## 2 Materials and Methods
In Fstat 2.9.4 [37], we estimated heterozygosity (\(H_{\text{O}}\)), expected heterozygosity (\(H_{\text{E}}\)), allele counts, and F-statistics for the 10 geographical locations sampled. GENEPOP 4.0.10 [38] was used to estimate the deviations from Hardy-Weinberg equilibrium and genotypic linkage disequilibrium using an exact (probability) test for locus and locations [39]. Correction for multiple testing was performed using the false discovery rate (FDR) in the FDR software [40] with the \"graphically sharpened method.\"  
The results from these initial tests of the 26 microsatellite loci showed that 49 pairwise tests of the population and loci exhibited deviations; however, after a correction using the FDR method (threshold \(<\) 0.0027), only 13 combinations exhibited deviations from Hardy-Weinberg equilibrium. There was no systematic combination of loci and population, and the deviations were possibly due to null alleles. Out of the 2760 combinations of loci and populations, only 158 combinations indicated significant linkage disequilibrium (LD) before FDR correction, and no pairwise combinations were in significant LD after an FDR correction (threshold \(<\) 0.000058). Thus, after this initial microsatellite quality assessment, a set of 24 interpreted neutral microsatellites (Supplementary Table S1) were used in all further population genetic analyses. \begin{table}
\begin{tabular}{c c c c c c c} \hline \hline
**Study Area** & **Country** & **Total N** & **N Males** & **N Females** & **GPS Fox** & **Shot Fox** \\ \hline Sweden N. & Sweden & 24 & 13 & 11 & 20 & 3 \\ Sweden S. 1 & Sweden & 14 & 3 & 11 & 13 & 1 \\ Sweden S. 2 & Sweden & 6 & 4 & 2 & 0 & 6 \\ Sweden S. 3 & Sweden & 5 & 3 & 2 & 0 & 5 \\ Hedmark N. 1 & Norway & 9 & 3 & 6 & 0 & 9 \\ Hedmark S. 1 & Norway & 8 & 3 & 5 & 0 & 8 \\ Hedmark S. 2 & Norway & 25 & 10 & 15 & 0 & 25 \\ Hedmark S. 3 & Norway & 19 & 9 & 10 & 0 & 19 \\ Hedmark N. 2 & Norway & 23 & 14 & 9 & 0 & 23 \\ Hedmark N. 3 & Norway & 17 & 9 & 8 & 0 & 17 \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Sampling information for the 150 red fox individuals from Norway and Sweden included in this study. Columns describes study area, country, total fox analyzed and separated into sex, the sampling method (GPS fox-trapped and released alive; shot fox). See also Figure 1 for geographical localization of all individual samples. \(F_{\rm ST}\) values among localities was calculated in FSTAT 2.9.4 [37]. In order to visualize the genetic differentiation of red fox individuals in the different study areas, we used the package Factoextra [41] in R [42] to construct a neighbor-joining tree with 1000 bootstraps. Genetic relationships among individuals and localities were analyzed in STRUCTURE 2.2.3 [43], revealing the most likely numbers of Hardy-Weinberg equilibrium clusters analyzed using an admixture model and correlated allele frequencies with 100,000 burn-in steps and 300,000 Markov chain Monte Carlo (MCMC) iterations and 10 replicates for each of the runs for K populations = 1-10. Three sets of analyses were performed, the first with and the second without the LOCPRIOR option (i.e., using geographical information of sampling localities to help STRUCTURE when low differentiation existed), and the third analysis was done in a hierarchical manner by removing one divergent area and then rerunning with the remaining samples (revealing the cumulative number of K groups). Evaluation of the most likely number of K was based on methods in [PERSON], et al. [44] and STRUCTURE-HARVESTER, version 0.6.1 [45]. Here, we particularly compared the patterns of InP (data) and \(\Delta\)K used for the inferences. The visual graphics from the best STRUCTURE run (most likely K) was added to the neighbor-joining tree (described above). To assign individuals based on both genetic and spatial information, the clustering software Geneland [46] was used for the four localities. Geneland offers the opportunity to both identify genetic clustering and to infer what influence spatial clustering has on the population structure [47].