonable doubt, or that plenty of intelligent people took the opposing side; Boas and Mead were definitely around to muddy the waters.

    But in the sense that it really was a different world, we now live in a world where people invoke arguments, quite regurlarly, that come from Gould, or Diamond, or King. Indeed, Diamond's work came out the last time I had an argument on this subject. These people may be dead, but they're not at all buried.

    "I might also add that Jared Diamond is not the sort of radical blank-slatist that some make him out to be."

    Diamond lost all credibility with me the moment I found him explaining how the Australian Aboriginals were actually smarter than Westerners. So whether Diamond is a radical blank-slatist or not doesn't really matter to me; his claims are still asinine.

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  10. Intelligence is multifaceted and IQ tests are likely to measure only one facet of it.

    For example, during my early exposures to 'diversity', I was curious to explore other ways of thinking, for example with jokes.
    I was no big fan of Chinese food, and neither was the Englishman who said this:
    "Chinese people call food: food"
    Can you say that in Chinese?
    Anyway, I told the joke to a Chinese colleague, a PhD guy with a higher IQ than mine I am sure, but who however, never got it.

    So I concluded that even an IQ of 150 isn't of much help if your language doesn't let you easily express that sort of recursive thinking.

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  11. Actually the joke was: "Chinese people call Chinese food: food"

    hope it makes it funnier…
    sorry I can't remember the author's name (my low IQ)

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  12. Interesting, as always. About the idea that mutations which have large effect, even if beneficial, are likely to be somewhat harmful in their interactions with other genes affecting other traits: how would this apply to the "over-clocking" Greg Cochran has talked about in relation to the rapid gains in IQ among Ashkenazi over the past thousand years or so? I am speculating that it may have distorted other personality traits, their variance in particular. Just a speculation.

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  13. Anon,

    In the late 1980s and early 1990s, I was willing to give "race realists" a fair hearing but, by and large, I found them unconvincing and often silly. One reason was the tendency towards grand theory (Rushton's r & K). Another reason was Lewontin's finding that there is much more genetic variation within human populations than between them. Still another was the tendency of race differences in IQ to be smaller in children than in adults. It seemed to me that many if not most alleged race différences had non-genetic causes. I think differently today, but the transition from then to now was gradual. Even today a lot of race realism seems to me poorly thought out.

    I agree that antiracism is often motivated by groupthink and conformity (plus cowardice) but that's not the whole story. There is also a lot more open-mindedness out there than you may think, and you would be surprised by the kind of people who read these blogs.

    You're wrong about Jared Diamond, but I don't have time to write more.

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  14. Race realism seems more an ad-hoc collection of facts to justify certain right-wing political positions and less a movement for honesty in scientific departments and news establishments.

    I mean do you really believe if white people were ruled by some alien race with 2x their IQ, and were given special admissions to alien university, that they would be so enthusiastic about the alien-white IQ gap?

    On the other hand they bring attention to the black-on-white crime discrepancy, but I don't see how IQ is directly related to this. The education gap though…

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  15. Someone said:

    "Another reason was Lewontin's finding that there is much more genetic variation within human populations than between them"

    Could someone explain how this logic was supposed to work?

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  16. Anonymous says:     Show CommentNext New Comment

    I'd place more validity in this if PISA, TIMSS etc. scores were actually IQ tests. Many of them show far greater variability than what some (IE a small number of racialist researchers and their fans on the internet) are willing to give them credit for, in relation to basic facts about the countries that have been tested (such as various SS african countries outscoring latin american ones, Kyrgyzstan scoring worse than any other country, countries like Norway and India have almost no advanced students etc.).

    It gets more complex when you look at less developed countries that use IQ actual tests (from their government) to assess the population, such as Thailand, which is at nearly 100 despite high rates of malnutrition and disease in some provinces:

    Correct for that, and Thailand might very well have an IQ over 100. It's likely brought up by over 10% of the population being chinese, but native thais probably have IQ's no less than the high 90's. And with that, it calls into question much of the research on southeast asian IQ.

    They at best have predictive validity for developed countries.

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