ABSTRACT
Neutral genetic diversity across the genome is determined by the complex interplay of mutation, demographic history, and natural selection. While the direct action of natural selection is limited to functional loci across the genome, its impact can have effects on nearby neutral loci due to genetic linkage. These effects of selection at linked sites, referred to as genetic hitchhiking and background selection (BGS), are pervasive across natural populations. However, only recently has there been a focus on the joint consequences of demography and selection at linked sites, and empirical studies have sometimes come to apparently contradictory conclusions. In order to understand the relationship between demography and linked selection, we conducted an extensive forward simulation study of BGS under a range of demographic models. We found that levels of diversity compared to an equilibrium population vary over time and that the initial dynamics after a population size change are often in the opposite direction of the long-term expected trajectory. Our detailed observations of the temporal dynamics of neutral diversity in the context of selection at linked sites in nonequilibrium populations provides new intuition about why patterns of diversity under BGS vary through time in natural populations and help reconcile previously contradictory observations. Most notably, our results highlight that classical models of BGS are poorly suited for predicting diversity in nonequilibrium populations.
Footnotes
↵† Department of Evolution and Ecology, University of California, Davis, CA, USA E-mail: rossibarra{at}ucdavis.edu; Department of Human Genetics, McGill University, Montreal, Canada E-mail: ryan.hernandez{at}me.com