Genome-wide scan of 29,141 African Americans finds no evidence of selection since admixture

TL;DR

A comprehensive genome-wide analysis of over 29,000 African Americans found no significant evidence of recent selection since admixture, contrasting with prior smaller studies and highlighting the importance of proper statistical correction.

Contribution

This study provides the largest analysis to date, demonstrating the absence of detectable recent selection in African Americans using rigorous multiple testing correction.

Findings

No genome-wide significant deviations in African ancestry proportions

Previous signals of selection are likely false positives due to inadequate correction

Most loci with differentiation are explained by selection in Africa before migration

Abstract

We scanned through the genomes of 29,141 African Americans, searching for loci where the average proportion of African ancestry deviates significantly from the genome-wide average. We failed to find any genome-wide significant deviations, and conclude that any selection in African Americans since admixture is sufficiently weak that it falls below the threshold of our power to detect it using a large sample size. These results stand in contrast to the findings of a recent study of selection in African Americans. That study, which had 15 times fewer samples, reported six loci with significant deviations. We show that the discrepancy is likely due to insufficient correction for multiple hypothesis testing in the previous study. The same study reported 14 loci that showed greater population differentiation between African Americans and Nigerian Yoruba than would be expected in the absence of natural selection. Four such loci were previously shown to be genome-wide significant and likely to be affected by selection, but we show that most of the 10 additional loci are likely to be false positives. Additionally, the most parsimonious explanation for the loci that have significant evidence of unusual differentiation in frequency between Nigerians and Africans Americans is selection in Africa prior to their forced migration to the Americas.