Signals of Human Polygenic Adaptation: Moving Beyond Single-Gene Methods and Controlling for Population-Specific Linkage Disequilibrium

Abstract

This research aimed to identify signals of polygenic adaptation in various phenotypes – such as educational attainment, height, and schizophrenia – by employing traditional Fst enrichment tests and polygenic score differentiation tests like Qst and Qx. Fst tests offered inconclusive evidence for over-differentiation in allele frequencies, while Qst tests indicated significant differences for cognitive traits but not for height. The investigation underscores that Fst underestimates the extent of phenotypic differentiation due to additive genetic influences because it fails to account for the covariance of allelic effects across populations. The research demonstrates that Bird's (2021) analysis of the genetic IQ disparity between Africans and Europeans is based on the incorrect assumption that Fst should be equal to the phenotypic variance between populations (Qst), assuming all between-group variation results from additive genetic effects. The findings emphasize the importance of considering both Fst and Qst values when assessing population genetic differentiation. They also stress the importance of controlling for population-specific Linkage Disequilibrium (LD) decay. Indeed, LD decay produced a pro-European bias in polygenic scores, inflating the European mean compared to Africans and East Asians. Finally, family based or multi-ancestry GWAS are needed to account for other sources of bias such as population stratification and ancestry-specific variants or effects. The currently available data does not allow us to provide accurate estimates of the genotypic potential of ancestral groups that are genetically very different from Europeans.