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Fig. S1 The position of male and female brown trout spawners in the Bellbekken stream during the 2002–2004 spawning seasons. Mature fish seem to cluster in three sections in the stream (1st section: 0–392 m, 2nd section: 452–800 m, 3rd section: 852–1420 m), marked by the dashed vertical lines in the figure.

Fig. S2 Distribution of pairwise distance comparisons between individuals assigned as full siblings. All individuals were sampled as 1+ in the spring from all the three seasons studied. The y-axis denotes the proportion of individuals in each category.

Fig. S3 Results of simulations performed to assess the accuracy of the full probability assignment model used in this study. Data was generated with 50 males and 50 females, 10 of which were designated as unsampled. The population level parameters (β) for the effect of male and female size are also shown. The real underlying values are denoted by the black vertical lines.

Table S1 Number of alleles and expected (He) and observed (Ho) microsatellite heterozygosity for the potential parental brown trout in the Bellbekken during the 2002–2004 spawning seasons. Also given are the expected exclusion probabilities of the first and second parent: the probability of excluding a randomly chosen non-parent and the probability of excluding a randomly chosen non-parent after the first parent has been assigned. These estimates are based on all potential parents of both sexes pooled across the three breeding seasons studied, as there was no difference between seasons or sex.

Appendix S1 Includes a section discussing the selective neutrality of the microsatellite markers and a section on the details on the full probability Bayesian model of parentage assignment.

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