Weak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome

Positive selection and purifying selection reduce levels of variation at linked neutral loci. One consequence of these processes is that the amount of neutral diversity and the meiotic recombination rate are predicted to be positively correlated across the genome—a prediction met in some species but not others. To better document the prevalence of selection at linked sites, we used new and published whole-genome sequences to survey nucleotide variation in population samples of the western European house mouse (Mus musculus domesticus) from Germany, France, and Gough Island, a remote volcanic island in the south Atlantic. Correlations between sequence variation and recombination rates estimated independently from dense linkage maps were consistently very weak (ρ ≤ 0.06), though they exceeded conventional significance thresholds. This pattern persisted in comparisons between genomic regions with the highest and lowest recombination rates, as well as in models incorporating the density of transcribed sites, the density of CpG dinucleotides, and divergence between mouse and rat as covariates. We conclude that natural selection affects linked neutral variation in a restricted manner in the western European house mouse.