Fig. S1 Genotype matrices for the BV transect (A) and the CZ transect (B). Each column is an individual mouse and each row is an individual SNP. Mice are arranged geographically from west (left) to east (right) and SNPs are arranged by chromosome. Genotypes are color-coded in the following way. Green is homozygous M.  m. domesticus, blue is homozygous M.  m. musculus, red is a heterozygous genotype, and white is missing data [Correction added after online publication 14 June 2011: the labelling in Fig. S1 was corrected].

Fig. S2 A comparison of geographic clines estimated using a 2-parameter model between the Bavaria and Czech transects. The autosomal clines were calculated based on median values of cline center and width for all SNPs (see Table 1). The X-linked clines were calculated for 84 or 85 SNP markers in the BV and CZ transects, respectively. For comparative purposes the median cline center, estimated from autosomal markers, was set to 0 km in both transects.

Fig. S3 Decay of LD for samples sizes of 10 (black), 15 (red) and 25 (blue) from a single population (Neufahrn) sampled in two separate years. Dashed lines = mice from 1984, solid lines = mice from 1985.

Table S1 ID’s (Field #), sex, locality information, collection year, heterozygosity and hybrid index for all samples.

Table S2 Sample ID’s and localities of mice genotyped with the Mouse Diversity Array and used to sort for fixed differences between M.  m. musculus and M.  m. domesticus mice.

Table S3 Result of Fst analyses using program DnaSP v. 5.10.

Table S4 List of SNP markers used in the study and their chromosomal locations (mouse genome-Build 37).

Table S5 Estimates of cline center and width for all autosomal and X-linked markers.

Table S6 Values of r2, D′, half-length of LD (HLD), estimated age in generations, for samples (n = 10, 15, 19 or 20) collected at specific localities in specific years. *Distance is calculated from the western-most locality. **Total number SNP comparisons at ≤2Mb distance are based on 100 permutations of samples at each locality. SNPs with minor allele frequency ≤0.05 and missing values >50% are excluded. ***The age, in generations, of each population was calculated based on the decline of r2 as described in the methods.

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