Table S1. List of sampling sites.

Table S2. List of analyzed markers (in parentheses, abbreviations used in the text).

Table S3. List of new insertions diagnostic for musculus/domesticus subspecies.

Table S4. Results of Barton's concordance analysis.

Figure S1. Individual-based estimates of heterozygote deficit (F) against individual hybrid index (HI), a treatment analogous to Barton's concordance approach for allele frequencies.

Figure S2. Genomic clines for all 24 loci.

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