  We report on a genome-wide scan for introgression in the house mouse (Mus
musculus domesticus) involving the Algerian mouse (Mus spretus), using samples
from the ranges of sympatry and allopatry in Africa and Europe. Our analysis
reveals wide variability in introgression signatures along the genomes, as well
as across the samples. We find that fewer than half of the autosomes in each
genome harbor all detectable introgression, while the X chromosome has none.
Further, European mice carry more M. spretus alleles than the sympatric African
ones. Using the length distribution and sharing patterns of introgressed
genomic tracts across the samples, we infer, first, that at least three
distinct hybridization events involving M. spretus have occurred, one of which
is ancient, and the other two are recent (one presumably due to warfarin
rodenticide selection). Second, several of the inferred introgressed tracts
contain genes that are likely to confer adaptive advantage. Third, introgressed
tracts might contain driver genes that determine the evolutionary fate of those
tracts. Further, functional analysis revealed introgressed genes that are
essential to fitness, including the Vkorc1 gene, which is implicated in
rodenticide resistance, and olfactory receptor genes. Our findings highlight
the extent and role of introgression in nature, and call for careful analysis
and interpretation of house mouse data in evolutionary and genetic studies.
