Missing Heritability – found?

There is an interesting new paper out on genetics and IQ. The claim is that they have found the missing heritability – in rare variants, generally different in each family.

Some of the variants, the ones we find with GWAS, are fairly common and fitness-neutral: the variant that slightly increases IQ confers the same fitness (or very close to the same) as the one that slightly decreases IQ – presumably because of other effects it has. If this weren’t the case, it would be impossible for both of the variants to remain common.

The rare variants that affect IQ will generally decrease IQ – and since pleiotropy is the norm, usually they’ll be deleterious in other ways as well. Genetic load.

This explains a few things. Studies have shown that people with high IQs are healthier and live longer. It doesn’t really look as if this was caused by smarter health decisions – so probably it’s because smart people, on average, have less genetic load. This explains why girls always run after the smartest guy in the room – at any rate it would explain that if it happened. It doesn’t.

There is a report of better sperm quality in high-IQ guys: that fits lower genetic load.

How does fit into observed IQ differences between groups? Well, selection could have favored IQ more in some places than others – or the mutation rate could have varied – or the efficiency of selection against deleterious mutations could have varied (more or less truncation-like) – or perhaps some mix of all three.

You could do an admixture analysis (how does IQ vary with different amounts of ancestry from group A and group B) without knowing the exact cause – it would still tell you if and to what extent racial genetic differences influenced IQ, even if you didn’t know the exact SNPs that made the difference.

In principle, you could get rid of the load by a kind of averaging process. More fun if the superman you create comes from way out in left field – say a super-Neanderthal, as I once suggested.

The rate at which new genetic load is generated, per generation, does not look to be too high (from the info we have), since the amount of observed IQ depression in the children of older fathers is, at this point, unobservably small.

If selection favors lower IQ, as it does today, you should see every IQ-negative allele increasing in frequency ( assuming that the side effects are not too awful): all of the GWAS fitness-neutral hits, and probably some of the mutational load alleles as well.  You can be sure that the current dysgenic trend (~ 1 point drop per generation, not counting immigration)  has not been operating too long, because if it had, we’d all be idiots, unable to read and understand past works of genius.  Hasn’t happened. Michael Woodley and Bruce Charlton think so, but they are mistaken.  Badly mistaken.

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35 Responses to Missing Heritability – found?

  1. Halvorson says:

    I’ve never heard you bring up archaic admixture as a factor in explaining continental IQ differences. I don’t know if recent findings have invalidated the model, but back in 2009 Jeffrey Wall, without ancient genomes to rely on, found signals of archaic mixture to be highest in West Africans when compared against Europeans and East Asians:


    Fossils degrade quickly in tropical Africa, so we don’t know exactly who was living there 40,000 years ago. The very archaic looking Iwo Eleru skull is only about 12-15,000 years old, though. It’s possible that archaic mixture in Africans is both more common and more recent than in Eurasians, which has given them less time for the archaic variants to be purged.

    If lower Sub-Saharan IQs were due to a higher mutational burden I’d think it was a weird coincidence they also have such extreme facial prognathism and small foreheads.

  2. Cloudswrest says:

    So if I understand this right there aren’t that many genes for “smartness”. Just a lot of broken genes for “dumbness”. And since genes can be broken in an almost infinite number of ways there’s no real smoking gun for dumbness. Just a lot of random, non-specific, genetic load, which varies from person to person.

  3. gcochran9 says:

    There are common alleles that influence IQ, no single one of which has a big effect. Your IQ is influenced by the number of such plus or minus alleles you have. Those are genes for ‘smartness’: they account for about 40% of the variance in IQ. The other 60% is a mess of somewhat broken genes. Identifiable, because they’re rare, and to some extent because we can sometimes figure out how they damage gene function. Assuming that this new paper is right.

  4. Douglas Knight says:

    Did you mean to link to this paper?

    I don’t see what’s new in it. It finds that 25% of the variance is due to common variants and 25% to “rare” variants in LD with common variants. Isn’t that an old result? And why would it, since the techniques are the same? The only innovation is to use related individuals to partition the 50% into the two halves. So that’s not finding missing heritability, but clarifying known heritability. And I thought that the partition was known by other methods.

    And how rare are these variants? The common SNPs on chips have MAF of 1%, right? There is a big range of variants too rare to appear on chips, but still too common to count as mutational load. The abstract claims that these variants are due to mutation-selection balance, but skimming the paper I don’t see the justification for this claim.

  5. whyteablog says:

    This makes me wonder why girls don’t chase after the smart cookies (excepting assortative mating). You’d think they’d prefer low genetic load. Is it possible that an inbuilt preference for high IQ males, independent of the woman’s own intelligence, simply never evolved?

    Let’s say, hypothetically, there’s a “sapiosexuality” allele which makes you want to have sex with smart people. In a period of positive selection on IQ, this allele would cause its carriers to seek high-fitness mates. It’d go up in frequency. Therefore you’d expect people to find intelligence attractive nowadays.

    Even if IQ was undergoing a very very small amount of negative selection, as long as the payoff of avoiding genetic load was greater, you’d still expect the allele to become more frequent over time. Furthermore, we have good reasons to believe that selection for high IQ has been generally positive for a pretty long time now.

    Is it possible that people don’t prefer smart partners irrespective of their own IQs because that trait simply never evolved?

    • gcochran9 says:

      There must have been some selection for IQ – without it, our brains would have disintegrated. But that selection can’t have been very strong, or intelligence would have gone up like a rocket. Today it’s going down at a rate of something like three points a century – think what would have happened if it had changed that rapidly, either up or down, over the last couple of millennia.

      • whyteablog says:

        Would you say that it’s a slow Explosion, having taken about 10,000 Years?

        Jokes aside. Even if selection for IQ was very little, the allele could still undergo positive selection because picking partners with low genetic load means having kids with low genetic load. These mechanisms may be too weak for the allele to have reached fixation, particularly if it showed up recently, but the allele would be out there today if it had ever evolved (unless genetic drift got rid of it early on?). You’d get a population somewhere out there where a sizable minority of them were really attracted to brains.

        • gkai says:

          Attractivity of success would filter the same, no? Probably more efficiently, as it is both easier to see, an maybe more robust. Plus it adds resources, which are beneficial for succesfully rearing children.
          I wonder if this is not the reason IQ attractiveness has not evolved, humans have been social for a long time so success (more precisely, success in the social hierarchy) seems better than IQ as a fitness indicator…
          Chasing the samrt cookie is not common. Chasing the top of social ladder, on the other hand…

          • whyteablog says:

            Again, you’d be incentivized to prefer high IQ even if it had nothing to do with success because it displays low genetic load. Even if other traits did the same, that doesn’t remove the positive selective pressure that should exist.

            IQ DID correlate with success- at least reproductive success- to varying degrees, for most of human history and prehistory.

      • Skunkworks22 says:

        Except that in the current ecology, high IQ people tend to have low reproductive success, thus selection may favour some increase in mutational load in multiple offspring than 1 healthier child.

    • Leonard says:

      There is modest selection for IQ, or at least for some penumbral forms of intelligence. Women love comedians. They also love socially dominant men. Both of these require a certain degree of intelligence.

      But low genetic load is displayed in many ways, not just intelligence. I.e., being symmetrical, general fitness, healthiness, strength. Women like these things too. Of course, most of these things are inherently useful for survival in their own right, not just as signals of genetic load. (Same with intelligence.) So I am not sure how one would prove that women like trait X because high X shows lower load as versus liking X because X might be used to provision or defend the woman and her children.

      • whyteablog says:

        Being selected to prefer one trait doesn’t prevent them from being selected to prefer another.

        And the reason that genetic load is relevant is pleiotropy. Dumber people should be less healthy if much of the differences between people in IQ boil down to genetic load. And as it stands, smart people live longer! Genes that make you dumb are disproportionately likely to have random negative effects on fitness.

        As for whether the selective pressure on genetic quality vs mate quality- provisioning and defending- you’d look at cultures where the men don’t provision for or defend their women.

    • Greying Wanderer says:

      if a man is smart and short does he have low genetic load?

      in a population with a high average height?

      in a population with a low average height?

      so women from a high average height population might perceive shortness as evidence of load even if it wasn’t


      do women chase after men who are 6′ – yes

      do women chase after men who are 7′ – not so much

      in my experience most women generally go for a balance, like:

      8/10 brains + 8/10 brawn > 10/10 brain + 6/10 brawn

      which is the fail-safe option.

      so maybe it’s the fail-safe option that is being selected for?

  6. Getting access to datasets with genomic data is hard, but we’re working on it. But we did get access to PING dataset which has precalculated ancestry estimates. It does show the ancestry relationships for IQ and parental social status (subjects were children). n ≈ 1400. The main limitation is the lack of controls for visual appearance, mainly skin tone, which some will try to claim as the causal confound.

    We also meta-analyzed published estimates of the relationship between genomic ancestry and social status. It’s pretty robust, r = .18 for European.


  7. pelekesi says:

    My guess is that IQ was selected for mostly for social competition/cooperation reasons not for physics or math ability. Lawyer and negotiator skills gave an edge not scientist skills. The latter stuff drafted off the g selected for because it made us better speakers.
    To know if someone was good at math or that sort of analytical skills and not good at faking it, you’d need to have a fair amount of ability yourself wouldn’t you? Then it would be an expensive and not a cheap way to select a good mate.

  8. You’re saying it like fitness was a linear function of alleles. Given the recent change from eugenic to dysgenic trend, speaking of fitness of IQ variants is…. insufficient at least

  9. JayMan says:

    Readers see also:

    IQ and Death

    This explains a few things. Studies have shown that people with high IQs are healthier and live longer. It doesn’t really look as if this was caused by smarter health decisions – so probably it’s because smart people, on average, have less genetic load.

    A lot of people don’t seem to want to believe me on intrinsic healthiness. They seem to believe that it’s because smart people make better lifestyle choices. But then why does the connection between many so-called markers of health disappear when you control for IQ?

    As well, the connection between IQ and health/lifespan itself disappears when you control for genes by looking at MZ twins. The “smarter” twin doesn’t seem to be any healthier.

    • pyrrhus says:

      Also there’s the fact that the definition of “healthy lifestyle” changes constantly over the years, but the results don’t.

  10. El Bow says:

    There’s a typo in the first sentence of the last paragraph.

  11. Gerhard says:

    It is perfectly expected that a lot of the genetic IQ variance (at least half, I would estimate) is caused by detrimental rare variants that have sometimes small and sometimes large effects. This is simply based on what we know about mutation rates and the presumed number of genes that need to be intact for optimal functioning of the brain. There is a huge mutational target size. Even many of the GWAS associations most likely are due to rare causal variants of relatively recent origin that are in linkage disequilibrium with more common tag SNPs that have been around since the Lower Palaeolithic. These are the associations that don’t replicate when the GWAS is repeated in populations from different geographic origins. That’s why we need to repeat association studies for IQ genes and educational attainment genes in Africans, East Asians, Papuans etc, and do the proper follow-up by sequencing those genes that are near the GWAS signals.
    The expectation is that differences in selection for higher or lower intelligence that persist for tens of thousands of years cause population differences in common variants with small effects. This is because the detrimental mutations that are under mutation-selection balance don’t survive so long anyhow. However, when selection is strong and acts over a shorter time period, such as a millennium, the prediction is that it has greater effects on mutational load than on common polymorphisms. This is because rare mutations have larger effects than common polymorphisms and therefore respond more strongly to selection. It’s simply the fastest way to respond to new selective pressures.
    In the same way, when it is desired to raise population IQ, the fastest way is to identify mutations in the important “IQ genes” that are predicted to disrupt the function of the encoded protein, and then select those embryos that don’t have these disruptive mutations. One advantage of this strategy would be that it reduces pleiotropic detrimental effects that many of these mutations have on non-cognitive traits. Such selection improves population health. Selection of embryos for polygenic scores would most likely have a smaller immediate effect, and there would be no beneficial side effects because in this case the low-IQ variants are not likely to have bad side effects on other traits. On the other hand, the effect would be more persistent across many generations.

  12. Greying Wanderer says:

    is selection in intelligent species different to selection in unintelligent species?

    (defining intelligence as the ability to create their own habitat)

    if a species is being selected for a single environment then isn’t a perfect fit the optimum?

    what’s the optimum in an intelligent species who can create their own environment – behavioral flexibility?

  13. marcel proust says:

    My grasp of the fine details of genetic load is shaky, but my understanding is that it is inferred from fitness (number of descendants) rather than observed directly from study of the genome or genotype . My question then is whether there is any indication that the genes thought to raise genetic load & lower IQ are those that directly affect intelligence or do they instead affect it indirectly through a more general affect on health and physiological function?

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  15. Rappaport says:

    In the past because most marriages was arranged nerds guys had a chance to mate. Most men were married and had kids. Arranged marriages has been extremely common in East Asian societies and they have the highest average IQ + directional selection to the academic skills. Today namely in the West because we live in societies that value beauty and popularity many nerd guys, usually the smartest ones, are in the ”friendzone”, out-reproducting. Western societies has been designed to the dysgenic path.

    If intelligence is correlated with neotenic personality traits or delayed psychological maturation so smarter people, on average, and specially men, are clearly in disadvantage because while they are designed to the low-speed lifestyle their rivals are in high-speed. We are living basically in the open competition specially white guys and against foreigners and we are taking note that higher intelligence at least by academic format make humans more dependent from advantageous cultural structures. It’s just to put a domesticated variant competing directly against a wild variant of the same species.

    And because nerds has been more troubles to find a mate early in life so they have married and start to have kids later probably increasing their mutational load and autism, clearly a aberrant form of nerdness.

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