Table S1 Primer sequences used for the nuclear genes.

Table S2 Percentages of variability shared between Mau and Rod or unique in one of the two populations for each nuclear gene (a) and each microsatellite locus (b).

Table S3 Tamura 3-parameters distances D with standard errors calculated with 1,000 bootstrap replications.

Fig. S1 Determination of the number of clusters using Structure software: graphs a and b show the mean Log-likelihood method and the method following Evanno et. al (2005) for microsatellite loci and graphs c and d show the same analyses for the X-linked dataset.

Fig. S2 Median-Joining networks for each nuclear gene.

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