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Fig. S1 Inference of genetic clusters in the study region using the Structure algorithm for the red deer (a and b) and wild boar (c and d) dataset both not using (a and c) and using (b and d) sampling location as a prior.

Fig. S2 Modal assignment of red deer to the two clusters (grey and black dots) inferred using program GENELAND.

Fig. S3 Analysis of the genetic composition of the 10 sub-samples of the red deer dataset consisting of 450 individuals each, using a standard Structure analysis without sampling locations as priors.

Fig. S4 Analysis of the genetic composition of the 10 sub-samples of the red deer dataset consisting of 300 individuals each, using a standard Structure analysis without sampling locations as priors.

Fig. S5 Analysis of the genetic composition of the 10 sub-samples of the red deer dataset consisting of 200 individuals each, using a standard Structure analysis without sampling locations as priors.

Fig. S6 Analysis of the genetic composition of the 10 sub-samples of the red deer dataset consisting of 100 individuals each, using a standard Structure analysis without sampling locations as priors.

Fig. S7 Analysis of the genetic composition of the 10 sub-samples of the red deer dataset consisting of 450 individuals each, using a Structure analysis with sampling locations as priors.

Fig. S8 Analysis of the genetic composition of the 10 sub-samples of the red deer dataset consisting of 300 individuals each, using a Structure analysis with sampling locations as priors.

Fig. S9 Analysis of the genetic composition of the 10 sub-samples of the red deer dataset consisting of 200 individuals each, using a Structure analysis with sampling locations as priors.

Fig. S10 Analysis of the genetic composition of the 10 sub-samples of the red deer dataset consisting of 100 individuals each, using a Structure analysis with sampling locations as priors.

Fig. S11 GENELAND analysis of the genetic composition of sub-samples of the red deer dataset.

Fig. S12 BAPS analysis of the genetic composition of sub-samples of the red deer dataset.

Fig. S13 Analysis of the genetic composition of sub-samples of the red deer dataset consisting of juveniles only and of adults of different sexes.

Table S1 Inferred population genetic structure using data sets consisting of juvenile red deer and adults of different sexes.

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