File S1 - The Genetic Integrity of the <i>Ex Situ</i> Population of the European Wildcat (<i>Felis silvestris silvestris</i>) Is Seriously Threatened by Introgression from Domestic Cats (<i>Felis silvestris catus</i>)

Text S1, Permits for sampling. Text S2, List of participating institutions for genetic analyses. Figure S3, Plots of LnP(D) and delta K (Evanno et al. 2005) for the microsatellite data obtained with STRUCTURE Harvester. Table S4, Sampling regime. 1) Most juveniles of sampled mothers and siblings were excluded from sequencing. Their haplotypes were inferred using their maternal relatives (number behind slash). 2) One captive individual was sampled twice and thus the duplicate sample was excluded. 3) The DNA quality of the sample from a preserved captive specimen was not sufficient for sequencing. Table S5, Information on the samples used in this study. The table contains all samples which were used in this study, together with their origin, the detected mtDNA haplotypes, the assignments to the STRUCTURE clusters at K = 2, K = 3 and K = 6 as well as the most probable assignment by NewHybrids. At K = 2 all individuals which qualify as hybrids based on qi <0.8 are marked with an *. These individuals were excluded for the analyses of population differentiation. For reasons of data protection the origin of the ex situ samples can only be given as encrypted information. Remarks: 1) DNA quality was too low for genotyping; 2) individual was classified as morphologically suspicious; 3) known hybrid; 4) domestic cat (this individual had a wildcat number as it was included in the wildcat samples as a control by the provider of in situ samples); 5) single samples from wild populations as reference for sequencing, but not suitable for population genetic approaches; 6) zoo located next to wild population in the Harz mountains; 7) foundling within region of the wild population Rhineland Palatinate; 8) the cat was transferred to a new zoo which also took a sample, the duplicate sample was excluded from analysis. (DOCX)