Comparing estimates of number of breeders <i>N</i>_b based on microsatellites and single nucleotide polymorphism of three groups of brown trout (<i>Salmo trutta</i> L.)

Abstract Microsatellites (10 MS s) and single nucleotide polymorphism (3871 SNP s) were analysed in three closely related, single‐cohort groups of brown trout, Salmo trutta L. Autumn (W/0+) and subsequent year (W/1+) samples of brown trout of the same stream were retrieved using electric fishing, and one sample of artificially reared brown trout (H/1+), bred from wild parents, was collected from a hatchery. The number of breeders, N b , was estimated based on each total sample set and from subsets of loci by means of the software LDN e, and by means of Colony2, NeEstimator and ON e SAMP softwares. MS ‐based estimates were consequently higher than those based on SNP s. ML ‐Relate and Colony2 software was used to estimate putative full‐sib pairs, and there was considerable variation between methods. For monitoring species and populations, both methods are recommended, but to compare N b across samples and years, the same markers of MS s or SNP s must be used as estimates varied across markers within sample.