Mouse samples and data sets.

We obtained a new mouse sample and also used existing mouse samples from previous studies. The array CEL files for existing mouse samples are available online (http://cgd.jax.org/datasets/diversityarray/CELfiles.shtml and by request from the authors of [38]). The introgression scans examined patterns of local phylogeny switching involving an M. m. domesticus sample from the region of sympatry with two M. spretus strains and a baseline M. m. domesticus sample from far away. The control scans utilized the two M. spretus strains along with two wild M. m. musculus mice that were known to not have introgressed with M. spretus.