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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.

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