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Table S1 Locality details and numbers of individuals sampled.

Table S2 PCR and extension primers used in the Sequenom's iPlex genotyping.

Table S3 Maximum likelihood estimates (MLE) for the two parameters of the non-geographic concordance analysis (α and β) and probability of non-concordant introgression patterns for each locus.

Fig. S1 Likelihood profiles for monotonic change in allele frequencies across the sampling area.

Fig. S2 A summary of clinal patterns for all individual loci without constraint to any particular model of monotonic change.

Fig. S3 Likelihood profiles for cline center (c) and cline width (w) estimated under the cline model retained for each locus.

Fig. S4 Consensus Hardy-Weinberg (FIS) values across the center of the rabbit hybrid zone (indicated by a solid vertical line).

Fig. S5 Scatterplot of cline width (km) versus net nucleotide divergence (Da; A) and locus specific estimates of gene flow between Oryctolagus algirus and O. c. cuniculus individuals sampled away from the hybrid zone (data from Carneiro et al. 2009, 2010).

Fig. S6 Map of the study area with major topographic features.

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