A review of intelligence GWAS hits: Their relationship to country IQ and the issue of spatial autocorrelation

Davide Piffer

doi:10.1016/j.intell.2015.08.008

Abstract

Published Genome Wide Association Studies (GWAS), reporting the presence of alleles exhibiting significant and replicable associations with IQ, are reviewed. The average between-population frequency (polygenic score) of nine alleles positively and significantly associated with intelligence is strongly correlated to country-level IQ (r=.91). Factor analysis of allele frequencies furthermore identified a metagene with a similar correlation to country IQ (r=.86). The majority of the alleles (seven out of nine) loaded positively on this metagene. Allele frequencies varied by continent in a way that corresponds with observed population differences in average phenotypic intelligence. Average allele frequencies for intelligence GWAS hits exhibited higher inter-population variability than random SNPs matched to the GWAS hits or GWAS hits for height. This indicates stronger directional polygenic selection for intelligence relative to height. Random sets of SNPs and Fst distances were employed to deal with the issue of autocorrelation due to population structure. GWAS hits were much stronger predictors of IQ than random SNPs. Regressing IQ on Fst distances did not significantly alter the results nonetheless it demonstrated that, whilst population structure due to genetic drift and migrations is indeed related to IQ differences between populations, the GWAS hit frequencies are independent predictors of aggregate IQ differences.

Highlights

Over the last few years, population geneticists have moved away from the study of genetic evolution using the single-gene, Mendelian approach, towards models that examine many genes together
A common factor was extracted from among the SNPs, utilizing unweighted least squares factor analysis, yielding a metagene — this being a term utilized in genetics to describe patterns of covariance among genes
Two alternative metagenes were constructed, one utilizing only the four SNPs exhibiting replicated Genome Wide Association Studies (GWAS) associations with g and related phenotypes ( “four SNPs metagene”; Piffer, 2015a), and a second utilizing all nine alleles discovered to date ( “nine SNP metagene”)

Summary

Introduction

Over the last few years, population geneticists have moved away from the study of genetic evolution using the single-gene, Mendelian approach, towards models that examine many genes together (i.e. polygenic models). The origin of this trend can be traced back to Fisher (1918). The first attempt at empirically identifying polygenic selection was made by Turchin et al (2012) utilizing height alleles (obtained from Genome Wide Association Studies, GWAS) and two large populations (Northern and Southern Europeans). It was found that the Northern European population exhibited higher frequencies of height-increasing alleles (obtained from GWAS studies) — suggesting greater polygenic selection for heightenhancing alleles in this population relative to the Southern Europeans.

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Conclusion