Parentage and pedigree

A combination of microsatellite genotypes (Table S1, Supporting information) and field observations, such as information on territorial, scent‐marking pairs (Wabakken et al. 2001), was used to determine parents and reconstruct the pedigree (Liberg et al. 2005). Territorial pairs were confirmed from snow tracking conducted within the joint Swedish‐Norwegian wolf monitoring programme (Wabakken et al. 2013). The parentage of individuals was determined by genetic exclusion (Table S2, Supporting information) both manually based on field observation data from genetically identified pairs and using cervus 3.0.3. Using cervus, we ran a simulation based on allele frequencies from the Scandinavian population with the purpose to estimate the critical values of the difference in log‐likelihood (LOD) values (delta) between different pairs, that is putative parents. In the simulations, we assumed the parental sexes to be known, with 200 candidate mothers and 200 candidate fathers and 95% of the parents sampled. Moreover, we assumed 73.5% of the loci to be typed (which corresponds to the average success rate of the noninvasive samples in the data set), and 2% of the loci to be mistyped. As it is not possible to define specific pairs as potential parents in cervus, we included all known pair members as potential parents for all individuals and chose the output to include all parents with positive LOD scores. Matching parents were checked manually for deviations from Mendelian inheritance, which could not be explained by allelic dropout.

Based on the reconstructed pedigree, we calculated the inbreeding coefficient using cfc v1.0 (Sargolzaei et al. 2005). For more detailed description of the reconstruction of the pedigree, see Appendix S1 (Supporting information).