The Allele Counting Begins

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
Davide Piffer

Weak widespread (polygenic) selection is a mechanism that acts on multiple SNPs simultaneously. The aim of this paper is to suggest a methodology to detect signals of polygenic selection using educational attainment as an example. Educational attainment is a polygenic phenotype, influenced by many genetic variants with small effects. Frequencies of 10 SNPs found to be associated with educational attainment in a recent genome-wide association study were obtained from HapMap, 1000 Genomes and ALFRED. Factor analysis showed that they are strongly statistically associated at the population level, and the resulting factor score was highly related to average population IQ (r=0.90). Moreover, allele frequencies were positively correlated with aggregate measures of educational attainment in the population, average IQ, and with two intelligence increasing alleles that had been identified in different studies. This paper provides a simple method for detecting signals of polygenic selection on genes with overlapping phenotypes but located on different chromosomes. The method is therefore different from traditional estimations of linkage disequilibrium. This method can also be used as a tool in gene discovery, potentially decreasing the number of SNPs that are included in a genome-wide association study, reducing the multiple-testing problem and required sample sizes and consequently, financial costs.

Correlation of the COMT Val158Met polymorphism with latitude and a hunter-gather lifestyle suggests culture–gene coevolution and selective pressure on cognition genes due to climate
Davide Piffer

Dual-inheritance theory posits that the genotype has an impact on the evolution of human behavior and that cultural traits can be constrained by genetic imperatives. A large body of studies provides evidence that the functional catechol-O-methyltransferase (COMT) Val158Met polymorphism is associated with executive function, working memory (WM), and intelligence. A survey of the population genetics database provides evidence that COMT gene frequencies vary across populations. The aim of the present study was to test the hypothesis that the COMT gene has an impact on cultural evolution, specifically on the adoption of an agricultural vs. a hunter-gatherer lifestyle. Statistically significant differences in COMT allele frequencies between hunter-gatherer and agricultural societies were found. Ethnic groups whose economy is based on farming have higher frequencies of the Met allele (symbol: A), whereas societies based on a hunter-gatherer economy have very low frequencies of the Met allele and a disproportionate predominance of the Val allele. Moreover, the frequency of the Met allele was positively correlated to the populations’ IQ (r = 0.57). The FNBP1L gene (rs236330) is associated with childhood and adult intelligence and it varies in frequency across populations. Frequency of rs236330 was also significantly correlated with the populations’ IQ (r = 0.81). COMT and FNBP1L had fairly similar geographical distributions (r = 0.44) although the result did not reach statistical significance. The results suggest that the genotype of a population influences its cultural development in fairly specific and predictable ways. Met allele frequency was positively correlated with latitude (r = 0.56), suggesting selective pressure due to climate.

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12 Responses to The Allele Counting Begins

  1. Garrett says:

    When reading through the charts, I was struck by this too:

    “Particularly interesting is the relatively low frequency of COMT in East Asian populations (range 0.22–0.30), which contrasts with their reported higher IQ (105).”

    The Senagalese apparently have a higher Met % than the Chinese or Koreans, Palestinians higher than Ashkenazi Jews…

    I’m also curious what “Amerindian” encompasses in Tables 3 and 4, since they’re the only group I see with a Met % of 1 rather than a decimal.

    • Chuck says:

      “The Senagalese apparently have a higher Met % than the Chinese or Koreans, Palestinians higher than Ashkenazi Jews…”

      What’s of interest is the method in the first paper and the fact that the second paper was published in Anthropological Science.

      • Garrett says:

        The author is a handsome fellow:

        http://gr.iqsociety.org/members/davide-piffer/

        While I’m at it, let me field this question: just what is the extent that IQ differences between ethnic groups influence economic outcomes? The example of the Chinese in Vietnam stirred my interest in this question:

        “In 1970 it was estimated that while Chinese Vietnamese made up only 5.3% of the total population, but reputedly controlled 70 to 80% of the commerce sector of Vietnam.[6][7] Chinese businesses controlled much of the commerce in Saigon in South Vietnam. Before the Fall of Saigon, ethnic Chinese controlled 40.9% of the small scale enterprises, 100% of the wholesale trade in South Vietnam, transitioning from smaller-scale retail firms to larger wholesale enterprises.[164] At the end of 1974 the Hoa controlled more than 80 percent of the food, textile, chemical, metallurgy, engineering, and electrical industries, 100 percent of wholesale trade, more than 50 percent of retail trade, and 90 percent of export-import trade. Dominance over the economy enabled the Hoa to “manipulate prices” of rice and other scarce goods.[165]

        In the South, they controlled more than 90% of the non-European capital, 80 percent of the food, textile, chemical, metallurgy, engineering, and electrical industries, 100% of the wholesale trade, more than 50% of the retail trade, and 90 percent of the import-export trade. Economic dominance presided accusations from the Vietnamese that the Hoa manipulated prices of rice and other scarce commodities. It was noted by 1983 that more than 60% of southern Vietnam’s bourgeoisie were of Chinese extraction.[168] They controlled the entire rice paddy market and obtained up to 80% of the bank loans in the south. Hoa also owned 42 of the 60 corporations having a large annual turnover of more than 1 million dong and investments accounted for two-thirds of the total investment in South Vietnam.[164][169]”

        This is curious to me because, in recent decades, the Vietnamese have proven themselves quite capable. Correct me if I’m wrong, but I believe their average IQ is about 99-100, which is on par with Europeans and only about 5 points behind East Asians. Can a 5 point gap really produce the wild disparity described in the above passage? East Asians in America do well, but do not dominate anywhere near that extent.

        • Chuck says:

          “Correct me if I’m wrong, but I believe their average IQ is about 99-100”

          Where did you get this estimate? I ask because many follow Lynn and put the measured South East Asian IQ at 90 or so. My own review — unpublished — based on some recent national and international surveys (based on IQ tests proper) put it at about 90-100, That is, East Asian (Mongoloid) regional IQs range from 90 to 110 with the upper values representing some P.R.C provinces. This is compared to West Eurasian (Caucasoid) regional IQs of 85 (South Asian, Middle East) to 105 (Northern Europe). And SubSaharan (Negroid) regional IQs of 65 to 85 (no obvious geographic pattern). (These of course are measured IQs — as “true scores” or invariant scores are not available.)

          But anyways, ya, the differences would be small. Though, small differences on the population level can mean a lot when groups are sufficiently cohesive. From what I recall when in South Asia, ethnic Hans tended to network perhaps a good degree less than Jews in the West, but more than other ethnos. If so, the small individual level advantages would amplify on the sub population level within nations, just as they do between nations. Generally, it’s a mistake (and a fallacy of composition) to reduce cultural group differences to individual ones, as if cultural groups merely represented arbitrary sets of individuals.

      • *** the fact that the second paper was published in Anthropological Science.***

        Yes, I would have thought that would have created quite a stir.

        I wonder if Nisbett, Flynn & co will alter their views based on these papers?

  2. Borris says:

    Lol on that amren site they completely left out that blacks have more of the cognitive flexibility gene.

    My prediction is that ll of this will account for about 5% in the difference between groups in IQ and that mixed people will be superior since they will have all the alleles and thus the most variation and balance… and ability.

    • Chuck says:

      Heterosis? Jensen made a case for that in context to Europeans and East Asians; see also here. As I noted in a comment above, I wouldn’t make much of the results; of interest is the method.

    • statsquatch says:

      “they will have all the alleles” or none of the alleles…depends on the luck of the draw…or if the trait is under positive selection pressure which it is not currently.

  3. Rohmer says:

    Out of curiosity, what would you make of the suggestion that East Asians do NOT have higher IQs than White? My feeling is that the average East Asian IQ is around 100, and not the 105-110 often claimed. I’ve spoken to some mainstream IQ researchers, and without going into too much detail, I’m willing to bet that I’ll be vindicated on this point. How would this impact some of your correlations?

    • Chuck says:

      I’ll take that bet — better, provide the researchers’ names and I will bet them directly. (Email at J122177(at)hotmail.com.) Anyways, the claim is that North East Asians have higher levels of psychometric intelligence (so some combination of g+broad factors+narrow abilities). See e.g., Christainsen (2013), Table 2. Since we are only dealing with a few countries (China (105.8), Taiwan (104.6), N/S Korean (104.6), Mongolia (100), and Japan (104.2) — L&V’s 2012 IQs in parentheses) and since two of these show large negative residuals (North Korea and China) i.e., they under-perform in a number of metrics relative to their said IQs, “my correlations” would not be affected much at all. As for cause, high North East Asian cognitive levels can be traced back to the 1500s (see: Baten and Sohn. (2013)); they show up in East Asian Diasporas around the world (see e.g., Canabana (2011); and they show up in transracial adoptions in the US and Europe (some unpublished, but at least 12 in total); so, as I said, I’ll take that bet.

      • Rohmer says:

        Ha, I claimed they have IQs around 100. You make it sound as if I claimed around 80. Though, yes, I too have noticed they underachieve in numerous areas given their supposed IQ advantage and their advantage in absolute numbers, I thought my hypothesis might actually clean up some of the outliers.

        I have to admit it’s ironic to see HBDers occasionally overstating the historical accomplishments of non-Whites just as PC liberals do. For example, Philippe Rushton himself claimed that China has been ahead of Europe for most of recorded history when that’s simply not the case:

        As Fjordman pointed out:

        “In sharp contrast to the impressive list of great practical inventions was the relative sparseness of major Chinese achievements in science and mathematics. They suffered from a general lack of interest in theory in the sciences. For instance, the Chinese were diligent in keeping astronomical records, but they never created any elaborate theoretical structure and never deduced that the Earth was round. Their failure to do so made significant progress in astronomy difficult. In 1600 AD, Chinese astronomy was at least 2000 years behind the West. The Chinese made no major contributions to physics, chemistry or geology, either.”

        “There were a few exceptions, mainly related to the introduction of Buddhism when some scholars went to India to study, but the Chinese usually showed little interest in exploration beyond this. There were the famous naval expeditions in the Indian Ocean during the Ming Dynasty in the early fifteenth century AD led by men such as the admiral Zheng He (1371-1433), which reached as far as the east coast of Africa. Yet the whole reason why these expeditions have generated so much attention is precisely because they constituted a rare event. The project happened comparatively late and was eventually discontinued.”

        “there were no Chinese equivalents to Copernicus, Newton, Bach, Mozart, Beethoven, Michelangelo, Leonardo da Vinci, Columbus or Magellan. In the ancient world, there were none to Pythagoras, Archimedes, Euclid, Hipparchus or Ptolemy, either.”

        “Arnold Pacey admits that “…the most significant developments in Asia were the technical books published in Japan during the seventeenth and eighteenth centuries, a handful of Chinese scientific works, and very occasional episodes in India such as the use of models in the design of the Taj Mahal in the 1630s, and the systematic use of scale drawings by some shipbuilders by the end of the eighteenth century. But such examples are few and isolated. The great preponderance of new technological potential generated by increased ability to conceptualize technical problems was accruing in the West.””

        “In the theoretical sciences, Europeans were ahead of East Asians throughout the late medieval and early modern periods, and the gap was rapidly increasing. These advances gradually affected applied technology as well. The Chinese had known about magnetism for centuries, yet they never discovered the connection between it and electricity, exemplified by telegraphy. Did Europeans have “easy access” to electromagnetism? Modern European studies of the speed and properties of light were far more advanced than Asian ones. Was this because Europeans had “easy access” to light? Didn’t they have light in Asia?”

        Michael Hart adds:

        “The Chinese were relatively late in making use of the arch and the dome; and although they did build many attractive homes and other buildings, they did not construct anything that rivals the Parthenon in Athens, Hagia Sophia in Constantinople, or the magnificent cathedrals of medieval Europe.”

        “The Chinese — virtually unaided by outsiders — created a complex and complete civilization, with a smoothly functioning government, and multitudinous achievements in technology, construction, literature, the arts, and philosophy. They had a wide variety of skilled craftsmen; they maintained large, powerful armies; and they created a school system, a network of roads, an elaborate (and delicious) cuisine, and all the other attributes of a sophisticated civilization. In general, the Chinese enjoyed more internal unity than Europe. Europe has usually consisted of many independent states, often fighting one another. In contrast, China has usually been politically unified. Between 600 and 1300 AD, China was clearly more prosperous than the West. Because of this, it has often been asserted that (until the rise of modern science in the last five centuries) China was usually more advanced than the West. However, that assertion is incorrect. In the first place, even during that period, China was far behind the West in mathematics and science. In the second place, the interval 600-1300 AD was atypical. For most of recorded history — and for most of the last ten thousand years — China has been well behind the Western world in both technology and the arts.”

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