Background selection under evolving recombination rates

Abstract

Background selection (BGS), the effect that purifying selection exerts on sites linked to deleterious alleles, is expected to be ubiquitous across eukaryotic genomes. The effects of BGS reflect the interplay of the rates and fitness effects of deleterious mutations with recombination. A fundamental assumption of BGS models is that recombination rates are invariant over time. However, in some lineages, recombination rates evolve rapidly, violating this central assumption. Here, we investigate how recombination rate evolution affects genetic variation under BGS. We show that recombination rate evolution modifies the effects of BGS in a manner similar to a localized change in the effective population size, potentially leading to underestimation or overestimation of the genome-wide effects of selection. Furthermore, we find evidence that recombination rate evolution in the ancestors of modern house mice may have impacted inferences of the genome-wide effects of selection in that species.

Keywords: Mus musculus; background selection; chromosomal rearrangements; evolutionary genetics; recombination rate.

Figure 1.

The effect of BGS on nucleotide diversity (π) over time after recombination rates change by a factor λ. The dashed lines were calculated using equation (2.1) and formulae from Nordborg et al. [32]. Points indicate the mean from 50 replicate simulations. Nucleotide diversity was calculated for neutral sites 10 000 bp away from sites subject to purifying selection. Points are shown with error bars indicating ± 1 standard error. (Online version in colour.)

Figure 2.

Spearman's correlation between nucleotide diversity (π) and recombination rate (r) over time after recombination rates evolve; (a) shows results for a broad-scale shift in the recombination landscape and (b) shows results for recombination rate evolution by the movement of hotspots. Results are shown for 10 kbp analysis windows. (Online version in colour.)