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Fig. S1 Neighbour-joining trees depicting the evolutionary relationships between all the haplotypes found at (a) Chrng, (b) Med19, (c) Prpf3, (d) Clcn6, (e) G6pdx, (f) Ocrl, (g) Jarid1d and (h) control region. Haplotypes found in Mus domesticus are followed by a white box, found in M. musculus by a black box and found in M. castaneus in a grey box. Numbers next to the haplotype boxes indicate the number of chromosomes in which the given haplotype was present and the populations where they were found. Bootstrap values equal or higher to 80 are shown next to branches. Whenever available, sequences of M. spretus, M. spicilegus and M. caroli were included.

Table S1 Populations and sampling localities for all the samples used in this study

Table S2 Amplicon and primer details

Table S3 Length, number of sites (SNPs) and number of chromosomes (Nx) of non-recombining data sets used for IM and IMa analyses after removing missing data

Table S4 Levels of polymorphism within populations of house mice, and divergence between these populations and Mus caroli

Table S5 Counts of exclusive (Sd, Sm, Sc), shared (Ss) and fixed (Sf) sites between species pairs of house mice

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