Human demographic history has amplified the effects of background selection across the genome
Patterns of genetic diversity within a species are affected at broad and fine scales by population size changes (“demography”) and natural selection. From both population genetics theory and observation on genomic sequence data, it is known that demography can alter genome-wide average neutral genetic diversity. Additionally, natural selection can affect neutral genetic diversity regionally across the genome via selection at linked sites. During this process, natural selection acting on adaptive or deleterious variants in the genome will also shape diversity at nearby neutral sites due to genetic linkage. However, less is known about the dynamic changes to diversity that occur in regions affected by selection at linked sites when a population undergoes a size change. We characterize these dynamic changes using thousands of human genomes and find that the population size changes experienced by humans have shaped the consequences of selection at linked sites across the genome. In particular, population contractions, such as those experienced by non-Africans, have disproportionately decreased neutral diversity in regions of the genome inferred to be under strong background selection (i.e., selection at linked sites that is caused by natural selection acting on deleterious variants), resulting in large differences between African and non-African populations.