The recombination landscape in wild house mice inferred using population genomic data

Abstract

Characterizing variation in the rate of recombination across the genome is important for understanding many evolutionary processes. The landscape of recombination has been studied previously in the house mouse, Mus musculus, and it is known that the different subspecies exhibit different suites of recombination hotspots. However, it is not established whether broad-scale variation in the rate of recombination is conserved between the subspecies. In this study, we construct a fine-scale recombination map for the Eastern house mouse subspecies, M. m. castaneus, using 10 individuals sampled from its ancestral range. After inferring phase, we use LDhelmet to construct recombination maps for each autosome. We find that the spatial distribution of recombination rate is strongly positively between our castaneus map and a map constructed using inbred lines of mice derived predominantly from M. m. domesticus. We also find that levels of genetic diversity in M. m. castaneus are positively correlated with the rate of recombination, consistent with pervasive natural selection acting in the genome. Our study suggests that recombination rate variation is conserved at broad scales between M. musculus subspecies.