Reproductive success was quantified as the number of offspring assigned to an adult, following parentage assignment of all offspring. Pedigrees were constructed for each parent-offspring cohort separately using the package MasterBayes v2.55 (43) in the program R (44). MasterBayes implements a Bayesian approach using Markov chain Monte Carlo (MCMC) sampling to estimate the most likely pedigree configuration while simultaneously estimating the unsampled population size, thus reducing bias in parentage assignments by allowing for uncertainty in all model parameters.

The pedigree model used fixed genotyping error rates in a two-level model, calculated by re-extracting and regenotyping 190 randomly chosen samples from 24 initial plate runs and comparing the two runs. Allelic dropout (E1) was calculated as the frequency of genotypes that were homozygous in one run and heterozygous in the other, which yielded more conservative error rates than MicroDrop, a dedicated tool to estimate allelic dropout in genetic data without repeat samples. Stochastic error rate (E2) was calculated as the frequency of alleles that were scored differently in the two runs, conservatively also including one allele from all putative cases of allelic dropout. E1 and E2 were calculated separately for each locus. Across all 13 loci, mean E1 was 0.20% and mean E2 was 0.24%.

We calculated allelic frequencies from the parental genotypes to prevent skewing by family groups produced by particularly fecund parents. Alleles from unsampled parents, present in the offspring but not in the parental genotypes, were added manually to the parental genotypes at low frequency. A simulation analysis showed that, among offspring with confidently assigned parents, this marker panel identified the true (positively identified or unsampled) mother with 96.6% accuracy and true father with 93.3% accuracy (10 pedigree runs on genotypes simulated from the final pedigree). Errors in the simulation involved unsampled parents or low confidence assignments, with different known parents assigned in different runs in only 0.2% of dam assignments and 0.3% of sire assignments. For offspring with 10 or 11 loci typed, one mismatch with potential parents was allowed, and for those with seven to nine loci typed, no mismatches were allowed. Among 2552 offspring typed at 10 or more loci and confidently assigned at least one parent, 30 of the 1192 dam assignments and 22 of the 1581 sire assignments had one mismatch between parent and offspring. Of 264 adults and 5341 offspring, 118 offspring with fewer than seven loci successfully genotyped were excluded; all parents were successfully typed with at least 11 loci (204 at all 13 loci). Final sample sizes and assignment probabilities are shown in tables S1 and S4.

Priors for the Bayesian inference were chosen to be broad but informative. The number of unsampled parents (unsampled population size) was estimated for both mothers and fathers in association with the pedigree estimation through MCMC sampling from the prior distribution, specified with a mean of four times the sampled population size (40), and variance calculated as 1.5 − 0.25 × sampled population size, which encompassed likely parameter space. The model was run for 70,000 iterations after a burn-in of 5000, thinning every two iterations (45). The modal pedigree configuration was extracted from the posterior distribution of pedigrees, and assignments with a likelihood of at least 90% were considered confident and were used in the analyses.

A total of 13 individuals (six females and seven males) that had spawned in a previous year as adults were identified on the basis of scale morphology (repeat spawners or kelts) and were captured at the lower Utsjoki location (4.9% of all adult individuals captured in this location). The mean sea age at maturity of repeat spawning females was 3.2 ± 0.4 SE (range, 2 to 4 SW), and all repeat spawning males spent 1 year at sea before the first spawning migration and another year at sea before returning to spawning for the second time (all repeat spawners were 2 SW). Only one repeat spawning female was a disperser, and all other individuals were local. In addition, adult genotypes were screened for recaptures using Allelematch (46). Allelematch identifies full and partial genotype matches based on genotype data. Using the criterion of up to two allele mismatches, we found no recaptured adults pooled across all cohort years (2010–2014).

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