Genes for IQ Differ Among Racial Groups
Table 1a. (above): Frequencies of alleles that had a positive association with educational attainment. Shaded columns, L-R: Racial Group; Average IQ; Average Allele Frequency.
The phenotype known as intelligence, as measured by IQ and IQ-like tests such as the SAT, admission tests, and so forth, is a highly heritable and polygenic trait, that is, no single gene is known to a have large effect — instead there are many genes involved, each with a very small effect.
Genome-Wide Association Studies (GWASs) are able to detect variants at genomic loci that are associated with complex traits in a population and, in particular, at detecting associations between common single-nucleotide polymorphisms (SNPs) and common diseases such as heart disease, diabetes, auto-immune diseases, and psychiatric disorders. GWASs have also been used to detect common variants for height and body mass index, not least intelligence.
More recent GWASs have identified several SNPs whose different alleles are associated with differences in performance on PISA or IQ tests, moreover, significant genetic correlations are found between the general (g) factor of cognitive ability and language, mathematics, and reading. A massive GWAS of over 100,000 individual genomes identified ten SNPs associated with educational attainment that reached suggestive genome-wide significance:
GWAS of 126,559 Individuals Identifies Genetic Variants Associated with Educational Attainment
The results support the findings from SNP-based heritability studies that a significant fraction of total genetic variance is due to common variants. Three of the genome-wide significant and replicable SNPs that influence educational performance were rs9320913, rs11584700 and rs4851266. Several other SNPs are associated with differences in performance on PISA or IQ tests, two of which include:
Rs236330, as tested in two separate studies:
Genome-wide association studies establish that human intelligence is highly heritable and polygenic
Childhood intelligence is heritable, highly polygenic and associated with FNBP1L
Rs324650, as replicated in four association studies:
Role of the cholinergic muscarinic 2 receptor (CHRM2) gene in cognition
Association of CHRM2 with IQ: converging evidence for a gene influencing intelligence
Association between the CHRM2 gene and intelligence in a sample of 304 Dutch families
Exploring the functional role of the CHRM2 gene in human cognition: results from a dense genotyping and brain expression study
Since intellectual capacity has risen through small incremental changes at very many genes, have these changes been the same in all human racial groups?
To test this, another study used seven SNPs (including rs9320913, rs11584700, rs4851266, rs236330, and rs324650) that are associated with differences in performance on PISA or IQ tests. The study then looked up the prevalence of each allele that seems to increase performance for a total of fifty human populations, and then calculated the average prevalence of these alleles at seven genes:
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:
The results are similar across the HapMap and 1000 Genomes data sets: East Asian populations (Japanese, Chinese) have the highest average frequency of “beneficial” alleles (39%), followed by Europeans (35.5%) and sub-Saharan Africans (16.4%). [...] 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. [...] The polygenic score of educational attainment alleles was a good predictor of PISA scores (r=0.84, p<.05).
Table 1a (above this post): Frequencies of alleles that had a positive association with educational attainment in the combined dataset in the large GWAS study of genetic variants associated with educational attainment. In the table:
AFR: African;
AMR: American;
ASN: Asian;
EUR: European;
ASW: African ancestry in SW USA; LWK: Luhya, Kenya; YRI: Yoruba, Nigeria; CLM: Colombian; MXL: Mexican ancestry from LA, California; PUR: Puerto Ricans from Puerto Rica; CHB: Han Chinese in Bejing, China; CHS: Southern Han Chinese; JPT: Japanese in Tokyo, Japan; CEU: Utah Residents with Northern and Western European Ancestry; FIN: Finnish in Finland; GBR: British in England and Scotland; IBS: Iberian population in Spain; TSI: Toscani in Italy.
Table 1c (below): Frequencies for the 50 populations, along with their factor score and estimated racial IQ:
As seen here, the average allele frequency for the selected SNPs is lowest among the San Bushmen and Mbuti Pygmies of sub-Saharan Africa.
Additionally, in early GWASs there was found to be no genome-wide significant variants determining height (also a polygenic trait whose allele frequencies differ among populations, not least between closely-related European populations) despite decades worth of studies finding height to be a highly heritable trait. It was only when larger sample sizes were used (>15,000 individuals) did GWASs start to find “GWAS hits” (SNP associations) affecting height -- lots, in fact:
Source: Five Years of GWAS Discovery
The prior cognitive enhancing-SNPs associated represent only a handful of total genome-wide variation, but much like with height, geneticists expect a steady accumulation of SNP 'hits' associated with intelligence once they pass the statistical power threshold. Since intelligence is a polygenic trait, a single SNP produces meager results, on the other hand, an accumulation of several more cognitive enhancing-SNPs than the average person produces notable differences — and the incidence of the current crop of such SNP variants differ among racial groups.
Finally, all but one of the ten alleles in the study were specific to humans and not shared with ancestral primates. Evidently, these are recent variants that arose independently during a time of recent and divergent human evolution and which show varying differences (on selection pressures) among human groups:
[Piffer, 2013] Nine of the 10 alleles associated with educational attainment were derived, thus unique to humans and not shared with non-human primates. This result was significant (p=0.01) and is predicted on the basis of the assumption that humans have evolved by natural selection to become more intelligent than their primate cousins. The results show that this evolutionary process, which was already far advanced at the time when modern humans spread across the globe approximately 65,000 years before present, has continued in modern human populations after that time. It invalidates theories that assume, explicitly or implicitly, that human cognitive evolution has ended with the first appearance of physically modern Homo sapiens (e.g., Tooby and Cosmides, 1992).
Ongoing Adaptive Evolution in Human Brain Size - Varying differences among human racial groups on gene variants that confer brain growth.